glydevkit 0.1-java → 0.2.beta.1-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f35fa57e6677d427e287dd2a019ab2894b6a6d65671c065f5457eebfd7eb8d28
-  data.tar.gz: dc0234344840c9d9970a9b9c90ec595982536252bd486dd6abc338ab8c20dddf
+  metadata.gz: c912a7e2a35037df8e3878dbd2afaaa8647034457ee4569ce84a8e78b1c6b3d8
+  data.tar.gz: f87718ac5617735afe4d38026cc66ebcf23bbd15d41b718515d15b248800a088
 SHA512:
-  metadata.gz: 179c8854710c3459b13259e026c2a49e06a7b67ed0649ec38ac9e3e111e73aa59b8cab39646df21dcd44d714ef810c80a961e740e0e406ff2e4b146e57b065ec
-  data.tar.gz: 8af420af02a32a1c1dc32de58fba405efe972150876eec903f2849c30bb6d65c4dccc2950e400d86a6ec1dd16f2a69e9c2a3241019b45931c3a62056f0930ab3
+  metadata.gz: aab88ca9b8ca7c18ff72c342ffa66ddb5649a76bba36c81de8d07f4b2654a9435c0d00b694620a365ad685b8e18670db4e470da5f3cab45599d1a5f1ab70e649
+  data.tar.gz: 4e44ccc0ebb190851a9e577d7cda0ac458821320df6c2d15f1675fe279bed673f7daa730ac4a06fa4e0e134a20f816f194c34795b73f4c376a4e530be9f1f3d3

data/jar.yml

@@ -14,8 +14,8 @@ libraries:
 
   - name: wurcsframework
     info: "https://gitlab.com/glycoinfo/wurcsframework"
-    version: 1.2.14
-    url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
+    version: 1.3.1
+    url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/127116856/download"
     file: "jar/wurcsframework.jar"
 
   - name: wurcsframework-1.2.14

data/lib/glydevkit/wurcs_frame_work.rb

@@ -7,70 +7,85 @@ module GlyDevKit
     require_relative  '../jar/wurcsframework.jar'
     java_import 'org.glycoinfo.WURCSFramework.util.validation.WURCSValidator'
     
-    def validator(w)
+    def validator(w,maxbranch)
       validator = WURCSValidator.new
+      validator.setMaxBranchCount(maxbranch)
       validator.start(w)
-      reports = {}
-      reports["VALIDATOR"] = ["WURCSFramework-1.2.14"]
-      reports["WARNING"] = validator.getReport().hasWarning()
-      reports["ERROR"] = validator.getReport().hasError()
-      reports["UNVERIFIABLE"] = validator.getReport().hasUnverifiable()
-      return {"message" => reports,
-            "StandardWURCS" => validator.getReport().standard_string(),
-            "RESULTS" => validator.getReport().getResults() }
+      report = validator.getReport()
+
+      {
+        "message" => {
+          "VALIDATOR" => ["WURCSFramework-1.2.14"],
+          "WARNING" => report.hasWarning(),
+          "ERROR" => report.hasError(),
+          "UNVERIFIABLE" => report.hasUnverifiable()
+        },
+        "StandardWURCS" => report.standard_string(),
+        "RESULTS" => report.getResults()
+      }
     end
 
     def to_graph(w)
-      g = nil
       wgn = WURCSGraphNormalizer.new
       begin
         factory = WURCSFactory.new(w)
-        g = factory.getGraph
-        wgn.start(g)
+        graph = factory.getGraph
+        wgn.start(graph)
+        graph
       rescue WURCSException => e
         e.printStackTrace
+        nil
       end
-      return g
     end
     
     def get_anomeric_status(a_o_backbone)
       a_o_backbone.get_backbone_carbons.each do |t_o_bc|
-        return "archetype_anomer" if t_o_bc.get_descriptor.get_char.chr == 'u'
-        return "archetype_anomer" if t_o_bc.get_descriptor.get_char.chr == 'U'
+        return "archetype_anomer" if %w[u U].include?(t_o_bc.get_descriptor.get_char.chr)
+      end
+
+      case a_o_backbone.get_anomeric_symbol.chr
+      when 'x'
+        "anomer_unknown"
+      when 'a'
+        "anomer_alpha"
+      when 'b'
+        "anomer_beta"
+      else
+        a_o_backbone.get_anomeric_position != 0 ? "openchain" : nil
       end
-      return "anomer_unknown" if a_o_backbone.get_anomeric_symbol.chr == 'x'
-      return "anomer_alpha" if a_o_backbone.get_anomeric_symbol.chr == 'a'
-      return "anomer_beta" if a_o_backbone.get_anomeric_symbol.chr == 'b'
-      return "openchain" if a_o_backbone.get_anomeric_position != 0
-      return nil
     end
 
     def get_ring_type(a_o_backbone)
       a_o_backbone.get_backbone_carbons.each do |t_o_bc|
-        return "archetype_ringtype" if t_o_bc.get_descriptor.get_char.chr == 'u'
-        return "archetype_ringtype" if t_o_bc.get_descriptor.get_char.chr == 'U'
+        return "archetype_ringtype" if %w[u U].include?(t_o_bc.get_descriptor.get_char.chr)
       end
-      for edge in a_o_backbone.get_edges 
-        if edge.is_anomeric && edge.get_modification.is_ring
-          ring_start = edge.get_linkages[0].get_backbone_position
-          ring_end = edge.get_modification.get_edges[1].get_linkages[0].get_backbone_position
-          if (ring_end - ring_start) == 6
-            return "octanose"
-          elsif (ring_end - ring_start) == 5
-            return "septanose"
-          elsif (ring_end - ring_start) == 4
-            return "pyranose"
-          elsif (ring_end - ring_start) == 3
-            return "furanose"
-          elsif (ring_end - ring_start) == 2
-            return "oxetose"
-          elsif (ring_end - ring_start) == 1
-            return "oxirose"
-          end
-        end
+
+      a_o_backbone.get_edges.each do |edge|
+        next unless edge.is_anomeric && edge.get_modification.is_ring
+
+        ring_start = edge.get_linkages[0].get_backbone_position
+        ring_end = edge.get_modification.get_edges[1].get_linkages[0].get_backbone_position
+        ring_size = ring_end - ring_start
+
+        return case ring_size
+               when 6 then "octanose"
+               when 5 then "septanose"
+               when 4 then "pyranose"
+               when 3 then "furanose"
+               when 2 then "oxetose"
+               when 1 then "oxirose"
+               end
       end
-      return nil
+      nil
     end
 
+    def getWURCSMass(w)
+      importer = WURCSImporter.new
+      wurcs_array = importer.extractWURCSArray(w)
+      WURCSMassCalculator.calcMassWURCS(wurcs_array)
+    rescue WURCSException, WURCSMassException, StandardError => e
+      e.printStackTrace
+      nil
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: glydevkit
 version: !ruby/object:Gem::Version
-  version: '0.1'
+  version: 0.2.beta.1
 platform: java
 authors:
 - Akihiro Fujita
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-07-07 00:00:00.000000000 Z
+date: 2024-08-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement