X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=87cd9a967b27b41045cc3cc0be5e3440cdeb742c;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=a76106b5ffda293ace91e7263683cd9552c38b3f;hpb=8fc68b43785ce4b8a9d068fbec43e52b4e8cbf20;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a76106b..87cd9a9 100755
--- 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");
   }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+  }
+
 
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
@@ -707,8 +712,9 @@ public class AlignFrame
         String newtitle = new String("Copied sequences");
 
         //>>>This is a fix for the moment, until a better solution is found!!<<<
-        FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-        fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
 
         if (title.startsWith("Copied sequences"))
         {
@@ -801,7 +807,7 @@ public class AlignFrame
 
     //Jalview no longer allows deletion of residues.
     //Check here whether any residues are in selection area
-    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
       for (int i = 0; i < sg.sequences.size(); i++)
       {
@@ -822,7 +828,7 @@ public class AlignFrame
           j++;
         }while(j<=sg.getEndRes());
       }
-    }
+    }*/
 
 
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
@@ -1207,8 +1213,8 @@ public class AlignFrame
 
     viewport.padGaps = padGapsMenuitem.isSelected();
 
-    if (viewport.padGaps)
-      alignmentChanged();
+   // if (viewport.padGaps)
+    alignmentChanged();
   }
 
   /**
@@ -2355,6 +2361,7 @@ public class AlignFrame
       {
         // Add any Multiple Sequence Alignment Services
         final JMenu msawsmenu = new JMenu("Alignment");
+        final AlignFrame af = this;
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2366,7 +2373,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset());
+                  false, true, viewport.getAlignment().getDataset(), af);
 
             }
 
@@ -2383,7 +2390,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset());
+                    true, true, viewport.getAlignment().getDataset(), af);
 
               }