JAL-1622 code tidy only, no functional change
[jalview.git] / src / jalview / structure / StructureSelectionManager.java
index ed5ee2d..ef4a7a5 100644 (file)
  */
 package jalview.structure;
 
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+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;
+import MCview.PDBChain;
+import MCview.PDBfile;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.commands.CommandI;
@@ -36,22 +53,10 @@ import jalview.io.AppletFormatAdapter;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
-import java.io.PrintStream;
-import java.util.ArrayList;
-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;
-import MCview.PDBChain;
-
 public class StructureSelectionManager
 {
+  public final static String NEWLINE = System.lineSeparator();
+
   static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
 
   private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
@@ -163,8 +168,9 @@ public class StructureSelectionManager
    * map between the PDB IDs (or structure identifiers) used by Jalview and the
    * absolute filenames for PDB data that corresponds to it
    */
-  HashMap<String, String> pdbIdFileName = new HashMap<String, String>(),
-          pdbFileNameId = new HashMap<String, String>();
+  Map<String, String> pdbIdFileName = new HashMap<String, String>();
+
+  Map<String, String> pdbFileNameId = new HashMap<String, String>();
 
   public void registerPDBFile(String idForFile, String absoluteFile)
   {
@@ -201,8 +207,11 @@ public class StructureSelectionManager
       {
         if (instances != null)
         {
-          throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
-                  new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
+          throw new Error(
+                  MessageManager
+                          .getString("error.implementation_error_structure_selection_manager_null"),
+                  new NullPointerException(MessageManager
+                          .getString("exception.ssm_context_is_null")));
         }
         else
         {
@@ -308,7 +317,7 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+  synchronized public PDBfile setMapping(SequenceI[] sequence,
           String[] targetChains, String pdbFile, String protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
@@ -332,15 +341,14 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public MCview.PDBfile setMapping(boolean forStructureView,
-          SequenceI[] sequence,
-          String[] targetChains, String pdbFile, String protocol)
+  synchronized public PDBfile setMapping(boolean forStructureView,
+          SequenceI[] sequence, String[] targetChains, String pdbFile,
+          String protocol)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
      * the tried and tested MCview pdb mapping
      */
-    MCview.PDBfile pdb = null;
     boolean parseSecStr = processSecondaryStructure;
     if (isPDBFileRegistered(pdbFile))
     {
@@ -359,8 +367,7 @@ public class StructureSelectionManager
             // false if any annotation present from this structure
             // JBPNote this fails for jmol/chimera view because the *file* is
             // passed, not the structure data ID -
-            if (MCview.PDBfile.isCalcIdForFile(ala,
-                    findIdForPDBFile(pdbFile)))
+            if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
             {
               parseSecStr = false;
             }
@@ -368,10 +375,11 @@ public class StructureSelectionManager
         }
       }
     }
+    PDBfile pdb = null;
     try
     {
-      pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
-              secStructServices, pdbFile, protocol);
+      pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+              pdbFile, protocol);
       if (pdb.id != null && pdb.id.trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
@@ -387,15 +395,16 @@ public class StructureSelectionManager
     for (int s = 0; s < sequence.length; s++)
     {
       boolean infChain = true;
+      final SequenceI seq = sequence[s];
       if (targetChains != null && targetChains[s] != null)
       {
         infChain = false;
         targetChain = targetChains[s];
       }
-      else if (sequence[s].getName().indexOf("|") > -1)
+      else if (seq.getName().indexOf("|") > -1)
       {
-        targetChain = sequence[s].getName().substring(
-                sequence[s].getName().lastIndexOf("|") + 1);
+        targetChain = seq.getName().substring(
+                seq.getName().lastIndexOf("|") + 1);
         if (targetChain.length() > 1)
         {
           if (targetChain.trim().length() == 0)
@@ -414,14 +423,17 @@ public class StructureSelectionManager
         targetChain = "";
       }
 
