pycompound 0.1.5__py3-none-any.whl → 0.1.7__py3-none-any.whl

app.py

@@ -1,16 +1,9 @@
 
 from shiny import App, ui, reactive, render, req
-from pycompound.spec_lib_matching import run_spec_lib_matching_on_HRMS_data 
-from pycompound.spec_lib_matching import run_spec_lib_matching_on_NRMS_data 
-from pycompound.spec_lib_matching import tune_params_on_HRMS_data_grid
-from pycompound.spec_lib_matching import tune_params_on_NRMS_data_grid
-from pycompound.spec_lib_matching import tune_params_on_HRMS_data_grid_shiny
-from pycompound.spec_lib_matching import tune_params_on_NRMS_data_grid_shiny
-from pycompound.spec_lib_matching import tune_params_DE
-from pycompound.plot_spectra import generate_plots_on_HRMS_data
-from pycompound.plot_spectra import generate_plots_on_NRMS_data
+from shiny.types import SilentException
 from pathlib import Path
 from contextlib import redirect_stdout, redirect_stderr
+import contextlib
 import subprocess
 import traceback
 import asyncio
@@ -24,10 +17,2320 @@ import netCDF4 as nc
 from pyteomics import mgf, mzml
 import ast
 from numbers import Real
-
+import logging
+from scipy.optimize import differential_evolution
+import scipy
+import scipy.stats
+from itertools import product
+import json
+import re
+import urllib.parse
+import urllib.request
+import matplotlib
+
+matplotlib.rcParams['svg.fonttype'] = 'none'
 
 _LOG_QUEUE: asyncio.Queue[str] = asyncio.Queue()
 
