Alignment Annotation added

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 00961d6..8c7c9be 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,7 +32,6 @@ public class AlignFrame extends GAlignFrame
   final AlignViewport viewport;\r
   public AlignFrame(AlignmentI al)\r
   {\r
-    super();\r
     viewport = new AlignViewport(al,true,true,false);\r
 \r
     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
@@ -45,6 +44,15 @@ public class AlignFrame extends GAlignFrame
     alignPanel = new AlignmentPanel(this, viewport);\r
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
 \r
+    // add conservation graph to alignment\r
+    viewport.updateConservation();\r
+    viewport.updateConsensus();\r
+\r
+    alignPanel.annotationPanel.adjustPanelHeight();\r
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+\r
+\r
     addInternalFrameListener(new InternalFrameAdapter()\r
    {\r
      public void internalFrameActivated(InternalFrameEvent evt)\r
@@ -227,6 +235,8 @@ public class AlignFrame extends GAlignFrame
       seq = (SequenceI[]) history[1];\r
       viewport.setAlignment( new Alignment(seq) );\r
       updateEditMenuBar();\r
+      viewport.updateConsensus();\r
+      alignPanel.RefreshPanels();\r
       alignPanel.RefreshPanels();\r
   }\r
 \r
@@ -339,12 +349,14 @@ public class AlignFrame extends GAlignFrame
         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
         if (newHeight > 500)\r
           newHeight = 500;\r
-        Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
+        Desktop.addInternalFrame(af, "Copied sequences", 700, 500);\r
       }\r
       else\r
       {\r
         viewport.setEndSeq(viewport.alignment.getHeight());\r
         viewport.alignment.getWidth();\r
+        viewport.updateConservation();\r
+        viewport.updateConsensus();\r
         alignPanel.RefreshPanels();\r
       }\r
 \r
@@ -386,6 +398,8 @@ public class AlignFrame extends GAlignFrame
      {\r
        this.setClosed(true);\r
      }catch(Exception ex){}\r
+   viewport.updateConservation();\r
+   viewport.updateConsensus();\r
      alignPanel.RefreshPanels();\r
 \r
   }\r
@@ -398,6 +412,8 @@ public class AlignFrame extends GAlignFrame
      SequenceI[] seq = (SequenceI[]) history[1];\r
      viewport.setAlignment( new Alignment(seq) );\r
      updateEditMenuBar();\r
+     viewport.updateConsensus();\r
+     alignPanel.RefreshPanels();\r
      alignPanel.RefreshPanels();\r
   }\r
 \r
@@ -508,6 +524,8 @@ public class AlignFrame extends GAlignFrame
   {\r
     addHistoryItem("delete gapped columns");\r
     viewport.getAlignment().removeGaps();\r
+    viewport.updateConservation();\r
+    viewport.updateConsensus();\r
     alignPanel.RefreshPanels();\r
   }\r
 \r
@@ -528,7 +546,8 @@ public class AlignFrame extends GAlignFrame
           jSize--;\r
         }\r
     }\r
-\r
+    viewport.updateConservation();\r
+    viewport.updateConsensus();\r
     alignPanel.RefreshPanels();\r
   }\r
 \r
@@ -616,9 +635,9 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();\r
   }\r
 \r
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
   }\r
 \r
   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
@@ -1109,11 +1128,13 @@ if ( viewport.getConservationSelected() )
          g.drawString("Clustal Alignment Web Service running", 30,30);\r
        }\r
   }\r
-  public void jpredMenuItem_actionPerformed(ActionEvent e)\r
-    {\r
-    //  JInternalFrame frame = new JInternalFrame();\r
-//      JPredClient ct = new JPredClient((SequenceI)\r
-    ///                                   viewport.getAlignment().getSequences().elementAt(0));\r
+  protected void jpred_actionPerformed(ActionEvent e)\r
+{\r
+\r
+\r
+      JInternalFrame frame = new JInternalFrame();\r
+      JPredClient ct = new JPredClient((SequenceI)\r
+                                       viewport.getAlignment().getSequences().elementAt(0));\r
     }\r
 \r
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r