+      /*
+       * Attempt pairwise alignment of the sequence with each chain in the PDB,
+       * and remember the highest scoring chain
+       */
       int max = -10;
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
       boolean first = true;
-      for (int i = 0; i < pdb.chains.size(); i++)
+      for (PDBChain chain : pdb.chains)
       {
-        PDBChain chain = (pdb.chains.elementAt(i));
         if (targetChain.length() > 0 && !targetChain.equals(chain.id)
                 && !infChain)
         {
@@ -429,12 +441,13 @@ public class StructureSelectionManager
         }
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
-        AlignSeq as = new AlignSeq(sequence[s],
-                pdb.chains.elementAt(i).sequence,
-                pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
-                        : AlignSeq.PEP);
-        as.calcScoreMatrix();
-        as.traceAlignment();
+        final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
+        AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
+                type);
+        // equivalent to:
+        // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
+        // as.calcScoreMatrix();
+        // as.traceAlignment();
 
         if (first || as.maxscore > max
                 || (as.maxscore == max && chain.id.equals(targetChain)))
@@ -450,11 +463,13 @@ public class StructureSelectionManager
       {
         continue;
       }
-      final StringBuffer mappingDetails = new StringBuffer();
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + maxChain.sequence.getSequenceAsString());
-      mappingDetails.append("\nNo of residues = "
-              + maxChain.residues.size() + "\n\n");
+      final StringBuilder mappingDetails = new StringBuilder(128);
+      mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+              .append(NEWLINE).append("Sequence = ")
+              .append(maxChain.sequence.getSequenceAsString());
+      mappingDetails.append(NEWLINE).append("No of residues = ")
+              .append(maxChain.residues.size()).append(NEWLINE)
+              .append(NEWLINE);
       PrintStream ps = new PrintStream(System.out)
       {
         @Override
@@ -466,35 +481,40 @@ public class StructureSelectionManager
         @Override
         public void println()
         {
-          mappingDetails.append("\n");
+          mappingDetails.append(NEWLINE);
         }
       };
 
       maxAlignseq.printAlignment(ps);
 
-      mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start
-              + " " + maxAlignseq.seq2end);
-      mappingDetails.append("\nSEQ start/end "
-              + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + " "
-              + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
+      mappingDetails.append(NEWLINE).append("PDB start/end ");
+      mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
+              " ");
+      mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+
+      mappingDetails.append(NEWLINE).append("SEQ start/end ");
+      mappingDetails.append(
+              String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
+              .append(" ");
+      mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+              + seq.getEnd() - 1));
 
-      maxChain.makeExactMapping(maxAlignseq, sequence[s]);
+      maxChain.makeExactMapping(maxAlignseq, seq);
       jalview.datamodel.Mapping sqmpping = maxAlignseq
               .getMappingFromS1(false);
       jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
               sqmpping.getMap().getInverse());
-      maxChain.transferRESNUMFeatures(sequence[s], null);
+      maxChain.transferRESNUMFeatures(seq, null);
 
       // allocate enough slots to store the mapping from positions in
       // sequence[s] to the associated chain
-      int[][] mapping = new int[sequence[s].findPosition(sequence[s]
-              .getLength()) + 2][2];
+      int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
       int resNum = -10000;
       int index = 0;
 
       do
       {
-        Atom tmp = (Atom) maxChain.atoms.elementAt(index);
+        Atom tmp = maxChain.atoms.elementAt(index);
         if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
         {
           resNum = tmp.resNumber;
@@ -509,9 +529,8 @@ public class StructureSelectionManager
       {
         pdbFile = "INLINE" + pdb.id;
       }
-      StructureMapping newMapping = new StructureMapping(sequence[s],
-              pdbFile, pdb.id, maxChainId, mapping,
-              mappingDetails.toString());
+      StructureMapping newMapping = new StructureMapping(seq, pdbFile,
+              pdb.id, maxChainId, mapping, mappingDetails.toString());
       if (forStructureView)
       {
         mappings.add(newMapping);
@@ -542,30 +561,30 @@ public class StructureSelectionManager
     {
       return;
     }
-    String[] handlepdbs;
-    Vector pdbs = new Vector();
-    for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
-    {
-      ;
-    }
+
+    /*
+     * Remove mappings to the closed listener's PDB files, but first check if
+     * another listener is still interested
+     */
+    List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+
     StructureListener sl;
     for (int i = 0; i < listeners.size(); i++)
     {
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        handlepdbs = sl.getPdbFile();
-        for (int j = 0; j < handlepdbs.length; j++)
+        for (String pdbfile : sl.getPdbFile())
         {
-          if (pdbs.contains(handlepdbs[j]))
-          {
-            pdbs.removeElement(handlepdbs[j]);
-          }
+          pdbs.remove(pdbfile);
         }
-
       }
     }
 
+    /*
+     * Rebuild the mappings set, retaining only those which are for 'other' PDB
+     * files
+     */
     if (pdbs.size() > 0)
     {
       List<StructureMapping> tmp = new ArrayList<StructureMapping>();
@@ -581,53 +600,75 @@ public class StructureSelectionManager
     }
   }
 