+_ADDUCT_PAT = re.compile(r"\s*(?:\[(M[^\]]+)\]|(M[+-][A-Za-z0-9]+)\+?)\s*$", re.IGNORECASE)
+
+def start_log_consumer():
+    if getattr(start_log_consumer, "_started", False):
+        return
+    start_log_consumer._started = True
+
+    async def _consume():
+        while True:
+            s = await _LOG_QUEUE.get()
+            match_log_rv.set(match_log_rv.get() + s)
+            await reactive.flush()
+
+    asyncio.create_task(_consume())
+
+
+def start_log_consumer():
+    if getattr(start_log_consumer, "_started", False):
+        return
+    start_log_consumer._started = True
+
+    async def _consume():
+        while True:
+            s = await _LOG_QUEUE.get()
+            match_log_rv.set(match_log_rv.get() + s)
+            await reactive.flush()
+
+    asyncio.create_task(_consume())
+
+
+
+def _strip_adduct(name: str) -> str:
+    return _ADDUCT_PAT.sub("", name).strip()
+
+def get_pubchem_url(query: str) -> str:
+    base_name = _strip_adduct(query)
+    endpoint = ("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/" + urllib.parse.quote(base_name) + "/cids/TXT")
+    try:
+        with urllib.request.urlopen(endpoint, timeout=10) as r:
+            txt = r.read().decode("utf-8").strip()
+        cid = txt.splitlines()[0].strip()
+        if cid.isdigit():
+            return f"https://pubchem.ncbi.nlm.nih.gov/compound/{cid}"
+    except Exception:
+        pass
+    q = urllib.parse.quote(base_name)
+    return f"https://pubchem.ncbi.nlm.nih.gov/#query={q}"
+
+
+
+def build_library_from_raw_data(input_path=None, output_path=None, is_reference=False):
+    if input_path is None:
+        print('Error: please specify input_path (i.e. the path to the input mgf, mzML, cdf, json, or msp file). Mandatory argument.')
+        sys.exit()
+
+    if output_path is None:
+        tmp = input_path.split('/')
+        tmp = tmp[(len(tmp)-1)]
+        basename = tmp.split('.')[0]
+        output_path = f'{Path.cwd()}/{basename}.csv'
+        print(f'Warning: no output_path specified, so library is written to {output_path}')
+
+    if is_reference not in [True,False]:
+        print('Error: is_reference must be either \'True\' or \'False\'.')
+        sys.exit()
+
+    last_three_chars = input_path[(len(input_path)-3):len(input_path)]
+    last_four_chars = input_path[(len(input_path)-4):len(input_path)]
+    if last_three_chars == 'mgf' or last_three_chars == 'MGF':
+        input_file_type = 'mgf'
+    elif last_four_chars == 'mzML' or last_four_chars == 'mzml' or last_four_chars == 'MZML':
+        input_file_type = 'mzML'
+    elif last_four_chars == 'json' or last_four_chars == 'JSON':
+        input_file_type = 'json'
+    elif last_three_chars == 'cdf' or last_three_chars == 'CDF':
+        input_file_type = 'cdf'
+    elif last_three_chars == 'msp' or last_three_chars == 'MSP':
+        input_file_type = 'msp'
+    else:
+        print('ERROR: either an \'mgf\', \'mzML\', \'cdf\', \'json\', or \'msp\' file must be passed to --input_path')
+        sys.exit()
+
+
+
+def generate_plots_on_HRMS_data(query_data=None, reference_data=None, precursor_ion_mz=None, precursor_ion_mz_tolerance=None, ionization_mode=None, collision_energy=None, spectrum_ID1=None, spectrum_ID2=None, print_url_spectrum1='No', print_url_spectrum2='No', similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FCNMWL', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, window_size_centroiding=0.5, window_size_matching=0.5, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, y_axis_transformation='normalized', output_path=None, return_plot=False):
+
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the TXT file of the query data.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = query_data[:-3] + 'txt'
+            #build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=True)
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_query = pd.read_csv(query_data, sep='\t')
+        unique_query_ids = df_query['id'].unique().tolist()
+        unique_query_ids = [str(tmp) for tmp in unique_query_ids]
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the TXT file of the reference data.')
+        sys.exit()
+    else:
+        extension = reference_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = reference_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=reference_data, output_path=output_path_tmp, is_reference=True)
+            df_reference = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_reference = pd.read_csv(reference_data, sep='\t')
+            cols_tmp = df_reference.columns.tolist()
+            if 'precursor_ion_mz' in cols_tmp and 'ionization_mode' in cols_tmp and 'collision_energy' in cols_tmp:
+                if precursor_ion_mz is not None and precursor_ion_mz_tolerance is not None:
+                    df_reference = df_reference.loc[(df_reference['precursor_ion_mz'] > (precursor_ion_mz-precursor_ion_mz_tolerance) & df_reference['precursor_ion_mz'] < (precursor_ion_mz+precursor_ion_mz_tolerance))]
+                if ionization_mode is not None:
+                    df_reference = df_reference.loc[df_reference['ionization_mode'==ionization_mode]]
+                if collision_energy is not None:
+                    df_reference = df_reference.loc[df_reference['collision_energy'==collision_energy]]
+                df_reference = df_reference.drop(columns=['precursor_ion_mz','ionization_mode','collision_energy'])
+        unique_reference_ids = df_reference['id'].unique().tolist()
+        unique_reference_ids = [str(tmp) for tmp in unique_reference_ids]
+
+    if spectrum_ID1 is not None:
+        spectrum_ID1 = str(spectrum_ID1)
+    else:
+        spectrum_ID1 = str(df_query['id'].iloc[0])
+        print('No argument passed to spectrum_ID1; using the first spectrum in query_data.')
+
+    if spectrum_ID2 is not None:
+        spectrum_ID2 = str(spectrum_ID2)
+    else:
+        spectrum_ID2 = str(df_reference['id'].iloc[0])
+        print('No argument passed to spectrum_ID2; using the first spectrum in reference_data.')
+
+    if spectrum_preprocessing_order is not None:
+        spectrum_preprocessing_order = list(spectrum_preprocessing_order)
+    else:
+        spectrum_preprocessing_order = ['F', 'C', 'N', 'M', 'W', 'L']
+    if 'M' not in spectrum_preprocessing_order:
+        print(f'Error: \'M\' must be a character in spectrum_preprocessing_order.')
+        sys.exit()
+    if 'C' in spectrum_preprocessing_order:
+        if spectrum_preprocessing_order.index('C') > spectrum_preprocessing_order.index('M'):
+            print(f'Error: \'C\' must come before \'M\' in spectrum_preprocessing_order.')
+            sys.exit()
+    if set(spectrum_preprocessing_order) - {'F','C','N','M','W','L'}:
+        print(f'Error: spectrum_preprocessing_order must contain only \'C\', \'F\', \'M\', \'N\', \'L\', \'W\'.')
+        sys.exit()
+
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger.')
+        sys.exit()
+
+    if isinstance(int_min,int) is True:
+        int_min = float(int_min)
+    if isinstance(int_max,int) is True:
+        int_max = float(int_max)
+    if isinstance(mz_min,int) is False or isinstance(mz_max,int) is False or isinstance(int_min,float) is False or isinstance(int_max,float) is False:
+        print('Error: mz_min must be a non-negative integer, mz_max must be a positive integer, int_min must be a non-negative float, and int_max must be a positive float')
+        sys.exit()
+    if mz_min < 0:
+        print('\nError: mz_min should be a non-negative integer')
+        sys.exit()
+    if mz_max <= 0:
+        print('\nError: mz_max should be a positive integer')
+        sys.exit()
+    if int_min < 0:
+        print('\nError: int_min should be a non-negative float')
+        sys.exit()
+    if int_max <= 0:
+        print('\nError: int_max should be a positive float')
+        sys.exit()
+
+    if isinstance(window_size_centroiding,float) is False or window_size_centroiding <= 0.0:
+        print('Error: window_size_centroiding must be a positive float.')
+        sys.exit()
+    if isinstance(window_size_matching,float) is False or window_size_matching<= 0.0:
+        print('Error: window_size_matching must be a positive float.')
+        sys.exit()
+
+    if isinstance(noise_threshold,int) is True:
+        noise_threshold = float(noise_threshold)
+    if isinstance(noise_threshold,float) is False or noise_threshold < 0:
+        print('Error: noise_threshold must be a positive float.')
+        sys.exit()
+
+    if isinstance(wf_intensity,int) is True:
+        wf_intensity = float(wf_intensity)
+    if isinstance(wf_mz,int) is True:
+        wf_mz = float(wf_mz)
+    if isinstance(wf_intensity,float) is False or isinstance(wf_mz,float) is False:
+        print('Error: wf_mz and wf_intensity must be integers or floats')
+        sys.exit()
+
+    if entropy_dimension <= 0:
+        print('\nError: entropy_dimension should be a positive float')
+        sys.exit()
+    else:
+        q = entropy_dimension
+
+    normalization_method = 'standard' #consider including additional normalization methods to transform intensities into a probability distribution; softmax results in many numerical errors/warnings
+
+    if y_axis_transformation not in ['normalized','none','log10','sqrt']:
+        print('Error: y_axis_transformation must be either \'normalized\', \'none\', \'log10\', or \'sqrt\'.')
+        sys.exit()
+
+    if output_path is None:
+        print(f'Warning: plots will be saved to the svg ./spectrum1_{spectrum_ID1}_spectrum2_{spectrum_ID2}.svg in the current working directory.')
+        output_path = f'{Path.cwd()}/spectrum1_{spectrum_ID1}_spectrum2_{spectrum_ID2}.svg'
+
+
+    if spectrum_ID1 in unique_query_ids and spectrum_ID2 in unique_query_ids:
+        query_idx = unique_query_ids.index(spectrum_ID1)
+        reference_idx = unique_query_ids.index(spectrum_ID2)
+        q_idxs_tmp = np.where(df_query.iloc[:,0].astype(str) == unique_query_ids[query_idx])[0]
+        r_idxs_tmp = np.where(df_query.iloc[:,0].astype(str) == unique_query_ids[reference_idx])[0]
+        q_spec = np.asarray(pd.concat([df_query.iloc[q_idxs_tmp,1], df_query.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        r_spec = np.asarray(pd.concat([df_query.iloc[r_idxs_tmp,1], df_query.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+    elif spectrum_ID1 in unique_reference_ids and spectrum_ID2 in unique_reference_ids:
+        query_idx = unique_reference_ids.index(spectrum_ID1)
+        reference_idx = unique_reference_ids.index(spectrum_ID2)
+        q_idxs_tmp = np.where(df_reference.iloc[:,0].astype(str) == unique_reference_ids[query_idx])[0]
+        r_idxs_tmp = np.where(df_reference.iloc[:,0].astype(str) == unique_reference_ids[reference_idx])[0]
+        q_spec = np.asarray(pd.concat([df_reference.iloc[q_idxs_tmp,1], df_reference.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        r_spec = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+    else:
+        if spectrum_ID1 in unique_reference_ids and spectrum_ID2 in unique_query_ids:
+            spec_tmp = spectrum_ID1
+            spectrum_ID1 = spectrum_ID2
+            spectrum_ID2 = spec_tmp
+        query_idx = unique_query_ids.index(spectrum_ID1)
+        reference_idx = unique_reference_ids.index(spectrum_ID2)
+        q_idxs_tmp = np.where(df_query['id'].astype(str) == unique_query_ids[query_idx])[0]
+        r_idxs_tmp = np.where(df_reference['id'].astype(str) == unique_reference_ids[reference_idx])[0]
+        q_spec = np.asarray(pd.concat([df_query['mz_ratio'].iloc[q_idxs_tmp], df_query['intensity'].iloc[q_idxs_tmp]], axis=1).reset_index(drop=True))
+        r_spec = np.asarray(pd.concat([df_reference['mz_ratio'].iloc[r_idxs_tmp], df_reference['intensity'].iloc[r_idxs_tmp]], axis=1).reset_index(drop=True))
+
+
+    q_spec_pre_trans = q_spec.copy()
+    r_spec_pre_trans = r_spec.copy()
+    q_spec_pre_trans[:,1] = q_spec_pre_trans[:,1].astype(float)
+    r_spec_pre_trans[:,1] = r_spec_pre_trans[:,1].astype(float)
+
+    if y_axis_transformation == 'normalized':
+        q_spec_pre_trans[:,1] = q_spec_pre_trans[:,1] / np.max(q_spec_pre_trans[:,1])
+        r_spec_pre_trans[:,1] = r_spec_pre_trans[:,1] / np.max(r_spec_pre_trans[:,1])
+        ylab = 'Normalized Intensity'
+    elif y_axis_transformation == 'log10':
+        q_spec_pre_trans[:,1] = np.log10(np.array(q_spec_pre_trans[:,1]+1,dtype=float))
+        r_spec_pre_trans[:,1] = np.log10(np.array(r_spec_pre_trans[:,1]+1,dtype=float))
+        ylab = 'log10(Intensity)'
+    elif y_axis_transformation == 'sqrt':
+        q_spec_pre_trans[:,1] = np.sqrt(np.array(q_spec_pre_trans[:,1],dtype=float))
+        r_spec_pre_trans[:,1] = np.sqrt(np.array(r_spec_pre_trans[:,1],dtype=float))
+        ylab = 'sqrt(Intensity)'
+    else:
+        ylab = 'Raw Intensity'
+
+    fig, axes = plt.subplots(nrows=2, ncols=1)
+
+    plt.subplot(2,1,1)
+    plt.vlines(x=q_spec_pre_trans[:,0], ymin=[0]*q_spec_pre_trans.shape[0], ymax=q_spec_pre_trans[:,1], linewidth=3, color='blue', label=f'Spectrum ID 1: {spectrum_ID1}')
+    plt.vlines(x=r_spec_pre_trans[:,0], ymin=[0]*r_spec_pre_trans.shape[0], ymax=-r_spec_pre_trans[:,1], linewidth=3, color='red', label=f'Spectrum ID 2: {spectrum_ID2}')
+    plt.xlabel('m/z',fontsize=7)
+    plt.ylabel(ylab, fontsize=7)
+    plt.xticks(fontsize=7)
+    plt.yticks(fontsize=7)
+    plt.title('Untransformed Spectra', fontsize=10)
+
+    mz_min_tmp_q = round(q_spec[:,0].min(),1)
+    mz_min_tmp_r = round(r_spec[:,0].min(),1)
+    int_min_tmp_q = round(q_spec[:,1].min(),1)
+    int_min_tmp_r = round(r_spec[:,1].min(),1)
+    mz_max_tmp_q = round(q_spec[:,0].max(),1)
+    mz_max_tmp_r = round(r_spec[:,0].max(),1)
+    int_max_tmp_q = round(q_spec[:,1].max(),1)
+    int_max_tmp_r = round(r_spec[:,1].max(),1)
+    mz_min_tmp = min([mz_min_tmp_q,mz_min_tmp_r])
+    mz_max_tmp = min([mz_max_tmp_q,mz_max_tmp_r])
+    int_min_tmp = min([int_min_tmp_q,int_min_tmp_r])
+    int_max_tmp = max([int_max_tmp_q,int_max_tmp_r])
+
+    is_matched = False
+    for transformation in spectrum_preprocessing_order:
+        if transformation == 'C' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+            q_spec = centroid_spectrum(q_spec, window_size=window_size_centroiding) 
+            r_spec = centroid_spectrum(r_spec, window_size=window_size_centroiding) 
+        if transformation == 'M' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+            m_spec = match_peaks_in_spectra(spec_a=q_spec, spec_b=r_spec, window_size=window_size_matching)
+            q_spec = m_spec[:,0:2]
+            r_spec = m_spec[:,[0,2]]
+            is_matched = True
+        if transformation == 'W' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+            q_spec[:,1] = wf_transform(q_spec[:,0], q_spec[:,1], wf_mz, wf_intensity)
+            r_spec[:,1] = wf_transform(r_spec[:,0], r_spec[:,1], wf_mz, wf_intensity)
+        if transformation == 'L' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+            q_spec[:,1] = LE_transform(q_spec[:,1], LET_threshold, normalization_method=normalization_method)
+            r_spec[:,1] = LE_transform(r_spec[:,1], LET_threshold, normalization_method=normalization_method)
+        if transformation == 'N' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+            q_spec = remove_noise(q_spec, nr = noise_threshold)
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
+                r_spec = remove_noise(r_spec, nr = noise_threshold)
+        if transformation == 'F' and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+            q_spec = filter_spec_lcms(q_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max, is_matched = is_matched)
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
+                r_spec = filter_spec_lcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max, is_matched = is_matched)
+
+    q_ints = q_spec[:,1]
+    r_ints = r_spec[:,1]
+
+    if np.sum(q_ints) != 0 and np.sum(r_ints) != 0 and q_spec.shape[0] > 1 and r_spec.shape[1] > 1:
+        similarity_score = get_similarity(similarity_measure, q_ints, r_ints, weights, entropy_dimension)
+    else:
+        similarity_score = 0
+
+    plt.subplot(2,1,2)
+
+    if q_spec.shape[0] > 1:
+        if np.max(q_spec[:,1]) == 0 or np.max(r_spec[:,1]) == 0:
+            plt.text(0.5, 0.5, 'The query and/or reference spectrum has no non-zero intensities after transformations.\n Change transformation parameters.', ha='center', va='center', fontsize=7, color='black')
+            plt.xticks([])
+            plt.yticks([])
+        else:
+            if y_axis_transformation == 'normalized':
+                q_spec[:,1] = q_spec[:,1] / np.max(q_spec[:,1])
+                r_spec[:,1] = r_spec[:,1] / np.max(r_spec[:,1])
+                ylab='Normalized Intensity'
+            elif y_axis_transformation == 'log10':
+                q_spec[:,1] = np.log10(q_spec[:,1]+1)
+                r_spec[:,1] = np.log10(r_spec[:,1]+1)
+                ylab='log10(Intensity)'
+            elif y_axis_transformation == 'sqrt':
+                q_spec[:,1] = np.sqrt(q_spec[:,1])
+                r_spec[:,1] = np.sqrt(r_spec[:,1])
+                ylab='sqrt(Intensity)'
+            else:
+                ylab = 'Raw Intensity'
+            plt.vlines(x=q_spec[:,0], ymin=[0]*q_spec.shape[0], ymax=q_spec[:,1], linewidth=3, color='blue')
+            plt.vlines(x=r_spec[:,0], ymin=[0]*r_spec.shape[0], ymax=-r_spec[:,1], linewidth=3, color='red')
+            plt.xlabel('m/z', fontsize=7)
+            plt.ylabel(ylab, fontsize=7)
+            plt.xticks(fontsize=7)
+            plt.yticks(fontsize=7)
+            plt.title(f'Transformed Spectra', fontsize=10)
+    else:
+        plt.text(0.5, 0.5, 'All points in the spectra were removed during preprocessing. \nChange the spectrum_preprocesing_order and/or change other spectrum-preprocessing parameters.', ha='center', va='center', fontsize=7, color='black')
+        plt.xticks([])
+        plt.yticks([])
+
+    plt.subplots_adjust(top=0.8, hspace=0.92, bottom=0.3)
+    plt.figlegend(loc='upper center')
+
+    fig.text(0.05, 0.20, f'Similarity Measure: {similarity_measure.capitalize()}', fontsize=7)
+    fig.text(0.05, 0.17, f'Similarity Score: {round(similarity_score, 4)}', fontsize=7)
+    fig.text(0.05, 0.14, f"Spectrum Preprocessing Order: {''.join(spectrum_preprocessing_order)}", fontsize=7)
+    fig.text(0.05, 0.11, f'High Quality Reference Library: {str(high_quality_reference_library)}', fontsize=7)
+    fig.text(0.05, 0.08, f'Window Size (Centroiding): {window_size_centroiding}', fontsize=7)
+    fig.text(0.05, 0.05, f'Window Size (Matching): {window_size_matching}', fontsize=7)
+    if similarity_measure == 'mixture':
+        fig.text(0.05, 0.02, f'Weights for mixture similarity: {weights}', fontsize=7)
+
+    fig.text(0.40, 0.20, f'Raw-Scale M/Z Range: [{mz_min_tmp},{mz_max_tmp}]', fontsize=7)
+    fig.text(0.40, 0.17, f'Raw-Scale Intensity Range: [{int_min_tmp},{int_max_tmp}]', fontsize=7)
+    fig.text(0.40, 0.14, f'Noise Threshold: {noise_threshold}', fontsize=7)
+    fig.text(0.40, 0.11, f'Weight Factors (m/z,intensity): ({wf_mz},{wf_intensity})', fontsize=7)
+    fig.text(0.40, 0.08, f'Low-Entropy Threshold: {LET_threshold}', fontsize=7)
+
+    if print_url_spectrum1 == 'Yes' and print_url_spectrum2 == 'Yes':
+        url_tmp1 = get_pubchem_url(query=spectrum_ID1)
+        url_tmp2 = get_pubchem_url(query=spectrum_ID2)
+        t1 = fig.text(0.40, 0.05, f'PubChem URL for {spectrum_ID1}: {url_tmp1}', fontsize=7)
+        t2 = fig.text(0.40, 0.02, f'PubChem URL for {spectrum_ID2}: {url_tmp2}', fontsize=7)
+        t1.set_url(url_tmp1)
+        t2.set_url(url_tmp2)
+
+    if print_url_spectrum1 == 'Yes' and print_url_spectrum2 == 'No':
+        url_tmp1 = get_pubchem_url(query=spectrum_ID1)
+        t1 = fig.text(0.40, 0.05, f'PubChem URL for {spectrum_ID1}: {url_tmp1}', fontsize=7)
+        t1.set_url(url_tmp1)
+
+    if print_url_spectrum1 == 'No' and print_url_spectrum2 == 'Yes':
+        url_tmp2 = get_pubchem_url(query=spectrum_ID2)
+        t2 = fig.text(0.40, 0.05, f'PubChem URL for {spectrum_ID2}: {url_tmp2}', fontsize=7)
+        t2.set_url(url_tmp2)
+
+    fig.savefig(output_path, format='svg')
+
+    if return_plot == True:
+        return fig
+
+
+
+
+def generate_plots_on_NRMS_data(query_data=None, reference_data=None, spectrum_ID1=None, spectrum_ID2=None, print_url_spectrum1='No', print_url_spectrum2='No', similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FNLW', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, y_axis_transformation='normalized', output_path=None, return_plot=False):
+
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the TXT file of the query data.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_query = pd.read_csv(query_data, sep='\t')
+        unique_query_ids = df_query['id'].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the TXT file of the reference data.')
+        sys.exit()
+    else:
+        extension = reference_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = reference_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=reference_data, output_path=output_path_tmp, is_reference=True)
+            df_reference = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_reference = pd.read_csv(reference_data, sep='\t')
+            unique_reference_ids = df_reference['id'].unique()
+
+
+    if spectrum_ID1 is not None:
+        spectrum_ID1 = str(spectrum_ID1)
+    else:
+        spectrum_ID1 = str(df_query.iloc[0,0])
+        print('No argument passed to spectrum_ID1; using the first spectrum in query_data.')
+
+    if spectrum_ID2 is not None:
+        spectrum_ID2 = str(spectrum_ID2)
+    else:
+        spectrum_ID2 = str(df_reference.iloc[0,0])
+        print('No argument passed to spectrum_ID2; using the first spectrum in reference_data.')
+
+    if spectrum_preprocessing_order is not None:
+        spectrum_preprocessing_order = list(spectrum_preprocessing_order)
+    else:
+        spectrum_preprocessing_order = ['F','N','W','L']
+    if set(spectrum_preprocessing_order) - {'F','N','W','L'}:
+        print(f'Error: spectrum_preprocessing_order must contain only \'F\', \'N\', \'W\', \'L\'.')
+        sys.exit()
+
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kulczynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger.')
+        sys.exit()
+
+    if isinstance(int_min,int) is True:
+        int_min = float(int_min)
+    if isinstance(int_max,int) is True:
+        int_max = float(int_max)
+    if isinstance(mz_min,int) is False or isinstance(mz_max,int) is False or isinstance(int_min,float) is False or isinstance(int_max,float) is False:
+        print('Error: mz_min must be a non-negative integer, mz_max must be a positive integer, int_min must be a non-negative float, and int_max must be a positive float')
+        sys.exit()
+    if mz_min < 0:
+        print('\nError: mz_min should be a non-negative integer')
+        sys.exit()
+    if mz_max <= 0:
+        print('\nError: mz_max should be a positive integer')
+        sys.exit()
+    if int_min < 0:
+        print('\nError: int_min should be a non-negative float')
+        sys.exit()
+    if int_max <= 0:
+        print('\nError: int_max should be a positive float')
+        sys.exit()
+
+    if isinstance(noise_threshold,int) is True:
+        noise_threshold = float(noise_threshold)
+    if isinstance(noise_threshold,float) is False or noise_threshold < 0:
+        print('Error: noise_threshold must be a positive float.')
+        sys.exit()
+
+    if isinstance(wf_intensity,int) is True:
+        wf_intensity = float(wf_intensity)
+    if isinstance(wf_mz,int) is True:
+        wf_mz = float(wf_mz)
+    if isinstance(wf_intensity,float) is False or isinstance(wf_mz,float) is False:
+        print('Error: wf_mz and wf_intensity must be integers or floats')
+        sys.exit()
+
+    if entropy_dimension <= 0:
+        print('\nError: entropy_dimension should be a positive float')
+        sys.exit()
+    else:
+        q = entropy_dimension
+
+    normalization_method = 'standard' #consider including additional normalization methods to transform intensities into a probability distribution; softmax results in many numerical errors/warnings
+
+    if y_axis_transformation not in ['normalized','none','log10','sqrt']:
+        print('Error: y_axis_transformation must be either \'normalized\', \'none\', \'log10\', or \'sqrt\'.')
+        sys.exit()
+
+    if output_path is None:
+        print(f'Warning: plots will be saved to the svg ./spectrum1_{spectrum_ID1}_spectrum2_{spectrum_ID2}.svg in the current working directory.')
+        output_path = f'{Path.cwd()}/spectrum1_{spectrum_ID1}_spectrum2_{spectrum_ID2}.svg'
+
+    min_mz = np.min([df_query['mz_ratio'].min(), df_reference['mz_ratio'].min()])
+    max_mz = np.max([df_query['mz_ratio'].max(), df_reference['mz_ratio'].max()])
+    mzs = np.linspace(min_mz,max_mz,(max_mz-min_mz+1))
+
+    unique_query_ids = df_query['id'].unique().tolist()
+    unique_reference_ids = df_reference['id'].unique().tolist()
+    unique_query_ids = [str(ID) for ID in unique_query_ids]
+    unique_reference_ids = [str(ID) for ID in unique_reference_ids]
+    common_IDs = np.intersect1d([str(ID) for ID in unique_query_ids], [str(ID) for ID in unique_reference_ids])
+    if len(common_IDs) > 0:
+        print(f'Warning: the query and reference library have overlapping IDs: {common_IDs}')
+
+    if spectrum_ID1 in unique_query_ids and spectrum_ID2 in unique_query_ids:
+        q_idxs_tmp = np.where(df_query.iloc[:,0].astype(str) == spectrum_ID1)[0]
+        r_idxs_tmp = np.where(df_query.iloc[:,0].astype(str) == spectrum_ID2)[0]
+        q_spec = np.asarray(pd.concat([df_query.iloc[q_idxs_tmp,1], df_query.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        r_spec = np.asarray(pd.concat([df_query.iloc[r_idxs_tmp,1], df_query.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+    elif spectrum_ID1 in unique_reference_ids and spectrum_ID2 in unique_reference_ids:
