-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * AM Waterhouse\r
- *******************/\r
-\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+\r
+import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
+\r
+\r
+\r
\r
-public class GAlignFrame extends JInternalFrame\r
+public class GAlignFrame\r
+ extends JInternalFrame\r
{\r
protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
protected JMenu fileMenu = new JMenu();\r
protected JMenuItem closeMenuItem = new JMenuItem();\r
protected JMenu editMenu = new JMenu();\r
- protected JMenu fontMenu = new JMenu();\r
protected JMenu viewMenu = new JMenu();\r
protected JMenu colourMenu = new JMenu();\r
protected JMenu calculateMenu = new JMenu();\r
- protected JMenu alignMenu = new JMenu();\r
- protected JMenuItem groupsMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\r
+ protected JMenu webService = new JMenu();\r
+ protected JMenuItem webServiceNoServices;\r
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deleteSelectedMenuItem = new JMenuItem();\r
- protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
- protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
- protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
- protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
- protected JMenuItem fontNameMenuItem = new JMenuItem();\r
- protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
- protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
protected JMenuItem sortIDMenuItem = new JMenuItem();\r
protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
- protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
protected JMenuItem PCAMenuItem = new JMenuItem();\r
protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
BorderLayout borderLayout1 = new BorderLayout();\r
public JLabel statusBar = new JLabel();\r
- protected JMenu saveAlignmentMenu = new JMenu();\r
+ protected JMenuItem saveAs = new JMenuItem();\r
protected JMenu outputTextboxMenu = new JMenu();\r
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new\r
+ JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
JMenuItem htmlMenuItem = new JMenuItem();\r
- JMenuItem schemeKeyMenuItem = new JMenuItem();\r
JMenuItem overviewMenuItem = new JMenuItem();\r
protected JMenuItem undoMenuItem = new JMenuItem();\r
protected JMenuItem redoMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem noColourmenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem pdbTest = new JMenuItem();\r
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
JMenuItem printMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem findMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
+ JMenuItem deleteGroups = new JMenuItem();\r
+ JMenuItem delete = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenu pasteMenu = new JMenu();\r
+ JMenuItem pasteNew = new JMenuItem();\r
+ JMenuItem pasteThis = new JMenuItem();\r
+ public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
+ JMenuItem createPNG = new JMenuItem();\r
+ protected JMenuItem font = new JMenuItem();\r
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
+ JMenuItem epsFile = new JMenuItem();\r
+ JMenuItem LoadtreeMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
+ protected JMenuItem modifyPID = new JMenuItem();\r
+ protected JMenuItem modifyConservation = new JMenuItem();\r
+ protected JMenu sortByTreeMenu = new JMenu();\r
+ protected JMenu sort = new JMenu();\r
+ JMenu calculate = new JMenu();\r
+ JMenu jMenu2 = new JMenu();\r
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
+ protected ButtonGroup colours = new ButtonGroup();\r
+ JMenuItem vamsasStore = new JMenuItem();\r
+ protected JMenuItem showTranslation = new JMenuItem();\r
+ public JMenuItem featureSettings = new JMenuItem();\r
+ JMenuItem fetchSequence = new JMenuItem();\r
+ JMenuItem annotationColour = new JMenuItem();\r
+ JMenuItem associatedData = new JMenuItem();\r
+ protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
+ JMenu addSequenceMenu = new JMenu();\r
+ JMenuItem addFromFile = new JMenuItem();\r
+ JMenuItem addFromText = new JMenuItem();\r
+ JMenuItem addFromURL = new JMenuItem();\r
+ JMenuItem exportAnnotations = new JMenuItem();\r
+ JMenuItem exportFeatures = new JMenuItem();\r
+ protected JPanel statusPanel = new JPanel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
+ JMenu jMenu3 = new JMenu();\r
+ JMenuItem showAllSeqs = new JMenuItem();\r
+ JMenuItem showAllColumns = new JMenuItem();\r
+ JMenu hideMenu = new JMenu();\r
+ JMenuItem hideSelSequences = new JMenuItem();\r
+ JMenuItem hideSelColumns = new JMenuItem();\r
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
+ JMenuItem invertColSel = new JMenuItem();\r
+ protected JTabbedPane tabbedPane = new JTabbedPane();\r
+ JMenuItem save = new JMenuItem();\r
+ JMenuItem jMenuItem1 = new JMenuItem();\r
+ protected JMenuItem reload = new JMenuItem();\r
+ JMenuItem newView = new JMenuItem();\r
+ JMenuItem textColour = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+ JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();\r
+ JMenu jMenu4 = new JMenu();\r
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
public GAlignFrame()\r
{\r
try\r
jbInit();\r
setJMenuBar(alignFrameMenuBar);\r
\r
- JMenuItem item;\r
// dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
- saveAlignmentMenu.add( item );\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAs_actionPerformed(e);\r
