JAL-1957 JAL-1479 Further optimisation of SIFTs Client and addition of support for...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 13aae26..3d5a975 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -326,7 +326,7 @@ public class StructureSelectionManager
    * @param forStructureView
    *          when true, record the mapping for use in mouseOvers
    * 
-   * @param sequence
+   * @param sequenceArray
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChains
    *          - optional chain specification for mapping each sequence to pdb
@@ -338,7 +338,7 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public PDBfile setMapping(boolean forStructureView,
-          SequenceI[] sequence, String[] targetChains, String pdbFile,
+          SequenceI[] sequenceArray, String[] targetChains, String pdbFile,
           String protocol)
   {
     /*
@@ -348,7 +348,7 @@ public class StructureSelectionManager
     boolean parseSecStr = processSecondaryStructure;
     if (isPDBFileRegistered(pdbFile))
     {
-      for (SequenceI sq : sequence)
+      for (SequenceI sq : sequenceArray)
       {
         SequenceI ds = sq;
         while (ds.getDatasetSequence() != null)
@@ -372,15 +372,25 @@ public class StructureSelectionManager
       }
     }
     PDBfile pdb = null;
+    boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
+            "MAP_WITH_SIFTS", "false"));
+    SiftsClient siftsClient = null;
     try
     {
       pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
               pdbFile, protocol);
+      if (isMapUsingSIFTs)
+      {
+        siftsClient = new SiftsClient(pdb);
+      }
       if (pdb.id != null && pdb.id.trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
         registerPDBFile(pdb.id.trim(), pdbFile);
       }
+    } catch (SiftsException e)
+    {
+      e.printStackTrace();
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -388,10 +398,10 @@ public class StructureSelectionManager
     }
 
     String targetChain;
-    for (int s = 0; s < sequence.length; s++)
+    for (int s = 0; s < sequenceArray.length; s++)
     {
       boolean infChain = true;
-      final SequenceI seq = sequence[s];
+      final SequenceI seq = sequenceArray[s];
       if (targetChains != null && targetChains[s] != null)
       {
         infChain = false;
@@ -465,16 +475,29 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
       }
 
-      StructureMapping seqToStrucMapping = null;
-      boolean isMapViaSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
-              "MAP_WITH_SIFTS", "false"));
-      if (isMapViaSIFTs)
+      ArrayList<StructureMapping> seqToStrucMapping = null;
+      if (isMapUsingSIFTs)
       {
-        SiftsClient siftsClient = new SiftsClient(pdb);
         try
         {
-          seqToStrucMapping = siftsClient.getSiftsStructureMapping(seq,
-                  pdbFile, maxChainId);
+          seqToStrucMapping = new ArrayList<StructureMapping>();
+          if (targetChain != null && !targetChain.trim().isEmpty())
+          {
+            maxChainId = targetChain;
+            StructureMapping curChainMapping = siftsClient
+                    .getSiftsStructureMapping(seq, pdbFile, targetChain);
+            seqToStrucMapping.add(curChainMapping);
+          }
+          else
+          {
+            for (PDBChain chain : pdb.chains)
+            {
+              maxChainId = chain.id;
+              StructureMapping curChainMapping = siftsClient
+                      .getSiftsStructureMapping(seq, pdbFile, chain.id);
+              seqToStrucMapping.add(curChainMapping);
+            }
+          }
         } catch (SiftsException e)
         {
           System.err
@@ -492,13 +515,15 @@ public class StructureSelectionManager
 
       if (forStructureView)
       {
-        mappings.add(seqToStrucMapping);
+        // mappings.add(seqToStrucMapping);
+        mappings.addAll(seqToStrucMapping);
       }
     }
     return pdb;
   }
 
-  private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+  private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+          String pdbFile,
           String maxChainId, PDBChain maxChain, PDBfile pdb,
           AlignSeq maxAlignseq)
   {
@@ -574,7 +599,9 @@ public class StructureSelectionManager
     StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
             pdb.id, maxChainId, mapping, mappingDetails.toString());
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-    return nwMapping;
+    ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
+    mappings.add(nwMapping);
+    return mappings;
   }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)