Reinstated 'create tree from selected region only' with better indication that only...

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index f44f990..85749a1 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -412,7 +412,7 @@ public class NJTree {
           if (j==i) {\r
             distance[i][i] = 0;\r
           } else {\r
-            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);\r
+            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j], start, end);\r
             distance[j][i] = distance[i][j];\r
           }\r
         }\r
@@ -423,14 +423,14 @@ public class NJTree {
       for (int i = 0; i < noseqs-1; i++) {\r
         for (int j = i; j < noseqs; j++) {\r
           int score = 0;\r
-          for (int k=0; k < sequence[i].getLength(); k++) {\r
+          for (int k=start; k < end; k++) {\r
             try{\r
               score +=\r
                   ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,\r
                   k + 1),\r
                                                 sequence[j].getSequence(k,\r
                   k + 1));\r
-            }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}\r
+            }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}\r
           }\r
           distance[i][j] = (float)score;\r
           if (score > maxscore) {\r
@@ -522,6 +522,11 @@ public class NJTree {
     return found;\r
   }\r
 \r
+  /**\r
+   * printNode is mainly for debugging purposes.\r
+   *\r
+   * @param node SequenceNode\r
+   */\r
   public void printNode(SequenceNode node) {\r
     if (node == null) {\r
       return;\r