+        q_idxs_tmp = np.where(df_reference.iloc[:,0].astype(str) == spectrum_ID1)[0]
+        r_idxs_tmp = np.where(df_reference.iloc[:,0].astype(str) == spectrum_ID2)[0]
+        q_spec = np.asarray(pd.concat([df_reference.iloc[q_idxs_tmp,1], df_reference.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        r_spec = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+    else:
+        if spectrum_ID1 in unique_reference_ids and spectrum_ID2 in unique_query_ids:
+            spec_tmp = spectrum_ID1
+            spectrum_ID1 = spectrum_ID2
+            spectrum_ID2 = spec_tmp
+        q_idxs_tmp = np.where(df_query['id'].astype(str) == spectrum_ID1)[0]
+        r_idxs_tmp = np.where(df_reference['id'].astype(str) == spectrum_ID2)[0]
+        q_spec = np.asarray(pd.concat([df_query['mz_ratio'].iloc[q_idxs_tmp], df_query['intensity'].iloc[q_idxs_tmp]], axis=1).reset_index(drop=True))
+        r_spec = np.asarray(pd.concat([df_reference['mz_ratio'].iloc[r_idxs_tmp], df_reference['intensity'].iloc[r_idxs_tmp]], axis=1).reset_index(drop=True))
+
+    q_spec = convert_spec(q_spec,mzs)
+    r_spec = convert_spec(r_spec,mzs)
+
+    int_min_tmp_q = min(q_spec[q_spec[:,1].nonzero(),1][0])
+    int_min_tmp_r = min(r_spec[r_spec[:,1].nonzero(),1][0])
+    int_max_tmp_q = max(q_spec[q_spec[:,1].nonzero(),1][0])
+    int_max_tmp_r = max(r_spec[r_spec[:,1].nonzero(),1][0])
+    int_min_tmp = int(min([int_min_tmp_q,int_min_tmp_r]))
+    int_max_tmp = int(max([int_max_tmp_q,int_max_tmp_r]))
+    
+    fig, axes = plt.subplots(nrows=2, ncols=1)
+
+    plt.subplot(2,1,1)
+
+    if np.max(q_spec[:,1]) == 0 or np.max(r_spec[:,1]) == 0:
+        plt.text(0.5, 0.5, 'The query and/or reference spectrum has no non-zero intensities after transformations.\n Change transformation parameters.', ha='center', va='center', fontsize=7, color='black')
+        plt.xticks([])
+        plt.yticks([])
+    else:
+        q_spec_pre_trans = q_spec.copy()
+        r_spec_pre_trans = r_spec.copy()
+        q_spec_pre_trans[:,1] = q_spec_pre_trans[:,1].astype(float)
+        r_spec_pre_trans[:,1] = r_spec_pre_trans[:,1].astype(float)
+
+        if y_axis_transformation == 'normalized':
+            q_spec_pre_trans[:,1] = q_spec_pre_trans[:,1] / np.max(q_spec_pre_trans[:,1])
+            r_spec_pre_trans[:,1] = r_spec_pre_trans[:,1] / np.max(r_spec_pre_trans[:,1])
+            ylab = 'Normalized Intensity'
+        elif y_axis_transformation == 'log10':
+            q_spec_pre_trans[:,1] = np.log10(q_spec_pre_trans[:,1]+1)
+            r_spec_pre_trans[:,1] = np.log10(r_spec_pre_trans[:,1]+1)
+            ylab = 'log10(Intensity)'
+        elif y_axis_transformation == 'sqrt':
+            q_spec_pre_trans[:,1] = np.sqrt(q_spec_pre_trans[:,1])
+            r_spec_pre_trans[:,1] = np.sqrt(r_spec_pre_trans[:,1])
+            ylab = 'sqrt(Intensity)'
+        else:
+            ylab = 'Raw Intensity'
+        plt.vlines(x=q_spec_pre_trans[:,0], ymin=[0]*len(q_spec_pre_trans[:,0]), ymax=q_spec_pre_trans[:,1], linewidth=3, color='blue', label=f'Spectrum ID1: {spectrum_ID1}')
+        plt.vlines(x=r_spec_pre_trans[:,0], ymin=[0]*len(r_spec_pre_trans[:,0]), ymax=-r_spec_pre_trans[:,1], linewidth=3, color='red', label=f'Spectrum ID2: {spectrum_ID2}')
+        plt.xlabel('m/z',fontsize=7)
+        plt.ylabel(ylab, fontsize=7)
+        plt.xticks(fontsize=7)
+        plt.yticks(fontsize=7)
+        plt.title('Untransformed Query and Reference Spectra', fontsize=10)
+
+    for transformation in spectrum_preprocessing_order:
+        if transformation == 'W':
+            q_spec[:,1] = wf_transform(q_spec[:,0], q_spec[:,1], wf_mz, wf_intensity)
+            r_spec[:,1] = wf_transform(r_spec[:,0], r_spec[:,1], wf_mz, wf_intensity)
+        if transformation == 'L':
+            q_spec[:,1] = LE_transform(q_spec[:,1], LET_threshold, normalization_method)
+            r_spec[:,1] = LE_transform(r_spec[:,1], LET_threshold, normalization_method)
+        if transformation == 'N':
+            q_spec = remove_noise(q_spec, nr = noise_threshold)
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
+                r_spec = remove_noise(r_spec, nr = noise_threshold)
+        if transformation == 'F':
+            q_spec = filter_spec_gcms(q_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
+            if high_quality_reference_library == False or high_quality_reference_library == 'False':
+                r_spec = filter_spec_gcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
+
+    if q_spec.shape[0] > 1:
+        similarity_score = get_similarity(similarity_measure, q_spec[:,1], r_spec[:,1], weights, entropy_dimension)
+    else:
+        similarity_score = 0
+
+ 
+    plt.subplot(2,1,2)
+
+    if q_spec.shape[0] == 0 or r_spec.shape[0] == 0:
+        plt.text(0.5, 0.5, 'The query and/or reference spectrum has no ion fragments left after transformations.\n Change transformation parameters.', ha='center', va='center', fontsize=7, color='black')
+        plt.xticks([])
+        plt.yticks([])
+    elif np.max(q_spec[:,1]) == 0 or np.max(r_spec[:,1]) == 0:
+        plt.text(0.5, 0.5, 'The query and/or reference spectrum has no non-zero intensities after transformations.\n Change transformation parameters.', ha='center', va='center', fontsize=7, color='black')
+        plt.xticks([])
+        plt.yticks([])
+    else:
+        if y_axis_transformation == 'normalized':
+            q_spec[:,1] = q_spec[:,1] / np.max(q_spec[:,1])
+            r_spec[:,1] = r_spec[:,1] / np.max(r_spec[:,1])
+            ylab='Normalized Intensity'
+        elif y_axis_transformation == 'log10':
+            q_spec[:,1] = np.log10(q_spec[:,1]+1)
+            r_spec[:,1] = np.log10(r_spec[:,1]+1)
+            ylab='log10(Intensity)'
+        elif y_axis_transformation == 'sqrt':
+            q_spec[:,1] = np.sqrt(q_spec[:,1])
+            r_spec[:,1] = np.sqrt(r_spec[:,1])
+            ylab='sqrt(Intensity)'
+        else:
+            ylab = 'Raw Intensity'
+        plt.vlines(x=mzs, ymin=[0]*len(mzs), ymax=q_spec[:,1], linewidth=3, color='blue')
+        plt.vlines(x=mzs, ymin=[0]*len(mzs), ymax=-r_spec[:,1], linewidth=3, color='red')
+        plt.xlabel('m/z', fontsize=7)
+        plt.ylabel(ylab, fontsize=7)
+        plt.xticks(fontsize=7)
+        plt.yticks(fontsize=7)
+        plt.title(f'Transformed Query and Reference Spectra', fontsize=10)
+
+    plt.subplots_adjust(top=0.8, hspace=0.92, bottom=0.3)
+    plt.figlegend(loc='upper center')
+
+    fig.text(0.05, 0.20, f'Similarity Measure: {similarity_measure.capitalize()}', fontsize=7)
+    fig.text(0.05, 0.17, f'Similarity Score: {round(similarity_score, 4)}', fontsize=7)
+    fig.text(0.05, 0.14, f"Spectrum Preprocessing Order: {''.join(spectrum_preprocessing_order)}", fontsize=7)
+    fig.text(0.05, 0.11, f'High Quality Reference Library: {str(high_quality_reference_library)}', fontsize=7)
+    fig.text(0.05, 0.08, f'Weight Factors (m/z,intensity): ({wf_mz},{wf_intensity})', fontsize=7)
+    if similarity_measure == 'mixture':
+        fig.text(0.05, 0.05, f'Weights for mixture similarity: {weights}', fontsize=7)
+
+    fig.text(0.40, 0.20, f'Raw-Scale M/Z Range: [{min_mz},{max_mz}]', fontsize=7)
+    fig.text(0.40, 0.17, f'Raw-Scale Intensity Range: [{int_min_tmp},{int_max_tmp}]', fontsize=7)
+    fig.text(0.40, 0.14, f'Noise Threshold: {noise_threshold}', fontsize=7)
+    fig.text(0.40, 0.11, f'Low-Entropy Threshold: {LET_threshold}', fontsize=7)
+
+    if print_url_spectrum1 == 'Yes' and print_url_spectrum2 == 'Yes':
+        url_tmp1 = get_pubchem_url(query=spectrum_ID1)
+        url_tmp2 = get_pubchem_url(query=spectrum_ID2)
+        t1 = fig.text(0.40, 0.08, f'PubChem URL for {spectrum_ID1}: {url_tmp1}', fontsize=7)
+        t2 = fig.text(0.40, 0.05, f'PubChem URL for {spectrum_ID2}: {url_tmp2}', fontsize=7)
+        t1.set_url(url_tmp1)
+        t2.set_url(url_tmp2)
+
+    if print_url_spectrum1 == 'Yes' and print_url_spectrum2 == 'No':
+        url_tmp1 = get_pubchem_url(query=spectrum_ID1)
+        t1 = fig.text(0.40, 0.08, f'PubChem URL for {spectrum_ID1}: {url_tmp1}', fontsize=7)
+        t1.set_url(url_tmp1)
+
+    if print_url_spectrum1 == 'No' and print_url_spectrum2 == 'Yes':
+        url_tmp2 = get_pubchem_url(query=spectrum_ID2)
+        t2 = fig.text(0.40, 0.08, f'PubChem URL for {spectrum_ID2}: {url_tmp2}', fontsize=7)
+        t2.set_url(url_tmp2)
+
+    fig.savefig(output_path, format='svg')
+
+    if return_plot == True:
+        return fig
+
+
+def wf_transform(spec_mzs, spec_ints, wf_mz, wf_int):
+    spec_ints = np.power(spec_mzs, wf_mz) * np.power(spec_ints, wf_int)
+    return(spec_ints)
+
+
+def LE_transform(intensity, thresh, normalization_method):
+    intensity_tmp = normalize(intensity, method=normalization_method)
+    if np.sum(intensity_tmp) > 0:
+        S = scipy.stats.entropy(intensity_tmp.astype('float'))
+        if S > 0 and S < thresh:
+            w = (1 + S) / (1 + thresh) 
+            intensity = np.power(intensity_tmp, w)
+    else:
+        intensity = np.zeros(len(intensity))
+    return intensity 
+
+
+def normalize(intensities,method='standard'):
+    if np.sum(intensities) > 0:
+        if method == 'softmax':
+            if np.any(intensities > 700):
+                print("Warning: some intensities are too large to exponentiate. Applying standard normalization.")
+                intensities /= np.sum(intensities)
+            else:
+                intensities2 = np.exp(intensities)
+                if np.isinf(intensities2).sum() == 0:
+                    intensities = intensities / np.sum(intensities2)
+        elif method == 'standard':
+            intensities /= np.sum(intensities)
+    return(intensities)
+
+
+def filter_spec_lcms(spec, mz_min = 0, mz_max = 999999999999, int_min = 0, int_max = 999999999999, is_matched = False):
+    if is_matched == False:
+        spec = spec[spec[:,0] >= mz_min]
+        spec = spec[spec[:,0] <= mz_max]
+        spec = spec[spec[:,1] >= int_min]
+        spec = spec[spec[:,1] <= int_max]
+    else:
+        spec = spec[spec[:,0] >= mz_min]
+        spec = spec[spec[:,0] <= mz_max]
+        spec[spec[:,1] >= int_min] = 0
+        spec[spec[:,1] <= int_max] = 0
+    return(spec)
+
+
+def filter_spec_gcms(spec, mz_min = 0, mz_max = 999999999999, int_min = 0, int_max = 999999999999):
+    spec[np.where(spec[:,0] < mz_min)[0],1] = 0
+    spec[np.where(spec[:,0] > mz_max)[0],1] = 0
+    spec[np.where(spec[:,1] < int_min)[0],1] = 0
+    spec[np.where(spec[:,1] > int_max)[0],1] = 0
+    return(spec)
+
+
+def remove_noise(spec, nr):
+    if spec.shape[0] > 1:
+        if nr is not None:
+            spec[np.where(spec[:,1] < np.max(spec[:,1]) * nr)[0]] = 0
+
+    return(spec)
+
+
+def centroid_spectrum(spec, window_size):
+    spec = spec[np.argsort(spec[:,0])]
+
+    mz_array = spec[:, 0]
+    need_centroid = 0
+    if mz_array.shape[0] > 1:
+        mz_delta = mz_array[1:] - mz_array[:-1]
+        if np.min(mz_delta) <= window_size:
+            need_centroid = 1
+
+    if need_centroid:
+        intensity_order = np.argsort(-spec[:, 1])
+        spec_new = []
+        for i in intensity_order:
+            mz_delta_allowed = window_size
+
+            if spec[i, 1] > 0:
+                i_left = i - 1
+                while i_left >= 0:
+                    mz_delta_left = spec[i, 0] - spec[i_left, 0]
+                    if mz_delta_left <= mz_delta_allowed:
+                        i_left -= 1
+                    else:
+                        break
+                i_left += 1
+
+                i_right = i + 1
+                while i_right < spec.shape[0]:
+                    mz_delta_right = spec[i_right, 0] - spec[i, 0]
+                    if mz_delta_right <= mz_delta_allowed:
+                        i_right += 1
+                    else:
+                        break
+
+                intensity_sum = np.sum(spec[i_left:i_right, 1])
+                intensity_weighted_sum = np.sum(spec[i_left:i_right, 0] * spec[i_left:i_right, 1])
+
+                spec_new.append([intensity_weighted_sum / intensity_sum, intensity_sum])
+                spec[i_left:i_right, 1] = 0
+
+        spec_new = np.array(spec_new)
+        spec_new = spec_new[np.argsort(spec_new[:, 0])]
+        if spec_new.shape[0] > 1:
+            spec_new = spec_new[np.argsort(spec_new[:, 0])]
+            return spec_new
+        else:
+            return np.array([[0,0]])
+    else:
+        return spec
+
+
+
+def match_peaks_in_spectra(spec_a, spec_b, window_size):
+    a = 0
+    b = 0
+
+    spec_merged = []
+    peak_b_int = 0.
+    while a < spec_a.shape[0] and b < spec_b.shape[0]:
+        mass_delta = spec_a[a, 0] - spec_b[b, 0]
+        
+        if mass_delta < -window_size:
+            spec_merged.append([spec_a[a, 0], spec_a[a, 1], peak_b_int])
+            peak_b_int = 0.
+            a += 1
+        elif mass_delta > window_size:
+            spec_merged.append([spec_b[b, 0], 0., spec_b[b, 1]])
+            b += 1
+        else:
+            peak_b_int += spec_b[b, 1]
+            b += 1
+
+    if peak_b_int > 0.:
+        spec_merged.append([spec_a[a, 0], spec_a[a, 1], peak_b_int])
+        peak_b_int = 0.
+        a += 1
+
+    if b < spec_b.shape[0]:
+        spec_merged += [[x[0], 0., x[1]] for x in spec_b[b:]]
+
+    if a < spec_a.shape[0]:
+        spec_merged += [[x[0], x[1], 0.] for x in spec_a[a:]]
+
+    if spec_merged:
+        spec_merged = np.array(spec_merged, dtype=np.float64)
+    else:
+        spec_merged = np.array([[0., 0., 0.]], dtype=np.float64)
+    return spec_merged
+
+
+
+def convert_spec(spec, mzs):
+    ints_tmp = []
+    for i in range(0,len(mzs)):
+        if mzs[i] in spec[:,0]:
+            int_tmp = spec[np.where(spec[:,0] == mzs[i])[0][0],1]
+        else:
+            int_tmp = 0
+        ints_tmp.append(int_tmp)
+    out = np.transpose(np.array([mzs,ints_tmp]))
+    return out
+
+
+def get_reference_df(reference_data, likely_reference_IDs=None):
+    extension = reference_data.rsplit('.',1)
+    extension = extension[(len(extension)-1)]
+    if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+        output_path_tmp = reference_data[:-3] + 'txt'
+        build_library_from_raw_data(input_path=reference_data, output_path=output_path_tmp, is_reference=True)
+        df_reference = pd.read_csv(output_path_tmp, sep='\t')
+    if extension == 'txt' or extension == 'TXT':
+        df_reference = pd.read_csv(reference_data, sep='\t')
+    if likely_reference_IDs is not None:
+        likely_reference_IDs = pd.read_csv(likely_reference_IDs, header=None)
+        df_reference = df_reference.loc[df_reference.iloc[:,0].isin(likely_reference_IDs.iloc[:,0].tolist())]
+    return df_reference
+
+
+
+def S_cos(ints_a, ints_b):
+    if np.sum(ints_a) == 0 or np.sum(ints_b) == 0:
+        return(0)
+    else:
+        return np.dot(ints_a,ints_b) / (np.sqrt(sum(np.power(ints_a,2))) * np.sqrt(sum(np.power(ints_b,2))))
+
+
+def ent_renyi(ints, q):
+    return np.log(sum(np.power(ints,q))) / (1-q)
+
+
+def ent_tsallis(ints, q):
+    return (sum(np.power(ints,q))-1) / (1-q)
+
+
+def S_shannon(ints_a, ints_b):
+    ent_a = scipy.stats.entropy(ints_a)
+    ent_b = scipy.stats.entropy(ints_b)
+    ent_ab = scipy.stats.entropy(ints_a + ints_b)
+    return(1 - (2 * ent_ab - ent_a - ent_b)/np.log(4))
+
+
+def S_renyi(ints_a, ints_b, q):
+    if q == 1:
+        print('Warning: the Renyi Entropy Similarity Measure is equivalent to the Shannon Entropy Similarity Measure when the entropy dimension is 1')
+        return S_shannon(ints_a, ints_b)
+    else:
+        ent_a = ent_renyi(ints_a, q)
+        ent_b = ent_renyi(ints_b, q)
+        ent_merg = ent_renyi(ints_a/2 + ints_b/2, q)
+        N = (1/(1-q)) * (2*np.log(np.sum(np.power(ints_a/2,q))+np.sum(np.power(ints_b/2,q))) - np.log(np.sum(np.power(ints_a,q))) - np.log(np.sum(np.power(ints_b,q))))
+        return 1 - (2 * ent_merg - ent_a - ent_b) / N
+
+
+def S_tsallis(ints_a, ints_b, q):
+    if q == 1:
+        print('Warning: the Tsallis Entropy Similarity Measure is equivalent to the Shannon Entropy Similarity Measure when the entropy dimension is 1')
+        return S_shannon(ints_a, ints_b)
+    else:
+        ent_a = ent_tsallis(ints_a, q)
+        ent_b = ent_tsallis(ints_b, q)
+        ent_merg = ent_tsallis(ints_a/2 + ints_b/2, q)
+        N = np.sum(2*np.power(ints_a/2,q)+2*np.power(ints_b/2,q)-np.power(ints_a,q)-np.power(ints_b,q)) / (1-q)
+        return 1 - (2 * ent_merg - ent_a - ent_b) / N
+
+def S_mixture(ints_a, ints_b, weights={'Cosine':0.25, 'Shannon':0.25, 'Renyi':0.25, 'Tsallis':0.25}, q=1.1):
+    if set(weights.keys()).issubset(set(['Cosine','Shannon','Renyi','Tsallis'])) is False:
+        print('Error: the keys to the weight parameter dict of the function S_mixture must be one of the four: Cosine, Shannon, Renyi, Tsallis')
+        sys.exit()
+
+    similarity = 0
+    for key, value in weights.items():
+        if key == 'Cosine':
+            similarity += value * S_cos(ints_a,ints_b)
+        if key == 'Shannon':
+            similarity += value * S_shannon(ints_a,ints_b)
+        if key == 'Renyi':
+            similarity += value * S_renyi(ints_a,ints_b,q)
+        if key == 'Tsallis':
+            similarity += value * S_tsallis(ints_a,ints_b,q)
+    return similarity
+
+
+def get_contingency_entries(ints_a, ints_b):
+    a = 0
+    b = 0
+    c = 0
+
+    for x, y in zip(ints_a, ints_b):
+        if x != 0 and y != 0:
+            c += 1
+        elif x != 0 and y == 0:
+            a += 1
+        elif x == 0  and y != 0:
+            b += 1
+    return [a,b,c]
+
+
+def S_jaccard(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = a + b + c
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = c / (a + b + c)
+    return similarity
+
+
+def S_dice(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = a + b + 2 * c
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = 2 * c / denom
+    return similarity
+
+
+def S_3w_jaccard(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = a + b + 3 * c
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = 3 * c / denom
+    return similarity
+
+
+def S_sokal_sneath(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = 2 * a + 2 * b + c
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = c / denom
+    return similarity
+
+
+def S_binary_cosine(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = np.sqrt((a + c) * (b + c))
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = c / denom
+    return similarity
+
+
+def S_mountford(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = c * (a + b) + 2 * a * b
+    if denom == 0:
+        similarity = 1
+    else:
+        similarity = 2 * c / denom
+    return similarity
+
+
+def S_mcconnaughey(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = (a + c) * (b + c)
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = (c**2 - a * b) / denom
+    return similarity
+
+
+def S_driver_kroeber(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = 2 * (a + c) * (b + c)
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = c * (a + b + 2 * c) / denom
+    return similarity
+
+
+def S_simpson(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = min(a + c, b + c)
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = c / denom
+    return similarity
+
+
+def S_braun_banquet(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = max(a + c, b + c)
+    if denom == 0:
+        similarity = 0
+    else:
+        similarity = c / denom
+    return similarity
+
+
+def S_fager_mcgowan(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom1 = np.sqrt((a + c) * (b + c))
+    denom2 = 2 * np.sqrt(max(a + c, b + c))
+    if denom1 == 0 or denom2 == 0:
+        similarity = 0
+    else:
+        similarity = c / denom1 - 1 / denom2
+    return similarity
+
+
+def S_kulczynski(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    denom = a + b
+    if denom == 0:
+        similarity = 1
+    else:
+        similarity = c / denom
+    return similarity
+
+
+def S_intersection(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    c = tmp[2]
+    return c
+
+
+def S_hamming(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    denom = a + b
+    if denom == 0:
+        similarity = 1
+    else:
+        similarity = 1 / denom
+    return similarity
+
+
+def S_hellinger(ints_a, ints_b):
+    tmp = get_contingency_entries(ints_a, ints_b)
+    a = tmp[0]
+    b = tmp[1]
+    c = tmp[2]
+    similarity = 1 - np.sqrt((1 - c / np.sqrt((a + c) * (b + c))))
+    return similarity
+
+
+def get_similarity(similarity_measure, q_ints, r_ints, weights, q):
+
+    if similarity_measure == 'cosine':
+        similarity = S_cos(q_ints, r_ints)
+
+    elif similarity_measure in ['shannon', 'renyi', 'tsallis']:
+            q_ints = normalize(q_ints, method = 'standard')
+            r_ints = normalize(r_ints, method = 'standard')
+            if similarity_measure == 'shannon':
+                similarity = S_shannon(q_ints, r_ints)
+            elif similarity_measure == 'renyi':
+                similarity = S_renyi(q_ints, r_ints, q)
+            elif similarity_measure == 'tsallis':
+                similarity = S_tsallis(q_ints, r_ints, q)
+
+    elif similarity_measure == 'mixture':
+        similarity = S_mixture(q_ints, r_ints, weights, q)
+
+    elif similarity_measure == 'jaccard':
+        similarity = S_jaccard(q_ints, r_ints)
+
+    elif similarity_measure == 'dice':
+        similarity = S_dice(q_ints, r_ints)
+
+    elif similarity_measure == '3w_jaccard':
+        similarity = S_3w_jaccard(q_ints, r_ints)
+
+    elif similarity_measure == 'sokal_sneath':
+        similarity = S_sokal_sneath(q_ints, r_ints)
+
+    elif similarity_measure == 'binary_cosine':
+        similarity = S_binary_cosine(q_ints, r_ints)
+
+    elif similarity_measure == 'mountford':
+        similarity = S_mountford(q_ints, r_ints)
+
+    elif similarity_measure == 'mcconnaughey':
+        similarity = S_mcconnaughey(q_ints, r_ints)
+
+    elif similarity_measure == 'driver_kroeber':
+        similarity = S_driver_kroeber(q_ints, r_ints)
+
+    elif similarity_measure == 'simpson':
+        similarity = S_simpson(q_ints, r_ints)
+
+    elif similarity_measure == 'braun_banquet':
+        similarity = S_braun_banquet(q_ints, r_ints)
+
+    elif similarity_measure == 'fager_mcgowan':
+        similarity = S_fager_mcgowan(q_ints, r_ints)
+
+    elif similarity_measure == 'kulczynski':
+        similarity = S_kulczynski(q_ints, r_ints)
+
+    elif similarity_measure == 'intersection':
+        similarity = S_intersection(q_ints, r_ints)
+
+    elif similarity_measure == 'hamming':
+        similarity = S_hamming(q_ints, r_ints)
+
+    elif similarity_measure == 'hellinger':
+        similarity = S_hellinger(q_ints, r_ints)
+
+    return similarity
+
+
+def _vector_to_full_params(X, default_params, optimize_params):
+    params = default_params.copy()
+    for name, val in zip(optimize_params, X):
+        params[name] = float(val)
+    return params
+
+
+def objective_function_HRMS(X, ctx):
+    p = _vector_to_full_params(X, ctx["default_params"], ctx["optimize_params"])
+    acc = get_acc_HRMS(
+        ctx["df_query"], ctx["df_reference"],
+        ctx["precursor_ion_mz_tolerance"], ctx["ionization_mode"], ctx["adduct"],
+        ctx["similarity_measure"], ctx["weights"], ctx["spectrum_preprocessing_order"],
+        ctx["mz_min"], ctx["mz_max"], ctx["int_min"], ctx["int_max"],
+        p["window_size_centroiding"], p["window_size_matching"], p["noise_threshold"],
+        p["wf_mz"], p["wf_int"], p["LET_threshold"],
+        p["entropy_dimension"],
+        ctx["high_quality_reference_library"],
+        verbose=False
+    )
+    print(f"\nparams({ctx['optimize_params']}) = {np.array(X)}\naccuracy: {acc*100}%")
+    return 1.0 - acc
+
+def objective_function_NRMS(X, ctx):
+    p = _vector_to_full_params(X, ctx["default_params"], ctx["optimize_params"])
+    acc = get_acc_NRMS(
+        ctx["df_query"], ctx["df_reference"],
+        ctx["unique_query_ids"], ctx["unique_reference_ids"],
+        ctx["similarity_measure"], ctx["weights"], ctx["spectrum_preprocessing_order"],
+        ctx["mz_min"], ctx["mz_max"], ctx["int_min"], ctx["int_max"],
+        p["noise_threshold"], p["wf_mz"], p["wf_int"], p["LET_threshold"], p["entropy_dimension"],
+        ctx["high_quality_reference_library"],
+        verbose=False
+    )
+    print(f"\nparams({ctx['optimize_params']}) = {np.array(X)}\naccuracy: {acc*100}%")
+    return 1.0 - acc
+
+
+
+def tune_params_DE(query_data=None, reference_data=None, precursor_ion_mz_tolerance=None, ionization_mode=None, adduct=None, chromatography_platform='HRMS', similarity_measure='cosine', weights=None, spectrum_preprocessing_order='CNMWL', mz_min=0, mz_max=999999999, int_min=0, int_max=999999999, high_quality_reference_library=False, optimize_params=["window_size_centroiding","window_size_matching","noise_threshold","wf_mz","wf_int","LET_threshold","entropy_dimension"], param_bounds={"window_size_centroiding":(0.0,0.5),"window_size_matching":(0.0,0.5),"noise_threshold":(0.0,0.25),"wf_mz":(0.0,5.0),"wf_int":(0.0,5.0),"LET_threshold":(0.0,5.0),"entropy_dimension":(1.0,3.0)}, default_params={"window_size_centroiding": 0.5, "window_size_matching":0.5, "noise_threshold":0.10, "wf_mz":0.0, "wf_int":1.0, "LET_threshold":0.0, "entropy_dimension":1.1}, maxiters=3, de_workers=1):
+
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the TXT file of the query data.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_query = pd.read_csv(query_data, sep='\t')
+        unique_query_ids = df_query.iloc[:,0].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the TXT file of the reference data.')
+        sys.exit()
