From 5a6113ce9fef6f59b895a40a69b55b120735c533 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 5 May 2005 13:15:25 +0000
Subject: [PATCH] Moved tree leafname to alignment set matching into
 SequenceIdMatcher class for use in other contexts.

---
 src/jalview/analysis/NJTree.java            |   62 +++---------
 src/jalview/analysis/SequenceIdMatcher.java |  137 +++++++++++++++++++++++++++
 2 files changed, 150 insertions(+), 49 deletions(-)
 create mode 100755 src/jalview/analysis/SequenceIdMatcher.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 8f3483d..7f4850e 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -48,69 +48,33 @@ public class NJTree {
     maxheight = findHeight(top);
 
   }
-  // Private SequenceID class to do fuzzy .equals() method for Hashtable.
-
-  private class SeqIdname {
-    String id;
-
-    SeqIdname(String s) {
-      id = new String(s);
-    }
-    public int hashCode() {
-      return (id.substring(0,4).hashCode());
-    }
-    public boolean equals(Object s) {
-      if (s instanceof SeqIdname) {
-        return this.equals((SeqIdname) s);
-      } else {
-        if (s instanceof String) {
-          return this.equals((String) s);
-        }
-      }
-      return false;
-    }
-
-
-    public boolean equals(SeqIdname s) {
-      if (id.startsWith(s.id) || s.id.startsWith(id)) {
-        return true;
-      }
-      return false;
-    }
-
-    public boolean equals(String s) {
-      if (id.startsWith(s) || s.startsWith(id)) {
-        return true;
-      }
-      return false;
-    }
-  }
 
   public NJTree(SequenceI[] seqs, NewickFile treefile) {
     top = treefile.getTree();
     maxheight = findHeight(top);
-    Hashtable names = new Hashtable();
-    for (int i = 0; i < seqs.length; i++)
-    {
-      names.put(new SeqIdname(seqs[i].getDisplayId()), seqs[i]);
-    }
+    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
+
     Vector leaves = new Vector();
     findLeaves(top, leaves);
+
     int i = 0;
     int namesleft = seqs.length;
+
     SequenceNode j;
-    SeqIdname nam;
+    SequenceI nam;
+    String realnam;
     while (i < leaves.size())
     {
       j = (SequenceNode) leaves.elementAt(i++);
-      nam = new SeqIdname(j.getName());
-      if ((namesleft>-1)
-          && names.containsKey(nam))
-      {
-        j.setElement(names.get(nam));
+      realnam = j.getName();
+      nam = null;
+      if (namesleft>-1)
+        nam = algnIds.findIdMatch(realnam);
+      if (nam != null) {
+        j.setElement(nam);
         namesleft--;
       } else {
-        j.setElement(new Sequence(nam.id, "THISISAPLACEHLDER"));
+        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
       }
     }
   }
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
new file mode 100755
index 0000000..03528db
--- /dev/null
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -0,0 +1,137 @@
+package jalview.analysis;
+
+import java.util.Vector;
+import java.util.Hashtable;
+import jalview.datamodel.SequenceI;
+
+/**
+ * <p>Title: </p>
+ * SequenceIdMatcher
+ * <p>Description: </p>
+ * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class SequenceIdMatcher
+{
+
+  private class SeqIdName
+  {
+    String id;
+
+    SeqIdName(String s)
+    {
+      id = new String(s);
+    }
+
+    public int hashCode()
+    {
+      return (id.substring(0, 4).hashCode());
+    }
+
+    public boolean equals(Object s)
+    {
+      if (s instanceof SeqIdName)
+      {
+        return this.equals( (SeqIdName) s);
+      }
+      else
+      {
+        if (s instanceof String)
+        {
+          return this.equals( (String) s);
+        }
+      }
+      return false;
+    }
+
+    public boolean equals(SeqIdName s)
+    {
+      if (id.startsWith(s.id) || s.id.startsWith(id))
+      {
+        return true;
+      }
+      return false;
+    }
+
+    public boolean equals(String s)
+    {
+      if (id.startsWith(s) || s.startsWith(id))
+      {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  private Hashtable names;
+
+  public SequenceIdMatcher(SequenceI[] seqs)
+  {
+    names = new Hashtable();
+    for (int i = 0; i < seqs.length; i++)
+    {
+      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+    }
+  }
+
+  SequenceI findIdMatch(SequenceI seq)
+  {
+    SeqIdName nam = new SeqIdName(seq.getName());
+    if (names.containsKey(nam))
+    {
+      return (SequenceI) names.get(nam);
+    }
+    return null;
+  }
+
+  SequenceI findIdMatch(String seqnam)
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
+    if (names.containsKey(nam))
+    {
+      return (SequenceI) names.get(nam);
+    }
+    return null;
+  }
+
+  /**
+   * @method findIdMatch
+   *
+   * Return pointers to sequences (or sequence object containers)
+   * which have same Id as a given set of different sequence objects
+   *
+   * @param seqs SequenceI[]
+   * @return SequenceI[]
+   */
+
+  SequenceI[] findIdMatch(SequenceI[] seqs)
+  {
+    SequenceI[] namedseqs = new SequenceI[seqs.length];
+
+    int i = 0;
+    SeqIdName nam;
+    if (seqs.length > 0)
+    {
+      do
+      {
+        nam = new SeqIdName(seqs[i].getName());
+        if (names.containsKey(nam))
+        {
+          namedseqs[i] = (SequenceI) names.get(nam);
+        }
+        else
+        {
+          namedseqs[i] = null;
+        }
+      }
+      while (i++ < seqs.length);
+    }
+    return namedseqs;
+  }
+
+}
-- 
1.7.10.2