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
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
seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.RefreshPanels();\r
alignPanel.RefreshPanels();\r
}\r
\r
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
{\r
this.setClosed(true);\r
}catch(Exception ex){}\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
\r
}\r
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
{\r
addHistoryItem("delete gapped columns");\r
viewport.getAlignment().removeGaps();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
jSize--;\r
}\r
}\r
-\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
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
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