X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=98886472f1de8e750b46438ddb1680a81fa206c8;hb=63cead20b09743e899a22cb89f1c09e4d41cc8c0;hp=cc2b4580e1ece76f02dbc7b6d499d8f68dfd1290;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index cc2b458..9888647 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,26 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Routines for approximate Sequence Id resolution by name using string
@@ -30,33 +37,97 @@ import jalview.datamodel.*;
  */
 public class SequenceIdMatcher
 {
-  private Hashtable names;
+  private HashMap<SeqIdName, List<SequenceI>> names;
 
-  public SequenceIdMatcher(SequenceI[] seqs)
+  private Map<SeqIdName, List<SequenceI>> excludes;
+
+  public SequenceIdMatcher(List<SequenceI> seqs)
+  {
+    names = new HashMap<>();
+    excludes = new HashMap<>();
+    addAll(seqs);
+  }
+
+  /**
+   * Adds sequences to this matcher
+   * 
+   * @param seqs
+   */
+  public void addAll(List<SequenceI> seqs)
   {
-    names = new Hashtable();
-    for (int i = 0; i < seqs.length; i++)
+    for (SequenceI seq : seqs)
     {
-      // 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)
+      add(seq);
+    }
+  }
+
+  /**
+   * Adds one sequence to this matcher
+   * 
+   * @param seq
+   */
+  public void add(SequenceI seq)
+  {
+    SeqIdName key = new SeqIdName(seq.getDisplayId(true));
+    addMatchCandidate(key, seq);
+    SequenceI dbseq = seq;
+    while (dbseq.getDatasetSequence() != null)
+    {
+      dbseq = dbseq.getDatasetSequence();
+    }
+    // add in any interesting identifiers
+    if (dbseq.getDBRefs() != null)
+    {
+      DBRefEntry dbr[] = dbseq.getDBRefs();
+      for (int r = 0; r < dbr.length; r++)
       {
-        DBRefEntry dbr[] = seqs[i].getDBRef();
-        SeqIdName sid = null;
-        for (int r = 0; r < dbr.length; r++)
+        DBRefEntry dbref = dbr[r];
+        SeqIdName sid = new SeqIdName(dbref.getAccessionId());
+        if (dbref.getMap() != null
+                && dbref.getMap().getMap().isTripletMap())
         {
-          sid = new SeqIdName(dbr[r].getAccessionId());
-          if (!names.contains(sid))
+          /*
+           * dbref with 3:1 or 1:3 mapping (e.g. CDS/protein);
+           * mark as not a valid match for this id
+           */
+          List<SequenceI> excluded = excludes.get(sid);
+          if (excluded == null)
           {
-            names.put(sid, seqs[i]);
+            excludes.put(sid, excluded = new ArrayList<>());
           }
+          excluded.add(seq);
+          System.out.println("Excluding " + sid + "->" + seq);
+          continue;
         }
+        addMatchCandidate(sid, seq);
       }
     }
   }
 
+  void addMatchCandidate(SeqIdName key, SequenceI seq)
+  {
+    List<SequenceI> namesList = names.get(key);
+    if (namesList == null)
+    {
+      names.put(key, namesList = new ArrayList<>());
+    }
+    if (!namesList.contains(seq))
+    {
+      namesList.add(seq);
+      System.out.println("Adding " + key + "->" + seq);
+    }
+  }
+
+  /**
+   * convenience method to make a matcher from concrete array
+   * 
+   * @param sequences
+   */
+  public SequenceIdMatcher(SequenceI[] sequences)
+  {
+    this(Arrays.asList(sequences));
+  }
+
   /**
    * returns the closest SequenceI in matches to SeqIdName and returns all the
    * matches to the names hash.
@@ -64,13 +135,14 @@ public class SequenceIdMatcher
    * @param candName
    *          SeqIdName
    * @param matches
-   *          Vector of SequenceI objects
+   *          List of SequenceI objects
    * @return SequenceI closest SequenceI to SeqIdName
    */
-  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+  private SequenceI pickbestMatch(SeqIdName candName,
+          List<SequenceI> matches)
   {
-    SequenceI[] st = pickbestMatches(candName, matches);
-    return st == null || st.length == 0 ? null : st[0];
+    List<SequenceI> st = pickbestMatches(candName, matches);
+    return st == null || st.size() == 0 ? null : st.get(0);
   }
 
   /**
@@ -84,31 +156,28 @@ public class SequenceIdMatcher
    * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
    *         ties }
    */
-  private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+  private List<SequenceI> pickbestMatches(SeqIdName candName,
+          List<SequenceI> matches)
   {
-    ArrayList best = new ArrayList();
-    SequenceI match = null;
+    List<SequenceI> best = new ArrayList<>();
     if (candName == null || matches == null || matches.size() == 0)
     {
       return null;
     }
-    match = (SequenceI) matches.elementAt(0);
-    matches.removeElementAt(0);
+    SequenceI match = matches.remove(0);
     best.add(match);
-    names.put(new SeqIdName(match.getName()), match);
+    addMatchCandidate(new SeqIdName(match.getName()), match);
     int matchlen = match.getName().length();
     int namlen = candName.id.length();
     while (matches.size() > 0)
     {
       // look through for a better one.
-      SequenceI cand = (SequenceI) matches.elementAt(0);
-      matches.remove(0);
-      names.put(new SeqIdName(cand.getName()), cand);
+      SequenceI cand = matches.remove(0);
+      addMatchCandidate(new SeqIdName(cand.getName()), cand);
       int q, w, candlen = cand.getName().length();
       // keep the one with an id 'closer' to the given seqnam string
-      if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
-              - namlen))
-              && candlen > matchlen)
+      if ((q = Math.abs(matchlen - namlen)) > (w = Math
+              .abs(candlen - namlen)) && candlen > matchlen)
       {
         best.clear();
         match = cand;
@@ -126,7 +195,7 @@ public class SequenceIdMatcher
       return null;
     }
     ;
-    return (SequenceI[]) best.toArray(new SequenceI[0]);
+    return best;
   }
 
