JAL-3253 miscellaneous tidying up before merge to JS-develop

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index d9e8c95..56d2e9b 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -25,7 +25,7 @@ import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -53,9 +53,9 @@ import java.util.List;
  * @author gmcarstairs
  *
  */
-public abstract class AAStructureBindingModel extends
-        SequenceStructureBindingModel implements StructureListener,
-        StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+        extends SequenceStructureBindingModel
+        implements StructureListener, StructureSelectionManagerProvider
 {
 
   private StructureSelectionManager ssm;
@@ -142,7 +142,6 @@ public abstract class AAStructureBindingModel extends
    * @param ssm
    * @param pdbentry
    * @param sequenceIs
-   * @param chains
    * @param protocol
    */
   public AAStructureBindingModel(StructureSelectionManager ssm,
@@ -154,8 +153,60 @@ public abstract class AAStructureBindingModel extends
     this.nucleotide = Comparison.isNucleotide(sequenceIs);
     this.pdbEntry = pdbentry;
     this.protocol = protocol;
+    resolveChains();
   }
 
+  private boolean resolveChains()
+  {
+    /**
+     * final count of chain mappings discovered
+     */
+    int chainmaps = 0;
+    // JBPNote: JAL-2693 - this should be a list of chain mappings per
+    // [pdbentry][sequence]
+    String[][] newchains = new String[pdbEntry.length][];
+    int pe = 0;
+    for (PDBEntry pdb : pdbEntry)
+    {
+      SequenceI[] seqsForPdb = sequence[pe];
+      if (seqsForPdb != null)
+      {
+        newchains[pe] = new String[seqsForPdb.length];
+        int se = 0;
+        for (SequenceI asq : seqsForPdb)
+        {
+          String chain = (chains != null && chains[pe] != null)
+                  ? chains[pe][se]
+                  : null;
+          SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+                  : asq.getDatasetSequence();
+          if (sq.getAllPDBEntries() != null)
+          {
+            for (PDBEntry pdbentry : sq.getAllPDBEntries())
+            {
+              if (pdb.getFile() != null && pdbentry.getFile() != null
+                      && pdb.getFile().equals(pdbentry.getFile()))
+              {
+                String chaincode = pdbentry.getChainCode();
+                if (chaincode != null && chaincode.length() > 0)
+                {
+                  chain = chaincode;
+                  chainmaps++;
+                  break;
+                }
+              }
+            }
+          }
+          newchains[pe][se] = chain;
+          se++;
+        }
+        pe++;
+      }
+    }
+
+    chains = newchains;
+    return chainmaps > 0;
+  }
   public StructureSelectionManager getSsm()
   {
     return ssm;
@@ -300,11 +351,12 @@ public abstract class AAStructureBindingModel extends
     {
       throw new Error(MessageManager.formatMessage(
               "error.implementation_error_no_pdbentry_from_index",
-              new Object[] { Integer.valueOf(pe).toString() }));
+              new Object[]
+              { Integer.valueOf(pe).toString() }));
     }
     final String nullChain = "TheNullChain";
-    List<SequenceI> s = new ArrayList<SequenceI>();
-    List<String> c = new ArrayList<String>();
+    List<SequenceI> s = new ArrayList<>();
+    List<String> c = new ArrayList<>();
     if (getChains() == null)
     {
       setChains(new String[getPdbCount()][]);
@@ -373,8 +425,8 @@ public abstract class AAStructureBindingModel extends
   public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
           SequenceI[][] seq, String[][] chns)
   {
-    List<PDBEntry> v = new ArrayList<PDBEntry>();
-    List<int[]> rtn = new ArrayList<int[]>();
+    List<PDBEntry> v = new ArrayList<>();
+    List<int[]> rtn = new ArrayList<>();
     for (int i = 0; i < getPdbCount(); i++)
     {
       v.add(getPdbEntry(i));
@@ -463,9 +515,7 @@ public abstract class AAStructureBindingModel extends
    * Returns a readable description of all mappings for the wrapped pdbfile to
    * any mapped sequences
    * 
-   * @param pdbfile
-   * @param seqs
-   * @return
+   * @return 
    */
   public String printMappings()
   {
@@ -638,8 +688,8 @@ public abstract class AAStructureBindingModel extends
 
     if (waiting)
     {
-      System.err
-              .println("Timed out waiting for structure viewer to load file "
+      System.err.println(
+              "Timed out waiting for structure viewer to load file "
                       + notLoaded);
       return false;
     }
@@ -657,10 +707,8 @@ public abstract class AAStructureBindingModel extends
         {
           for (SequenceI s : seqs)
           {
-            if (s == seq
-                    || (s.getDatasetSequence() != null && s
-                            .getDatasetSequence() == seq
-                            .getDatasetSequence()))
+            if (s == seq || (s.getDatasetSequence() != null
+                    && s.getDatasetSequence() == seq.getDatasetSequence()))
             {
               return true;
             }
@@ -716,8 +764,8 @@ public abstract class AAStructureBindingModel extends
    *          an array of corresponding hidden columns for each alignment
    * @return
    */
-  public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
-          ColumnSelection[] hiddenCols);
+  public abstract String superposeStructures(AlignmentI[] alignments,
+          int[] structureIndices, HiddenColumns[] hiddenCols);
 
   public abstract void setBackgroundColour(Color col);
 
@@ -732,7 +780,8 @@ public abstract class AAStructureBindingModel extends
    * 
    * @return
    */
-  public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+  public abstract SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment);
 
   protected abstract void colourBySequence(
           StructureMappingcommandSet[] colourBySequenceCommands);
@@ -757,9 +806,9 @@ public abstract class AAStructureBindingModel extends
       return;
     }
     String[] files = getStructureFiles();
-  
+
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
-  
+
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
             files, sr, alignmentv);
     colourBySequence(colourBySequenceCommands);