Parsing features file - dont adjust for alignment position

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 46a2ced..40dfc9b 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -60,6 +60,10 @@ public class NJTree
     Object leaves = null;\r
     int start;\r
     int end;\r
+    boolean hasDistances = true; // normal case for jalview trees\r
+       boolean hasBootstrap = false; // normal case for jalview trees\r
+\r
+    private boolean hasRootDistance = true;\r
 \r
     /**\r
      * Creates a new NJTree object.\r
@@ -81,6 +85,11 @@ public class NJTree
     public NJTree(SequenceI[] seqs, NewickFile treefile)\r
     {\r
         top = treefile.getTree();\r
+\r
+        hasDistances = treefile.HasDistances();\r
+        hasBootstrap = treefile.HasBootstrap();\r
+        hasRootDistance = treefile.HasRootDistance();\r
+\r
         maxheight = findHeight(top);\r
 \r
         SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
@@ -375,7 +384,7 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,\r
         float dist)\r
     {\r
-     \r
+\r
         tmpi.dist = ((dist + ri) - rj) / 2;\r
         tmpj.dist = (dist - tmpi.dist);\r
 \r
@@ -658,7 +667,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
                     as.calcScoreMatrix();\r
                     as.traceAlignment();\r
-                    as.printAlignment();\r
+                    as.printAlignment(System.out);\r
                     distance[i][j] = (float) as.maxscore;\r
 \r
                     if (max < distance[i][j])\r
@@ -1134,6 +1143,27 @@ public class NJTree
     {\r
         return top;\r
     }\r
+    /**\r
+     *\r
+     * @return true if tree has real distances\r
+     */\r
+    public boolean isHasDistances() {\r
+      return hasDistances;\r
+    }\r
+\r
+    /**\r
+     *\r
+     * @return true if tree has real bootstrap values\r
+     */\r
+    public boolean isHasBootstrap() {\r
+      return hasBootstrap;\r
+    }\r
+\r
+  public boolean isHasRootDistance()\r
+  {\r
+    return hasRootDistance;\r
+  }\r
+\r
 }\r
 \r
 \r