- }\r
- });\r
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
\r
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
\r
- outputTextboxMenu.add( item );\r
+ outputTextboxMenu.add(item);\r
}\r
-\r
}\r
- catch(Exception e)\r
+ catch (Exception e)\r
+ {\r
+ }\r
+\r
+ if (!System.getProperty("os.name").startsWith("Mac"))\r
{\r
- e.printStackTrace();\r
+ closeMenuItem.setMnemonic('C');\r
+ outputTextboxMenu.setMnemonic('T');\r
+ undoMenuItem.setMnemonic('Z');\r
+ redoMenuItem.setMnemonic('0');\r
+ copy.setMnemonic('C');\r
+ cut.setMnemonic('U');\r
+ pasteMenu.setMnemonic('P');\r
+ reload.setMnemonic('R');\r
}\r
\r
- ButtonGroup colours = new ButtonGroup();\r
+\r
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+ "Remove from default list?",\r
+ "Remove user defined colour",\r
+ JOptionPane.YES_NO_OPTION);\r
+ if(option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\r
+ colours.add(noColourmenuItem);\r
colours.add(clustalColour);\r
colours.add(zappoColour);\r
colours.add(taylorColour);\r
colours.add(strandColour);\r
colours.add(turnColour);\r
colours.add(buriedColour);\r
- colours.add(abovePIDColour);\r
colours.add(userDefinedColour);\r
colours.add(PIDColour);\r
colours.add(BLOSUM62Colour);\r
+ colours.add(nucleotideColour);\r
+\r
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
+\r
+\r
}\r
- private void jbInit() throws Exception\r
+\r
+ public void setColourSelected(String defaultColour)\r
+ {\r
+\r
+ if (defaultColour != null)\r
+ {\r
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+\r
+ switch (index)\r
+ {\r
+ case ColourSchemeProperty.NONE:\r
+ noColourmenuItem.setSelected(true);\r
+ break;\r
+ case ColourSchemeProperty.CLUSTAL:\r
+ clustalColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BLOSUM:\r
+ BLOSUM62Colour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.PID:\r
+ PIDColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.ZAPPO:\r
+ zappoColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TAYLOR:\r
+ taylorColour.setSelected(true);\r
+ break;\r
+\r
+ case ColourSchemeProperty.HYDROPHOBIC:\r
+ hydrophobicityColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HELIX:\r
+ helixColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.STRAND:\r
+ strandColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TURN:\r
+ turnColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BURIED:\r
+ buriedColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.NUCLEOTIDE:\r
+ nucleotideColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.USER_DEFINED:\r
+ userDefinedColour.setSelected(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
- fileMenu.setMnemonic('F');\r
fileMenu.setText("File");\r
- saveAlignmentMenu.setMnemonic('L');\r
- saveAlignmentMenu.setText("Save alignment to local file");\r
- closeMenuItem.setMnemonic('C');\r
+ saveAs.setText("Save As...");\r
+ saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_S,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+ saveAs.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ saveAs_actionPerformed(e);\r
+ }\r
+ });\r
closeMenuItem.setText("Close");\r
+ closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- closeMenuItem_actionPerformed(e);\r
+ closeMenuItem_actionPerformed(false);\r
}\r
});\r
editMenu.setText("Edit");\r
- fontMenu.setText("Font");\r
viewMenu.setText("View");\r
colourMenu.setText("Colour");\r
calculateMenu.setText("Calculate");\r
- alignMenu.setText("Web Service");\r
- groupsMenuItem.setText("Groups");\r
- groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ webService.setText("Web Service");\r
+ selectAllSequenceMenuItem.setText("Select All");\r
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_A,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupsMenuItem_actionPerformed(e);\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- groupEditingMenuItem.setText("Group editing mode");\r
- groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ deselectAllSequenceMenuItem.setText("Deselect All");\r
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
+ getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupEditingMenuItem_actionPerformed(e);\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- selectAllSequenceMenuItem.setText("Select all sequences");\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ invertSequenceMenuItem.setText("Invert Sequence Selection");\r
+ invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_I,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
+ invertSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ remove2LeftMenuItem.setText("Remove Left");\r
+ remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+ awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
+ remove2LeftMenuItem_actionPerformed(e);\r
}\r
});\r
- invertSequenceMenuItem.setText("Invert sequence selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ remove2RightMenuItem.setText("Remove Right");\r
+ remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+ awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- invertSequenceMenuItem_actionPerformed(e);\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
+ getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
}\r
});\r
- deleteSelectedMenuItem.setText("Delete selected sequences");\r
- deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ removeAllGapsMenuItem.setText("Remove All Gaps");\r
+ removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_E,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- deleteSelectedMenuItem_actionPerformed(e);\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
}\r
});\r
- moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
- moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ viewBoxesMenuItem.setText("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- moveSelectedMenuItem_actionPerformed(e);\r
+ viewBoxesMenuItem_actionPerformed(e);\r
}\r
});\r
- copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
- copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ viewTextMenuItem.setText("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- copySelectedMenuItem_actionPerformed(e);\r
+ viewTextMenuItem_actionPerformed(e);\r
}\r
});\r
- deselectAllColumnsMenuItem.setText("Deselect all columns");\r
- deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ sortPairwiseMenuItem.setText("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- deselectAllColumnsMenuItem_actionPerformed(e);\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
}\r
});\r
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ sortIDMenuItem.setText("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- remove2LeftMenuItem_actionPerformed(e);\r
+ sortIDMenuItem_actionPerformed(e);\r
}\r
});\r
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ sortGroupMenuItem.setText("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- remove2RightMenuItem_actionPerformed(e);\r
+ sortGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- removeGappedColumnMenuItem.setText("Remove gapped columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+ removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
}\r
});\r
- removeAllGapsMenuItem.setText("Remove all gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- removeAllGapsMenuItem_actionPerformed(e);\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
}\r
});\r
- setGapCharMenuItem.setText("Set gap character to \"-\"");\r
- setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ PCAMenuItem.setText("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- setGapCharMenuItem_actionPerformed(e);\r
+ PCAMenuItem_actionPerformed(e);\r
}\r
});\r
- fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ averageDistanceTreeMenuItem.setText(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- fontNameMenuItem_actionPerformed(e);\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
}\r
});\r
- fontSizeMenuItem.setText("10");\r
- fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- fontSizeMenuItem_actionPerformed(e);\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
}\r
});\r
- fontStyleMenuItem.setText("Plain");\r
- fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ this.getContentPane().setLayout(borderLayout1);\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setText("Output to Textbox");\r
+ clustalColour.setText("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- fontStyleMenuItem_actionPerformed(e);\r
+ clustalColour_actionPerformed(e);\r
}\r
});\r
- viewBoxesMenuItem.setText("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ zappoColour.setText("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- viewBoxesMenuItem_actionPerformed(e);\r
+ zappoColour_actionPerformed(e);\r
}\r
});\r
- viewTextMenuItem.setText("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ taylorColour.setText("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- viewTextMenuItem_actionPerformed(e);\r
+ taylorColour_actionPerformed(e);\r
}\r
});\r
- sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sortPairwiseMenuItem_actionPerformed(e);\r
+ hydrophobicityColour_actionPerformed(e);\r
}\r
});\r
- sortIDMenuItem.setText("Sort by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ helixColour.setText("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sortIDMenuItem_actionPerformed(e);\r
+ helixColour_actionPerformed(e);\r
}\r
});\r
- sortGroupMenuItem.setText("Sort by group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ strandColour.setText("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sortGroupMenuItem_actionPerformed(e);\r
+ strandColour_actionPerformed(e);\r
}\r
});\r
- sortTreeOrderMenuItem.setText("Sort by tree order");\r
- sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ turnColour.setText("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sortTreeOrderMenuItem_actionPerformed(e);\r
+ turnColour_actionPerformed(e);\r
}\r
});\r
- removeRedundancyMenuItem.setText("Remove redundancy");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ buriedColour.setText("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- removeRedundancyMenuItem_actionPerformed(e);\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setText("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setText("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setText("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setText(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setText("Show Annotations");\r
+ annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ annotationPanelMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ colourTextMenuItem.setText("Colour Text");\r
+ colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ colourTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ htmlMenuItem.setText("HTML");\r
