retrieve all sequences matching a particular name (JAL-872)

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0a3bd39..25a3dc6 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -45,6 +45,9 @@ public class Atom
 
   public String chain;
 
+  /**
+   * this is a temporary value - designed to store the position in sequence that this atom corresponds to after aligning the chain to a SequenceI object. Do not rely on its value being correct when visualizing sequence colourings on the structure - use the StructureSelectionManager's mapping instead.
+   */
   public int alignmentMapping = -1;
 
   public int atomIndex;

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index d5597de..65504e4 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -99,7 +99,7 @@ public class PDBChain
   /**
    * Annotate the residues with their corresponding positions in s1 using the
    * alignment in as
-   * 
+   * NOTE: This clears all atom.alignmentMapping values on the structure.
    * @param as
    * @param s1
    */
@@ -107,7 +107,11 @@ public class PDBChain
   {
     int pdbpos = as.getSeq2Start() - 2;
     int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+    // first clear out any old alignmentMapping values:
+    for (Atom atom: (Vector<Atom>) atoms) { 
+      atom.alignmentMapping=-1;
+    }
+    // and now trace the alignment onto the atom set.
     for (int i = 0; i < as.astr1.length(); i++)
     {
       if (as.astr1.charAt(i) != '-')

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 71b2754..5bde225 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -53,7 +53,8 @@ public class SequenceIdMatcher
     names = new Hashtable();
     for (int i = 0; i < seqs.length; i++)
     {
-      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+      // TODO: deal with ID collisions - SequenceI should be appended to list associated with this key.
+      names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
       // add in any interesting identifiers
       if (seqs[i].getDBRef() != null)
       {
@@ -83,6 +84,22 @@ public class SequenceIdMatcher
    */
   private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
   {
+    SequenceI[] st= pickbestMatches(candName, matches);
+    return st==null || st.length==0 ? null : st[0];
+  }
+  /**
+   * returns the closest SequenceI in matches to SeqIdName and returns all the
+   * matches to the names hash.
+   * 
+   * @param candName
+   *          SeqIdName
+   * @param matches
+   *          Vector of SequenceI objects
+   * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[] ties }
+   */
+  private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+  {
+    ArrayList best=new ArrayList();
     SequenceI match = null;
     if (candName == null || matches == null || matches.size() == 0)
     {
@@ -90,6 +107,7 @@ public class SequenceIdMatcher
     }
     match = (SequenceI) matches.elementAt(0);
     matches.removeElementAt(0);
+    best.add(match);
     names.put(new SeqIdName(match.getName()), match);
     int matchlen = match.getName().length();
     int namlen = candName.id.length();
@@ -97,17 +115,26 @@ public class SequenceIdMatcher
     {
       // look through for a better one.
       SequenceI cand = (SequenceI) matches.elementAt(0);
+      matches.remove(0);
       names.put(new SeqIdName(cand.getName()), cand);
-      int candlen = cand.getName().length();
+      int q,w,candlen = cand.getName().length();
       // keep the one with an id 'closer' to the given seqnam string
-      if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen)
+      if ((q=Math.abs(matchlen - namlen)) > (w=Math.abs(candlen - namlen))
               && candlen > matchlen)
       {
+        best.clear();
         match = cand;
         matchlen = candlen;
+        best.add(match);
+      }
+      if (q==w && candlen==matchlen)
+      {
+        // record any ties
+        best.add(cand);
       }
     }
-    return match;
+    if (best.size()==0) { return null; };
+    return (SequenceI[]) best.toArray(new SequenceI[0]);
   }
 
   /**
@@ -130,6 +157,17 @@ public class SequenceIdMatcher
   }
 
   /**
+   *  Find all matches for a given sequence name.
+   *  @param seqnam string to query Matcher with.
+   */
+  public SequenceI[] findAllIdMatches(String seqnam)
+  {
+
+    SeqIdName nam = new SeqIdName(seqnam);
+    return findAllIdMatches(nam);
+  }
+
+  /**
    * findIdMatch
    * 
    * Return pointers to sequences (or sequence object containers) which have
@@ -183,6 +221,25 @@ public class SequenceIdMatcher
     }
     return pickbestMatch(nam, matches);
   }
+  /**
+   * core findIdMatch search method for finding all equivalent matches
+   * 
+   * @param nam
+   *          SeqIdName
+   * @return SequenceI[]
+   */
+  private SequenceI[] findAllIdMatches(
+          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+  {
+    Vector matches = new Vector();
+    while (names.containsKey(nam))
+    {
+      matches.addElement(names.remove(nam));
+    }
+    SequenceI[] r=pickbestMatches(nam, matches);
+    return r;
+  }
+
 
   private class SeqIdName
   {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b658ffb..06272c3 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4513,7 +4513,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           if (pdbfn.length() > 0)
           {
             // attempt to find a match in the alignment
-            SequenceI mtch = idm.findIdMatch(pdbfn);
+            SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
             int l = 0, c = pdbfn.indexOf(".");
             while (mtch == null && c != -1)
             {
@@ -4525,7 +4525,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 pdbfn = pdbfn.substring(0, l);
               }
-              mtch = idm.findIdMatch(pdbfn);
+              mtch = idm.findAllIdMatches(pdbfn);
             }
             if (mtch != null)
             {
@@ -4570,17 +4570,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               // try and associate
               // TODO: may want to set a standard ID naming formalism for
               // associating PDB files which have no IDs.
+              for (SequenceI toassoc: (SequenceI[])fm[2]) {
               PDBEntry pe = new AssociatePdbFileWithSeq()
                       .associatePdbWithSeq((String) fm[0], (String) fm[1],
-                              (SequenceI) fm[2], false);
+                              toassoc, false);
               if (pe != null)
               {
                 System.err
                         .println("Associated file : " + ((String) fm[0])
                                 + " with "
-                                + ((SequenceI) fm[2]).getDisplayId(true));
+                                + toassoc.getDisplayId(true));
                 assocfiles++;
               }
+              }
               alignPanel.paintAlignment(true);
             }
           }