JAL-2046 stack trace for implementation warning

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 28fc3d1..be042e6 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -385,7 +385,11 @@ public class StructureSelectionManager
     try
     {
 
     try
     {
 

-      if (pdbFile != null && isCIFFile(pdbFile))
+      boolean isParseWithJMOL = StructureImportSettings
+              .getDefaultPDBFileParser().equalsIgnoreCase(
+                      StructureImportSettings.StructureParser.JMOL_PARSER
+                              .toString());
+      if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))

       {
         pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
                 secStructServices, pdbFile, protocol);
       {
         pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
                 secStructServices, pdbFile, protocol);

@@ -501,29 +505,67 @@ public class StructureSelectionManager
       if (isMapUsingSIFTs)
       {
         setProgressBar(null);
       if (isMapUsingSIFTs)
       {
         setProgressBar(null);

-        setProgressBar("Obtaining mapping with SIFTS");
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_sifts"));

         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
         {
         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
         {

-          StructureMapping mapping = getStructureMapping(seq, pdbFile,
-                  targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
-          seqToStrucMapping.add(mapping);
+          StructureMapping siftsMapping;
+          try
+          {
+            siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+                    pdb, maxChain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(siftsMapping);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null);
+            maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+          } catch (SiftsException e)
+          {
+            // fall back to NW alignment
+            System.err.println(e.getMessage());
+            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                    targetChainId, maxChain, pdb, maxAlignseq);
+            seqToStrucMapping.add(nwMapping);
+          }

         }
         else
         {
         }
         else
         {

+          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();

           for (PDBChain chain : pdb.getChains())
           {
           for (PDBChain chain : pdb.getChains())
           {

-            StructureMapping mapping = getStructureMapping(seq, pdbFile,
-                    chain.id, pdb, chain, sqmpping, maxAlignseq);
-            seqToStrucMapping.add(mapping);
+            try
+            {
+              StructureMapping siftsMapping = getStructureMapping(seq,
+                      pdbFile,
+                      chain.id, pdb, chain, sqmpping, maxAlignseq);
+              foundSiftsMappings.add(siftsMapping);
+            } catch (SiftsException e)
+            {
+              System.err.println(e.getMessage());
+            }
+          }
+          if (!foundSiftsMappings.isEmpty())
+          {
+            seqToStrucMapping.addAll(foundSiftsMappings);
+            maxChain.makeExactMapping(maxAlignseq, seq);
+            maxChain.transferRESNUMFeatures(seq, null);
+            maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+                    sqmpping);
+          }
+          else
+          {
+            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                    maxChainId, maxChain, pdb, maxAlignseq);
+            seqToStrucMapping.add(nwMapping);

           }
         }
       }
       else
       {
         setProgressBar(null);
           }
         }
       }
       else
       {
         setProgressBar(null);

-        setProgressBar("Obtaining mapping with NW alignment");
+        setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_nw_alignment"));

         seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
                 maxChain, pdb, maxAlignseq));
       }
         seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
                 maxChain, pdb, maxAlignseq));
       }

@@ -546,11 +588,8 @@ public class StructureSelectionManager
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,

-          AlignSeq maxAlignseq)
+          AlignSeq maxAlignseq) throws SiftsException

   {
   {

-    String maxChainId = targetChainId;
-    try
-    {

       StructureMapping curChainMapping = siftsClient
               .getSiftsStructureMapping(seq, pdbFile, targetChainId);
       try
       StructureMapping curChainMapping = siftsClient
               .getSiftsStructureMapping(seq, pdbFile, targetChainId);
       try

@@ -565,15 +604,6 @@ public class StructureSelectionManager
         e.printStackTrace();
       }
       return curChainMapping;
         e.printStackTrace();
       }
       return curChainMapping;

-    } catch (SiftsException e)
-    {
-      System.err.println(e.getMessage());
-      System.err.println(">>> Now switching mapping with NW alignment...");
-      setProgressBar(null);
-      setProgressBar(">>> Now switching mapping with NW alignment...");
-      return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
-              maxAlignseq);
-    }

   }
 
   private StructureMapping getNWMappings(SequenceI seq,
   }
 
   private StructureMapping getNWMappings(SequenceI seq,

@@ -1290,6 +1320,10 @@ public class StructureSelectionManager
 
   public void setProgressBar(String message)
   {
 
   public void setProgressBar(String message)
   {

+    if (progressIndicator == null)
+    {
+      return;
+    }

     progressIndicator.setProgressBar(message, progressSessionId);
   }
 
     progressIndicator.setProgressBar(message, progressSessionId);
   }