some JavaDoc provided

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java

@@ -246,6 +246,18 @@ public class CellDesignerElementCollection {
   private Map<String, String> modificationResidueIdByHash = new HashMap<>();
   private Set<String> usedModificationResidueIds = new HashSet<>();
 
+  /**
+   * This method computes modificationResidueId that should be used when exporting
+   * modification residue to CellDesigner. The identifier relies on type and
+   * position on the list of modification
+   * 
+   * @param region
+   *          {@link ModificationResidue} for which we want to find out identifier
+   * @param number
+   *          position on which this {@link ModificationResidue} is located in
+   *          species
+   * @return identifier that can be used in CellDesigner
+   */
   public String getModificationResidueId(ModificationResidue region, int number) {
     String hash = region.getClass().getSimpleName() + "\n" + number;
     String result = modificationResidueIdByHash.get(hash);

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java

@@ -31,7 +31,7 @@ public class ModificationResidueXmlParser extends XmlParser {
   }
 
   /**
-   * Transforms AntisenseRnaRegion into CellDEsigner xml representation.
+   * Transforms ModificationResidue into CellDssigner xml representation.
    * 
    * @param region
    *          object to be transformed
@@ -86,28 +86,37 @@ public class ModificationResidueXmlParser extends XmlParser {
     return result;
   }
 
+  /**
+   * This method computes modificationResidueId that should be used when exporting
+   * modification residue to CellDesigner. It cannot be taken from data structure
+   * because we have to merge elements when exporting to CellDesigner and this
+   * might introduce inconsistent identifiers.
+   * 
+   * @param region {@link ModificationResidue} for which we want to find out identifier
+   * @return identifier that can be used in CellDesigner
+   */
   private String computeModificationResidueId(ModificationResidue region) {
     List<? extends ModificationResidue> modificationResidues;
     if (region.getSpecies() instanceof Protein) {
-      modificationResidues = ((Protein)region.getSpecies()).getModificationResidues();
+      modificationResidues = ((Protein) region.getSpecies()).getModificationResidues();
     } else if (region.getSpecies() instanceof Rna) {
-      modificationResidues = ((Rna)region.getSpecies()).getRegions();
+      modificationResidues = ((Rna) region.getSpecies()).getRegions();
     } else if (region.getSpecies() instanceof AntisenseRna) {
-      modificationResidues = ((AntisenseRna)region.getSpecies()).getRegions();
+      modificationResidues = ((AntisenseRna) region.getSpecies()).getRegions();
     } else if (region.getSpecies() instanceof Gene) {
-      modificationResidues = ((Gene)region.getSpecies()).getModificationResidues();
+      modificationResidues = ((Gene) region.getSpecies()).getModificationResidues();
     } else {
       throw new NotImplementedException();
     }
     int number = -1;
-    int i=0;
-    for (ModificationResidue mr: modificationResidues) {
+    int i = 0;
+    for (ModificationResidue mr : modificationResidues) {
       if (mr.getIdModificationResidue().equals(region.getIdModificationResidue())) {
-        number= i;
+        number = i;
       }
       i++;
     }
-    if (i<0) {
+    if (i < 0) {
       throw new InvalidArgumentException("ModificationResidue is not on the species list");
     }
     return elements.getModificationResidueId(region, number);