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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ccf7303..87cd9a9 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -195,6 +195,11 @@ public class AlignFrame
     return  jalview.bin.Cache.getProperty("VERSION");\r
   }\r
 \r
+  public FeatureRenderer getFeatureRenderer()\r
+  {\r
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+  }\r
+\r
 \r
   public void fetchSequence_actionPerformed(ActionEvent e)\r
   {\r
@@ -707,8 +712,9 @@ public class AlignFrame
         String newtitle = new String("Copied sequences");\r
 \r
         //>>>This is a fix for the moment, until a better solution is found!!<<<\r
-        FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
-        fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
 \r
         if (title.startsWith("Copied sequences"))\r
         {\r
@@ -801,7 +807,7 @@ public class AlignFrame
 \r
     //Jalview no longer allows deletion of residues.\r
     //Check here whether any residues are in selection area\r
-    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
+   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
     {\r
       for (int i = 0; i < sg.sequences.size(); i++)\r
       {\r
@@ -822,7 +828,7 @@ public class AlignFrame
           j++;\r
         }while(j<=sg.getEndRes());\r
       }\r
-    }\r
+    }*/\r
 \r
 \r
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
@@ -2355,6 +2361,7 @@ public class AlignFrame
       {\r
         // Add any Multiple Sequence Alignment Services\r
         final JMenu msawsmenu = new JMenu("Alignment");\r
+        final AlignFrame af = this;\r
         for (int i = 0, j = msaws.size(); i < j; i++)\r
         {\r
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
@@ -2366,7 +2373,7 @@ public class AlignFrame
             {\r
               SequenceI[] msa = gatherSequencesForAlignment();\r
               new jalview.ws.MsaWSClient(sh, title, msa,\r
-                  false, true, viewport.getAlignment().getDataset());\r
+                  false, true, viewport.getAlignment().getDataset(), af);\r
 \r
             }\r
 \r
@@ -2383,7 +2390,7 @@ public class AlignFrame
               {\r
                 SequenceI[] msa = gatherSequencesForAlignment();\r
                 new jalview.ws.MsaWSClient(sh, title, msa,\r
-                    true, true, viewport.getAlignment().getDataset());\r
+                    true, true, viewport.getAlignment().getDataset(), af);\r
 \r
               }\r
 \r