glydevkit 0.2.beta.1-java → 0.2.0.pre.beta.2-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: d379ce557d17df7d8d4252253ed401ba2fd8efdcccd085d02e57d2761d073939
+  data.tar.gz: 26c01118b88face8d7e17f55e314d449e47f292d29c18bd3e876cd93045c5206
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+  data.tar.gz: 04613f824cac68e2fc989f0dff84d271bcd25f09de2b5cefab8aea44b4f8c857176ac95ab2eb53b0eee3378ec6116fb5a2b8bffc8677feca395fbcb968b5fd02

data/lib/glydevkit/gly_tou_can.rb

@@ -8,9 +8,18 @@ java_import 'org.glycoinfo.WURCSFramework.wurcs.graph.WURCSGraph'
 java_import 'org.glycoinfo.WURCSFramework.util.WURCSException'
 
 module GlyDevKit
-class GlyTouCan
-  def archetype(w)
-    Hash[Archetype.beBorn(w)]
+  class GlyTouCan
+    # Converts a WURCS string to its archetype representation.
+    #
+    # @param w [String] The WURCS string.
+    # @return [Hash] The archetype representation of the WURCS string.
+    #
+    # @example
+    #   require glydevkit
+    #   glytoucan = GlyDevKit::GlyTouCan.new
+    #   archetype = glytoucan.archetype("WURCS=2.0/...")
+    def archetype(w)
+      Hash[Archetype.beBorn(w)]
+    end
   end
 end
-end

data/lib/glydevkit/glycan_format_converter.rb

@@ -8,69 +8,136 @@ java_import 'org.glycoinfo.GlycanFormatconverter.io.GlycoCT.WURCSToGlycoCT'
 java_import 'org.glycoinfo.GlycanFormatconverter.io.IUPAC.IUPACStyleDescriptor'
 java_import 'org.glycoinfo.GlycanFormatconverter.io.WURCS.WURCSImporter'
 java_import 'org.glycoinfo.GlycanFormatconverter.util.ExporterEntrance'
-
+java_import 'org.glycoinfo.GlycanFormatconverter.Glycan.GlyContainer'
+java_import 'org.glycoinfo.GlycanFormatconverter.Glycan.GlycanException'
+java_import 'org.glycoinfo.GlycanFormatconverter.io.GlyCoExporterException'
+java_import 'org.glycoinfo.GlycanFormatconverter.io.GlyCoImporterException'
+java_import 'org.glycoinfo.GlycanFormatconverter.io.IUPAC.IUPACStyleDescriptor'
+java_import 'org.glycoinfo.GlycanFormatconverter.io.IUPAC.condensed.IUPACCondensedImporter'
+java_import 'org.glycoinfo.GlycanFormatconverter.io.IUPAC.extended.IUPACExtendedImporter'
+    
 module GlyDevKit
-class GlycanFormatConverter
+  class GlycanFormatConverter
 
-def wurcs2iupac(wurcs,style)
-  ret = {}
-  ret["input"] =  wurcs
-   
-  begin
-    wi = WURCSImporter.new
-    gc = wi.start(wurcs)
-    ee = ExporterEntrance.new(gc)
+    # Converts a WURCS string to IUPAC format.
+    #
+    # @param wurcs [String] The WURCS string to be converted.
+    # @param style [String] The desired IUPAC style ("condensed", "extended", or "glycam").
+    # @return [Hash] A hash containing the input WURCS string and the resulting IUPAC format.
+    #
+    # @example
+    #   converter = GlyDevKit::GlycanFormatConverter.new
+    #   result = converter.wurcs2iupac("WURCS=2.0/...", "condensed")
+    def wurcs2iupac(wurcs, style)
+      ret = {}
+      ret["input"] = wurcs
 
-    if style == "condensed"
-      iupaccondensed = ee.toIUPAC(IUPACStyleDescriptor::CONDENSED)
-      ret["IUPACcondensed"] = iupaccondensed
-    elsif style == "extended"
-      iupacextended = ee.toIUPAC(IUPACStyleDescriptor::GREEK)
-      ret["IUPACextended"] = iupacextended
-    else
-      glycam = ee.toIUPAC(IUPACStyleDescriptor::GLYCANWEB)
-      ret["GLYCAM"] = glycam
-    end
+      begin
+        wi = WURCSImporter.new
+        gc = wi.start(wurcs)
+        ee = ExporterEntrance.new(gc)
 
-  rescue GlyCoExporterException, GlycanException, TrivialNameException, WURCSException => e
-    logger.error("{}", e)
-    ret["message"] = e.to_s
-  rescue Exception => e
-    logger.error("{}", e)
-    ret["message"] = e.to_s
-  end
-  return ret
-end
+        if style == "condensed"
+          iupaccondensed = ee.toIUPAC(IUPACStyleDescriptor::CONDENSED)
+          ret["IUPACcondensed"] = iupaccondensed
+        elsif style == "extended"
+          iupacextended = ee.toIUPAC(IUPACStyleDescriptor::GREEK)
+          ret["IUPACextended"] = iupacextended
+        else
+          glycam = ee.toIUPAC(IUPACStyleDescriptor::GLYCANWEB)
+          ret["GLYCAM"] = glycam
+        end
 
-def wurcs2glycoct(wurcs)
-    ret = {}
-    ret["input"] =  wurcs
-  begin
-    converter = WURCSToGlycoCT.new
-    converter.start(wurcs)
-    message = converter.getErrorMessages
-  if message.empty?
-      ret["GlycoCT"] = converter.getGlycoCT
-      ret["message"] = ""
-    else
-      ret["GlycoCT"] = ""
-      ret["message"] = message
+      rescue GlyCoExporterException, GlycanException, TrivialNameException, WURCSException => e
+        logger.error("{}", e)
+        ret["message"] = e.to_s
+      rescue Exception => e
+        logger.error("{}", e)
+        ret["message"] = e.to_s
+      end
+      return ret
     end
+
+    # Converts a WURCS string to GlycoCT format.
+    #
+    # @param wurcs [String] The WURCS string to be converted.
+    # @return [Hash] A hash containing the input WURCS string and the resulting GlycoCT format.
+    #
+    # @example
+    #   converter = GlyDevKit::GlycanFormatConverter.new
+    #   result = converter.wurcs2glycoct("WURCS=2.0/...")
+    def wurcs2glycoct(wurcs)
+      ret = {}
+      ret["input"] = wurcs
+      begin
+        converter = WURCSToGlycoCT.new
+        converter.start(wurcs)
+        message = converter.getErrorMessages
+        if message.empty?
+          ret["GlycoCT"] = converter.getGlycoCT
+          ret["message"] = ""
+        else
+          ret["GlycoCT"] = ""
+          ret["message"] = message
+        end
       rescue Exception => e
-              ret["GlycoCT"] = ""
-    ret["message"] =  e.to_s
+        ret["GlycoCT"] = ""
+        ret["message"] = e.to_s
+      end
+      return ret
+    end
+
+    # Converts a WURCS string to GLYCAM format.
+    #
+    # @param wurcs [String] The WURCS string to be converted.
+    # @return [String] The resulting GLYCAM format string.
+    #
+    # @example
+    #   converter = GlyDevKit::GlycanFormatConverter.new
+    #   result = converter.wurcs2glycam("WURCS=2.0/...")
+    def wurcs2glycam(wurcs)
+      wi = WURCSImporter.new
+      ee = ExporterEntrance.new(wi.start(wurcs))
+      begin
+        ee.toIUPAC(IUPACStyleDescriptor::GLYCANWEB)
+      rescue => e
+        e.printStackTrace()
+      end
+    end
+
+    # Converts an IUPAC string to WURCS format.
+    #
+    # @param iupac [String] The IUPAC string to be converted.
+    # @param style [String] The style of the IUPAC string ("condensed" or "extended").
+    # @return [Hash] A hash containing the input IUPAC string and the resulting WURCS format.
+    #
+    # @example
+    #   converter = GlyDevKit::GlycanFormatConverter.new
+    #   result = converter.iupac2wurcs("Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-", "condensed")
+    def iupac2wurcs(iupac, style)
+        ret = {}
+        ret["input"] = iupac
+      
+        begin
+          if style == "condensed"
+            ici = IUPACCondensedImporter.new
+            gc = ici.start(iupac)
+          else
+            iei = IUPACExtendedImporter.new
+            gc = iei.start(iupac)
+          end
+      
+          ee = ExporterEntrance.new(gc)
+          wurcs = ee.toWURCS
+          ret["wurcs"] = wurcs
+      
+        rescue GlyCoImporterException, GlycanException, WURCSException => e
+          ret["message"] = e.to_s
+        rescue StandardError => e
+          ret["message"] = e.to_s
+        end
+        return ret
     end
-  return ret
-end
 
