Moved tree leafname to alignment set matching into SequenceIdMatcher class for

[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 8f3483d..7f4850e 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -48,69 +48,33 @@ public class NJTree {
     maxheight = findHeight(top);\r
 \r
   }\r
-  // Private SequenceID class to do fuzzy .equals() method for Hashtable.\r
-\r
-  private class SeqIdname {\r
-    String id;\r
-\r
-    SeqIdname(String s) {\r
-      id = new String(s);\r
-    }\r
-    public int hashCode() {\r
-      return (id.substring(0,4).hashCode());\r
-    }\r
-    public boolean equals(Object s) {\r
-      if (s instanceof SeqIdname) {\r
-        return this.equals((SeqIdname) s);\r
-      } else {\r
-        if (s instanceof String) {\r
-          return this.equals((String) s);\r
-        }\r
-      }\r
-      return false;\r
-    }\r
-\r
-\r
-    public boolean equals(SeqIdname s) {\r
-      if (id.startsWith(s.id) || s.id.startsWith(id)) {\r
-        return true;\r
-      }\r
-      return false;\r
-    }\r
-\r
-    public boolean equals(String s) {\r
-      if (id.startsWith(s) || s.startsWith(id)) {\r
-        return true;\r
-      }\r
-      return false;\r
-    }\r
-  }\r
 \r
   public NJTree(SequenceI[] seqs, NewickFile treefile) {\r
     top = treefile.getTree();\r
     maxheight = findHeight(top);\r
-    Hashtable names = new Hashtable();\r
-    for (int i = 0; i < seqs.length; i++)\r
-    {\r
-      names.put(new SeqIdname(seqs[i].getDisplayId()), seqs[i]);\r
-    }\r
+    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
+\r
     Vector leaves = new Vector();\r
     findLeaves(top, leaves);\r
+\r
     int i = 0;\r
     int namesleft = seqs.length;\r
+\r
     SequenceNode j;\r
-    SeqIdname nam;\r
+    SequenceI nam;\r
+    String realnam;\r
     while (i < leaves.size())\r
     {\r
       j = (SequenceNode) leaves.elementAt(i++);\r
-      nam = new SeqIdname(j.getName());\r
-      if ((namesleft>-1)\r
-          && names.containsKey(nam))\r
-      {\r
-        j.setElement(names.get(nam));\r
+      realnam = j.getName();\r
+      nam = null;\r
+      if (namesleft>-1)\r
+        nam = algnIds.findIdMatch(realnam);\r
+      if (nam != null) {\r
+        j.setElement(nam);\r
         namesleft--;\r
       } else {\r
-        j.setElement(new Sequence(nam.id, "THISISAPLACEHLDER"));\r
+        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
       }\r
     }\r
   }\r