JAL-1807

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 3470dbc..16395c2 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -31,13 +31,14 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.io.NewickFile;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
 
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
 
 /**
- * DOCUMENT ME!
+ * NeighborJoining tree
  * 
  * @author $author$
  * @version $Revision$
@@ -116,7 +117,7 @@ public class NJTree
     }
     /*
      * sequenceString = new String[odata.length]; char gapChar =
-     * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
+     * Comparison.GapChars.charAt(0); for (int i = 0; i <
      * odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
      * sequenceString[i] = oseq_aligned.getSequence(); }
      */
@@ -179,8 +180,8 @@ public class NJTree
         if (one2many.contains(nam))
         {
           countOne2Many++;
-          // if (jalview.bin.Cache.log.isDebugEnabled())
-          // jalview.bin.Cache.log.debug("One 2 many relationship for
+          // if (Cache.log.isDebugEnabled())
+          // Cache.log.debug("One 2 many relationship for
           // "+nam.getName());
         }
         else
@@ -195,8 +196,8 @@ public class NJTree
         j.setPlaceholder(true);
       }
     }
-    // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
-    // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+    // if (Cache.log.isDebugEnabled() && countOne2Many>0) {
+    // Cache.log.debug("There were "+countOne2Many+" alignment
     // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
     // more leaves.");
     // }
@@ -284,7 +285,7 @@ public class NJTree
    */
   public String toString()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+    NewickFile fout = new NewickFile(getTopNode());
 
     return fout.print(isHasBootstrap(), isHasDistances(),
             isHasRootDistance()); // output all data available for tree
@@ -1068,8 +1069,7 @@ public class NJTree
     String[] seqdatas = seqData.getSequenceStrings(gapChar);
     for (int i = 0; i < seqdatas.length; i++)
     {
-      sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
-              .getName()));
+      sb.append(new Format("%-" + 15 + "s").form(sequence[i].getName()));
       sb.append(" " + seqdatas[i] + "\n");
     }
     return sb.toString();