Merge branch 'develop' into features/JAL-250_hideredundantseqs

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 65fd5e7..fbfa486 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -29,12 +29,14 @@ 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;
@@ -159,8 +161,8 @@ public class StructureSelectionManager
     }
     else
     {
-      System.err.println("reportMapping: There are " + mappings.size()
-              + " mappings.");
+      System.err.println(
+              "reportMapping: There are " + mappings.size() + " mappings.");
       int i = 0;
       for (StructureMapping sm : mappings)
       {
@@ -212,9 +214,8 @@ public class StructureSelectionManager
       {
         if (instances != null)
         {
-          throw new Error(
-                  MessageManager
-                          .getString("error.implementation_error_structure_selection_manager_null"),
+          throw new Error(MessageManager.getString(
+                  "error.implementation_error_structure_selection_manager_null"),
                   new NullPointerException(MessageManager
                           .getString("exception.ssm_context_is_null")));
         }
@@ -384,6 +385,7 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
+      sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
@@ -430,8 +432,8 @@ public class StructureSelectionManager
       }
       else if (seq.getName().indexOf("|") > -1)
       {
-        targetChainId = seq.getName().substring(
-                seq.getName().lastIndexOf("|") + 1);
+        targetChainId = seq.getName()
+                .substring(seq.getName().lastIndexOf("|") + 1);
         if (targetChainId.length() > 1)
         {
           if (targetChainId.trim().length() == 0)
@@ -454,7 +456,7 @@ 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;
@@ -574,8 +576,8 @@ public class StructureSelectionManager
         setProgressBar(null);
         setProgressBar(MessageManager
                 .getString("status.obtaining_mapping_with_nw_alignment"));
-        StructureMapping nwMapping = getNWMappings(seq, pdbFile,
-                maxChainId, maxChain, pdb, maxAlignseq);
+        StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
+                maxChain, pdb, maxAlignseq);
         seqToStrucMapping.add(nwMapping);
         ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
@@ -589,11 +591,9 @@ 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);
   }
 
   /**
@@ -636,8 +636,8 @@ public class StructureSelectionManager
           AlignSeq maxAlignseq)
   {
     final StringBuilder mappingDetails = new StringBuilder(128);
-    mappingDetails.append(NEWLINE).append(
-            "Sequence \u27f7 Structure mapping details");
+    mappingDetails.append(NEWLINE)
+            .append("Sequence \u27f7 Structure mapping details");
     mappingDetails.append(NEWLINE);
     mappingDetails
             .append("Method: inferred with Needleman & Wunsch alignment");
@@ -669,11 +669,12 @@ public class StructureSelectionManager
             .append(" ");
     mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
     mappingDetails.append(NEWLINE).append("SEQ start/end ");
-    mappingDetails.append(
-            String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+    mappingDetails
+            .append(String
+                    .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
             .append(" ");
-    mappingDetails.append(String.valueOf(maxAlignseq.seq1end
-            + (seq.getStart() - 1)));
+    mappingDetails.append(
+            String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1)));
     mappingDetails.append(NEWLINE);
     maxChain.makeExactMapping(maxAlignseq, seq);
     jalview.datamodel.Mapping sqmpping = maxAlignseq
@@ -695,8 +696,9 @@ public class StructureSelectionManager
         insCode = tmp.insCode;
         if (tmp.alignmentMapping >= -1)
         {
-          mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
-              tmp.atomIndex });
+          mapping.put(tmp.alignmentMapping + 1,
+                  new int[]
+                  { tmp.resNumber, tmp.atomIndex });
         }
       }
 
@@ -741,7 +743,7 @@ 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);
         }
@@ -774,7 +776,8 @@ public class StructureSelectionManager
    * @param chain
    * @param pdbfile
    */
-  public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+  public void mouseOverStructure(int pdbResNum, String chain,
+          String pdbfile)
   {
     AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
     List<AtomSpec> atoms = Collections.singletonList(atomSpec);
@@ -806,6 +809,28 @@ public class StructureSelectionManager
       return;
     }
 
+    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)
     {
@@ -831,13 +856,7 @@ public class StructureSelectionManager
         }
       }
     }
-    for (Object li : listeners)
-    {
-      if (li instanceof SequenceListener)
-      {
-        ((SequenceListener) li).highlightSequence(results);
-      }
-    }
+    return results;
   }
 
   /**
@@ -934,8 +953,7 @@ public class StructureSelectionManager
     List<AtomSpec> atoms = new ArrayList<AtomSpec>();
     for (StructureMapping sm : mappings)
     {
-      if (sm.sequence == seq
-              || sm.sequence == seq.getDatasetSequence()
+      if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
               || (sm.sequence.getDatasetSequence() != null && sm.sequence
                       .getDatasetSequence() == seq.getDatasetSequence()))
       {
@@ -945,8 +963,8 @@ public class StructureSelectionManager
 
           if (atomNo > 0)
           {
-            atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
-                    .getPDBResNum(index), atomNo));
+            atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+                    sm.getPDBResNum(index), atomNo));
           }
         }
       }
@@ -1188,13 +1206,14 @@ 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);
       }
     }
   }
@@ -1311,8 +1330,8 @@ public class StructureSelectionManager
   {
     if (command instanceof EditCommand)
     {
-      return MappingUtils.mapEditCommand((EditCommand) command, undo,
-              mapTo, gapChar, seqmappings);
+      return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo,
+              gapChar, seqmappings);
     }
     else if (command instanceof OrderCommand)
     {