When saving, use print instead of println

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fc59062..bdcea36 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -97,11 +97,9 @@ public class AlignFrame
   /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
   private void addServiceListeners()\r
   {\r
-\r
-    final AlignFrame thisFrame = this;\r
     final java.beans.PropertyChangeListener thisListener;\r
     // Do this once to get current state\r
-    thisFrame.BuildWebServiceMenu();\r
+    BuildWebServiceMenu();\r
     Desktop.discoverer.addPropertyChangeListener(\r
         thisListener = new java.beans.PropertyChangeListener()\r
     {\r
@@ -111,7 +109,7 @@ public class AlignFrame
         if (evt.getPropertyName().equals("services"))\r
         {\r
           // System.out.println("Rebuilding web service menu");\r
-          thisFrame.BuildWebServiceMenu();\r
+          BuildWebServiceMenu();\r
         }\r
       }\r
     });\r
@@ -123,6 +121,7 @@ public class AlignFrame
       {\r
         // System.out.println("deregistering discoverer listener");\r
         Desktop.discoverer.removePropertyChangeListener(thisListener);\r
+        closeMenuItem_actionPerformed(null);\r
       }\r
       ;\r
     });\r
@@ -264,7 +263,8 @@ public class AlignFrame
       {\r
         java.io.PrintWriter out = new java.io.PrintWriter(\r
             new java.io.FileWriter(file));\r
-        out.println(output);\r
+\r
+        out.print(output);\r
         out.close();\r
         return true;\r
       }\r
@@ -348,6 +348,7 @@ public class AlignFrame
   {\r
     try\r
     {\r
+      PaintRefresher.components.remove(viewport.alignment);\r
       this.setClosed(true);\r
     }\r
     catch (Exception ex)\r
@@ -1448,7 +1449,9 @@ public class AlignFrame
           }\r
         }\r
 \r
-        if (viewport.getAbovePIDThreshold())\r
+        if (viewport.getAbovePIDThreshold()\r
+            || cs instanceof PIDColourScheme\r
+            || cs instanceof Blosum62ColourScheme)\r
         {\r
          sg.cs.setThreshold(threshold,\r
                 viewport.getIgnoreGapsConsensus());\r
@@ -2109,6 +2112,11 @@ public class AlignFrame
     }\r
   }\r
 \r
+\r
+  public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+  {\r
+    return ShowNewickTree(nf,title,600,500,4,5);\r
+  }\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -2117,7 +2125,7 @@ public class AlignFrame
    *\r
    * @return DOCUMENT ME!\r
    */\r
-  public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)\r
   {\r
     TreePanel tp = null;\r
 \r
@@ -2131,7 +2139,14 @@ public class AlignFrame
                            viewport.getAlignment().getSequences(), nf,\r
                            "FromFile",\r
                            title);\r
-        Desktop.addInternalFrame(tp, title, 600, 500);\r
+\r
+        tp.setSize(w,h);\r
+\r
+        if(x>0 && y>0)\r
+          tp.setLocation(x,y);\r
+\r
+\r
+        Desktop.addInternalFrame(tp, title, w, h);\r
         addTreeMenuItem(tp, title);\r
       }\r
     }\r