-def wurcs2glycam(wurcs)
-  wi = WURCSImporter.new
-  ee = ExporterEntrance.new(wi.start(wurcs))
-  begin
-    ee.toIUPAC(IUPACStyleDescriptor::GLYCANWEB)
-  rescue => e
-    e.printStackTrace()
   end
 end
-end
-end

data/lib/glydevkit/wurcs_frame_work.rb

@@ -2,12 +2,22 @@ require 'java'
 
 module GlyDevKit
 
-  class WurcsFrameWork
+  class WURCSFramework
 
-    require_relative  '../jar/wurcsframework.jar'
+    # Import the JAR file
+    require_relative '../jar/wurcsframework.jar'
     java_import 'org.glycoinfo.WURCSFramework.util.validation.WURCSValidator'
-    
-    def validator(w,maxbranch)
+
+    # Validates a WURCS data string.
+    #
+    # @param w [String] The WURCS string to be validated.
+    # @param maxbranch [Integer] The maximum allowed branch count for validation.
+    # @return [Hash] A hash containing the validation results, including any warnings, errors, and unverifiable issues.
+    #
+    # @example
+    #   wurcs = "WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1"
+    #   result = validator(wurcs, 10)
+    def validator(w, maxbranch)
       validator = WURCSValidator.new
       validator.setMaxBranchCount(maxbranch)
       validator.start(w)
@@ -25,6 +35,11 @@ module GlyDevKit
       }
     end
 
+
+    # Converts WURCS data to a graph object.
+    #
+    # @param w [String] WURCS format data
+    # @return [Object, nil] Graph object or nil if an error occurs
     def to_graph(w)
       wgn = WURCSGraphNormalizer.new
       begin
@@ -38,6 +53,12 @@ module GlyDevKit
       end
     end
     
+    # Retrieves the anomeric status of a backbone.
+    # @param a_o_backbone [Backbone] The backbone object to evaluate.
+    # @return [String, nil] A string representing the anomeric status, or nil if it cannot be determined.
+    #
+    # @example
+    #   status = get_anomeric_status(backbone)
     def get_anomeric_status(a_o_backbone)
       a_o_backbone.get_backbone_carbons.each do |t_o_bc|
         return "archetype_anomer" if %w[u U].include?(t_o_bc.get_descriptor.get_char.chr)
@@ -55,6 +76,11 @@ module GlyDevKit
       end
     end
 
+
+    # Retrieves the ring type of a backbone.
+    #
+    # @param a_o_backbone [Object] Backbone object
+    # @return [String, nil] Ring type as a string or nil if not applicable
     def get_ring_type(a_o_backbone)
       a_o_backbone.get_backbone_carbons.each do |t_o_bc|
         return "archetype_ringtype" if %w[u U].include?(t_o_bc.get_descriptor.get_char.chr)
@@ -79,6 +105,10 @@ module GlyDevKit
       nil
     end
 
+    # Calculates the mass of a WURCS data string.
+    #
+    # @param w [String] WURCS format data
+    # @return [Float, nil] Mass or nil if an error occurs
     def getWURCSMass(w)
       importer = WURCSImporter.new
       wurcs_array = importer.extractWURCSArray(w)

data/lib/glydevkit.rb

@@ -11,4 +11,4 @@ require 'glydevkit/mol_wurcs'
 require 'open-uri'
 require 'net/http'
 require 'fileutils'
-require 'yaml'
+require 'yaml'

data/lib/init.rb

@@ -4,32 +4,11 @@ require 'fileutils'
 require 'yaml'
 
 module Init
-  def self.load_settings(file_path, flag)
-    downloads = []
-
-    unless Dir.exist?(ENV['HOME'] + "/.glycobook")
-      Dir.mkdir(ENV['HOME'] + "/.glycobook")
-    end
-
-    folder_path = File.dirname(__FILE__) + "/jar"
-    unless Dir.exist?(folder_path)
-      FileUtils.mkdir_p(folder_path)
-    end
-
-    if File.exist?(file_path)
-      downloads = YAML.load_file(file_path)
-    else
-      FileUtils.cp(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
-    end
-
-    if flag
-      FileUtils.cp(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
-      downloads = YAML.load_file(file_path)
-    end
-
-    downloads
-  end
 