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ htmlMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ overviewMenuItem.setText("Overview Window");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_Z,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText("Redo");\r
+ redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setText("By Conservation");\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ noColourmenuItem.setText("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setText("Wrap");\r
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ wrapMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ printMenuItem.setText("Print");\r
+ printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ printMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setText("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ renderGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ findMenuItem.setText("Find...");\r
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_F,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ abovePIDThreshold.setText("Above Identity Threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ abovePIDThreshold_actionPerformed(e);\r
+ }\r
+ });\r
+ showSeqFeatures.setText("Show Sequence Features");\r
+ showSeqFeatures.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ showSeqFeatures_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ nucleotideColour.setText("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setText("Undefine groups");\r
+ deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_C,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+\r
+ copy.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setText("Cut");\r
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_X,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ cut.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setText("Delete");\r
+ delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_BACK_SPACE, 0, false));\r
+ delete.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteMenu.setText("Paste");\r
+ pasteNew.setText("To New Alignment");\r
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_V,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.ALT_MASK, false));\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setText("Add To This Alignment");\r
+ pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_V,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setText("Apply Colour To All Groups");\r
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ applyToAllGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createPNG(null);\r
+ }\r
+ });\r
+ createPNG.setActionCommand("Save As PNG Image");\r
+ createPNG.setText("PNG");\r
+ font.setText("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ seqLimits.setText("Show Sequence Limits");\r
+ seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
+ seqLimits.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ seqLimit_actionPerformed(e);\r
+ }\r
+ });\r
+ epsFile.setText("EPS");\r
+ epsFile.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createEPS(null);\r
}\r
});\r
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
+ LoadtreeMenuItem.setText("Load Associated Tree");\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ LoadtreeMenuItem_actionPerformed(e);\r
}\r
});\r
- PCAMenuItem.setText("Principal component analysis");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ scaleAbove.setVisible(false);\r
+ scaleAbove.setText("Scale Above");\r
+ scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- PCAMenuItem_actionPerformed(e);\r
+ scaleAbove_actionPerformed(e);\r
}\r
});\r
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ scaleLeft.setVisible(false);\r
+ scaleLeft.setSelected(true);\r
+ scaleLeft.setText("Scale Left");\r
+ scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
+ scaleLeft_actionPerformed(e);\r
}\r
});\r
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ scaleRight.setVisible(false);\r
+ scaleRight.setSelected(true);\r
+ scaleRight.setText("Scale Right");\r
+ scaleRight.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- neighbourTreeMenuItem_actionPerformed(e);\r
+ scaleRight_actionPerformed(e);\r
}\r
});\r
- clustalAlignMenuItem.setText("Clustal alignment");\r
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ modifyPID.setText("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- clustalAlignMenuItem_actionPerformed(e);\r
+ modifyPID_actionPerformed(e);\r
}\r
});\r
- this.getContentPane().setLayout(borderLayout1);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setMnemonic('T');\r
- outputTextboxMenu.setText("Output alignment via textbox");\r
- clustalColour.setEnabled(false);\r
- clustalColour.setSelected(false);\r
- clustalColour.setText("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
+ modifyConservation.setText("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- clustalColour_actionPerformed(e);\r
+ modifyConservation_actionPerformed(e);\r
}\r
});\r
- zappoColour.setSelected(true);\r
- zappoColour.setText("Zappo colour scheme");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
+ sortByTreeMenu.setText("By Tree Order");\r
+ sort.setText("Sort");\r
+ calculate.setText("Calculate Tree");\r
+\r
+ jMenu2.setText("Export Image");\r
+ padGapsMenuitem.setText("Pad Gaps");\r
+ padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