+    else:
+        if isinstance(reference_data,str):
+            df_reference = get_reference_df(reference_data=reference_data)
+            unique_reference_ids = df_reference.iloc[:,0].unique()
+        else:
+            dfs = []
+            unique_reference_ids = []
+            for f in reference_data:
+                tmp = get_reference_df(reference_data=f)
+                dfs.append(tmp)
+                unique_reference_ids.extend(tmp.iloc[:,0].unique())
+            df_reference = pd.concat(dfs, axis=0, ignore_index=True)
+
+    if 'ionization_mode' in df_reference.columns.tolist() and ionization_mode != None and ionization_mode != 'N/A':
+        df_reference = df_reference.loc[df_reference['ionization_mode']==ionization_mode]
+    if 'adduct' in df_reference.columns.tolist() and adduct != None and adduct != 'N/A':
+        df_reference = df_reference.loc[df_reference['adduct']==adduct]
+
+    unique_query_ids = df_query['id'].unique().tolist()
+    unique_reference_ids = df_reference['id'].unique().tolist()
+
+    ctx = dict(
+        df_query=df_query,
+        df_reference=df_reference,
+        precursor_ion_mz_tolerance=precursor_ion_mz_tolerance,
+        ionization_mode=ionization_mode,
+        adduct=adduct,
+        similarity_measure=similarity_measure,
+        weights=weights,
+        spectrum_preprocessing_order=spectrum_preprocessing_order,
+        mz_min=mz_min, mz_max=mz_max, int_min=int_min, int_max=int_max,
+        high_quality_reference_library=high_quality_reference_library,
+        default_params=default_params,
+        optimize_params=optimize_params,
+    )
+
+    bounds = [param_bounds[p] for p in optimize_params]
+
+    if chromatography_platform == 'HRMS':
+        result = differential_evolution(objective_function_HRMS, bounds=bounds, args=(ctx,), maxiter=maxiters, tol=0.0, workers=de_workers, seed=1)
+    else:
+        result = differential_evolution(objective_function_NRMS, bounds=bounds, args=(ctx,), maxiter=maxiters, tol=0.0, workers=de_workers, seed=1)
+
+    best_full_params = _vector_to_full_params(result.x, default_params, optimize_params)
+    best_acc = 100.0 - (result.fun * 100.0)
+
+    print("\n=== Differential Evolution Result ===")
+    print(f"Optimized over: {optimize_params}")
+    print("Best values (selected params):")
+    for name in optimize_params:
+        print(f"  {name}: {best_full_params[name]}")
+    print("\nFull parameter set used in final evaluation:")
+    for k, v in best_full_params.items():
+        print(f"  {k}: {v}")
+    print(f"\nBest accuracy: {best_acc:.3f}%")
+    _log(f"best = {result.x}, acc={100*(1-result.fun):.3f}%")
+
+
+default_HRMS_grid = {'similarity_measure':['cosine'], 'weight':[{'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}], 'spectrum_preprocessing_order':['FCNMWL'], 'mz_min':[0], 'mz_max':[9999999], 'int_min':[0], 'int_max':[99999999], 'window_size_centroiding':[0.5], 'window_size_matching':[0.5], 'noise_threshold':[0.0], 'wf_mz':[0.0], 'wf_int':[1.0], 'LET_threshold':[0.0], 'entropy_dimension':[1.1], 'high_quality_reference_library':[False]}
+default_NRMS_grid = {'similarity_measure':['cosine'], 'weight':[{'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}], 'spectrum_preprocessing_order':['FCNMWL'], 'mz_min':[0], 'mz_max':[9999999], 'int_min':[0], 'int_max':[99999999], 'noise_threshold':[0.0], 'wf_mz':[0.0], 'wf_int':[1.0], 'LET_threshold':[0.0], 'entropy_dimension':[1.1], 'high_quality_reference_library':[False]}
+
+
+def _eval_one_HRMS(df_query, df_reference,
+              precursor_ion_mz_tolerance_tmp, ionization_mode_tmp, adduct_tmp,
+              similarity_measure_tmp, weight,
+              spectrum_preprocessing_order_tmp, mz_min_tmp, mz_max_tmp,
+              int_min_tmp, int_max_tmp, noise_threshold_tmp,
+              window_size_centroiding_tmp, window_size_matching_tmp,
+              wf_mz_tmp, wf_int_tmp, LET_threshold_tmp,
+              entropy_dimension_tmp, high_quality_reference_library_tmp):
+
+    acc = get_acc_HRMS(
+        df_query=df_query, df_reference=df_reference,
+        precursor_ion_mz_tolerance=precursor_ion_mz_tolerance_tmp,
+        ionization_mode=ionization_mode_tmp, adduct=adduct_tmp,
+        similarity_measure=similarity_measure_tmp, weights=weight,
+        spectrum_preprocessing_order=spectrum_preprocessing_order_tmp,
+        mz_min=mz_min_tmp, mz_max=mz_max_tmp,
+        int_min=int_min_tmp, int_max=int_max_tmp,
+        window_size_centroiding=window_size_centroiding_tmp,
+        window_size_matching=window_size_matching_tmp,
+        noise_threshold=noise_threshold_tmp,
+        wf_mz=wf_mz_tmp, wf_int=wf_int_tmp,
+        LET_threshold=LET_threshold_tmp,
+        entropy_dimension=entropy_dimension_tmp,
+        high_quality_reference_library=high_quality_reference_library_tmp,
+        verbose=False
+    )
+
+    return (
+        acc, similarity_measure_tmp, json.dumps(weight), spectrum_preprocessing_order_tmp,
+        mz_min_tmp, mz_max_tmp, int_min_tmp, int_max_tmp,
+        noise_threshold_tmp, window_size_centroiding_tmp, window_size_matching_tmp,
+        wf_mz_tmp, wf_int_tmp, LET_threshold_tmp, entropy_dimension_tmp,
+        high_quality_reference_library_tmp
+    )
+
+
+def _eval_one_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids,
+              similarity_measure_tmp, weight,
+              spectrum_preprocessing_order_tmp, mz_min_tmp, mz_max_tmp,
+              int_min_tmp, int_max_tmp, noise_threshold_tmp,
+              wf_mz_tmp, wf_int_tmp, LET_threshold_tmp,
+              entropy_dimension_tmp, high_quality_reference_library_tmp):
+
+    acc = get_acc_NRMS(
+        df_query=df_query, df_reference=df_reference,
+        unique_query_ids=unique_query_ids, unique_reference_ids=unique_reference_ids,
+        similarity_measure=similarity_measure_tmp, weights=weight,
+        spectrum_preprocessing_order=spectrum_preprocessing_order_tmp,
+        mz_min=mz_min_tmp, mz_max=mz_max_tmp,
+        int_min=int_min_tmp, int_max=int_max_tmp,
+        noise_threshold=noise_threshold_tmp,
+        wf_mz=wf_mz_tmp, wf_int=wf_int_tmp,
+        LET_threshold=LET_threshold_tmp,
+        entropy_dimension=entropy_dimension_tmp,
+        high_quality_reference_library=high_quality_reference_library_tmp,
+    )
+
+    return (
+        acc, similarity_measure_tmp, json.dumps(weight), spectrum_preprocessing_order_tmp,
+        mz_min_tmp, mz_max_tmp, int_min_tmp, int_max_tmp, noise_threshold_tmp, 
+        wf_mz_tmp, wf_int_tmp, LET_threshold_tmp, entropy_dimension_tmp, high_quality_reference_library_tmp
+    )
+
+
+
+
+def tune_params_on_HRMS_data_grid_shiny(query_data=None, reference_data=None, precursor_ion_mz_tolerance=None, ionization_mode=None, adduct=None, grid=None, output_path=None, return_output=False):
+    local_grid = {**default_HRMS_grid, **(grid or {})}
+    for key, value in local_grid.items():
+        globals()[key] = value
+
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the data file.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.', 1)[-1]
+        if extension in ('mgf','MGF','mzML','mzml','MZML','cdf','CDF'):
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        elif extension in ('txt','TXT'):
+            df_query = pd.read_csv(query_data, sep='\t')
+        else:
+            print(f'\nError: Unsupported query_data extension: {extension}')
+            sys.exit()
+        unique_query_ids = df_query.iloc[:, 0].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the data file(s).')
+        sys.exit()
+    else:
+        if isinstance(reference_data, str):
+            df_reference = get_reference_df(reference_data=reference_data)
+            unique_reference_ids = df_reference.iloc[:, 0].unique()
+        else:
+            dfs = []
+            unique_reference_ids = []
+            for f in reference_data:
+                tmp = get_reference_df(reference_data=f)
+                dfs.append(tmp)
+                unique_reference_ids.extend(tmp.iloc[:, 0].unique())
+            df_reference = pd.concat(dfs, axis=0, ignore_index=True)
+
+    print(f'\nNote that there are {len(unique_query_ids)} unique query spectra, '
+          f'{len(unique_reference_ids)} unique reference spectra, and '
+          f'{len(set(unique_query_ids) & set(unique_reference_ids))} of the query and reference spectra IDs are in common.\n')
+
+    if 'ionization_mode' in df_reference.columns.tolist() and ionization_mode != None and ionization_mode != 'N/A':
+        df_reference = df_reference.loc[df_reference['ionization_mode']==ionization_mode]
+    if 'adduct' in df_reference.columns.tolist() and adduct != None and adduct != 'N/A':
+        df_reference = df_reference.loc[df_reference['adduct']==adduct]
+
+    if output_path is None:
+        output_path = f'{Path.cwd()}/tuning_param_output.txt'
+        print(f'Warning: since output_path=None, the output will be written to the current working directory: {output_path}')
+
+    param_grid = product(
+        similarity_measure, weight, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max,
+        noise_threshold, window_size_centroiding, window_size_matching, wf_mz, wf_int, LET_threshold,
+        entropy_dimension, high_quality_reference_library
+    )
+
+    results = []
+    total = (
+        len(similarity_measure) * len(weight) * len(spectrum_preprocessing_order) * len(mz_min) * len(mz_max) *
+        len(int_min) * len(int_max) * len(noise_threshold) * len(window_size_centroiding) *
+        len(window_size_matching) * len(wf_mz) * len(wf_int) * len(LET_threshold) *
+        len(entropy_dimension) * len(high_quality_reference_library)
+    )
+    done = 0
+    for params in param_grid:
+        res = _eval_one_HRMS(df_query, df_reference, precursor_ion_mz_tolerance, ionization_mode, adduct, *params)
+        results.append(res)
+        done += 1
+        print(f'Completed {done}/{total} grid combinations.\n', flush=True)
+
+    df_out = pd.DataFrame(results, columns=[
+        'ACC','SIMILARITY.MEASURE','WEIGHT','SPECTRUM.PROCESSING.ORDER','MZ.MIN','MZ.MAX',
+        'INT.MIN','INT.MAX','NOISE.THRESHOLD','WINDOW.SIZE.CENTROIDING','WINDOW.SIZE.MATCHING',
+        'WF.MZ','WF.INT','LET.THRESHOLD','ENTROPY.DIMENSION','HIGH.QUALITY.REFERENCE.LIBRARY'
+    ])
+
+    if 'WEIGHT' in df_out.columns:
+        df_out['WEIGHT'] = (
+            df_out['WEIGHT'].astype(str)
+                .str.replace("\"","",regex=False)
+                .str.replace("{","",regex=False)
+                .str.replace("}","",regex=False)
+                .str.replace(":","",regex=False)
+                .str.replace("Cosine","",regex=False)
+                .str.replace("Shannon","",regex=False)
+                .str.replace("Renyi","",regex=False)
+                .str.replace("Tsallis","",regex=False)
+                .str.replace(" ","",regex=False)
+        )
+
+    if return_output:
+        return df_out
+    else:
+        df_out.to_csv(output_path, index=False, sep='\t', quoting=csv.QUOTE_NONE)
+        print(f'Wrote results to {output_path}')
+
+
+
+def tune_params_on_NRMS_data_grid(query_data=None, reference_data=None, grid=None, output_path=None, return_output=False):
+    grid = {**default_NRMS_grid, **(grid or {})}
+    for key, value in grid.items():
+        globals()[key] = value
+
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the TXT file of the query data.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_query = pd.read_csv(query_data, sep='\t')
+        unique_query_ids = df_query.iloc[:,0].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the TXT file of the reference data.')
+        sys.exit()
+    else:
+        if isinstance(reference_data,str):
+            df_reference = get_reference_df(reference_data=reference_data)
+            unique_reference_ids = df_reference.iloc[:,0].unique()
+        else:
+            dfs = []
+            unique_reference_ids = []
+            for f in reference_data:
+                tmp = get_reference_df(reference_data=f)
+                dfs.append(tmp)
+                unique_reference_ids.extend(tmp.iloc[:,0].unique())
+            df_reference = pd.concat(dfs, axis=0, ignore_index=True)
+
+    print(f'\nNote that there are {len(unique_query_ids)} unique query spectra, {len(unique_reference_ids)} unique reference spectra, and {len(set(unique_query_ids) & set(unique_reference_ids))} of the query and reference spectra IDs are in common.\n')
+
+    if output_path is None:
+        output_path = f'{Path.cwd()}/tuning_param_output.txt'
+        print(f'Warning: since output_path=None, the output will be written to the current working directory: {output_path}')
+
+    param_grid = product(similarity_measure, weight, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max,
+                         noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library)
+    results = Parallel(n_jobs=-1, verbose=10)(delayed(_eval_one_NRMS)(df_query, df_reference, unique_query_ids, unique_reference_ids, *params) for params in param_grid)
+
+    df_out = pd.DataFrame(results, columns=[
+        'ACC','SIMILARITY.MEASURE','WEIGHT','SPECTRUM.PROCESSING.ORDER', 'MZ.MIN','MZ.MAX','INT.MIN','INT.MAX',
+        'NOISE.THRESHOLD','WF.MZ','WF.INT','LET.THRESHOLD','ENTROPY.DIMENSION', 'HIGH.QUALITY.REFERENCE.LIBRARY'
+    ])
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("\"","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("{","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("}","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace(":","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("Cosine","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("Shannon","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("Renyi","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace("Tsallis","",regex=False)
+    df_out['WEIGHT'] = df_out['WEIGHT'].str.replace(" ","",regex=False)
+    if return_output is False:
+        df_out.to_csv(output_path, index=False, sep='\t', quoting=csv.QUOTE_NONE)
+    else:
+        return df_out
+
+
+
+def tune_params_on_NRMS_data_grid_shiny(query_data=None, reference_data=None, grid=None, output_path=None, return_output=False):
+    local_grid = {**default_NRMS_grid, **(grid or {})}
+    for key, value in local_grid.items():
+        globals()[key] = value
+
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the data file.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.', 1)[-1]
+        if extension in ('mgf','MGF','mzML','mzml','MZML','cdf','CDF'):
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        elif extension in ('txt','TXT'):
+            df_query = pd.read_csv(query_data, sep='\t')
+        else:
+            print(f'\nError: Unsupported query_data extension: {extension}')
+            sys.exit()
+        unique_query_ids = df_query.iloc[:, 0].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the data file(s).')
+        sys.exit()
+    else:
+        if isinstance(reference_data, str):
+            df_reference = get_reference_df(reference_data=reference_data)
+            unique_reference_ids = df_reference.iloc[:, 0].unique()
+        else:
+            dfs = []
+            unique_reference_ids = []
+            for f in reference_data:
+                tmp = get_reference_df(reference_data=f)
+                dfs.append(tmp)
+                unique_reference_ids.extend(tmp.iloc[:, 0].unique())
+            df_reference = pd.concat(dfs, axis=0, ignore_index=True)
+
+    print(f'\nNote that there are {len(unique_query_ids)} unique query spectra, '
+          f'{len(unique_reference_ids)} unique reference spectra, and '
+          f'{len(set(unique_query_ids) & set(unique_reference_ids))} of the query and reference spectra IDs are in common.\n')
+
+    if output_path is None:
+        output_path = f'{Path.cwd()}/tuning_param_output.txt'
+        print(f'Warning: since output_path=None, the output will be written to the current working directory: {output_path}')
+
+    param_grid = product(
+        similarity_measure, weight, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max,
+        noise_threshold, wf_mz, wf_int, LET_threshold,
+        entropy_dimension, high_quality_reference_library
+    )
+
+    results = []
+    total = (
+        len(similarity_measure) * len(weight) * len(spectrum_preprocessing_order) * len(mz_min) * len(mz_max) * len(int_min) *
+        len(int_max) * len(noise_threshold) * len(wf_mz) * len(wf_int) * len(LET_threshold) * len(entropy_dimension) * len(high_quality_reference_library)
+    )
+    done = 0
+    for params in param_grid:
+        res = _eval_one_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids, *params)
+        results.append(res)
+        done += 1
+        print(f'Completed {done}/{total} grid combinations.\n', flush=True)
+
+    df_out = pd.DataFrame(results, columns=[
+        'ACC','SIMILARITY.MEASURE','WEIGHT','SPECTRUM.PROCESSING.ORDER','MZ.MIN','MZ.MAX',
+        'INT.MIN','INT.MAX','NOISE.THRESHOLD','WF.MZ','WF.INT','LET.THRESHOLD','ENTROPY.DIMENSION','HIGH.QUALITY.REFERENCE.LIBRARY'
+    ])
+
+    if 'WEIGHT' in df_out.columns:
+        df_out['WEIGHT'] = (
+            df_out['WEIGHT'].astype(str)
+                .str.replace("\"","",regex=False)
+                .str.replace("{","",regex=False)
+                .str.replace("}","",regex=False)
+                .str.replace(":","",regex=False)
+                .str.replace("Cosine","",regex=False)
+                .str.replace("Shannon","",regex=False)
+                .str.replace("Renyi","",regex=False)
+                .str.replace("Tsallis","",regex=False)
+                .str.replace(" ","",regex=False)
+        )
+
+    if return_output:
+        return df_out
+    else:
+        df_out.to_csv(output_path, index=False, sep='\t', quoting=csv.QUOTE_NONE)
+        print(f'Wrote results to {output_path}')
+
+
+
+
+def get_acc_HRMS(df_query, df_reference, precursor_ion_mz_tolerance, ionization_mode, adduct, similarity_measure, weights, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max, window_size_centroiding, window_size_matching, noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library, verbose=True):
+    n_top_matches_to_save = 1
+    unique_reference_ids = df_reference['id'].dropna().astype(str).unique().tolist()
+    unique_query_ids = df_query['id'].dropna().astype(str).unique().tolist()
+    all_similarity_rows = []
+
+    for query_idx, qid in enumerate(unique_query_ids):
+        if verbose:
+            print(f'query spectrum #{query_idx} is being identified')
+
+        q_mask = (df_query['id'] == qid)
+        q_idxs = np.where(q_mask)[0]
+        if q_idxs.size == 0:
+            all_similarity_rows.append([0.0]*len(unique_reference_ids))
+            continue
+
+        q_spec_base = np.asarray(pd.concat([df_query['mz_ratio'].iloc[q_idxs], df_query['intensity'].iloc[q_idxs]], axis=1).reset_index(drop=True))
+
+        if 'precursor_ion_mz' in df_query.columns and 'precursor_ion_mz' in df_reference.columns and precursor_ion_mz_tolerance is not None:
+            precursor = float(df_query['precursor_ion_mz'].iloc[q_idxs[0]])
+            df_reference_tmp = df_reference.loc[df_reference['precursor_ion_mz'].between(precursor - precursor_ion_mz_tolerance, precursor + precursor_ion_mz_tolerance, inclusive='both'), ['id', 'mz_ratio', 'intensity']].copy()
+        else:
+            df_reference_tmp = df_reference[['id','mz_ratio','intensity']].copy()
+
+        if df_reference_tmp.empty:
+            all_similarity_rows.append([0.0]*len(unique_reference_ids))
+            continue
+
+        ref_groups = dict(tuple(df_reference_tmp.groupby('id', sort=False)))
+
+        similarity_by_ref = {}
+
+        for ref_id, r_df in ref_groups.items():
+            q_spec = q_spec_base.copy()
+            r_spec = np.asarray(pd.concat([r_df['mz_ratio'], r_df['intensity']], axis=1).reset_index(drop=True))
+
+            is_matched = False
+            for transformation in spectrum_preprocessing_order:
+                if np.isinf(q_spec[:, 1]).any():
+                    q_spec[:, 1] = 0.0
+                if np.isinf(r_spec[:, 1]).any():
+                    r_spec[:, 1] = 0.0
+
+                if transformation == 'C' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec = centroid_spectrum(q_spec, window_size=window_size_centroiding)
+                    r_spec = centroid_spectrum(r_spec, window_size=window_size_centroiding)
+
+                if transformation == 'M' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    m_spec = match_peaks_in_spectra(
+                        spec_a=q_spec, spec_b=r_spec, window_size=window_size_matching
+                    )
+                    if m_spec.size == 0:
+                        q_spec = np.empty((0,2))
+                        r_spec = np.empty((0,2))
+                    else:
+                        q_spec = m_spec[:, 0:2]
+                        r_spec = m_spec[:, [0, 2]]
+                    is_matched = True
+
+                if transformation == 'W' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec[:, 1] = wf_transform(q_spec[:, 0], q_spec[:, 1], wf_mz, wf_int)
+                    r_spec[:, 1] = wf_transform(r_spec[:, 0], r_spec[:, 1], wf_mz, wf_int)
+
+                if transformation == 'L' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec[:, 1] = LE_transform(q_spec[:, 1], LET_threshold, normalization_method='standard')
+                    r_spec[:, 1] = LE_transform(r_spec[:, 1], LET_threshold, normalization_method='standard')
+
+                if transformation == 'N' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec = remove_noise(q_spec, nr=noise_threshold)
+                    if not high_quality_reference_library:
+                        r_spec = remove_noise(r_spec, nr=noise_threshold)
+
+                if transformation == 'F' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec = filter_spec_lcms(
+                        q_spec, mz_min=mz_min, mz_max=mz_max, int_min=int_min, int_max=int_max, is_matched=is_matched
+                    )
+                    if not high_quality_reference_library:
+                        r_spec = filter_spec_lcms(
+                            r_spec, mz_min=mz_min, mz_max=mz_max, int_min=int_min, int_max=int_max, is_matched=is_matched
+                        )
+
+            if q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                q_ints = q_spec[:, 1]
+                r_ints = r_spec[:, 1]
+                if np.sum(q_ints) != 0 and np.sum(r_ints) != 0:
+                    sim = get_similarity(similarity_measure, q_ints, r_ints, weights, entropy_dimension)
+                else:
+                    sim = 0.0
+            else:
+                sim = 0.0
+
+            similarity_by_ref[str(ref_id)] = float(sim)
+
+        row = [similarity_by_ref.get(ref_id, 0.0) for ref_id in unique_reference_ids]
+        all_similarity_rows.append(row)
+
+    df_scores = pd.DataFrame(all_similarity_rows, index=unique_query_ids, columns=unique_reference_ids)
+    df_scores.index.name = 'QUERY.SPECTRUM.ID'
+
+    top_idx = df_scores.values.argmax(axis=1)
+    top_scores = df_scores.values[np.arange(df_scores.shape[0]), top_idx]
+    top_ids = [df_scores.columns[i] for i in top_idx]
+
+    df_tmp = pd.DataFrame({'TRUE.ID': df_scores.index.to_list(), 'PREDICTED.ID': top_ids, 'SCORE': top_scores})
+    if verbose:
+        print(df_tmp)
+
+    acc = (df_tmp['TRUE.ID'] == df_tmp['PREDICTED.ID']).mean()
+    return acc
+
+
+
+def get_acc_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids, similarity_measure, weights, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max, noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library, verbose=True):
+
+    n_top_matches_to_save = 1
+
+    min_mz = int(np.min([np.min(df_query.iloc[:,1]), np.min(df_reference.iloc[:,1])]))
+    max_mz = int(np.max([np.max(df_query.iloc[:,1]), np.max(df_reference.iloc[:,1])]))
+    mzs = np.linspace(min_mz,max_mz,(max_mz-min_mz+1))
+
+    all_similarity_scores =  []
+    for query_idx in range(0,len(unique_query_ids)):
+        q_idxs_tmp = np.where(df_query.iloc[:,0] == unique_query_ids[query_idx])[0]
+        q_spec_tmp = np.asarray(pd.concat([df_query.iloc[q_idxs_tmp,1], df_query.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        q_spec_tmp = convert_spec(q_spec_tmp,mzs)
+
+        similarity_scores = []
+        for ref_idx in range(0,len(unique_reference_ids)):
+            q_spec = q_spec_tmp
+            if verbose is True and ref_idx % 1000 == 0:
+                print(f'Query spectrum #{query_idx} has had its similarity with {ref_idx} reference library spectra computed')
+            r_idxs_tmp = np.where(df_reference.iloc[:,0] == unique_reference_ids[ref_idx])[0]
+            r_spec_tmp = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+            r_spec = convert_spec(r_spec_tmp,mzs)
+
+            for transformation in spectrum_preprocessing_order:
+                if np.isinf(q_spec[:,1]).sum() > 0:
+                    q_spec[:,1] = np.zeros(q_spec.shape[0])
+                if np.isinf(r_spec[:,1]).sum() > 0:
+                    r_spec[:,1] = np.zeros(r_spec.shape[0])
+                if transformation == 'W':
+                    q_spec[:,1] = wf_transform(q_spec[:,0], q_spec[:,1], wf_mz, wf_int)
+                    r_spec[:,1] = wf_transform(r_spec[:,0], r_spec[:,1], wf_mz, wf_int)
+                if transformation == 'L':
+                    q_spec[:,1] = LE_transform(q_spec[:,1], LET_threshold, normalization_method='standard')
+                    r_spec[:,1] = LE_transform(r_spec[:,1], LET_threshold, normalization_method='standard')
+                if transformation == 'N':
+                    q_spec = remove_noise(q_spec, nr = noise_threshold)
+                    if high_quality_reference_library == False:
+                        r_spec = remove_noise(r_spec, nr = noise_threshold)
