JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7456304..65df679 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -285,7 +285,8 @@ public class StructureSelectionManager
   }
 
   /**
-   * Returns the file name for a mapped PDB id (or null if not mapped).
+   * Returns the filename the PDB id is already mapped to if known, or null if
+   * it is not mapped
    * 
    * @param pdbid
    * @return
@@ -294,7 +295,7 @@ public class StructureSelectionManager
   {
     for (StructureMapping sm : mappings)
     {
-      if (sm.getPdbId().equals(pdbid))
+      if (sm.getPdbId().equalsIgnoreCase(pdbid))
       {
         return sm.pdbfile;
       }
@@ -397,8 +398,11 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
+      pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {
@@ -612,7 +616,10 @@ public class StructureSelectionManager
       }
       if (forStructureView)
       {
-        mappings.addAll(seqToStrucMapping);
+        for (StructureMapping sm : seqToStrucMapping)
+        {
+          addStructureMapping(sm); // not addAll!
+        }
       }
       if (progress != null)
       {
@@ -664,7 +671,10 @@ public class StructureSelectionManager
 
   public void addStructureMapping(StructureMapping sm)
   {
-    mappings.add(sm);
+    if (!mappings.contains(sm))
+    {
+      mappings.add(sm);
+    }
   }
 
   /**
@@ -848,13 +858,14 @@ public class StructureSelectionManager
    * @param pdbResNum
    * @param chain
    * @param pdbfile
+   * @return
    */
-  public void mouseOverStructure(int pdbResNum, String chain,
+  public String mouseOverStructure(int pdbResNum, String chain,
           String pdbfile)
   {
     AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
     List<AtomSpec> atoms = Collections.singletonList(atomSpec);
-    mouseOverStructure(atoms);
+    return mouseOverStructure(atoms);
   }
 
   /**
@@ -862,12 +873,12 @@ public class StructureSelectionManager
    * 
    * @param atoms
    */
-  public void mouseOverStructure(List<AtomSpec> atoms)
+  public String mouseOverStructure(List<AtomSpec> atoms)
   {
     if (listeners == null)
     {
       // old or prematurely sent event
-      return;
+      return null;
     }
     boolean hasSequenceListener = false;
     for (int i = 0; i < listeners.size(); i++)
@@ -879,18 +890,24 @@ public class StructureSelectionManager
     }
     if (!hasSequenceListener)
     {
-      return;
+      return null;
     }
 
     SearchResultsI results = findAlignmentPositionsForStructurePositions(
             atoms);
+    String result = null;
     for (Object li : listeners)
     {
       if (li instanceof SequenceListener)
       {
-        ((SequenceListener) li).highlightSequence(results);
+        String s = ((SequenceListener) li).highlightSequence(results);
+        if (s != null)
+        {
+          result = s;
+        }
       }
     }
+    return result;
   }
 
   /**