   /**
@@ -153,12 +222,18 @@ public class SequenceIdMatcher
    * 
    * @param seqnam
    *          string to query Matcher with.
+   * @return a new array or (possibly) null
    */
   public SequenceI[] findAllIdMatches(String seqnam)
   {
 
     SeqIdName nam = new SeqIdName(seqnam);
-    return findAllIdMatches(nam);
+    List<SequenceI> m = findAllIdMatches(nam);
+    if (m != null)
+    {
+      return m.toArray(new SequenceI[m.size()]);
+    }
+    return null;
   }
 
   /**
@@ -205,13 +280,22 @@ public class SequenceIdMatcher
    *          SeqIdName
    * @return SequenceI
    */
-  private SequenceI findIdMatch(
-          jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+  private SequenceI findIdMatch(SeqIdName nam)
   {
-    Vector matches = new Vector();
+    List<SequenceI> matches = new ArrayList<>();
     while (names.containsKey(nam))
     {
-      matches.addElement(names.remove(nam));
+      List<SequenceI> candidates = names.remove(nam);
+      List<SequenceI> except = excludes.get(nam);
+      int j = candidates.size();
+      for (int i = 0; i < j; i++)
+      {
+        SequenceI candidate = candidates.get(i);
+        if (!except.contains(candidate))
+        {
+          matches.add(candidate);
+        }
+      }
     }
     return pickbestMatch(nam, matches);
   }
@@ -223,19 +307,19 @@ public class SequenceIdMatcher
    *          SeqIdName
    * @return SequenceI[]
    */
-  private SequenceI[] findAllIdMatches(
+  private List<SequenceI> findAllIdMatches(
           jalview.analysis.SequenceIdMatcher.SeqIdName nam)
   {
-    Vector matches = new Vector();
+    List<SequenceI> matches = new ArrayList<>();
     while (names.containsKey(nam))
     {
-      matches.addElement(names.remove(nam));
+      matches.addAll(names.remove(nam));
     }
-    SequenceI[] r = pickbestMatches(nam, matches);
+    List<SequenceI> r = pickbestMatches(nam, matches);
     return r;
   }
 
-  private class SeqIdName
+  class SeqIdName
   {
     String id;
 
@@ -243,7 +327,7 @@ public class SequenceIdMatcher
     {
       if (s != null)
       {
-        id = new String(s);
+        id = s.toLowerCase();
       }
       else
       {
@@ -251,23 +335,29 @@ public class SequenceIdMatcher
       }
     }
 
+    @Override
     public int hashCode()
     {
-      return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
-              .hashCode());
+      return ((id.length() >= 4) ? id.substring(0, 4).hashCode()
+              : id.hashCode());
     }
 
+    @Override
     public boolean equals(Object s)
     {
+      if (s == null)
+      {
+        return false;
+      }
       if (s instanceof SeqIdName)
       {
-        return this.equals((SeqIdName) s);
+        return this.stringequals(((SeqIdName) s).id);
       }
       else
       {
         if (s instanceof String)
         {
-          return this.equals((String) s);
+          return this.stringequals(((String) s).toLowerCase());
         }
       }
 
@@ -289,37 +379,33 @@ public class SequenceIdMatcher
      * todo: (JBPNote) Set separator characters appropriately
      * 
      * @param s
-     *          SeqIdName
      * @return boolean
      */
-    public boolean equals(SeqIdName s)
+    private boolean stringequals(String s)
     {
-      // TODO: JAL-732 patch for cases when name includes a list of IDs, and the
-      // match contains one ID flanked
-      if (id.length() > s.id.length())
+      if (id.length() > s.length())
       {
-        return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
-                .length())) > -1) : false;
+        return id.startsWith(s)
+                ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+                : false;
       }
       else
       {
-        return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
-                .indexOf(s.id.charAt(id.length())) > -1)) : false;
+        return s.startsWith(id)
+                ? (s.equals(id) ? true
+                        : (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
+                : false;
       }
     }
 
-    public boolean equals(String s)
+    /**
+     * toString method returns the wrapped sequence id. For debugging purposes
+     * only, behaviour not guaranteed not to change.
+     */
+    @Override
+    public String toString()
     {
-      if (id.length() > s.length())
-      {
-        return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
-                : false;
-      }
-      else
-      {
-        return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
-                .indexOf(s.charAt(id.length())) > -1)) : false;
-      }
+      return id;
     }
   }
 }