From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 27 Jun 2024 16:45:08 +0000 (+0100)
Subject: Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=33ea95be162c87b303b091399ac0ee98dbde9c03;p=jalview.git

Merge branch 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' into spike/JAL-4386_generate_multiple_leaves_for_ss_sources
---

33ea95be162c87b303b091399ac0ee98dbde9c03
diff --cc src/jalview/structure/StructureSelectionManager.java
index 95f93ea,cade4f6..731d82f
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@@ -708,24 -708,29 +708,41 @@@ public class StructureSelectionManage
          ssAnnotDescriptionInPDB = ssAnnotationsInPDB[0].description;
        }
        
--      //Match the PDB entry using file path in the pdb data model and get the provider
-       Vector<PDBEntry> pdbEntries = seq.getDatasetSequence().getAllPDBEntries();
-       for(PDBEntry pdbEntry : pdbEntries) {        
-         if(ssStructFilePathNameInPDB!=null && pdbEntry.getFile()!=null && ssStructFilePathNameInPDB.startsWith(pdbEntry.getFile())) {
-           provider = pdbEntry.getProvider();
-           break;
-         }        
-       }
-       
-       //Add provider value as property to the ss annotation 
-       if(provider != null) {
-         AlignmentAnnotation[] ssAnnotList = ds.getAnnotation(Constants.SS_ANNOTATION_LABEL);
-         if(ssAnnotList != null) {
-           for(AlignmentAnnotation ssAnnot : ssAnnotList) {
-             //Match the annotation description with the annotation in pdb data object  
-             if(ssAnnot.getProperty(Constants.SS_PROVIDER_PROPERTY) == null 
-                     && ssAnnot.description.equals(ssAnnotDescriptionInPDB)) {
-               ssAnnot.setProperty(Constants.SS_PROVIDER_PROPERTY, provider);
 -      if(seq.getDatasetSequence() != null) {
 -        Vector<PDBEntry> pdbEntries = seq.getDatasetSequence().getAllPDBEntries();
 -        if(pdbEntries != null) {
 -          for(PDBEntry pdbEntry : pdbEntries) {        
 -            if(ssStructFilePathNameInPDB.startsWith(pdbEntry.getFile())) {
 -              provider = pdbEntry.getProvider();
 -              break;
 -            }        
++      // Match the PDB entry using file path in the pdb data model and get the
++      // provider
++      if (seq.getDatasetSequence() != null)
++      {
++        Vector<PDBEntry> pdbEntries = seq.getDatasetSequence()
++                .getAllPDBEntries();
++        for (PDBEntry pdbEntry : pdbEntries)
++        {
++          if (ssStructFilePathNameInPDB != null
++                  && pdbEntry.getFile() != null && ssStructFilePathNameInPDB
++                          .startsWith(pdbEntry.getFile()))
++          {
++            provider = pdbEntry.getProvider();
++            break;
+           }
 -          
 -          
 -          //Add provider value as property to the ss annotation 
 -          if(provider != null) {
 -            AlignmentAnnotation[] ssAnnotList = ds.getAnnotation(Constants.SS_ANNOTATION_LABEL);
 -            if(ssAnnotList != null) {
 -              for(AlignmentAnnotation ssAnnot : ssAnnotList) {
 -                //Match the annotation description with the annotation in pdb data object  
 -                if(ssAnnot.getProperty(Constants.SS_PROVIDER_PROPERTY) == null 
 -                        && ssAnnot.description.equals(ssAnnotDescriptionInPDB)) {
 -                  ssAnnot.setProperty(Constants.SS_PROVIDER_PROPERTY, provider);
 -                }
++        }
++        // Add provider value as property to the ss annotation
++        if (provider != null)
++        {
++          AlignmentAnnotation[] ssAnnotList = ds
++                  .getAnnotation(Constants.SS_ANNOTATION_LABEL);
++          if (ssAnnotList != null)
++          {
++            for (AlignmentAnnotation ssAnnot : ssAnnotList)
++            {
++              // Match the annotation description with the annotation in pdb
++              // data object
++              if (ssAnnot
++                      .getProperty(Constants.SS_PROVIDER_PROPERTY) == null
++                      && ssAnnot.description
++                              .equals(ssAnnotDescriptionInPDB))
++              {
++                ssAnnot.setProperty(Constants.SS_PROVIDER_PROPERTY,
++                        provider);
+               }
              }
            }
          }