- }\r
-\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete columns");\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- int max = colSel.getMax();\r
- if(max>1)\r
- viewport.getAlignment().trimRight(max);\r
-\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- }\r
-\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete gapped columns");\r
- viewport.getAlignment().removeGaps();\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete all gaps");\r
- SequenceI current;\r
- int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
- jSize = current.getLength();\r
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
- }\r
- }\r
-\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- char thisChar = '-';\r
- char nextChar = '.';\r
- if(viewport.getGapCharacter()=='-')\r
- {\r
- thisChar = '.';\r
- nextChar = '-';\r
- }\r
- setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
- viewport.setGapCharacter(thisChar);\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane op = new JOptionPane();\r
- JInternalFrame frame = op.createInternalFrame(this, "Find");\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setClosable(true);\r
- frame.setContentPane(finder);\r
- frame.setSize(340,110);\r
- frame.setVisible(true);\r
- }\r
-\r
-\r
-\r
- public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
-\r
-\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font",\r
- "Font selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,fonts\r
- ,fontNameMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontNameMenuItem.setText(selection);\r
- SetFont();\r
- }\r
-\r
- }\r
-\r
- public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,fontSizeMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontSizeMenuItem.setText(selection);\r
- SetFont();\r
- }\r
- }\r
-\r
- public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font style",\r
- "Font style",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"plain", "bold", "italic"}\r
- ,fontStyleMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontStyleMenuItem.setText(selection);\r
- SetFont();\r
- }\r
-\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText( colourTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- void SetFont()\r
- {\r
- int style = java.awt.Font.PLAIN;\r
- if(fontStyleMenuItem.getText().equals("bold"))\r
- style = java.awt.Font.BOLD;\r
- else if(fontStyleMenuItem.getText().equals("italic"))\r
- style = java.awt.Font.ITALIC;\r
-\r
- viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
- style,\r
- Integer.parseInt(fontSizeMenuItem.getText())));\r
- alignPanel.RefreshPanels();\r
-\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText( viewTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
- if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
- {\r
- AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
- ((Alignment)viewport.alignment).featuresAdded = true;\r
- }\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- return;\r
-\r
- JInternalFrame frame = new JInternalFrame();\r
- OverviewPanel overview = alignPanel.getOverviewPanel();\r
- try{\r
- overview = new OverviewPanel(alignPanel, viewport);\r
- frame.setContentPane(overview);\r
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
- frame.getWidth(), frame.getHeight());\r
- frame.pack();\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- };\r
- });\r
- alignPanel.setOverviewPanel( overview );\r