JAL-2446 merged to spike branch

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7e691be..db0b47e 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -29,12 +29,15 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
@@ -322,7 +325,7 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
-          String[] targetChains, String pdbFile, String protocol)
+          String[] targetChains, String pdbFile, DataSourceType protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
@@ -341,13 +344,13 @@ public class StructureSelectionManager
    *          (may be nill, individual elements may be nill)
    * @param pdbFile
    *          - structure data resource
-   * @param protocol
+   * @param sourceType
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile, String protocol)
+          String pdbFile, DataSourceType sourceType)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
@@ -383,15 +386,16 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new JmolParser(pdbFile, protocol);
+      sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
+      pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
-              && AppletFormatAdapter.FILE.equals(protocol))
+              && DataSourceType.FILE == sourceType)
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
       // if PDBId is unavailable then skip SIFTS mapping execution path
-      isMapUsingSIFTs = pdb.isPPDBIdAvailable();
+      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
 
     } catch (Exception ex)
     {
@@ -453,7 +457,7 @@ public class StructureSelectionManager
        * Attempt pairwise alignment of the sequence with each chain in the PDB,
        * and remember the highest scoring chain
        */
-      int max = -10;
+      float max = -10;
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
@@ -490,12 +494,12 @@ public class StructureSelectionManager
         continue;
       }
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (sourceType == DataSourceType.PASTE)
       {
         pdbFile = "INLINE" + pdb.getId();
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+      List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
         setProgressBar(null);
@@ -533,7 +537,7 @@ public class StructureSelectionManager
         }
         else
         {
-          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
           for (PDBChain chain : pdb.getChains())
           {
             try
@@ -588,11 +592,9 @@ public class StructureSelectionManager
     return pdb;
   }
 
-  private boolean isCIFFile(String filename)
+  public void addStructureMapping(StructureMapping sm)
   {
-    String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
-            filename.length());
-    return "cif".equalsIgnoreCase(fileExt);
+    mappings.add(sm);
   }
 
   /**
@@ -740,7 +742,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        for (String pdbfile : sl.getPdbFile())
+        for (String pdbfile : sl.getStructureFiles())
         {
           pdbs.remove(pdbfile);
         }
@@ -805,7 +807,28 @@ public class StructureSelectionManager
       return;
     }
 
-    SearchResults results = new SearchResults();
+    SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+    for (Object li : listeners)
+    {
+      if (li instanceof SequenceListener)
+      {
+        ((SequenceListener) li).highlightSequence(results);
+      }
+    }
+  }
+
+  /**
+   * Constructs a SearchResults object holding regions (if any) in the Jalview
+   * alignment which have a mapping to the structure viewer positions in the
+   * supplied list
+   * 
+   * @param atoms
+   * @return
+   */
+  public SearchResultsI findAlignmentPositionsForStructurePositions(
+          List<AtomSpec> atoms)
+  {
+    SearchResultsI results = new SearchResults();
     for (AtomSpec atom : atoms)
     {
       SequenceI lastseq = null;
@@ -830,13 +853,7 @@ public class StructureSelectionManager
         }
       }
     }
-    for (Object li : listeners)
-    {
-      if (li instanceof SequenceListener)
-      {
-        ((SequenceListener) li).highlightSequence(results);
-      }
-    }
+    return results;
   }
 
   /**
@@ -855,7 +872,7 @@ public class StructureSelectionManager
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();
-    SearchResults results = null;
+    SearchResultsI results = null;
     if (seqPos == -1)
     {
       seqPos = seq.findPosition(indexpos);
@@ -1187,13 +1204,14 @@ public class StructureSelectionManager
 
   public synchronized void sendSelection(
           jalview.datamodel.SequenceGroup selection,
-          jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+          jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     for (SelectionListener slis : sel_listeners)
     {
       if (slis != source)
       {
-        slis.selection(selection, colsel, source);
+        slis.selection(selection, colsel, hidden, source);
       }
     }
   }