JAL-2009 Codes to enable storing inserted residues as features to their base residue...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 678bf3b..9d06aef 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -32,6 +32,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
@@ -70,6 +71,12 @@ public class StructureSelectionManager
 
   private boolean addTempFacAnnot = false;
 
+  private IProgressIndicator progressIndicator;
+
+  private SiftsClient siftsClient = null;
+
+  private long progressSessionId;
+
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
@@ -375,7 +382,6 @@ public class StructureSelectionManager
     }
     PDBfile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
-    SiftsClient siftsClient = null;
     try
     {
       pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
@@ -482,63 +488,73 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = null;
+      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs)
       {
-        try
+        setProgressBar(null);
+        setProgressBar("Obtaining mapping with SIFTS");
+        jalview.datamodel.Mapping sqmpping = maxAlignseq
+                .getMappingFromS1(false);
+        if (targetChainId != null && !targetChainId.trim().isEmpty())
         {
-          jalview.datamodel.Mapping sqmpping = maxAlignseq
-                  .getMappingFromS1(false);
-          seqToStrucMapping = new ArrayList<StructureMapping>();
-          if (targetChainId != null && !targetChainId.trim().isEmpty())
-          {
-            StructureMapping curChainMapping = siftsClient
-                    .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-            seqToStrucMapping.add(curChainMapping);
-            maxChainId = targetChainId;
-            PDBChain chain = pdb.findChain(targetChainId);
-            if (chain != null)
-            {
-              chain.transferResidueAnnotation(curChainMapping, sqmpping);
-            }
-          }
-          else
+          StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                  targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
+          seqToStrucMapping.add(mapping);
+        }
+        else
+        {
+          for (PDBChain chain : pdb.chains)
           {
-            for (PDBChain chain : pdb.chains)
-            {
-              StructureMapping curChainMapping = siftsClient
-                      .getSiftsStructureMapping(seq, pdbFile, chain.id);
-              seqToStrucMapping.add(curChainMapping);
-              maxChainId = chain.id;
-              chain.transferResidueAnnotation(curChainMapping, sqmpping);
-            }
+            StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                    chain.id, pdb, chain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(mapping);
           }
-        } catch (SiftsException e)
-        {
-          e.printStackTrace();
-          System.err
-                  .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
-          seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
-                  maxChain, pdb, maxAlignseq);
         }
       }
       else
       {
-        seqToStrucMapping = getNWMappings(seq, pdbFile,
-                maxChainId, maxChain, pdb,
-                maxAlignseq);
+        setProgressBar(null);
+        setProgressBar("Obtaining mapping with NW alignment");
+        seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
+                maxChain, pdb, maxAlignseq));
       }
 
       if (forStructureView)
       {
-        // mappings.add(seqToStrucMapping);
         mappings.addAll(seqToStrucMapping);
       }
     }
     return pdb;
   }
 
-  private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+  private StructureMapping getStructureMapping(SequenceI seq,
+          String pdbFile, String targetChainId, PDBfile pdb,
+          PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+          AlignSeq maxAlignseq)
+  {
+    String maxChainId = targetChainId;
+    try
+    {
+      StructureMapping curChainMapping = siftsClient
+              .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+      PDBChain chain = pdb.findChain(targetChainId);
+      if (chain != null)
+      {
+        chain.transferResidueAnnotation(curChainMapping, sqmpping);
+      }
+      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,
           String pdbFile,
           String maxChainId, PDBChain maxChain, PDBfile pdb,
           AlignSeq maxAlignseq)
@@ -591,17 +607,18 @@ public class StructureSelectionManager
     HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
     int resNum = -10000;
     int index = 0;
+    char insCode = ' ';
 
     do
     {
       Atom tmp = maxChain.atoms.elementAt(index);
-      if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+      if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+              && tmp.alignmentMapping != -1)
       {
         resNum = tmp.resNumber;
+        insCode = tmp.insCode;
         if (tmp.alignmentMapping >= -1)
         {
-          // TODO (JAL-1836) address root cause: negative residue no in PDB
-          // file
           mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
               tmp.atomIndex });
         }
@@ -613,9 +630,7 @@ public class StructureSelectionManager
     StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
             pdb.id, maxChainId, mapping, mappingDetails.toString());
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-    ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
-    mappings.add(nwMapping);
-    return mappings;
+    return nwMapping;
   }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
@@ -1224,4 +1239,30 @@ public class StructureSelectionManager
     }
     return null;
   }
+
+  public IProgressIndicator getProgressIndicator()
+  {
+    return progressIndicator;
+  }
+
+  public void setProgressIndicator(IProgressIndicator progressIndicator)
+  {
+    this.progressIndicator = progressIndicator;
+  }
+
+  public long getProgressSessionId()
+  {
+    return progressSessionId;
+  }
+
+  public void setProgressSessionId(long progressSessionId)
+  {
+    this.progressSessionId = progressSessionId;
+  }
+
+  public void setProgressBar(String message)
+  {
+    progressIndicator.setProgressBar(message, progressSessionId);
+  }
+
 }