New feature type, new colour set

[jalview.git] / src / jalview / ws / MsaWSThread.java

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index e87bcf3..3fd5fbc 100644 (file)
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -339,6 +339,7 @@ class MsaWSThread
     OutputHeader = wsInfo.getProgressText();
     alTitle = title;
     dataset = seqset;
+
     SequenceI[][] conmsa = _msa.getVisibleContigs('-');
     if (conmsa != null)
     {
@@ -589,7 +590,7 @@ class MsaWSThread
     Vector alorders = new Vector();
     SequenceI[][] results=new SequenceI[jobs.length][];
     AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
-    SequenceI[] first=null;
+
     for (int j=0; j<jobs.length; j++) {
       if (jobs[j].hasResults()) {
         Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
@@ -643,7 +644,7 @@ class MsaWSThread
           {
             String orderName = new String(" Region " + i);
             int j = i + 1;
-            int r = l;
+
             while (j < l)
             {
               if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
@@ -694,4 +695,4 @@ class MsaWSThread
   {
     return false;
   }
-}
\ No newline at end of file
+}