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 c38f901..3fd5fbc 100644 (file)
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
 import java.util.*;
@@ -321,6 +339,7 @@ class MsaWSThread
     OutputHeader = wsInfo.getProgressText();
     alTitle = title;
     dataset = seqset;
+
     SequenceI[][] conmsa = _msa.getVisibleContigs('-');
     if (conmsa != null)
     {
@@ -571,7 +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();
@@ -601,7 +620,9 @@ class MsaWSThread
 
     if (newFrame)
     {
-      AlignFrame af = new AlignFrame(al, columnselection);
+      AlignFrame af = new AlignFrame(al, columnselection,
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT);
 
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
@@ -623,7 +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( ( (
@@ -659,8 +680,8 @@ class MsaWSThread
       }
 
       Desktop.addInternalFrame(af, alTitle,
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
+                               AlignFrame.DEFAULT_WIDTH,
+                               AlignFrame.DEFAULT_HEIGHT);
 
     }
     else