+  /**
+   * Propagate mouseover of a single position in a structure
+   * 
+   * @param pdbResNum
+   * @param chain
+   * @param pdbfile
+   */
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
+    AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
+    List<AtomSpec> atoms = Collections.singletonList(atomSpec);
+    mouseOverStructure(atoms);
+  }
+
+  /**
+   * Propagate mouseover or selection of multiple positions in a structure
+   * 
+   * @param atoms
+   */
+  public void mouseOverStructure(List<AtomSpec> atoms)
+  {
     if (listeners == null)
     {
       // old or prematurely sent event
       return;
     }
-    SearchResults results = null;
-    SequenceI lastseq = null;
-    int lastipos = -1, indexpos;
+    boolean hasSequenceListener = false;
     for (int i = 0; i < listeners.size(); i++)
     {
       if (listeners.elementAt(i) instanceof SequenceListener)
       {
-        if (results == null)
-        {
-          results = new SearchResults();
-        }
-        for (StructureMapping sm : mappings)
+        hasSequenceListener = true;
+      }
+    }
+    if (!hasSequenceListener)
+    {
+      return;
+    }
+
+    SearchResults results = new SearchResults();
+    for (AtomSpec atom : atoms)
+    {
+      SequenceI lastseq = null;
+      int lastipos = -1;
+      for (StructureMapping sm : mappings)
+      {
+        if (sm.pdbfile.equals(atom.getPdbFile())
+                && sm.pdbchain.equals(atom.getChain()))
         {
-          if (sm.pdbfile.equals(pdbfile) && sm.pdbchain.equals(chain))
+          int indexpos = sm.getSeqPos(atom.getPdbResNum());
+          if (lastipos != indexpos && lastseq != sm.sequence)
           {
-            indexpos = sm.getSeqPos(pdbResNum);
-            if (lastipos != indexpos && lastseq != sm.sequence)
+            results.addResult(sm.sequence, indexpos, indexpos);
+            lastipos = indexpos;
+            lastseq = sm.sequence;
+            // construct highlighted sequence list
+            for (AlignedCodonFrame acf : seqmappings)
             {
-              results.addResult(sm.sequence, indexpos, indexpos);
-              lastipos = indexpos;
-              lastseq = sm.sequence;
-              // construct highlighted sequence list
-              for (AlignedCodonFrame acf : seqmappings)
-              {
-                acf.markMappedRegion(sm.sequence, indexpos, results);
-              }
+              acf.markMappedRegion(sm.sequence, indexpos, results);
             }
           }
         }
       }
     }
-    if (results != null)
+    for (Object li : listeners)
     {
-      for (int i = 0; i < listeners.size(); i++)
+      if (li instanceof SequenceListener)
       {
-        Object li = listeners.elementAt(i);
-        if (li instanceof SequenceListener)
-        {
-          ((SequenceListener) li).highlightSequence(results);
-        }
+        ((SequenceListener) li).highlightSequence(results);
       }
     }
   }
@@ -821,25 +862,43 @@ public class StructureSelectionManager
   {
     List<StructureMapping> tmp = new ArrayList<StructureMapping>();
     for (StructureMapping sm : mappings)
-      {
+    {
       if (sm.pdbfile.equals(pdbfile))
-        {
+      {
         tmp.add(sm);
-        }
+      }
     }
     return tmp.toArray(new StructureMapping[tmp.size()]);
   }
 
-  public String printMapping(String pdbfile)
+  /**
+   * Returns a readable description of all mappings for the given pdbfile to any
+   * of the given sequences
+   * 
+   * @param pdbfile
+   * @param seqs
+   * @return
+   */
+  public String printMappings(String pdbfile, List<SequenceI> seqs)
   {
+    if (pdbfile == null || seqs == null || seqs.isEmpty())
+    {
+      return "";
+    }
+
     StringBuilder sb = new StringBuilder(64);
     for (StructureMapping sm : mappings)
     {
-      if (sm.pdbfile.equals(pdbfile))
+      if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
       {
         sb.append(sm.mappingDetails);
+        sb.append(NEWLINE);
+        // separator makes it easier to read multiple mappings
+        sb.append("=====================");
+        sb.append(NEWLINE);
       }
     }
+    sb.append(NEWLINE);
 
     return sb.toString();
   }