+                if transformation == 'F':
+                    q_spec = filter_spec_gcms(q_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
+                    if high_quality_reference_library == False:
+                        r_spec = filter_spec_gcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
+
+            q_ints = q_spec[:,1]
+            r_ints = r_spec[:,1]
+
+            if np.sum(q_ints) != 0 and np.sum(r_ints) != 0:
+                similarity_score = get_similarity(similarity_measure, q_spec[:,1], r_spec[:,1], weights, entropy_dimension)
+            else:
+                similarity_score = 0
+
+            similarity_scores.append(similarity_score)
+        all_similarity_scores.append(similarity_scores)
+
+    df_scores = pd.DataFrame(all_similarity_scores, columns = unique_reference_ids)
+    df_scores.index = unique_query_ids
+    df_scores.index.names = ['QUERY.SPECTRUM.ID']
+
+    preds = []
+    scores = []
+    for i in range(0, df_scores.shape[0]):
+        df_scores_tmp = df_scores
+        preds_tmp = []
+        scores_tmp = []
+        for j in range(0, n_top_matches_to_save):
+            top_ref_specs_tmp = df_scores_tmp.iloc[i,np.where(df_scores_tmp.iloc[i,:] == np.max(df_scores_tmp.iloc[i,:]))[0]]
+            cols_to_keep = np.where(df_scores_tmp.iloc[i,:] != np.max(df_scores_tmp.iloc[i,:]))[0]
+            df_scores_tmp = df_scores_tmp.iloc[:,cols_to_keep]
+
+            preds_tmp.append(';'.join(map(str,top_ref_specs_tmp.index.to_list())))
+            if len(top_ref_specs_tmp.values) == 0:
+                scores_tmp.append(0)
+            else:
+                scores_tmp.append(top_ref_specs_tmp.values[0])
+        preds.append(preds_tmp)
+        scores.append(scores_tmp)
+
+    preds = np.array(preds)
+    scores = np.array(scores)
+    out = np.c_[unique_query_ids,preds,scores]
+    df_tmp = pd.DataFrame(out, columns=['TRUE.ID','PREDICTED.ID','SCORE'])
+    acc = (df_tmp['TRUE.ID']==df_tmp['PREDICTED.ID']).mean()
+    return acc
+
+
+
+def run_spec_lib_matching_on_HRMS_data_shiny(query_data=None, reference_data=None, precursor_ion_mz_tolerance=None, ionization_mode=None, adduct=None, likely_reference_ids=None, similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FCNMWL', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, window_size_centroiding=0.5, window_size_matching=0.5, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None, return_ID_output=False, verbose=True):
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the CSV file of the query data.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            #build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=True)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_query = pd.read_csv(query_data, sep='\t')
+        unique_query_ids = df_query['id'].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the reference data.')
+        sys.exit()
+    else:
+        if isinstance(reference_data,str):
+            df_reference = get_reference_df(reference_data,likely_reference_ids)
+        else:
+            dfs = []
+            for f in reference_data:
+                tmp = get_reference_df(f,likely_reference_ids)
+                dfs.append(tmp)
+            df_reference = pd.concat(dfs, axis=0, ignore_index=True)
+
+    if 'ionization_mode' in df_reference.columns.tolist() and ionization_mode != 'N/A':
+        df_reference = df_reference.loc[df_reference['ionization_mode']==ionization_mode]
+    if 'adduct' in df_reference.columns.tolist() and adduct != 'N/A':
+        df_reference = df_reference.loc[df_reference['adduct']==adduct]
+
+    if spectrum_preprocessing_order is not None:
+        spectrum_preprocessing_order = list(spectrum_preprocessing_order)
+    else:
+        spectrum_preprocessing_order = ['F', 'C', 'N', 'M', 'W', 'L']
+    if 'M' not in spectrum_preprocessing_order:
+        print(f'Error: \'M\' must be a character in spectrum_preprocessing_order.')
+        sys.exit()
+    if 'C' in spectrum_preprocessing_order:
+        if spectrum_preprocessing_order.index('C') > spectrum_preprocessing_order.index('M'):
+            print(f'Error: \'C\' must come before \'M\' in spectrum_preprocessing_order.')
+            sys.exit()
+    if set(spectrum_preprocessing_order) - {'F','C','N','M','W','L'}:
+        print(f'Error: spectrum_preprocessing_order must contain only \'C\', \'F\', \'M\', \'N\', \'L\', \'W\'.')
+        sys.exit()
+
+
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kuldzynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger')
+        sys.exit()
+
+    if isinstance(int_min,int) is True:
+        int_min = float(int_min)
+    if isinstance(int_max,int) is True:
+        int_max = float(int_max)
+    if isinstance(mz_min,int) is False or isinstance(mz_max,int) is False or isinstance(int_min,float) is False or isinstance(int_max,float) is False:
+        print('Error: mz_min must be a non-negative integer, mz_max must be a positive integer, int_min must be a non-negative float, and int_max must be a positive float')
+        sys.exit()
+    if mz_min < 0:
+        print('\nError: mz_min should be a non-negative integer')
+        sys.exit()
+    if mz_max <= 0:
+        print('\nError: mz_max should be a positive integer')
+        sys.exit()
+    if int_min < 0:
+        print('\nError: int_min should be a non-negative float')
+        sys.exit()
+    if int_max <= 0:
+        print('\nError: int_max should be a positive float')
+        sys.exit()
+
+    if isinstance(window_size_centroiding,float) is False or window_size_centroiding <= 0.0:
+        print('Error: window_size_centroiding must be a positive float.')
+        sys.exit()
+    if isinstance(window_size_matching,float) is False or window_size_matching<= 0.0:
+        print('Error: window_size_matching must be a positive float.')
+        sys.exit()
+
+    if isinstance(noise_threshold,int) is True:
+        noise_threshold = float(noise_threshold)
+    if isinstance(noise_threshold,float) is False or noise_threshold < 0:
+        print('Error: noise_threshold must be a positive float.')
+        sys.exit()
+
+    if isinstance(wf_intensity,int) is True:
+        wf_intensity = float(wf_intensity)
+    if isinstance(wf_mz,int) is True:
+        wf_mz = float(wf_mz)
+    if isinstance(wf_intensity,float) is False or isinstance(wf_mz,float) is False:
+        print('Error: wf_mz and wf_intensity must be integers or floats')
+        sys.exit()
+
+    if entropy_dimension <= 0:
+        print('\nError: entropy_dimension should be a positive float')
+        sys.exit()
+    else:
+        q = entropy_dimension
+
+    normalization_method = 'standard'
+
+    if n_top_matches_to_save <= 0 or isinstance(n_top_matches_to_save,int)==False:
+        print('\nError: n_top_matches_to_save should be a positive integer')
+        sys.exit()
+
+    if isinstance(print_id_results,bool)==False:
+        print('\nError: print_id_results must be either True or False')
+        sys.exit()
+    
+    if output_identification is None:
+        output_identification = f'{Path.cwd()}/output_identification.txt'
+        print(f'Warning: writing identification output to {output_identification}')
+
+    if output_similarity_scores is None:
+        output_similarity_scores = f'{Path.cwd()}/output_all_similarity_scores.txt'
+        print(f'Warning: writing similarity scores to {output_similarity_scores}')
+
+
+    unique_reference_ids = df_reference['id'].unique().tolist()
+    all_similarity_scores = []
+
+    for query_idx in range(len(unique_query_ids)):
+        if verbose:
+            print(f'query spectrum #{query_idx} is being identified')
+
+        q_mask = (df_query['id'] == unique_query_ids[query_idx])
+        q_idxs_tmp = np.where(q_mask)[0]
+        q_spec_tmp = np.asarray(pd.concat([df_query['mz_ratio'].iloc[q_idxs_tmp], df_query['intensity'].iloc[q_idxs_tmp]], axis=1).reset_index(drop=True))
+
+        if 'precursor_ion_mz' in df_query.columns.tolist() and 'precursor_ion_mz' in df_reference.columns.tolist() and precursor_ion_mz_tolerance != None:
+            precursor_ion_mz_tmp = df_query['precursor_ion_mz'].iloc[q_idxs_tmp[0]]
+            df_reference_tmp = df_reference.loc[df_reference['precursor_ion_mz'].between(precursor_ion_mz_tmp-precursor_ion_mz_tolerance, precursor_ion_mz_tmp+precursor_ion_mz_tolerance, inclusive='both'),['id','mz_ratio','intensity']].copy()
+        else:
+            df_reference_tmp = df_reference.copy()
+
+        ref_groups = dict(tuple(df_reference_tmp.groupby('id', sort=False)))
+        unique_reference_ids_tmp = list(ref_groups.keys())
+
+        similarity_by_ref = {}
+        for ref_id in unique_reference_ids_tmp:
+            q_spec = q_spec_tmp.copy()
+            r_df = ref_groups[ref_id]
+            r_spec = np.asarray(pd.concat([r_df['mz_ratio'], r_df['intensity']], axis=1).reset_index(drop=True))
+
+            is_matched = False
+
+            for transformation in spectrum_preprocessing_order:
+                if np.isinf(q_spec[:, 1]).sum() > 0:
+                    q_spec[:, 1] = np.zeros(q_spec.shape[0])
+                if np.isinf(r_spec[:, 1]).sum() > 0:
+                    r_spec[:, 1] = np.zeros(r_spec.shape[0])
+
+                if transformation == 'C' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec = centroid_spectrum(q_spec, window_size=window_size_centroiding)
+                    r_spec = centroid_spectrum(r_spec, window_size=window_size_centroiding)
+
+                if transformation == 'M' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    m_spec = match_peaks_in_spectra(spec_a=q_spec, spec_b=r_spec, window_size=window_size_matching)
+                    q_spec = m_spec[:, 0:2]
+                    r_spec = m_spec[:, [0, 2]]
+                    is_matched = True
+
+                if transformation == 'W' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec[:, 1] = wf_transform(q_spec[:, 0], q_spec[:, 1], wf_mz, wf_intensity)
+                    r_spec[:, 1] = wf_transform(r_spec[:, 0], r_spec[:, 1], wf_mz, wf_intensity)
+
+                if transformation == 'L' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec[:, 1] = LE_transform(q_spec[:, 1], LET_threshold, normalization_method=normalization_method)
+                    r_spec[:, 1] = LE_transform(r_spec[:, 1], LET_threshold, normalization_method=normalization_method)
+
+                if transformation == 'N' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec = remove_noise(q_spec, nr=noise_threshold)
+                    if not high_quality_reference_library:
+                        r_spec = remove_noise(r_spec, nr=noise_threshold)
+
+                if transformation == 'F' and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                    q_spec = filter_spec_lcms(
+                        q_spec, mz_min=mz_min, mz_max=mz_max, int_min=int_min, int_max=int_max, is_matched=is_matched
+                    )
+                    if not high_quality_reference_library:
+                        r_spec = filter_spec_lcms(
+                            r_spec, mz_min=mz_min, mz_max=mz_max, int_min=int_min, int_max=int_max, is_matched=is_matched
+                        )
+
+            q_ints = q_spec[:, 1]
+            r_ints = r_spec[:, 1]
+
+            if np.sum(q_ints) != 0 and np.sum(r_ints) != 0 and q_spec.shape[0] > 1 and r_spec.shape[0] > 1:
+                sim = get_similarity(similarity_measure, q_ints, r_ints, weights, entropy_dimension)
+            else:
+                sim = 0.0
+
+            similarity_by_ref[ref_id] = sim
+
+        row_scores = [similarity_by_ref.get(ref_id, 0.0) for ref_id in unique_reference_ids]
+        all_similarity_scores.append(row_scores)
+
+    df_scores = pd.DataFrame(all_similarity_scores, index=unique_query_ids, columns=unique_reference_ids)
+    df_scores.index = unique_query_ids
+    df_scores.index.names = ['QUERY.SPECTRUM.ID']
+
+
+    preds = []
+    scores = []
+    for i in range(0, df_scores.shape[0]):
+        df_scores_tmp = df_scores
+        preds_tmp = []
+        scores_tmp = []
+        for j in range(0, n_top_matches_to_save):
+            top_ref_specs_tmp = df_scores_tmp.iloc[i,np.where(df_scores_tmp.iloc[i,:] == np.max(df_scores_tmp.iloc[i,:]))[0]]
+            cols_to_keep = np.where(df_scores_tmp.iloc[i,:] != np.max(df_scores_tmp.iloc[i,:]))[0]
+            df_scores_tmp = df_scores_tmp.iloc[:,cols_to_keep]
+
+            preds_tmp.append(';'.join(map(str,top_ref_specs_tmp.index.to_list())))
+            if len(top_ref_specs_tmp.values) == 0:
+                scores_tmp.append(0)
+            else:
+                scores_tmp.append(top_ref_specs_tmp.values[0])
+        preds.append(preds_tmp)
+        scores.append(scores_tmp)
+
+    preds = np.array(preds)
+    scores = np.array(scores)
+    out = np.c_[preds,scores]
+
+    cnames_preds = []
+    cnames_scores = []
+    for i in range(0,n_top_matches_to_save):
+        cnames_preds.append(f'RANK.{i+1}.PRED')
+        cnames_scores.append(f'RANK.{i+1}.SIMILARITY.SCORE')
+
+    df_top_ref_specs = pd.DataFrame(out, columns = [*cnames_preds, *cnames_scores])
+    df_top_ref_specs.index = unique_query_ids
+    df_top_ref_specs.index.names = ['QUERY.SPECTRUM.ID']
+
+    df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
+
+    if print_id_results == True:
+        print(df_top_ref_specs.to_string())
+
+    if return_ID_output is False:
+        df_top_ref_specs.to_csv(output_identification, sep='\t')
+        df_scores.to_csv(output_similarity_scores, sep='\t')
+    else:
+        return df_top_ref_specs
+
+
+
+
+def run_spec_lib_matching_on_NRMS_data_shiny(query_data=None, reference_data=None, likely_reference_ids=None, spectrum_preprocessing_order='FNLW', similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None, return_ID_output=False, verbose=True):
+    if query_data is None:
+        print('\nError: No argument passed to the mandatory query_data. Please pass the path to the TXT file of the query data.')
+        sys.exit()
+    else:
+        extension = query_data.rsplit('.',1)
+        extension = extension[(len(extension)-1)]
+        if extension == 'mgf' or extension == 'MGF' or extension == 'mzML' or extension == 'mzml' or extension == 'MZML' or extension == 'cdf' or extension == 'CDF' or extension == 'msp' or extension == 'MSP' or extension == 'json' or extension == 'JSON':
+            output_path_tmp = query_data[:-3] + 'txt'
+            build_library_from_raw_data(input_path=query_data, output_path=output_path_tmp, is_reference=False)
+            df_query = pd.read_csv(output_path_tmp, sep='\t')
+        if extension == 'txt' or extension == 'TXT':
+            df_query = pd.read_csv(query_data, sep='\t')
+        unique_query_ids = df_query.iloc[:,0].unique()
+
+    if reference_data is None:
+        print('\nError: No argument passed to the mandatory reference_data. Please pass the path to the TXT file of the reference data.')
+        sys.exit()
+    else:
+        if isinstance(reference_data,str):
+            df_reference = get_reference_df(reference_data,likely_reference_ids)
+            unique_reference_ids = df_reference.iloc[:,0].unique()
+        else:
+            dfs = []
+            unique_reference_ids = []
+            for f in reference_data:
+                tmp = get_reference_df(f,likely_reference_ids)
+                dfs.append(tmp)
+                unique_reference_ids.extend(tmp.iloc[:,0].unique())
+            df_reference = pd.concat(dfs, axis=0, ignore_index=True)
+
+
+    if spectrum_preprocessing_order is not None:
+        spectrum_preprocessing_order = list(spectrum_preprocessing_order)
+    else:
+        spectrum_preprocessing_order = ['F','N','W','L']
+    if set(spectrum_preprocessing_order) - {'F','N','W','L'}:
+        print(f'Error: spectrum_preprocessing_order must contain only \'F\', \'N\', \'W\', \'L\'.')
+        sys.exit()
+
+    if similarity_measure not in ['cosine','shannon','renyi','tsallis','mixture','jaccard','dice','3w_jaccard','sokal_sneath','binary_cosine','mountford','mcconnaughey','driver_kroeber','simpson','braun_banquet','fager_mcgowan','kuldzynski','intersection','hamming','hellinger']:
+        print('\nError: similarity_measure must be either cosine, shannon, renyi, tsallis, mixture, jaccard, dice, 3w_jaccard, sokal_sneath, binary_cosine, mountford, mcconnaughey, driver_kroeber, simpson, braun_banquet, fager_mcgowan, kulczynski, intersection, hamming, or hellinger')
+        sys.exit()
+
+    if isinstance(int_min,int) is True:
+        int_min = float(int_min)
+    if isinstance(int_max,int) is True:
+        int_max = float(int_max)
+    if isinstance(mz_min,int) is False or isinstance(mz_max,int) is False or isinstance(int_min,float) is False or isinstance(int_max,float) is False:
+        print('Error: mz_min must be a non-negative integer, mz_max must be a positive integer, int_min must be a non-negative float, and int_max must be a positive float')
+        sys.exit()
+    if mz_min < 0:
+        print('\nError: mz_min should be a non-negative integer')
+        sys.exit()
+    if mz_max <= 0:
+        print('\nError: mz_max should be a positive integer')
+        sys.exit()
+    if int_min < 0:
+        print('\nError: int_min should be a non-negative float')
+        sys.exit()
+    if int_max <= 0:
+        print('\nError: int_max should be a positive float')
+        sys.exit()
+
+    if isinstance(noise_threshold,int) is True:
+        noise_threshold = float(noise_threshold)
+    if isinstance(noise_threshold,float) is False or noise_threshold < 0:
+        print('Error: noise_threshold must be a positive float.')
+        sys.exit()
+
+    if isinstance(wf_intensity,int) is True:
+        wf_intensity = float(wf_intensity)
+    if isinstance(wf_mz,int) is True:
+        wf_mz = float(wf_mz)
+    if isinstance(wf_intensity,float) is False or isinstance(wf_mz,float) is False:
+        print('Error: wf_mz and wf_intensity must be integers or floats')
+        sys.exit()
+
+    if entropy_dimension <= 0:
+        print('\nError: entropy_dimension should be a positive float')
+        sys.exit()
+    else:
+        q = entropy_dimension
+
+    normalization_method = 'standard' 
+
+    if n_top_matches_to_save <= 0 or isinstance(n_top_matches_to_save,int)==False:
+        print('\nError: n_top_matches_to_save should be a positive integer')
+        sys.exit()
+
+    if isinstance(print_id_results,bool)==False:
+        print('\nError: print_id_results must be either True or False')
+        sys.exit()
+    
+    if output_identification is None:
+        output_identification = f'{Path.cwd()}/output_identification.txt'
+        print(f'Warning: writing identification output to {output_identification}')
+
+    if output_similarity_scores is None:
+        output_similarity_scores = f'{Path.cwd()}/output_all_similarity_scores.txt'
+        print(f'Warning: writing similarity scores to {output_similarity_scores}')
+
+
+
+    min_mz = int(np.min([np.min(df_query.iloc[:,1]), np.min(df_reference.iloc[:,1])]))
+    max_mz = int(np.max([np.max(df_query.iloc[:,1]), np.max(df_reference.iloc[:,1])]))
+    mzs = np.linspace(min_mz,max_mz,(max_mz-min_mz+1))
+
+    all_similarity_scores =  []
+    for query_idx in range(0,len(unique_query_ids)):
+        q_idxs_tmp = np.where(df_query.iloc[:,0] == unique_query_ids[query_idx])[0]
+        q_spec_tmp = np.asarray(pd.concat([df_query.iloc[q_idxs_tmp,1], df_query.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        q_spec_tmp = convert_spec(q_spec_tmp,mzs)
+
+        similarity_scores = []
+        for ref_idx in range(0,len(unique_reference_ids)):
+            if verbose is True and ref_idx % 1000 == 0:
+                print(f'Query spectrum #{query_idx} has had its similarity with {ref_idx} reference library spectra computed')
+            q_spec = q_spec_tmp
+            r_idxs_tmp = np.where(df_reference.iloc[:,0] == unique_reference_ids[ref_idx])[0]
+            r_spec_tmp = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+            r_spec = convert_spec(r_spec_tmp,mzs)
+
+            for transformation in spectrum_preprocessing_order:
+                if np.isinf(q_spec[:,1]).sum() > 0:
+                    q_spec[:,1] = np.zeros(q_spec.shape[0])
+                if np.isinf(r_spec[:,1]).sum() > 0:
+                    r_spec[:,1] = np.zeros(r_spec.shape[0])
+                if transformation == 'W': 
+                    q_spec[:,1] = wf_transform(q_spec[:,0], q_spec[:,1], wf_mz, wf_intensity)
+                    r_spec[:,1] = wf_transform(r_spec[:,0], r_spec[:,1], wf_mz, wf_intensity)
+                if transformation == 'L': 
+                    q_spec[:,1] = LE_transform(q_spec[:,1], LET_threshold, normalization_method=normalization_method)
+                    r_spec[:,1] = LE_transform(r_spec[:,1], LET_threshold, normalization_method=normalization_method)
+                if transformation == 'N': 
+                    q_spec = remove_noise(q_spec, nr = noise_threshold)
+                    if high_quality_reference_library == False:
+                        r_spec = remove_noise(r_spec, nr = noise_threshold)
+                if transformation == 'F':
+                    q_spec = filter_spec_gcms(q_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
+                    if high_quality_reference_library == False:
+                        r_spec = filter_spec_gcms(r_spec, mz_min = mz_min, mz_max = mz_max, int_min = int_min, int_max = int_max)
+
+            q_ints = q_spec[:,1]
+            r_ints = r_spec[:,1]
+
+            if np.sum(q_ints) != 0 and np.sum(r_ints) != 0:
+                similarity_score = get_similarity(similarity_measure, q_spec[:,1], r_spec[:,1], weights, entropy_dimension)
+            else:
+                similarity_score = 0
+
+            similarity_scores.append(similarity_score)
+        all_similarity_scores.append(similarity_scores)
+
+    df_scores = pd.DataFrame(all_similarity_scores, columns = unique_reference_ids)
+    df_scores.index = unique_query_ids
+    df_scores.index.names = ['QUERY.SPECTRUM.ID']
+
+    preds = []
+    scores = []
+    for i in range(0, df_scores.shape[0]):
+        df_scores_tmp = df_scores
+        preds_tmp = []
+        scores_tmp = []
+        for j in range(0, n_top_matches_to_save):
+            top_ref_specs_tmp = df_scores_tmp.iloc[i,np.where(df_scores_tmp.iloc[i,:] == np.max(df_scores_tmp.iloc[i,:]))[0]]
+            cols_to_keep = np.where(df_scores_tmp.iloc[i,:] != np.max(df_scores_tmp.iloc[i,:]))[0]
+            df_scores_tmp = df_scores_tmp.iloc[:,cols_to_keep]
+
+            preds_tmp.append(';'.join(map(str,top_ref_specs_tmp.index.to_list())))
+            if len(top_ref_specs_tmp.values) == 0:
+                scores_tmp.append(0)
+            else:
+                scores_tmp.append(top_ref_specs_tmp.values[0])
+        preds.append(preds_tmp)
+        scores.append(scores_tmp)
+
+    preds = np.array(preds)
+    scores = np.array(scores)
+    out = np.c_[preds,scores]
+
+    cnames_preds = []
+    cnames_scores = []
+    for i in range(0,n_top_matches_to_save):
+        cnames_preds.append(f'RANK.{i+1}.PRED')
+        cnames_scores.append(f'RANK.{i+1}.SIMILARITY.SCORE')
+
+    df_top_ref_specs = pd.DataFrame(out, columns = [*cnames_preds, *cnames_scores])
+    df_top_ref_specs.index = unique_query_ids
+    df_top_ref_specs.index.names = ['QUERY.SPECTRUM.ID']
+
+    if print_id_results == True:
+        print(df_top_ref_specs.to_string())
+
+    df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
+
+    if return_ID_output is False:
+        df_top_ref_specs.to_csv(output_identification, sep='\t')
+        df_scores.columns = ['Reference Spectrum ID: ' + col for col in  list(map(str,df_scores.columns.tolist()))]
+        df_scores.to_csv(output_similarity_scores, sep='\t')
+    else:
+        return df_top_ref_specs
+
+
+class _UIWriter:
+    def __init__(self, loop, q: asyncio.Queue[str]):
+        self._loop = loop
+        self._q = q
+    def write(self, s: str):
+        if s:
+            self._loop.call_soon_threadsafe(self._q.put_nowait, s)
+        return len(s)
+    def flush(self):
+        pass
+
+
+def attach_logging_to_writer(writer):
+    handler = logging.StreamHandler(writer)
+    handler.setLevel(logging.INFO)
+    root = logging.getLogger()
+    root.addHandler(handler)
+    root.setLevel(logging.INFO)
+    return handler, root
+
+
+
 def _run_with_redirects(fn, writer, *args, **kwargs):
     with redirect_stdout(writer), redirect_stderr(writer):
         return fn(*args, **kwargs)
@@ -64,19 +2367,21 @@ def strip_weights(s):
 def build_library(input_path=None, output_path=None):
     last_three_chars = input_path[(len(input_path)-3):len(input_path)]
     last_four_chars = input_path[(len(input_path)-4):len(input_path)]
-    if last_three_chars == 'csv' or last_three_chars == 'CSV':
-        return pd.read_csv(input_path)
+    if last_three_chars == 'txt' or last_three_chars == 'TXT':
+        return pd.read_csv(input_path, sep='\t')
     else:
         if last_three_chars == 'mgf' or last_three_chars == 'MGF':
             input_file_type = 'mgf'
         elif last_four_chars == 'mzML' or last_four_chars == 'mzml' or last_four_chars == 'MZML':
             input_file_type = 'mzML'
+        elif last_four_chars == 'json' or last_four_chars == 'JSON':
+            input_file_type = 'json'
         elif last_three_chars == 'cdf' or last_three_chars == 'CDF':
             input_file_type = 'cdf'
         elif last_three_chars == 'msp' or last_three_chars == 'MSP':
             input_file_type = 'msp'
         else:
-            print('ERROR: either an \'mgf\', \'mzML\', \'cdf\', or \'msp\' file must be passed to --input_path')
+            print('ERROR: either an \'mgf\', \'mzML\', \'cdf\', \'msp\', \'json\', or \'txt\' file must be passed to --input_path')
             sys.exit()
 
         spectra = []
@@ -146,6 +2451,23 @@ def build_library(input_path=None, output_path=None):
                         except ValueError:
                             continue
 
+        if input_file_type == 'json':
+            data = json.load(open(input_path))
+            ids = []
+            mzs = []
+            ints = []
+            for i in range(0,len(data)):
+                spec_ID_tmp = data[i]['spectrum_id']
+                tmp = data[i]['peaks_json']
+                tmp = tmp[1:-1].split(",")
+                tmp = [a.replace("[","") for a in tmp]
+                tmp = [a.replace("]","") for a in tmp]
+                mzs_tmp = tmp[0::2]
+                ints_tmp = tmp[1::2]
+                ids.extend([spec_ID_tmp] * len(mzs_tmp))
+                mzs.extend(mzs_tmp)
+                ints.extend(ints_tmp)
+
         df = pd.DataFrame({'id':ids, 'mz_ratio':mzs, 'intensity':ints})
         return df
 
@@ -154,9 +2476,12 @@ def build_library(input_path=None, output_path=None):
 def extract_first_column_ids(file_path: str, max_ids: int = 20000):
     suffix = Path(file_path).suffix.lower()
 
-    if suffix == ".csv":
-        df = pd.read_csv(file_path, usecols=[0])
-        ids = df.iloc[:, 0].astype(str).dropna()
+    if suffix == ".txt":
+        df = pd.read_csv(file_path, sep='\t')
+        if 'id' in df.columns.tolist():
+            ids = df['id'].astype(str).dropna()
+        else:
+            ids = df.iloc[:, 0].astype(str).dropna()
         ids = [x for x in ids if x.strip() != ""]
         seen = set()
         uniq = []
@@ -191,17 +2516,17 @@ def extract_first_column_ids(file_path: str, max_ids: int = 20000):
     return []
 
 
-def _open_plot_window(session, png_bytes: bytes, title: str = "plot.png"):
-    """Send PNG bytes to browser and open in a new window as a data URL."""
-    b64 = base64.b64encode(png_bytes).decode("ascii")
-    data_url = f"data:image/png;base64,{b64}"
-    session.send_custom_message("open-plot-window", {"png": data_url, "title": title})
+def _open_plot_window(session, svg_bytes: bytes, title: str = "plot.svg"):
+    """Send SVG bytes to browser and open in a new window as a data URL."""
+    b64 = base64.b64encode(svg_bytes).decode("ascii")
+    data_url = f"data:image/svg;base64,{b64}"
+    session.send_custom_message("open-plot-window", {"svg": data_url, "title": title})
 
 
 def plot_spectra_ui(platform: str):
     base_inputs = [
-        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
-        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
+        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or txt):"),
+        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or txt):"),
         ui.input_selectize(
             "spectrum_ID1",
             "Select spectrum ID 1 (default is the first spectrum in the library):",
@@ -216,6 +2541,8 @@ def plot_spectra_ui(platform: str):
             multiple=False,
             options={"placeholder": "Upload a library..."},
         ),
+        ui.input_select('print_url_spectrum1', 'Print PubChem URL for spectrum 1:', ['No', 'Yes']),
+        ui.input_select('print_url_spectrum2', 'Print PubChem URL for spectrum 2:', ['No', 'Yes']),
         ui.input_select("similarity_measure", "Select similarity measure:", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"]),
         ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
         ui.input_select(
@@ -227,21 +2554,13 @@ def plot_spectra_ui(platform: str):
 
     if platform == "HRMS":
         extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.",
-                "FCNMWL",
-            ),
+            ui.input_text("spectrum_preprocessing_order", "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.", "FCNMWL",),
             ui.input_numeric("window_size_centroiding", "Centroiding window-size:", 0.5),
             ui.input_numeric("window_size_matching", "Matching window-size:", 0.5),
         ]
     else:
         extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (F (filtering), N (noise removal), L (low-entropy transformation), W (weight factor transformation)).",
-                "FNLW",
-            )
+            ui.input_text("spectrum_preprocessing_order", "Sequence of characters for preprocessing order (F (filtering), N (noise removal), L (low-entropy transformation), W (weight factor transformation)).", "FNLW",)
         ]
 
     numeric_inputs = [
@@ -256,11 +2575,7 @@ def plot_spectra_ui(platform: str):
         ui.input_numeric("entropy_dimension", "Entropy dimension (Renyi/Tsallis only):", 1.1),
     ]
 
-    select_input = ui.input_select(
-        "y_axis_transformation",
-        "Transformation to apply to intensity axis:",
-        ["normalized", "none", "log10", "sqrt"],
-    )
+    select_input = ui.input_select("y_axis_transformation", "Transformation to apply to intensity axis:", ["normalized", "none", "log10", "sqrt"])
 
     run_button_plot_spectra = ui.download_button("run_btn_plot_spectra", "Run", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
@@ -268,15 +2583,15 @@ def plot_spectra_ui(platform: str):
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
             ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([base_inputs[6:7], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div(numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([numeric_inputs[5:10], select_input], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([base_inputs[6:9], extra_inputs[0]], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(extra_inputs[1:3], numeric_inputs[0:3], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([numeric_inputs[3:10], select_input], style="display:flex; flex-direction:column; gap:10px;"),
             col_widths=(3,3,3,3),
         )
     elif platform == "NRMS":
         inputs_columns = ui.layout_columns(
             ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([base_inputs[6:7], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([base_inputs[6:9], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
             ui.div(numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
             ui.div([numeric_inputs[5:10], select_input], style="display:flex; flex-direction:column; gap:10px;"),
             col_widths=(3,3,3,3),
@@ -297,49 +2612,29 @@ def plot_spectra_ui(platform: str):
 
 def run_spec_lib_matching_ui(platform: str):
     base_inputs = [
-        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
-        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
+        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or txt):"),
+        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or txt):"),
         ui.input_select("similarity_measure", "Select similarity measure:", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"]),
         ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
-        ui.input_selectize(
-            "spectrum_ID1",
-            "Select spectrum ID 1 (only applicable for plotting; default is the first spectrum in the query library):",
-            choices=[],
-            multiple=False,
-            options={"placeholder": "Upload a library..."},
-        ),
-        ui.input_selectize(
-            "spectrum_ID2",
-            "Select spectrum ID 2 (only applicable for plotting; default is the first spectrum in the reference library):",
-            choices=[],
-            multiple=False,
-            options={"placeholder": "Upload a library..."},
-        ),
-        ui.input_select(
-            "high_quality_reference_library",
-            "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.",
-            [False, True],
-        )
+        ui.input_file('compound_ID_output_file', 'Upload output from spectral library matching to plot top matches (optional)'),
+        ui.input_selectize("q_spec", "Select query spectrum (only applicable for plotting; default is the first spectrum in the compound ID output):", choices=[], multiple=False, options={"placeholder": "Upload compound ID output..."}),
+        ui.input_selectize("r_spec", "Select reference spectrum (only applicable for plotting; default is the rank 1 reference spectrum):", choices=[], multiple=False, options={"placeholder": "Upload compound ID output..."}),
+        ui.input_select('print_url_spectrum1', 'Print PubChem URL for query spectrum (only applicable for plotting):', ['No', 'Yes']),
+        ui.input_select('print_url_spectrum2', 'Print PubChem URL for reference spectrum (only applicable for plotting):', ['No', 'Yes']),
+        ui.input_select("high_quality_reference_library", "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.", [False, True])
     ]
 
     if platform == "HRMS":
         extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.",
-                "FCNMWL",
-            ),
+            ui.input_numeric("precursor_ion_mz_tolerance", "Precursor ion mass tolerance (leave blank if not applicable):", None),
+            ui.input_select("ionization_mode", "Ionization mode:", ['Positive','Negative','N/A'], selected='N/A'),
+            ui.input_select("adduct", "Adduct:", ['H','NH3','NH4','Na','K','N/A'], selected='N/A'),
+            ui.input_text("spectrum_preprocessing_order","Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.","FCNMWL"),
             ui.input_numeric("window_size_centroiding", "Centroiding window-size:", 0.5),
             ui.input_numeric("window_size_matching", "Matching window-size:", 0.5),
         ]
     else:
-        extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (F (filtering), N (noise removal), L (low-entropy transformation), W (weight factor transformation)).",
-                "FNLW",
-            )
-        ]
+        extra_inputs = [ui.input_text("spectrum_preprocessing_order","Sequence of characters for preprocessing order (F (filtering), N (noise removal), L (low-entropy transformation), W (weight factor transformation)).","FNLW")]
 
     numeric_inputs = [
         ui.input_numeric("mz_min", "Minimum m/z for filtering:", 0),
@@ -361,16 +2656,16 @@ def run_spec_lib_matching_ui(platform: str):
 
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
-            ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([base_inputs[6:7], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div(numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div(numeric_inputs[5:10], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([base_inputs[0:2], extra_inputs[0:3], base_inputs[2:4]], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([base_inputs[4:10]], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([extra_inputs[3:6], numeric_inputs[0:3]], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(numeric_inputs[3:10], style="display:flex; flex-direction:column; gap:10px;"),
             col_widths=(3,3,3,3)
         )
     elif platform == "NRMS":
         inputs_columns = ui.layout_columns(
             ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([base_inputs[6:7], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div([base_inputs[6:10], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
             ui.div(numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
             ui.div(numeric_inputs[5:10], style="display:flex; flex-direction:column; gap:10px;"),
             col_widths=(3,3,3,3)
@@ -397,8 +2692,8 @@ def run_spec_lib_matching_ui(platform: str):
 
 def run_parameter_tuning_grid_ui(platform: str):
     base_inputs = [
-        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
-        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
+        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or txt):"),
+        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or txt):"),
         ui.input_selectize("similarity_measure", "Select similarity measure(s):", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"], multiple=True, selected='cosine'),
         ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '((0.25, 0.25, 0.25, 0.25))'),
         ui.input_text("high_quality_reference_library", "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.", '[True]')
@@ -406,11 +2701,10 @@ def run_parameter_tuning_grid_ui(platform: str):
 
     if platform == "HRMS":
         extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.",
-                "[FCNMWL,CWM]",
-            ),
+            ui.input_numeric("precursor_ion_mz_tolerance", "Precursor ion mass tolerance (leave blank if not applicable):", None),
+            ui.input_select("ionization_mode", "Ionization mode:", ['Positive','Negative','N/A'], selected='N/A'),
+            ui.input_select("adduct", "Adduct:", ['H','NH3','NH4','Na','K','N/A'], selected='N/A'),
+            ui.input_text("spectrum_preprocessing_order", "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.", "[FCNMWL,CWM]"),
             ui.input_text("window_size_centroiding", "Centroiding window-size:", "[0.5]"),
             ui.input_text("window_size_matching", "Matching window-size:", "[0.1,0.5]"),
         ]
@@ -464,7 +2758,7 @@ def run_parameter_tuning_grid_ui(platform: str):
 
     return ui.div(
         ui.TagList(
-            ui.h2("Tune parameters"),
+            ui.h2("Tune parameters (grid search)"),
             inputs_columns,
             run_button_parameter_tuning_grid,
             back_button,
@@ -492,83 +2786,71 @@ PARAMS_NRMS = {
     "entropy_dimension":       (1.0, 3.0)
 }
 
+
 def run_parameter_tuning_DE_ui(platform: str):
-    if platform == 'HRMS':
-        PARAMS=PARAMS_HRMS
+    # Pick param set per platform
+    if platform == "HRMS":
+        PARAMS = PARAMS_HRMS
     else:
-        PARAMS=PARAMS_NRMS
+        PARAMS = PARAMS_NRMS
 
     base_inputs = [
-        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
-        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
+        ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or txt):"),
+        ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or txt):"),
         ui.input_select("similarity_measure", "Select similarity measure:", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"]),
-        ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
-        ui.input_select("high_quality_reference_library", "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.", [False, True],),
-    ]
+        ui.input_text("weights", "Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):", "0.25, 0.25, 0.25, 0.25"),
+        ui.input_select("high_quality_reference_library", "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.", [False, True])]
 
     if platform == "HRMS":
         extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.",
-                "FCNMWL",
-            ),
+            ui.input_numeric("precursor_ion_mz_tolerance", "Precursor ion mass tolerance (leave blank if not applicable):", None),
+            ui.input_select("ionization_mode", "Ionization mode:", ['Positive','Negative','N/A'], selected='N/A'),
+            ui.input_select("adduct", "Adduct:", ['H','NH3','NH4','Na','K','N/A'], selected='N/A'),
+            ui.input_text("spectrum_preprocessing_order", "Sequence of characters for preprocessing order (C (centroiding), F (filtering), M (matching), N (noise removal), L (low-entropy transformation), W (weight factor transformation)). M must be included, C before M if used.", "FCNMWL"),
             ui.input_numeric("window_size_centroiding", "Centroiding window-size:", 0.5),
             ui.input_numeric("window_size_matching", "Matching window-size:", 0.5),
         ]
     else:
-        extra_inputs = [
-            ui.input_text(
-                "spectrum_preprocessing_order",
-                "Sequence of characters for preprocessing order (F (filtering), N (noise removal), L (low-entropy transformation), W (weight factor transformation)).",
-                "FNLW",
-            )
-        ]
+        extra_inputs = [ui.input_text("spectrum_preprocessing_order", "Sequence of characters for preprocessing order (F (filtering), N (noise removal), L (low-entropy transformation), W (weight factor transformation)).", "FNLW")]
 
     numeric_inputs = [
         ui.input_numeric("mz_min", "Minimum m/z for filtering:", 0),
-        ui.input_numeric("mz_max", "Maximum m/z for filtering:", 99999999),
+        ui.input_numeric("mz_max", "Maximum m/z for filtering:", 99_999_999),
         ui.input_numeric("int_min", "Minimum intensity for filtering:", 0),
-        ui.input_numeric("int_max", "Maximum intensity for filtering:", 999999999),
+        ui.input_numeric("int_max", "Maximum intensity for filtering:", 999_999_999),
         ui.input_numeric("noise_threshold", "Noise removal threshold:", 0.0),
         ui.input_numeric("wf_mz", "Mass/charge weight factor:", 0.0),
         ui.input_numeric("wf_int", "Intensity weight factor:", 1.0),
         ui.input_numeric("LET_threshold", "Low-entropy threshold:", 0.0),
         ui.input_numeric("entropy_dimension", "Entropy dimension (Renyi/Tsallis only):", 1.1),
+        ui.input_numeric("max_iterations", "Maximum number of iterations:", 5),
     ]
 
-
-    #run_button_parameter_tuning_DE = ui.download_button("run_btn_parameter_tuning_DE", "Tune parameters (differential evolution optimization)", style="font-size:16px; padding:15px 30px; width:300px; height:100px")
     run_button_parameter_tuning_DE = ui.input_action_button("run_btn_parameter_tuning_DE", "Tune parameters (differential evolution optimization)", style="font-size:16px; padding:15px 30px; width:300px; height:100px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:300px; height:100px")
 
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
-            ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([base_inputs[6:7], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div(numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([numeric_inputs[5:10]], style="display:flex; flex-direction:column; gap:10px;"),
-            col_widths=(3,3,3,3),
+            ui.div(*base_inputs, style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(*extra_inputs, style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(*numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(*numeric_inputs[5:11], style="display:flex; flex-direction:column; gap:10px;"),
+            col_widths=(3, 3, 3, 3),
         )
-    elif platform == "NRMS":
+    else:
         inputs_columns = ui.layout_columns(
-            ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([base_inputs[6:7], *extra_inputs], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div(numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
-            ui.div([numeric_inputs[5:10]], style="display:flex; flex-direction:column; gap:10px;"),
-            col_widths=(3,3,3,3),
+            ui.div(*base_inputs, style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(*extra_inputs, style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(*numeric_inputs[0:5], style="display:flex; flex-direction:column; gap:10px;"),
+            ui.div(*numeric_inputs[5:11], style="display:flex; flex-direction:column; gap:10px;"),
+            col_widths=(3, 3, 3, 3),
         )
 
     return ui.page_fillable(
         ui.layout_sidebar(
             ui.sidebar(
-                ui.h3("Select parameters"),
-                ui.input_checkbox_group(
-                    "params",
-                    None,
-                    choices=list(PARAMS.keys()),
-                    selected=["noise_threshold","LET_threshold"],
-                ),
+                ui.h3("Select continuous parameters to optimize"),
+                ui.input_checkbox_group("params", None, choices=list(PARAMS.keys()), selected=["noise_threshold", "LET_threshold"]),
                 ui.hr(),
                 ui.h4("Bounds for selected parameters"),
                 ui.output_ui("bounds_inputs"),
@@ -576,23 +2858,30 @@ def run_parameter_tuning_DE_ui(platform: str):
             ),
             ui.div(
                 ui.h2("Tune parameters (differential evolution optimization)"),
-                *(inputs_columns if isinstance(inputs_columns, (list, tuple)) else [inputs_columns]),
-                run_button_parameter_tuning_DE,
-                back_button,
+                inputs_columns,
+                ui.div(run_button_parameter_tuning_DE, back_button, style=("display:flex; flex-direction:row; gap:12px; align-items:center; flex-wrap:wrap;")),
+                ui.br(),
+                ui.card(
+                    ui.card_header("Live log"),
+                    ui.output_text_verbatim("run_log"),
+                ),
+                style="display:flex; flex-direction:column; gap:16px;",
             ),
         )
     )
 
 
 
-
 app_ui = ui.page_fluid(
     ui.head_content(ui.tags.link(rel="icon", href="emblem.png")),
+    ui.div(ui.output_image("image"), style=("display:block; margin:20px auto; max-width:320px; height:auto; text-align:center")),
     ui.output_ui("main_ui"),
-    ui.output_text("status_output")
+    ui.output_text("status_output"),
 )
 
 
+
+
 def server(input, output, session):
 
     current_page = reactive.Value("main_menu")
@@ -611,7 +2900,7 @@ def server(input, output, session):
     match_log_rv = reactive.Value("")
     is_matching_rv = reactive.Value(False)
     is_any_job_running = reactive.Value(False)
-    latest_csv_path_rv = reactive.Value("")
+    latest_txt_path_rv = reactive.Value("")
     latest_df_rv = reactive.Value(None)
     is_running_rv = reactive.Value(False)
 
@@ -627,6 +2916,106 @@ def server(input, output, session):
     converted_query_path_rv = reactive.Value(None)
     converted_reference_path_rv = reactive.Value(None)
 
+    df_rv = reactive.Value(None)
+
+
+    def _discover_rank_cols(df: pd.DataFrame):
+        pred_pat = re.compile(r"^RANK\.(\d+)\.PRED$")
+        score_pat = re.compile(r"^RANK\.(\d+)\.SIMILARITY\.SCORE$")
+        pred_map, score_map = {}, {}
+        for c in df.columns:
+            m = pred_pat.match(c)
+            if m: pred_map[int(m.group(1))] = c
+            m = score_pat.match(c)
+            if m: score_map[int(m.group(1))] = c
+        return [(k, pred_map[k], score_map.get(k)) for k in sorted(pred_map)]
+
+
+    def _rank_choices_for_query(df: pd.DataFrame, qid: str):
+        sub = df.loc[df["QUERY.SPECTRUM.ID"].astype(str) == str(qid)]
+        if sub.empty:
+            return {}, None
+        row = sub.iloc[0]
+        rank_cols = _discover_rank_cols(df)
+        if not rank_cols:
+            return {}, None
+
+        choices = {}
+        default_value = None
+        for (k, pred_col, score_col) in rank_cols:
+            pred = row.get(pred_col, None)
+            if pd.isna(pred):
+                continue
+            pred = str(pred)
+            score = row.get(score_col, None) if score_col else None
+            score_str = f"{float(score):.6f}" if (score is not None and pd.notna(score)) else "NA"
+            label = f"Rank {k} — {score_str} — {pred}"
+            choices[label] = pred                 # values are plain names
+            if k == 1:
+                default_value = pred              # default = Rank 1 name
+
+        if default_value is None and choices:
+            default_value = next(iter(choices.values()))
+        return choices, default_value
+
+
+    @reactive.effect
+    @reactive.event(input.compound_ID_output_file)
+    async def _populate_ids_from_compound_ID_output_upload():
+        files = input.compound_ID_output_file()
+        if not files:
+            return
+
+        in_path = Path(files[0]["datapath"])
+        try:
+            query_status_rv.set(f"Reading table from: {in_path.name} …")
+            await reactive.flush()
+
+            df = await asyncio.to_thread(pd.read_csv, in_path, sep="\t", header=0)
+
+            if "QUERY.SPECTRUM.ID" not in df.columns:
+                raise ValueError("Missing required column: QUERY.SPECTRUM.ID")
+            if not _discover_rank_cols(df):
+                raise ValueError("No columns matching RANK.<k>.PRED found.")
+
+            df_rv.set(df)
+
+            ids = df["QUERY.SPECTRUM.ID"].astype(str).tolist()
+            unique_ids_in_order = list(dict.fromkeys(ids))
+
+            choices_dict, default_rank_value = _rank_choices_for_query(df, ids[0])
+            choices_values = [str(v).strip() for v in choices_dict.values()]
+            default_rank_value = str(default_rank_value).strip() if default_rank_value is not None else None
+
+            ui.update_selectize("q_spec", choices=unique_ids_in_order, selected=ids[0])
+            await reactive.flush()
+
+            ui.update_selectize("r_spec", choices=choices_values, selected=choices_values[0])
+            await reactive.flush()
+
+        except Exception as e:
+            query_status_rv.set(f"❌ Failed: {e}")
+            await reactive.flush()
+            raise
+
+
+    @reactive.effect
+    @reactive.event(input.q_spec)
+    async def _update_rank_choices_on_compound_ID_change():
+        df = df_rv.get()
+        if df is None:
+            return
+        qid = input.q_spec()
+        if not qid:
+            return
+
+        choices, default_rank_value = _rank_choices_for_query(df, qid)
+        choices = list(choices.values())
+        ui.update_selectize('r_spec', choices=choices, selected=default_rank_value)
+        await reactive.flush()
+
+
+
     @output
     @render.ui
     def bounds_inputs():
@@ -769,6 +3158,11 @@ def server(input, output, session):
         def flush(self):
             pass
 
+    def _run_with_redirects(func, writer: ReactiveWriter, **kwargs):
+        with contextlib.redirect_stdout(writer), contextlib.redirect_stderr(writer):
+            return func(**kwargs)
+
+
 
     @reactive.effect
     async def _pump_logs():
@@ -865,7 +3259,7 @@ def server(input, output, session):
     @render.image
     def image():
         dir = Path(__file__).resolve().parent
-        img: ImgData = {"src": str(dir / "www/emblem.png"), "width": "320px", "height": "250px"}
+        img: ImgData = {"src": str(dir / "www/emblem.png"), "width": "250px", "height": "250px"}
         return img
 
     @output
@@ -874,30 +3268,10 @@ def server(input, output, session):
         if current_page() == "main_menu":
             return ui.page_fluid(
                 ui.h2("Main Menu"),
-                ui.div(
-                    ui.output_image("image"),
-                    #ui.img(src="emblem.png", width="320px", height="250px"),
-                    style=(
-                        "position:fixed; top:0; left:50%; transform:translateX(-50%); "
-                        "z-index:1000; text-align:center; padding:10px; background-color:white;"
-                    ),
-                ),
-                ui.div(
-                    "Overview:",
-                    style="text-align:left; font-size:24px; font-weight:bold; margin-top:350px"
-                ),
-                ui.div(
-                    "PyCompound is a Python-based tool designed for performing spectral library matching on either high-resolution mass spectrometry data (HRMS) or low-resolution mass spectrometry data (NRMS). PyCompound offers a range of spectrum preprocessing transformations and similarity measures. These spectrum preprocessing transformations include filtering on mass/charge and/or intensity values, weight factor transformation, low-entropy transformation, centroiding, noise removal, and matching. The available similarity measures include the canonical Cosine similarity measure, three entropy-based similarity measures, and a variety of binary similarity measures: Jaccard, Dice, 3W-Jaccard, Sokal-Sneath, Binary Cosine, Mountford, McConnaughey, Driver-Kroeber, Simpson, Braun-Banquet, Fager-McGowan, Kulczynski, Intersection, Hamming, and Hellinger.",
-                    style="margin-top:10px; text-align:left; font-size:16px; font-weight:500"
-                ),
-                ui.div(
-                    "Select options:",
-                    style="margin-top:30px; text-align:left; font-size:24px; font-weight:bold"
-                ),
-                ui.div(
-                    ui.input_radio_buttons("chromatography_platform", "Specify chromatography platform:", ["HRMS","NRMS"]),
-                    style="font-size:18px; margin-top:10px; max-width:none"
-                ),
+                ui.div("Overview:", style="text-align:left; font-size:24px; font-weight:bold"),
+                ui.div("PyCompound is a Python-based tool designed for performing spectral library matching on either high-resolution mass spectrometry data (HRMS) or low-resolution mass spectrometry data (NRMS). PyCompound offers a range of spectrum preprocessing transformations and similarity measures. These spectrum preprocessing transformations include filtering on mass/charge and/or intensity values, weight factor transformation, low-entropy transformation, centroiding, noise removal, and matching. The available similarity measures include the canonical Cosine similarity measure, three entropy-based similarity measures, and a variety of binary similarity measures: Jaccard, Dice, 3W-Jaccard, Sokal-Sneath, Binary Cosine, Mountford, McConnaughey, Driver-Kroeber, Simpson, Braun-Banquet, Fager-McGowan, Kulczynski, Intersection, Hamming, and Hellinger.", style="margin-top:10px; text-align:left; font-size:16px; font-weight:500"),
+                ui.div("Select options:", style="margin-top:30px; text-align:left; font-size:24px; font-weight:bold"),
+                ui.div(ui.input_radio_buttons("chromatography_platform", "Specify chromatography platform:", ["HRMS","NRMS"]), style="font-size:18px; margin-top:10px; max-width:none"),
                 ui.input_action_button("plot_spectra", "Plot two spectra before and after preprocessing transformations.", style="font-size:18px; padding:20px 40px; width:550px; height:100px; margin-top:10px; margin-right:50px"),
                 ui.input_action_button("run_spec_lib_matching", "Run spectral library matching to perform compound identification on a query library of spectra.", style="font-size:18px; padding:20px 40px; width:550px; height:100px; margin-top:10px; margin-right:50px"),
                 ui.input_action_button("run_parameter_tuning_grid", "Grid search: Tune parameters to maximize accuracy of compound identification given a query library with known spectrum IDs.", style="font-size:18px; padding:20px 40px; width:450px; height:120px; margin-top:10px; margin-right:50px"),
@@ -970,36 +3344,36 @@ def server(input, output, session):
         suffix = in_path.suffix.lower()
 
         try:
-            if suffix == ".csv":
-                csv_path = in_path
-                converted_query_path_rv.set(str(csv_path))
+            if suffix == ".txt":
+                txt_path = in_path
+                converted_query_path_rv.set(str(txt_path))
             else:
-                query_status_rv.set(f"Converting {in_path.name} → CSV …")
+                query_status_rv.set(f"Converting {in_path.name} →  TXT…")
                 await reactive.flush()
 
-                tmp_csv_path = in_path.with_suffix(".converted.csv")
+                tmp_txt_path = in_path.with_suffix(".converted.txt")
 
-                out_obj = await asyncio.to_thread(build_library, str(in_path), str(tmp_csv_path))
+                out_obj = await asyncio.to_thread(build_library, str(in_path), str(tmp_txt_path))
 
                 if isinstance(out_obj, (str, os.PathLike, Path)):
-                    csv_path = Path(out_obj)
+                    txt_path = Path(out_obj)
                 elif isinstance(out_obj, pd.DataFrame):
-                    out_obj.to_csv(tmp_csv_path, index=False, sep='\t')
-                    csv_path = tmp_csv_path
+                    out_obj.to_csv(tmp_txt_path, index=False, sep='\t')
+                    txt_path = tmp_txt_path
                 else:
                     raise TypeError(f"build_library returned unsupported type: {type(out_obj)}")
 
-                converted_query_path_rv.set(str(csv_path))
+                converted_query_path_rv.set(str(txt_path))
 
-            query_status_rv.set(f"Reading IDs from: {csv_path.name} …")
+            query_status_rv.set(f"Reading IDs from: {txt_path.name} …")
             await reactive.flush()
 