+  # Runs the initialization process to resolve Java dependencies.
+  #
+  # Prompts the user for input on whether to resolve dependencies and set recommended versions.
+  # Downloads the necessary libraries based on the settings in the YAML file.
   def self.run
     puts <<-EOT
 Would you like to resolve Java dependencies? (No/yes)
@@ -56,7 +35,7 @@ Set recommended Java library version? (No/yes)
 
     downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml", flag)
 
-    # ダウンロードを実行する
+    # Execute the downloads
     downloads["libraries"].each do |download|
       url = URI(download["url"])
       http = Net::HTTP.new(url.host, url.port)
@@ -88,5 +67,35 @@ Set recommended Java library version? (No/yes)
       end
     end
   end
-end
 
+  # Loads the settings from a YAML file and prepares the environment.
+  #
+  # @param file_path [String] The path to the settings file.
+  # @param flag [Boolean] Whether to use the recommended Java library version.
+  # @return [Array<Hash>] The list of downloads specified in the settings file.
+  def self.load_settings(file_path, flag)
+    downloads = []
+
+    unless Dir.exist?(ENV['HOME'] + "/.glycobook")
+      Dir.mkdir(ENV['HOME'] + "/.glycobook")
+    end
+
+    folder_path = File.dirname(__FILE__) + "/jar"
+    unless Dir.exist?(folder_path)
+      FileUtils.mkdir_p(folder_path)
+    end
+
+    if File.exist?(file_path)
+      downloads = YAML.load_file(file_path)
+    else
+      FileUtils.cp(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
+    end
+
+    if flag
+      FileUtils.cp(File.dirname(File.expand_path(__FILE__)) + "/../jar.yml", file_path)
+      downloads = YAML.load_file(file_path)
+    end
+
+    downloads
+  end
+end

data/lib/wurcsverify.rb

@@ -17,6 +17,10 @@ class WurcsVerify
   @@v130 = "1.3.0"
   @@v131 = "1.3.1"
 
+  # Initializes the WurcsVerify class.
+  #
+  # Sets up custom class loaders for different versions of the WURCS Framework.
+  # Loads the WURCSValidator classes for each version.
   def initialize
       @wfw_glytoucan_loader = self.create_custom_classloader("jar/wurcsframework-" + @@gtc_version + ".jar")
       @wfw_v131_loader = self.create_custom_classloader("jar/wurcsframework-" + @@v131 + ".jar")
@@ -30,13 +34,22 @@ class WurcsVerify
       @validator_v1215 = java.lang.Class.forName("org.glycoinfo.WURCSFramework.util.validation.WURCSValidator", true, @wfw_v1215_loader)
   end
 
+  # Creates a custom class loader for a given JAR file.
+  #
+  # @param jar_path [String] The path to the JAR file.
+  # @return [URLClassLoader] The custom class loader.
   def create_custom_classloader(jar_path)
     absolute_path = File.dirname(File.expand_path(__FILE__)) + "/" + jar_path
     url = URL.new("file:#{absolute_path}")
     URLClassLoader.newInstance([url].to_java(URL), java.lang.Thread.currentThread.getContextClassLoader)
   end
 
-  def validatorVerify(w,style)
+  # Verifies the WURCS string using different versions of the WURCS Framework.
+  #
+  # @param w [String] The WURCS string to verify.
+  # @param style [String] The verification style ("v3" or "wfw").
+  # @return [Hash] The verification results.
+  def validatorVerify(w, style)
     v_glytoucan = @validator_glytoucan.new_instance
     v_glytoucan.start(w)
 
