Draw an offscreen Image

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a76106b..a73958d 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -54,9 +54,6 @@ public class AlignFrame
   AlignmentPanel alignPanel;\r
   AlignViewport viewport;\r
 \r
-  Vector viewports = new Vector();\r
-  Vector alignPanels = new Vector();\r
-\r
   /** DOCUMENT ME!! */\r
   public String currentFileFormat = null;\r
   Stack historyList = new Stack();\r
@@ -72,7 +69,6 @@ public class AlignFrame
   public AlignFrame(AlignmentI al)\r
   {\r
     viewport = new AlignViewport(al);\r
-    viewports.add(viewport);\r
 \r
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
 \r
@@ -88,7 +84,6 @@ public class AlignFrame
     }\r
 \r
     alignPanel = new AlignmentPanel(this, viewport);\r
-    alignPanels.add(alignPanel);\r
 \r
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
 \r
@@ -195,6 +190,11 @@ 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 +707,9 @@ 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 +802,7 @@ 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 +823,7 @@ public class AlignFrame
           j++;\r
         }while(j<=sg.getEndRes());\r
       }\r
-    }\r
+    }*/\r
 \r
 \r
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
@@ -1207,8 +1208,8 @@ public class AlignFrame
 \r
     viewport.padGaps = padGapsMenuitem.isSelected();\r
 \r
-    if (viewport.padGaps)\r
-      alignmentChanged();\r
+   // if (viewport.padGaps)\r
+    alignmentChanged();\r
   }\r
 \r
   /**\r
@@ -1943,6 +1944,10 @@ public class AlignFrame
   public void autoCalculate_actionPerformed(ActionEvent e)\r
   {\r
     viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
+    if(viewport.autoCalculateConsensus)\r
+    {\r
+      alignmentChanged();\r
+    }\r
   }\r
 \r
 \r
@@ -2355,6 +2360,7 @@ 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 +2372,7 @@ 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 +2389,7 @@ 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
@@ -2507,42 +2513,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
   jalview.datamodel.AlignmentAnnotation[] annotations\r
       = viewport.alignment.getAlignmentAnnotation();\r
   int a, aSize;\r
-  for (int i = 0; i < annotations.length; i++)\r
+  if(annotations!=null)\r
   {\r
-\r
-    if (annotations[i].label.equals("Quality") ||\r
-        annotations[i].label.equals("Conservation") ||\r
-        annotations[i].label.equals("Consensus"))\r
+    for (int i = 0; i < annotations.length; i++)\r
     {\r
-      continue;\r
-    }\r
-\r
+      if (annotations[i].label.equals("Quality") ||\r
+          annotations[i].label.equals("Conservation") ||\r
+          annotations[i].label.equals("Consensus"))\r
+      {\r
+        continue;\r
+      }\r
 \r
-    aSize = viewport.alignment.getWidth()/3;\r
-    jalview.datamodel.Annotation [] anots =\r
-        new jalview.datamodel.Annotation[aSize];\r
+      aSize = viewport.alignment.getWidth() / 3;\r
+      jalview.datamodel.Annotation[] anots =\r
+          new jalview.datamodel.Annotation[aSize];\r
 \r
-    for(a=0; a<viewport.alignment.getWidth(); a++)\r
-    {\r
-     if( annotations[i].annotations[a]==null\r
-      || annotations[i].annotations[a]==null)\r
-       continue;\r
+      for (a = 0; a < viewport.alignment.getWidth(); a++)\r
+      {\r
+        if (annotations[i].annotations[a] == null\r
+            || annotations[i].annotations[a] == null)\r
+          continue;\r
 \r
-      anots[a/3] = new Annotation(\r
-     annotations[i].annotations[a].displayCharacter,\r
-     annotations[i].annotations[a].description,\r
-     annotations[i].annotations[a].secondaryStructure,\r
-     annotations[i].annotations[a].value,\r
-     annotations[i].annotations[a].colour);\r
-    }\r
+        anots[a / 3] = new Annotation(\r
+            annotations[i].annotations[a].displayCharacter,\r
+            annotations[i].annotations[a].description,\r
+            annotations[i].annotations[a].secondaryStructure,\r
+            annotations[i].annotations[a].value,\r
+            annotations[i].annotations[a].colour);\r
+      }\r
 \r
-    jalview.datamodel.AlignmentAnnotation aa\r
+      jalview.datamodel.AlignmentAnnotation aa\r
           = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
-       annotations[i].description, anots );\r
-     al.addAnnotation(aa);\r
+          annotations[i].description, anots);\r
+      al.addAnnotation(aa);\r
+    }\r
   }\r
 \r
-\r
     AlignFrame af = new AlignFrame(al);\r
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
                              NEW_WINDOW_WIDTH,\r