+ padGapsMenuitem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- zappoColour_actionPerformed(e);\r
+ padGapsMenuitem_actionPerformed(e);\r
}\r
});\r
- taylorColour.setText("Taylor colour scheme");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
+ vamsasStore.setVisible(false);\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- taylorColour_actionPerformed(e);\r
+ vamsasStore_actionPerformed(e);\r
}\r
});\r
- hydrophobicityColour.setText("By hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- hydrophobicityColour_actionPerformed(e);\r
+ showTranslation_actionPerformed(e);\r
}\r
});\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
+\r
+\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- helixColour_actionPerformed(e);\r
+ featureSettings_actionPerformed(e);\r
}\r
});\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
+ fetchSequence.setText("Fetch Sequence(s)...");\r
+ fetchSequence.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- strandColour_actionPerformed(e);\r
+ fetchSequence_actionPerformed(e);\r
}\r
});\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
+\r
+ annotationColour.setText("By Annotation...");\r
+ annotationColour.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- turnColour_actionPerformed(e);\r
+ annotationColour_actionPerformed(e);\r
}\r
});\r
- buriedColour.setText("Buried index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
+ associatedData.setText("Load Features / Annotations");\r
+ associatedData.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- buriedColour_actionPerformed(e);\r
+ associatedData_actionPerformed(e);\r
}\r
});\r
- abovePIDColour.setEnabled(false);\r
- abovePIDColour.setText("Above PID threshold only");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ autoCalculate.setText("Autocalculate Consensus");\r
+ autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+ autoCalculate.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- abovePIDColour_actionPerformed(e);\r
+ autoCalculate_actionPerformed(e);\r
}\r
});\r
- userDefinedColour.setText("User defined colours");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
+ addSequenceMenu.setText("Add Sequences");\r
+ addFromFile.setText("From File");\r
+ addFromFile.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- userDefinedColour_actionPerformed(e);\r
+ addFromFile_actionPerformed(e);\r
}\r
});\r
- PIDColour.setEnabled(false);\r
- PIDColour.setText("By PID");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ addFromText.setText("From Textbox");\r
+ addFromText.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- PIDColour_actionPerformed(e);\r
+ addFromText_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("By BLOSUM62 score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
+ addFromURL.setText("From URL");\r
+ addFromURL.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- BLOSUM62Colour_actionPerformed(e);\r
+ addFromURL_actionPerformed(e);\r
}\r
});\r
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ exportFeatures.setText("Export Features...");\r
+ exportFeatures.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
+ exportFeatures_actionPerformed(e);\r
}\r
});\r
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ exportAnnotations.setText("Export Annotations...");\r
+ exportAnnotations.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
+ exportAnnotations_actionPerformed(e);\r
}\r
});\r
- conservationColourIncMenuItem.setEnabled(false);\r
- conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
- conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ statusPanel.setLayout(gridLayout1);\r
+ jMenu3.setText("Show");\r
+ showAllSeqs.setText("All Sequences");\r
+ showAllSeqs.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- conservationColourIncMenuItem_actionPerformed(e);\r
+ showAllSeqs_actionPerformed(e);\r
}\r
});\r
- consensusGraphMenuItem.setActionCommand("");\r
- consensusGraphMenuItem.setText("Consensus graph");\r
- consensusGraphMenuItem.setState(true);\r
- consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ showAllColumns.setText("All Columns");\r
+ showAllColumns.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- consensusGraphMenuItem_actionPerformed(e);\r
+ showAllColumns_actionPerformed(e);\r
}\r
});\r
- colourTextMenuItem.setText("Colour text");\r
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ hideMenu.setText("Hide");\r
+ hideSelSequences.setText("Selected Sequences");\r
+ hideSelSequences.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- colourTextMenuItem_actionPerformed(e);\r
+ hideSelSequences_actionPerformed(e);\r
}\r
});\r
- htmlMenuItem.setText("Output as HTML");\r
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ hideSelColumns.setText("Selected Columns");\r
+ hideSelColumns.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- htmlMenuItem_actionPerformed(e);\r
+ hideSelColumns_actionPerformed(e);\r
}\r
});\r
- schemeKeyMenuItem.setText("Colour Scheme Key");\r
- schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ hiddenMarkers.setText("Show Hidden Markers");\r
+ hiddenMarkers.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- schemeKeyMenuItem_actionPerformed(e);\r
+ hiddenMarkers_actionPerformed(e);\r
}\r
});\r
- overviewMenuItem.setText("Overview window");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ invertColSel.setText("Invert Column Selection");\r
+ invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ invertColSel.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- overviewMenuItem_actionPerformed(e);\r
+ invertColSel_actionPerformed(e);\r
}\r
});\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setMnemonic('Z');\r
- undoMenuItem.setText("Undo");\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ JTabbedPane pane = (JTabbedPane)evt.getSource();\r
+ int sel = pane.getSelectedIndex();\r
+ tabSelectionChanged(sel);\r
+ }\r
+ });\r
+ tabbedPane.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent e)\r
{\r
- undoMenuItem_actionPerformed(e);\r
+ tabbedPane_mousePressed(e);\r
}\r
});\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setMnemonic('0');\r
- redoMenuItem.setText("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ tabbedPane.addFocusListener(new FocusAdapter()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void focusGained(FocusEvent e)\r
{\r
- redoMenuItem_actionPerformed(e);\r
+ tabbedPane_focusGained(e);\r
}\r
});\r
- conservationMenuItem.setText("By conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ save.setText("Save");\r
+ save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ save.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- conservationMenuItem_actionPerformed(e);\r
+ save_actionPerformed(e);\r
}\r
});\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ reload.setEnabled(false);\r
+ reload.setText("Reload");\r
+ reload.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- noColourmenuItem_actionPerformed(e);\r
+ reload_actionPerformed(e);\r
}\r
});\r
- wrapMenuItem.setEnabled(false);\r
- wrapMenuItem.setText("Wrap alignment");\r
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ newView.setText("New View");\r
+ newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ newView.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- wrapMenuItem_actionPerformed(e);\r
+ newView_actionPerformed(e);\r
}\r
});\r
- pdbTest.setText("PDB Test Viewer");\r
- pdbTest.addActionListener(new java.awt.event.ActionListener()\r
+ tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
+ +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- pdbTest_actionPerformed(e);\r
+ textColour_actionPerformed(e);\r
}\r
});\r
- printMenuItem.setText("Print");\r
- printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ jMenu1.setText("Format");\r
+ jCheckBoxMenuItem1.setText("Right Align Ids");\r
+ jMenu4.setText("Select");\r
+ idRightAlign.setText("Right Align Sequence Id");\r
+ idRightAlign.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- printMenuItem_actionPerformed(e);\r
+ idRightAlign_actionPerformed(e);\r
}\r
});\r
+\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(fontMenu);\r
+ alignFrameMenuBar.add(jMenu4);\r
alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(jMenu1);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(alignMenu);\r
- fileMenu.add(saveAlignmentMenu);\r
+ alignFrameMenuBar.add(webService);\r
+ fileMenu.add(fetchSequence);\r
+ fileMenu.add(addSequenceMenu);\r
+ fileMenu.add(reload);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(vamsasStore);\r
+ fileMenu.add(save);\r
+ fileMenu.add(saveAs);\r
fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(htmlMenuItem);\r
fileMenu.add(printMenuItem);\r
fileMenu.addSeparator();\r
+ fileMenu.add(jMenu2);\r
+ fileMenu.add(exportFeatures);\r
+ fileMenu.add(exportAnnotations);\r
+ fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.add(associatedData);\r
+ fileMenu.addSeparator();\r
fileMenu.add(closeMenuItem);\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\r
+ editMenu.add(delete);\r
editMenu.addSeparator();\r
- editMenu.add(groupsMenuItem);\r
- editMenu.add(groupEditingMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(copySelectedMenuItem);\r
- editMenu.add(moveSelectedMenuItem);\r
- editMenu.add(deleteSelectedMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(deselectAllColumnsMenuItem);\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\r
- editMenu.addSeparator();\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(setGapCharMenuItem);\r
- fontMenu.add(fontNameMenuItem);\r
- fontMenu.add(fontSizeMenuItem);\r
- fontMenu.add(fontStyleMenuItem);\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(consensusGraphMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ editMenu.addSeparator();\r
+ editMenu.add(padGapsMenuitem);\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(jMenu3);\r
+ viewMenu.add(hideMenu);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(showSeqFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.add(textColour);\r
+ colourMenu.addSeparator();\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
colourMenu.add(zappoColour);\r
colourMenu.add(taylorColour);\r
colourMenu.add(hydrophobicityColour);\r
colourMenu.add(strandColour);\r
colourMenu.add(turnColour);\r
colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
colourMenu.add(userDefinedColour);\r
colourMenu.addSeparator();\r
colourMenu.add(conservationMenuItem);\r
- colourMenu.add(conservationColourIncMenuItem);\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(schemeKeyMenuItem);\r
- calculateMenu.add(sortPairwiseMenuItem);\r
- calculateMenu.add(sortIDMenuItem);\r
- calculateMenu.add(sortGroupMenuItem);\r
- calculateMenu.add(sortTreeOrderMenuItem);\r
