@datagrok/peptides 1.17.3 → 1.17.5

package/src/widgets/settings.ts

@@ -19,6 +19,7 @@ export enum SETTINGS_PANES {
   VIEWERS = 'Viewers',
   COLUMNS = 'Columns',
   SEQUENCE_SPACE = 'Sequence space',
+  MCL = 'MCL',
 }
 
 export enum GENERAL_INPUTS {
@@ -44,12 +45,22 @@ export enum SEQUENCE_SPACE_INPUTS {
   FINGERPRINT_TYPE = 'Fingerprint type',
 }
 
+export enum MCL_INPUTS {
+  DISTANCE_FUNCTION = 'Distance function',
+  GAP_OPEN = 'Gap open penalty',
+  GAP_EXTEND = 'Gap extend penalty',
+  FINGERPRINT_TYPE = 'Fingerprint type',
+  THRESHOLD = 'Similarity threshold',
+  MAX_ITERATIONS = 'Max iterations',
+}
+
 
 export const PANES_INPUTS = {
   [SETTINGS_PANES.GENERAL]: GENERAL_INPUTS,
   [SETTINGS_PANES.VIEWERS]: VIEWERS_INPUTS,
   [SETTINGS_PANES.COLUMNS]: COLUMNS_INPUTS,
   [SETTINGS_PANES.SEQUENCE_SPACE]: SEQUENCE_SPACE_INPUTS,
+  [SETTINGS_PANES.MCL]: MCL_INPUTS,
 };
 
 /**
@@ -69,7 +80,7 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
   const result: type.PartialPeptidesSettings = {};
   const inputs: PaneInputs = {};
   const seqSpaceParams = settings?.sequenceSpaceParams ?? new type.SequenceSpaceParams();
-
+  const mclParams = settings?.mclSettings ?? new type.MCLSettings();
   // General pane options
   const activityCol = ui.columnInput(GENERAL_INPUTS.ACTIVITY, model.df,
     model.df.getCol(model.settings!.activityColumnName!), () => result.activityColumnName = activityCol.value!.name,
@@ -102,10 +113,23 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
   const isDendrogramEnabled = wu(model.analysisView.viewers).some((v) => v.type === VIEWER_TYPE.DENDROGRAM);
   const dendrogram = ui.boolInput(VIEWER_TYPE.DENDROGRAM, isDendrogramEnabled ?? false,
     () => result.showDendrogram = dendrogram.value) as DG.InputBase<boolean>;
+  const showSeqSpace = ui.boolInput('Sequence space', !!settings?.showSequenceSpace, () => {
+    result.showSequenceSpace = showSeqSpace.value ?? undefined;
+    if (showSeqSpace.value) {
+      seqSpacePane.root.style.display = 'flex';
+      if (!settings?.showSequenceSpace)
+        result.sequenceSpaceParams = seqSpaceParams;
+    } else {
+      seqSpacePane.root.style.display = 'none';
+      delete result.sequenceSpaceParams;
+    }
+    if (result.showSequenceSpace === settings?.showSequenceSpace)
+      delete result.showSequenceSpace;
+  });
   dendrogram.setTooltip('Show dendrogram viewer');
   dendrogram.enabled = getTreeHelperInstance() !== null;
 
-  accordion.addPane(SETTINGS_PANES.VIEWERS, () => ui.inputs([dendrogram]), true);
+  accordion.addPane(SETTINGS_PANES.VIEWERS, () => ui.inputs([dendrogram, showSeqSpace]), true);
   inputs[SETTINGS_PANES.VIEWERS] = [dendrogram];
 
   // Columns to include pane options
@@ -182,7 +206,7 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
         input.root.style.display = 'none';
     });
   }
-
+  // SEQ SPACE INPUTS
   const distanceFunctionInput = ui.choiceInput(SEQUENCE_SPACE_INPUTS.DISTANCE_FUNCTION, seqSpaceParams.distanceF,
     [distFNames.NEEDLEMANN_WUNSCH, distFNames.HAMMING, distFNames.LEVENSHTEIN, distFNames.MONOMER_CHEMICAL_DISTANCE],
     () => onSeqSpaceParamsChange('distanceF', distanceFunctionInput.value));
@@ -203,7 +227,8 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
     () => onSeqSpaceParamsChange('minPts', minPtsInput.value));
   minPtsInput.setTooltip('Minimum number of points in a cluster');
   const fingerprintTypesInput = ui.choiceInput('Fingerprint type', seqSpaceParams.fingerprintType,
-    ['Morgan', 'RDKit', 'Pattern'], () => onSeqSpaceParamsChange('fingerprintType', fingerprintTypesInput.value));
+    ['Morgan', 'RDKit', 'Pattern', 'AtomPair', 'MACCS', 'TopologicalTorsion'],
+    () => onSeqSpaceParamsChange('fingerprintType', fingerprintTypesInput.value));
   function correctSeqSpaceInputs(): void {
     toggleInputs([gapOpenInput, gapExtendInput], distanceFunctionInput.value === distFNames.NEEDLEMANN_WUNSCH);
     toggleInputs([epsilonInput, minPtsInput], clusterEmbeddingsInput.value === true);
@@ -212,14 +237,70 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
       distanceFunctionInput.value === distFNames.NEEDLEMANN_WUNSCH);
   }
   correctSeqSpaceInputs();
+  // END OF SEQ SPACE INPUTS
+
+  //MCL INPUTS
+
+  const modifiedMCLParams: Partial<type.MCLSettings> = {};
+  function onMCLParamsChange(fieldName: keyof type.MCLSettings, value: any): void {
+    correctMCLInputs();
+    //correctSeqSpaceInputs();
+    if (value === null || value === undefined || value === '')
+      return;
+    modifiedMCLParams[fieldName] = value;
+    let isAllSame = true;
+    for (const [key, val] of Object.entries(modifiedMCLParams)) {
+      if (val !== mclParams[key as keyof type.MCLSettings]) {
+        isAllSame = false;
+        break;
+      }
+    }
+    if (isAllSame)
+      delete result.mclSettings;
+    else
+      result.mclSettings = {...mclParams, ...modifiedMCLParams};
+  }
+
+  function correctMCLInputs(): void {
+    toggleInputs([mclGapOpenInput, mclGapExtendInput], mclDistanceFunctionInput.value === distFNames.NEEDLEMANN_WUNSCH);
+    toggleInputs([mclFingerprintTypesInput],
+      mclDistanceFunctionInput.value === distFNames.MONOMER_CHEMICAL_DISTANCE ||
+      mclDistanceFunctionInput.value === distFNames.NEEDLEMANN_WUNSCH);
+  }
+
+  const mclDistanceFunctionInput = ui.choiceInput(SEQUENCE_SPACE_INPUTS.DISTANCE_FUNCTION, mclParams.distanceF,
+    [distFNames.NEEDLEMANN_WUNSCH, distFNames.MONOMER_CHEMICAL_DISTANCE, distFNames.HAMMING, distFNames.LEVENSHTEIN],
+    () => onMCLParamsChange('distanceF', mclDistanceFunctionInput.value));
+  const mclGapOpenInput = ui.floatInput(SEQUENCE_SPACE_INPUTS.GAP_OPEN, mclParams.gapOpen,
+    () => onMCLParamsChange('gapOpen', mclGapOpenInput.value));
+  const mclGapExtendInput = ui.floatInput(SEQUENCE_SPACE_INPUTS.GAP_EXTEND, mclParams.gapExtend,
+    () => onMCLParamsChange('gapExtend', mclGapExtendInput.value));
+  const mclFingerprintTypesInput = ui.choiceInput('Fingerprint type', mclParams.fingerprintType,
+    ['Morgan', 'RDKit', 'Pattern', 'AtomPair', 'MACCS', 'TopologicalTorsion'],
+    () => onMCLParamsChange('fingerprintType', mclFingerprintTypesInput.value));
+  const mclThresholdInput = ui.intInput('Similarity threshold', mclParams.threshold ?? 80,
+    () => onMCLParamsChange('threshold', mclThresholdInput.value));
+  const mclMaxIterationsInput = ui.intInput('Max iterations', mclParams.maxIterations ?? 5,
+    () => onMCLParamsChange('maxIterations', mclMaxIterationsInput.value));
+  correctMCLInputs();
+
+  const mclInputs = [mclThresholdInput, mclDistanceFunctionInput, mclFingerprintTypesInput,
+    mclGapOpenInput, mclGapExtendInput, mclMaxIterationsInput];
+
+  accordion.addPane(SETTINGS_PANES.MCL, () => ui.inputs(mclInputs), true);
+  inputs[SETTINGS_PANES.MCL] = mclInputs;
+  // END OF MCL INPUTS
 
   const seqSpaceInputs = [distanceFunctionInput, fingerprintTypesInput, gapOpenInput,
     gapExtendInput, clusterEmbeddingsInput, epsilonInput, minPtsInput];
-  accordion.addPane(SETTINGS_PANES.SEQUENCE_SPACE, () => ui.inputs(seqSpaceInputs), true);
+  const seqSpacePane = accordion.addPane(SETTINGS_PANES.SEQUENCE_SPACE, () => ui.inputs(seqSpaceInputs), true);
   inputs[SETTINGS_PANES.SEQUENCE_SPACE] = seqSpaceInputs;
+  showSeqSpace.fireChanged();
   const dialog = ui.dialog('Peptides settings').add(accordion);
   dialog.root.style.width = '400px';
-  dialog.onOK(() => model.settings = result);
+  dialog.onOK(() => {
+    model.settings = result;
+  });
   dialog.show();
 
   return {dialog, accordion, inputs};

package/webpack.config.js

@@ -29,7 +29,7 @@ module.exports = {
     ],
   },
   resolve: {
-    extensions: ['.mjs', '.js', '.json', '.ts', '.tsx'],
+    extensions: ['.mjs', '.ts', '.js', '.json', '.tsx'],
   },
   devtool: 'inline-source-map',
   externals: {