JAL-1919 code improvement to make PDB sequence fetcher file format configurable....

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 380c99b..6bb04ab 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -34,6 +34,7 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.sifts.SiftsClient;
@@ -47,10 +48,8 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.IdentityHashMap;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.Vector;
 
 import MCview.Atom;
@@ -80,7 +79,7 @@ public class StructureSelectionManager
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
-  public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
 
   private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
 
@@ -321,12 +320,13 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public PDBfile setMapping(SequenceI[] sequence,
+  synchronized public StructureFile setMapping(SequenceI[] sequence,
           String[] targetChains, String pdbFile, String protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
+
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -345,7 +345,7 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public PDBfile setMapping(boolean forStructureView,
+  synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile,
           String protocol)
@@ -380,12 +380,21 @@ public class StructureSelectionManager
         }
       }
     }
-    PDBfile pdb = null;
+    StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
-              pdbFile, protocol);
+
+      if (pdbFile != null && isCIFFile(pdbFile))
+      {
+        pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
+                secStructServices, pdbFile, protocol);
+      }
+      else
+      {
+        pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+                pdbFile, protocol);
+      }
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
@@ -527,8 +536,15 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  private boolean isCIFFile(String filename)
+  {
+    String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+            filename.length());
+    return "cif".equalsIgnoreCase(fileExt);
+  }
+
   private StructureMapping getStructureMapping(SequenceI seq,
-          String pdbFile, String targetChainId, PDBfile pdb,
+          String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
           AlignSeq maxAlignseq)
   {
@@ -562,7 +578,7 @@ public class StructureSelectionManager
 
   private StructureMapping getNWMappings(SequenceI seq,
           String pdbFile,
-          String maxChainId, PDBChain maxChain, PDBfile pdb,
+          String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {
     final StringBuilder mappingDetails = new StringBuilder(128);
@@ -777,19 +793,19 @@ public class StructureSelectionManager
    *          the sequence that the mouse over occurred on
    * @param indexpos
    *          the absolute position being mouseovered in seq (0 to seq.length())
-   * @param index
+   * @param seqPos
    *          the sequence position (if -1, seq.findPosition is called to
    *          resolve the residue number)
    */
-  public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+  public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos,
           VamsasSource source)
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();
     SearchResults results = null;
-    if (index == -1)
+    if (seqPos == -1)
     {
-      index = seq.findPosition(indexpos);
+      seqPos = seq.findPosition(indexpos);
     }
     for (int i = 0; i < listeners.size(); i++)
     {
@@ -802,7 +818,7 @@ public class StructureSelectionManager
       }
       if (listener instanceof StructureListener)
       {
-        highlightStructure((StructureListener) listener, seq, index);
+        highlightStructure((StructureListener) listener, seq, seqPos);
       }
       else
       {
@@ -816,12 +832,12 @@ public class StructureSelectionManager
             {
               if (results == null)
               {
-                results = MappingUtils.buildSearchResults(seq, index,
+                results = MappingUtils.buildSearchResults(seq, seqPos,
                         seqmappings);
               }
               if (handlingVamsasMo)
               {
-                results.addResult(seq, index, index);
+                results.addResult(seq, seqPos, seqPos);
 
               }
               if (!results.isEmpty())
@@ -839,7 +855,7 @@ public class StructureSelectionManager
         else if (listener instanceof SecondaryStructureListener)
         {
           ((SecondaryStructureListener) listener).mouseOverSequence(seq,
-                  indexpos, index);
+                  indexpos, seqPos);
         }
       }
     }
@@ -847,14 +863,14 @@ public class StructureSelectionManager
 
   /**
    * Send suitable messages to a StructureListener to highlight atoms
-   * corresponding to the given sequence position.
+   * corresponding to the given sequence position(s)
    * 
    * @param sl
    * @param seq
-   * @param index
+   * @param positions
    */
-  protected void highlightStructure(StructureListener sl, SequenceI seq,
-          int index)
+  public void highlightStructure(StructureListener sl, SequenceI seq,
+          int... positions)
   {
     if (!sl.isListeningFor(seq))
     {
@@ -866,12 +882,15 @@ public class StructureSelectionManager
     {
       if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
       {
-        atomNo = sm.getAtomNum(index);
-
-        if (atomNo > 0)
+        for (int index : positions)
         {
-          atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
-                  .getPDBResNum(index), atomNo));
+          atomNo = sm.getAtomNum(index);
+
+          if (atomNo > 0)
+          {
+            atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+                    .getPDBResNum(index), atomNo));
+          }
         }
       }
     }
@@ -1027,13 +1046,13 @@ public class StructureSelectionManager
   /**
    * Add each of the given codonFrames to the stored set, if not aready present.
    * 
-   * @param set
+   * @param mappings
    */
-  public void registerMappings(Set<AlignedCodonFrame> set)
+  public void registerMappings(List<AlignedCodonFrame> mappings)
   {
-    if (set != null)
+    if (mappings != null)
     {
-      for (AlignedCodonFrame acf : set)
+      for (AlignedCodonFrame acf : mappings)
       {
         registerMapping(acf);
       }
@@ -1271,4 +1290,9 @@ public class StructureSelectionManager
     progressIndicator.setProgressBar(message, progressSessionId);
   }
 
+  public List<AlignedCodonFrame> getSequenceMappings()
+  {
+    return seqmappings;
+  }
+
 }