@@ -53,18 +66,20 @@ class WurcsVerify
     v_1215.start(w)
 
     if (style == "v3")
-      ret = {@@gtc_version => self.dovalidatorv3(v_glytoucan,@@gtc_version),
-        @@v131  => self.dovalidatorv3(v_131, @@v131),
-        @@v130  => self.dovalidatorv3(v_130, @@v130),
+      ret = {
+        @@gtc_version => self.dovalidatorv3(v_glytoucan, @@gtc_version),
+        @@v131 => self.dovalidatorv3(v_131, @@v131),
+        @@v130 => self.dovalidatorv3(v_130, @@v130),
         @@v1215 => self.dovalidatorv3(v_1215, @@v1215),
         @@v1216 => self.dovalidatorv3(v_1216, @@v1216)
       }
     elsif (style == "wfw")
-      ret = {@@gtc_version => self.dovalidator(v_glytoucan,@@gtc_version),
-      @@v131  => self.dovalidator(v_131, @@v131),
-      @@v130  => self.dovalidator(v_130, @@v130),
-      @@v1215 => self.dovalidator(v_1215, @@v1215),
-      @@v1216 => self.dovalidator(v_1216, @@v1216)
+      ret = {
+        @@gtc_version => self.dovalidator(v_glytoucan, @@gtc_version),
+        @@v131 => self.dovalidator(v_131, @@v131),
+        @@v130 => self.dovalidator(v_130, @@v130),
+        @@v1215 => self.dovalidator(v_1215, @@v1215),
+        @@v1216 => self.dovalidator(v_1216, @@v1216)
       }
     else
       pp "strange second paramerters"
@@ -72,23 +87,40 @@ class WurcsVerify
     return ret
   end
 
-  def dovalidatorv3(validator,version)
+  # Performs validation and returns detailed reports for v3 style.
+  #
+  # @param validator [Object] The validator instance.
+  # @param version [String] The version of the WURCS Framework.
+  # @return [Hash] The validation report.
+  def dovalidatorv3(validator, version)
     if validator.getReport().respond_to?(:isStandardized)
       flag = validator.getReport().isStandardized()
     else
       flag = "undef"
     end
-    reports = { "VALIDATOR" => ["WURCSFramework-" + version],
-                "WARNING" => validator.getReport().hasWarning(),
-                "FLAG" => flag,
-                "ERROR" => validator.getReport().hasError(),
-                "UNVERIFIABLE" => validator.getReport().hasUnverifiable() }
-    return {"message" => reports,
-            "StandardWURCS" => validator.getReport().standard_string(),
-            "RESULTS" => validator.getReport().getResults() }
+    reports = { 
+      "VALIDATOR" => ["WURCSFramework-" + version],
+      "WARNING" => validator.getReport().hasWarning(),
+      "FLAG" => flag,
+      "ERROR" => validator.getReport().hasError(),
+      "UNVERIFIABLE" => validator.getReport().hasUnverifiable() 
+    }
+    return { 
+      "message" => reports,
+      "StandardWURCS" => validator.getReport().standard_string(),
+      "RESULTS" => validator.getReport().getResults() 
+    }
   end
-  def dovalidator(validator,version)
-    return {"VALIDATOR" => ["WURCSFramework-" + version],
-            "Report" => validator.getReport().getResults()}
+  
+  # Performs validation and returns basic reports.
+  #
+  # @param validator [Object] The validator instance.
+  # @param version [String] The version of the WURCS Framework.
+  # @return [Hash] The validation report.
+  def dovalidator(validator, version)
+    return { 
+      "VALIDATOR" => ["WURCSFramework-" + version],
+      "Report" => validator.getReport().getResults() 
+    }
   end
 end

metadata

@@ -1,22 +1,22 @@
 --- !ruby/object:Gem::Specification
 name: glydevkit
 version: !ruby/object:Gem::Version
-  version: 0.2.beta.1
+  version: 0.2.0.pre.beta.2
 platform: java
 authors:
 - Akihiro Fujita
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-08-27 00:00:00.000000000 Z
+date: 2024-10-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
+  name: java
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.0.2
-  name: java
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -48,7 +48,7 @@ licenses:
 metadata:
   source_code_uri: https://github.com/akihirof0005/glydevkit
   homepage_uri: https://github.com/akihirof0005/glydevkit/blob/main/README.md
-  changelog_uri: https://github.com/akihirof0005/glycobooks
+  changelog_uri: https://github.com/akihirof0005/glydevkit
 post_install_message:
 rdoc_options: []
 require_paths:
@@ -64,7 +64,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.6
+rubygems_version: 3.5.18
 signing_key:
 specification_version: 4
 summary: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glycaninformatics