-            ids = await asyncio.to_thread(extract_first_column_ids, str(csv_path))
+            ids = await asyncio.to_thread(extract_first_column_ids, str(txt_path))
             query_ids_rv.set(ids)
 
             ui.update_selectize("spectrum_ID1", choices=ids, selected=(ids[0] if ids else None))
 
-            query_status_rv.set(f"✅ Loaded {len(ids)} IDs from {csv_path.name}" if ids else f"⚠️ No IDs found in {csv_path.name}")
+            query_status_rv.set(f"✅ Loaded {len(ids)} IDs from {txt_path.name}" if ids else f"⚠️ No IDs found in {txt_path.name}")
             await reactive.flush()
 
         except Exception as e:
@@ -1019,37 +3393,37 @@ def server(input, output, session):
         suffix = in_path.suffix.lower()
 
         try:
-            if suffix == ".csv":
-                csv_path = in_path
-                converted_reference_path_rv.set(str(csv_path))
+            if suffix == ".txt":
+                txt_path = in_path
+                converted_reference_path_rv.set(str(txt_path))
             else:
-                reference_status_rv.set(f"Converting {in_path.name} → CSV …")
+                reference_status_rv.set(f"Converting {in_path.name} →  TXT…")
                 await reactive.flush()
 
-                tmp_csv_path = in_path.with_suffix(".converted.csv")
+                tmp_txt_path = in_path.with_suffix(".converted.txt")
 
-                out_obj = await asyncio.to_thread(build_library, str(in_path), str(tmp_csv_path))
+                out_obj = await asyncio.to_thread(build_library, str(in_path), str(tmp_txt_path))
 
                 if isinstance(out_obj, (str, os.PathLike, Path)):
-                    csv_path = Path(out_obj)
+                    txt_path = Path(out_obj)
                 elif isinstance(out_obj, pd.DataFrame):
-                    out_obj.to_csv(tmp_csv_path, index=False, sep='\t')
-                    csv_path = tmp_csv_path
+                    out_obj.to_csv(tmp_txt_path, index=False, sep='\t')
+                    txt_path = tmp_txt_path
                 else:
                     raise TypeError(f"build_library returned unsupported type: {type(out_obj)}")
 
-                converted_reference_path_rv.set(str(csv_path))
+                converted_reference_path_rv.set(str(txt_path))
 
-            reference_status_rv.set(f"Reading IDs from: {csv_path.name} …")
+            reference_status_rv.set(f"Reading IDs from: {txt_path.name} …")
             await reactive.flush()
 
-            ids = await asyncio.to_thread(extract_first_column_ids, str(csv_path))
+            ids = await asyncio.to_thread(extract_first_column_ids, str(txt_path))
             reference_ids_rv.set(ids)
 
             ui.update_selectize("spectrum_ID2", choices=ids, selected=(ids[0] if ids else None))
 
             reference_status_rv.set(
-                f"✅ Loaded {len(ids)} IDs from {csv_path.name}" if ids else f"⚠️ No IDs found in {csv_path.name}"
+                f"✅ Loaded {len(ids)} IDs from {txt_path.name}" if ids else f"⚠️ No IDs found in {txt_path.name}"
             )
             await reactive.flush()
 
@@ -1059,7 +3433,7 @@ def server(input, output, session):
             raise
 
 
-    @render.download(filename=lambda: f"plot.png")
+    @render.download(filename=lambda: f"plot.svg")
     def run_btn_plot_spectra():
         spectrum_ID1 = input.spectrum_ID1() or None
         spectrum_ID2 = input.spectrum_ID2() or None
@@ -1071,22 +3445,20 @@ def server(input, output, session):
         if input.high_quality_reference_library() != 'False':
             high_quality_reference_library_tmp2 = True
 
-        print(input.high_quality_reference_library())
-        print(high_quality_reference_library_tmp2)
-
         if input.chromatography_platform() == "HRMS":
-            fig = generate_plots_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), weights=weights, spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), window_size_centroiding=input.window_size_centroiding(), window_size_matching=input.window_size_matching(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
+            fig = generate_plots_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, print_url_spectrum1=input.print_url_spectrum1(), print_url_spectrum2=input.print_url_spectrum2(), similarity_measure=input.similarity_measure(), weights=weights, spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), window_size_centroiding=input.window_size_centroiding(), window_size_matching=input.window_size_matching(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
             plt.show()
         elif input.chromatography_platform() == "NRMS":
-            fig = generate_plots_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
+            fig = generate_plots_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, print_url_spectrum1=input.print_url_spectrum1(), print_url_spectrum2=input.print_url_spectrum2(), similarity_measure=input.similarity_measure(), spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
             plt.show()
         with io.BytesIO() as buf:
-            fig.savefig(buf, format="png", dpi=150, bbox_inches="tight")
+            fig.savefig(buf, format="svg", dpi=150, bbox_inches="tight")
             plt.close()
             yield buf.getvalue()
 
 
 
+
     @render.download(filename="identification_output.txt")
     async def run_btn_spec_lib_matching():
         match_log_rv.set("Running identification...\n")
@@ -1099,7 +3471,7 @@ def server(input, output, session):
             hq = bool(hq)
 
         weights = [float(weight.strip()) for weight in input.weights().split(",") if weight.strip()]
-        weights = {'Cosine':weights[0], 'Shannon':weights[1], 'Renyi':weights[2], 'Tsallis':weights[3]}
+        weights = {'Cosine': weights[0], 'Shannon': weights[1], 'Renyi': weights[2], 'Tsallis': weights[3]}
 
         common_kwargs = dict(
             query_data=input.query_data()[0]["datapath"],
@@ -1121,37 +3493,81 @@ def server(input, output, session):
             return_ID_output=True,
         )
 
+        # --- streaming setup (same pattern as your DE block) ---
         loop = asyncio.get_running_loop()
-        rw = ReactiveWriter(loop)
+        q: asyncio.Queue[str | None] = asyncio.Queue()
+
+        class UIWriter(io.TextIOBase):
+            def write(self, s: str):
+                if s:
+                    loop.call_soon_threadsafe(q.put_nowait, s)
+                return len(s)
+            def flush(self): pass
+
+        async def _drain():
+            while True:
+                msg = await q.get()
+                if msg is None:
+                    break
+                match_log_rv.set(match_log_rv.get() + msg)
+                await reactive.flush()
+
+        drain_task = asyncio.create_task(_drain())
+        writer = UIWriter()
+
+        # --- worker wrappers that install redirects INSIDE the thread ---
+        def _run_hrms():
+            with redirect_stdout(writer), redirect_stderr(writer):
+                # optional heartbeat
+                print(">> Starting HRMS identification ...", flush=True)
+                return run_spec_lib_matching_on_HRMS_data_shiny(
+                    precursor_ion_mz_tolerance=input.precursor_ion_mz_tolerance(),
+                    ionization_mode=input.ionization_mode(),
+                    adduct=input.adduct(),
+                    window_size_centroiding=input.window_size_centroiding(),
+                    window_size_matching=input.window_size_matching(),
+                    **common_kwargs
+                )
+
+        def _run_nrms():
+            with redirect_stdout(writer), redirect_stderr(writer):
+                print(">> Starting NRMS identification ...", flush=True)
+                return run_spec_lib_matching_on_NRMS_data_shiny(**common_kwargs)
 
+        # --- run in worker thread and stream output live ---
         try:
-            with redirect_stdout(rw), redirect_stderr(rw):
-                if input.chromatography_platform() == "HRMS":
-                    df_out = await asyncio.to_thread(
-                        run_spec_lib_matching_on_HRMS_data,
-                        window_size_centroiding=input.window_size_centroiding(),
-                        window_size_matching=input.window_size_matching(),
-                        **common_kwargs
-                    )
-                else:
-                    df_out = await asyncio.to_thread(run_spec_lib_matching_on_NRMS_data, **common_kwargs)
+            if input.chromatography_platform() == "HRMS":
+                df_out = await asyncio.to_thread(_run_hrms)
+            else:
+                df_out = await asyncio.to_thread(_run_nrms)
+
             match_log_rv.set(match_log_rv.get() + "\n✅ Identification finished.\n")
             await reactive.flush()
+
         except Exception as e:
-            match_log_rv.set(match_log_rv.get() + f"\n❌ Error: {e}\n")
+            import traceback
+            tb = "".join(traceback.format_exception(type(e), e, e.__traceback__))
+            match_log_rv.set(match_log_rv.get() + f"\n❌ {type(e).__name__}: {e}\n{tb}\n")
             await reactive.flush()
+            # make sure to stop the drainer before re-raising
+            await q.put(None); await drain_task
             raise
 
-        yield df_out.to_csv(index=True, sep='\t')
+        finally:
+            await q.put(None)
+            await drain_task
+
+        yield df_out.to_csv(index=True, sep="\t")
+
 
 
 
-    @render.download(filename="plot.png")
+    @render.download(filename="plot.svg")
     def run_btn_plot_spectra_within_spec_lib_matching():
         req(input.query_data(), input.reference_data())
 
-        spectrum_ID1 = input.spectrum_ID1() or None
-        spectrum_ID2 = input.spectrum_ID2() or None
+        spectrum_ID1 = input.q_spec() or None
+        spectrum_ID2 = input.r_spec() or None
 
         hq = input.high_quality_reference_library()
         if isinstance(hq, str):
@@ -1167,6 +3583,8 @@ def server(input, output, session):
             reference_data=input.reference_data()[0]['datapath'],
             spectrum_ID1=spectrum_ID1,
             spectrum_ID2=spectrum_ID2,
+            print_url_spectrum1=input.print_url_spectrum1(),
+            print_url_spectrum2=input.print_url_spectrum2(), 
             similarity_measure=input.similarity_measure(),
             weights=weights,
             spectrum_preprocessing_order=input.spectrum_preprocessing_order(),
@@ -1192,7 +3610,7 @@ def server(input, output, session):
             plt.show()
 
         with io.BytesIO() as buf:
-            fig.savefig(buf, format="png", dpi=150, bbox_inches="tight")
+            fig.savefig(buf, format="svg", dpi=150, bbox_inches="tight")
             plt.close()
             yield buf.getvalue()
 
@@ -1230,6 +3648,9 @@ def server(input, output, session):
 
         try:
             if input.chromatography_platform() == "HRMS":
+                precursor_ion_mz_tolerance = float(input.precursor_ion_mz_tolerance())
+                ionization_mode = str(input.ionization_mode())
+                adduct = str(input.adduct())
                 window_size_centroiding_tmp = strip_numeric(input.window_size_centroiding())
                 window_size_matching_tmp = strip_numeric(input.window_size_matching())
                 grid = {
@@ -1249,7 +3670,7 @@ def server(input, output, session):
                     'window_size_centroiding': window_size_centroiding_tmp,
                     'window_size_matching': window_size_matching_tmp,
                 }
-                df_out = await asyncio.to_thread(_run_with_redirects, tune_params_on_HRMS_data_grid_shiny, rw, **common_kwargs, grid=grid)
+                df_out = await asyncio.to_thread(_run_with_redirects, tune_params_on_HRMS_data_grid_shiny, rw, **common_kwargs, grid=grid, precursor_ion_mz_tolerance=precursor_ion_mz_tolerance, ionization_mode=ionization_mode, adduct=adduct)
             else:
                 grid = {
                     'similarity_measure': similarity_measure_tmp,
@@ -1277,43 +3698,147 @@ def server(input, output, session):
             is_any_job_running.set(False)
             await reactive.flush()
 
-        yield df_out.to_csv(index=False).encode("utf-8", sep='\t')
+        yield df_out.to_csv(index=False, sep='\t').encode("utf-8")
+
 
 
     @reactive.effect
     @reactive.event(input.run_btn_parameter_tuning_DE)
-    def _run_btn_parameter_tuning_DE():
+    async def run_btn_parameter_tuning_DE():
+        match_log_rv.set("Tuning specified continuous parameters using differential evolution...\n")
         is_any_job_running.set(True)
         is_tuning_DE_running.set(True)
-        match_log_rv.set("Tuning specified continuous parameters using differential evolution...\n")
+        await reactive.flush()
 
-        #print('\nhere!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
-        weights = [float(weight.strip()) for weight in input.weights().split(",") if weight.strip()]
-        weights = {'Cosine':weights[0], 'Shannon':weights[1], 'Renyi':weights[2], 'Tsallis':weights[3]}
-        opt_params, bounds_dict, bounds_list = _read_bounds()
-        #print(input.params())
-        #print("Optimizing over:", opt_params)
-        #print("Bounds list:", bounds_list)
-        #print("Bounds dict:", bounds_dict)
-        #tmp = {"window_size_centroiding":input.window_size_centroiding(), "window_size_matching":input.window_size_matching(), "noise_threshold":input.noise_threshold(), "wf_mz":input.wf_mz(), "wf_int":input.wf_int(), "LET_threshold":input.LET_threshold(), "entropy_dimension":input.entropy_dimension()}
-        #print(tmp)
-        if input.chromatography_platform() == 'HRMS':
-            tune_params_DE(query_data=input.query_data()[0]["datapath"],
-                           reference_data=input.reference_data()[0]["datapath"],
-                           similarity_measure=input.similarity_measure(),
-                           weights=weights,
-                           spectrum_preprocessing_order=input.spectrum_preprocessing_order(),
-                           mz_min=input.mz_min(),
-                           mz_max=input.mz_max(),
-                           int_min=input.int_min(),
-                           int_max=input.int_max(),
-                           high_quality_reference_library=input.high_quality_reference_library(),
-                           optimize_params=list(input.params()),
-                           param_bounds={"window_size_matching":(0.0,0.5),"noise_threshold":(0.0,0.25),"wf_mz":(0.0,5.0),"wf_int":(0.0,5.0)},
-                           #param_bounds=bounds_dict,
-                           default_params={"window_size_centroiding":input.window_size_centroiding(), "window_size_matching":input.window_size_matching(), "noise_threshold":input.noise_threshold(), "wf_mz":input.wf_mz(), "wf_int":input.wf_int(), "LET_threshold":input.LET_threshold(), "entropy_dimension":input.entropy_dimension()})
-        #print('here!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
+        def _safe_float(v, default):
+            try:
+                if v is None:
+                    return default
+                return float(v)
+            except Exception:
+                return default
+
+        def _iget(id, default=None):
+            if id in input:
+                try:
+                    return input[id]()
+                except SilentException:
+                    return default
+            return default
+
+        loop = asyncio.get_running_loop()
+        q: asyncio.Queue[str | None] = asyncio.Queue()
+
+        class UIWriter(io.TextIOBase):
+            def write(self, s: str):
+                if s:
+                    loop.call_soon_threadsafe(q.put_nowait, s)
+                return len(s)
+            def flush(self): pass
+
+        async def _drain():
+            while True:
+                msg = await q.get()
+                if msg is None:
+                    break
+                match_log_rv.set(match_log_rv.get() + msg)
+                await reactive.flush()
+
+        drain_task = asyncio.create_task(_drain())
+        writer = UIWriter()
+
+        try:
+            qfile = _iget("query_data")[0]["datapath"]
+            rfile = _iget("reference_data")[0]["datapath"]
 
+            platform = _iget("chromatography_platform", "HRMS")
+            sim = _iget("similarity_measure", "cosine")
+            spro = _iget("spectrum_preprocessing_order", "FCNMWL")
+
+            hq_raw = _iget("high_quality_reference_library", False)
+            if isinstance(hq_raw, str):
+                hq = hq_raw.lower() == "true"
+            else:
+                hq = bool(hq_raw)
+
+            mz_min = _safe_float(_iget("mz_min", 0.0), 0.0)
+            mz_max = _safe_float(_iget("mz_max", 99_999_999.0), 99_999_999.0)
+            int_min = _safe_float(_iget("int_min", 0.0), 0.0)
+            int_max = _safe_float(_iget("int_max", 999_999_999.0), 999_999_999.0)
+
+            w_text = _iget("weights", "") or ""
+            w_list = [float(w.strip()) for w in w_text.split(",") if w.strip()]
+            w_list = (w_list + [0.0, 0.0, 0.0, 0.0])[:4]
+            weights = {"Cosine": w_list[0], "Shannon": w_list[1], "Renyi": w_list[2], "Tsallis": w_list[3]}
+
+            opt_params = tuple(_iget("params", ()) or ())
+            bounds_dict = {}
+            param_defaults = PARAMS_HRMS if platform == "HRMS" else PARAMS_NRMS
+            for p in opt_params:
+                lo = _safe_float(_iget(f"min_{p}", param_defaults.get(p, (0.0, 1.0))[0]),
+                                 param_defaults.get(p, (0.0, 1.0))[0])
+                hi = _safe_float(_iget(f"max_{p}", param_defaults.get(p, (0.0, 1.0))[1]),
+                                 param_defaults.get(p, (0.0, 1.0))[1])
+                if lo > hi:
+                    lo, hi = hi, lo
+                bounds_dict[p] = (lo, hi)
+
+            defaults = {
+                "window_size_centroiding": _safe_float(_iget("window_size_centroiding", 0.5), 0.5),
+                "window_size_matching":    _safe_float(_iget("window_size_matching",    0.5), 0.5),
+                "noise_threshold":         _safe_float(_iget("noise_threshold",         0.0), 0.0),
+                "wf_mz":                   _safe_float(_iget("wf_mz",                   0.0), 0.0),
+                "wf_int":                  _safe_float(_iget("wf_int",                  1.0), 1.0),
+                "LET_threshold":           _safe_float(_iget("LET_threshold",           0.0), 0.0),
+                "entropy_dimension":       _safe_float(_iget("entropy_dimension",       1.1), 1.1),
+            }
+            if platform == "NRMS":
+                defaults.pop("window_size_centroiding", None)
+                defaults.pop("window_size_matching", None)
+
+        except Exception as e:
+            import traceback
+            tb = "".join(traceback.format_exception(type(e), e, e.__traceback__))
+            match_log_rv.set(match_log_rv.get() + f"\n❌ Input snapshot failed:\n{tb}\n")
+            is_tuning_DE_running.set(False); is_any_job_running.set(False)
+            await q.put(None); await drain_task; await reactive.flush()
+            return
+
+        def _run():
+            with redirect_stdout(writer), redirect_stderr(writer):
+                return tune_params_DE(
+                    query_data=qfile,
+                    reference_data=rfile,
+                    precursor_ion_mz_tolerance=float(input.precursor_ion_mz_tolerance()),
+                    ionization_mode=input.ionization_mode(),
+                    adduct=input.adduct(),
+                    chromatography_platform=input.chromatography_platform(),
+                    similarity_measure=sim,
+                    weights=weights,
+                    spectrum_preprocessing_order=spro,
+                    mz_min=mz_min, mz_max=mz_max,
+                    int_min=int_min, int_max=int_max,
+                    high_quality_reference_library=hq,
+                    optimize_params=list(opt_params),
+                    param_bounds=bounds_dict,
+                    default_params=defaults,
+                    de_workers=1,
+                    maxiters=input.max_iterations()
+                )
+
+        try:
+            _ = await asyncio.to_thread(_run)
+            match_log_rv.set(match_log_rv.get() + "\n✅ Differential evolution finished.\n")
+        except Exception as e:
+            import traceback
+            tb = "".join(traceback.format_exception(type(e), e, e.__traceback__))
+            match_log_rv.set(match_log_rv.get() + f"\n❌ {type(e).__name__}: {e}\n{tb}\n")
+        finally:
+            await q.put(None)
+            await drain_task
+            is_tuning_DE_running.set(False)
+            is_any_job_running.set(False)
+            await reactive.flush()
 
 
     @reactive.effect
@@ -1335,8 +3860,12 @@ def server(input, output, session):
         return run_status_parameter_tuning_grid.get()
         return run_status_parameter_tuning_DE.get()
 
+    @output
+    @render.text
+    def run_log():
+        return match_log_rv.get()
 
-app = App(app_ui, server)
 
+app = App(app_ui, server)