- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340, 110);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
-\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- FontChooser fc = new FontChooser(alignPanel);\r
- }\r
-\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowFullId(fullSeqId.isSelected());\r
-\r
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText(colourTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
- scaleAbove.setVisible(wrapMenuItem.isSelected());\r
- scaleLeft.setVisible(wrapMenuItem.isSelected());\r
- scaleRight.setVisible(wrapMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText(viewTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
-\r
- if (viewport.showSequenceFeatures &&\r
- ! ( (Alignment) viewport.alignment).featuresAdded)\r
- {\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
- alignment,\r
- alignPanel);\r
- ( (Alignment) viewport.alignment).featuresAdded = true;\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (annotationPanelMenuItem.isSelected() &&\r
- viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setSelected(false);\r
-\r
- return;\r
- }\r
-\r
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- {\r
- return;\r
- }\r
-\r
- JInternalFrame frame = new JInternalFrame();\r
- OverviewPanel overview = new OverviewPanel(alignPanel);\r
- frame.setContentPane(overview);\r
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
- frame.getWidth(), frame.getHeight());\r
- frame.pack();\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- }\r
- ;\r
- });\r
-\r
- alignPanel.setOverviewPanel(overview);\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(null);\r
- }\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ClustalxColourScheme(\r
- viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
- }\r
-\r
- void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
- "Background");\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
- }\r