- calculateMenu.add(removeRedundancyMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ colourMenu.add(annotationColour);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
calculateMenu.addSeparator();\r
- calculateMenu.add(averageDistanceTreeMenuItem);\r
- calculateMenu.add(neighbourTreeMenuItem);\r
- calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
- calculateMenu.add(njTreeBlosumMenuItem);\r
- alignMenu.add(clustalAlignMenuItem);\r
- alignMenu.add(pdbTest);\r
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ calculateMenu.add(showTranslation);\r
+ calculateMenu.add(autoCalculate);\r
+ webServiceNoServices=new JMenuItem("<No Services>");\r
+ webService.add(webServiceNoServices);pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ jMenu2.add(htmlMenuItem);\r
+ jMenu2.add(epsFile);\r
+ jMenu2.add(createPNG);\r
+ addSequenceMenu.add(addFromFile);\r
+ addSequenceMenu.add(addFromText);\r
+ addSequenceMenu.add(addFromURL);\r
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
+ statusPanel.add(statusBar, null);\r
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
+ jMenu3.add(showAllColumns);\r
+ jMenu3.add(showAllSeqs);\r
+ hideMenu.add(hideSelColumns);\r
+ hideMenu.add(hideSelSequences);\r
+ jMenu1.add(font);\r
+ jMenu1.addSeparator();\r
+ jMenu1.add(wrapMenuItem);\r
+ jMenu1.add(scaleAbove);\r
+ jMenu1.add(scaleLeft);\r
+ jMenu1.add(scaleRight);\r
+ jMenu1.add(seqLimits);\r
+ jMenu1.add(idRightAlign);\r
+ jMenu1.add(hiddenMarkers);\r
+ jMenu1.add(viewBoxesMenuItem);\r
+ jMenu1.add(viewTextMenuItem);\r
+ jMenu1.add(colourTextMenuItem);\r
+ jMenu1.add(renderGapsMenuItem);\r
+ jMenu4.add(findMenuItem);\r
+ jMenu4.addSeparator();\r
+ jMenu4.add(selectAllSequenceMenuItem);\r
+ jMenu4.add(deselectAllSequenceMenuItem);\r
+ jMenu4.add(invertSequenceMenuItem);\r
+ jMenu4.add(invertColSel);\r
+ jMenu4.add(deleteGroups);\r
}\r
\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
- protected void outputText_actionPerformed(ActionEvent e)\r
+ public void addFromFile_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ public void addFromText_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
-\r
-\r
-\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
+ public void addFromURL_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ public void exportFeatures_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ public void exportAnnotations_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
-\r
- protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void closeMenuItem_actionPerformed(boolean b)\r
+ {\r
}\r
\r
- protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
- protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
+ protected void zappoColour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ protected void strandColour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ protected void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void findMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
{\r
+ }\r
\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ protected void cut_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ public void createPNG(java.io.File f)\r
+ {\r
}\r
\r
- protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
+ protected void font_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ public void seqDBRef_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void createEPS(java.io.File f)\r
{\r
+ }\r
\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
+ {\r
\r
+ }\r
\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
\r
+ }\r
\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
+ public void smoothFont_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
+ public void annotationColour_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ public void associatedData_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
+ public void showAllSeqs_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
+ public void showAllColumns_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
+ public void hideSelSequences_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ public void hideSelColumns_actionPerformed(ActionEvent e)\r
+ {\r
\r
- protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ }\r
\r
- }\r
+ public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+ {\r
\r
+ }\r
\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ public void findPdbId_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ public void enterPdbId_actionPerformed(ActionEvent e)\r
+ {\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+ }\r
+\r
+ public void pdbFile_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
+ public void invertColSel_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ public void tabSelectionChanged(int sel)\r
{\r
\r
}\r
\r
- protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
+ public void tabbedPane_mousePressed(MouseEvent e)\r
{\r
\r
}\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ public void tabbedPane_focusGained(FocusEvent e)\r
+ {\r
+ requestFocus();\r
+ }\r
+\r
+ public void save_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ public void reload_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void pdbTest_actionPerformed(ActionEvent e)\r
+ public void newView_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
+ public void textColour_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ public void idRightAlign_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff