/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
+import javax.swing.event.*;\r
\r
import jalview.schemes.*;\r
\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 JMenuItem saveAlignmentMenu = new JMenuItem();\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
JMenuItem printMenuItem = new JMenuItem();\r
public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
JMenuItem findMenuItem = new JMenuItem();\r
- JMenu searchMenu = new JMenu();\r
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
JMenuItem delete = new JMenuItem();\r
JMenuItem copy = new JMenuItem();\r
JMenuItem cut = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
+ JMenu pasteMenu = new JMenu();\r
JMenuItem pasteNew = new JMenuItem();\r
JMenuItem pasteThis = new JMenuItem();\r
public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
protected ButtonGroup colours = new ButtonGroup();\r
JMenuItem vamsasStore = new JMenuItem();\r
- protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+ protected JMenuItem showTranslation = new JMenuItem();\r
public JMenuItem featureSettings = new JMenuItem();\r
JMenuItem fetchSequence = new JMenuItem();\r
- protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
JMenuItem annotationColour = new JMenuItem();\r
- JMenuItem fetchSeqFeatures = new JMenuItem();\r
-\r
-\r
-\r
JMenuItem associatedData = new JMenuItem();\r
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
JMenu addSequenceMenu = new JMenu();\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
+ protected JMenuItem reload = new JMenuItem();\r
+ JMenuItem newView = new JMenuItem();\r
+ JMenuItem textColour = new JMenuItem();\r
+ JMenu formatMenu = new JMenu();\r
+ JMenu selectMenu = new JMenu();\r
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
+ protected JMenuItem gatherViews = new JMenuItem();\r
+ protected JMenuItem expandViews = new JMenuItem();\r
+ JMenuItem pageSetup = new JMenuItem();\r
public GAlignFrame()\r
{\r
-\r
-\r
try\r
{\r
jbInit();\r
setJMenuBar(alignFrameMenuBar);\r
\r
// dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
{\r
- JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
- elementAt(\r
- i));\r
+ JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.\r
+ WRITEABLE_FORMATS[i]);\r
+\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
}\r
\r
+ if (!System.getProperty("os.name").startsWith("Mac"))\r
+ {\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
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\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
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(\r
+ 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
- public void mousePressed(MouseEvent evt)\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.\r
+ 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(\r
+ radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
{\r
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ radioItem.addActionListener(new ActionListener()\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
+ public void actionPerformed(ActionEvent evt)\r
{\r
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
- colourMenu.remove(radioItem);\r
+ userDefinedColour_actionPerformed(evt);\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
- });\r
+ }\r
+ }\r
+ });\r
radioItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent evt)\r
\r
setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
\r
-\r
}\r
\r
public void setColourSelected(String defaultColour)\r
switch (index)\r
{\r
case ColourSchemeProperty.NONE:\r
- noColourmenuItem.setSelected(true);\r
- break;\r
+ noColourmenuItem.setSelected(true);\r
+ break;\r
case ColourSchemeProperty.CLUSTAL:\r
clustalColour.setSelected(true);\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 As");\r
- saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
- awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
- saveAlignmentMenu.addActionListener(new ActionListener()\r
+ saveAs.setText("Save As...");\r
+ saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_S,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+ java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+ saveAs.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- saveAlignmentMenu_actionPerformed(e);\r
+ saveAs_actionPerformed(e);\r
}\r
});\r
- closeMenuItem.setMnemonic('C');\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
colourMenu.setText("Colour");\r
calculateMenu.setText("Calculate");\r
webService.setText("Web Service");\r
- selectAllSequenceMenuItem.setText("Select all");\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
deselectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- invertSequenceMenuItem.setText("Invert Selection");\r
+ invertSequenceMenuItem.setText("Invert Sequence Selection");\r
+ invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_I,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
remove2LeftMenuItem.setText("Remove Left");\r
+ remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+ awt.event.KeyEvent.VK_L,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
remove2RightMenuItem.setText("Remove Right");\r
+ remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+ awt.event.KeyEvent.VK_R,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent 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
}\r
});\r
removeAllGapsMenuItem.setText("Remove All Gaps");\r
+ removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_E,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+ java.awt.event.KeyEvent.SHIFT_MASK, false));\r
removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+ removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_D,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
ActionListener()\r
{\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 to Textbox");\r
clustalColour.setText("Clustalx");\r
\r
});\r
annotationPanelMenuItem.setActionCommand("");\r
annotationPanelMenuItem.setText("Show Annotations");\r
- annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
+ annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(\r
+ "SHOW_ANNOTATIONS", true));\r
annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
undoMenuItem.setEnabled(false);\r
- undoMenuItem.setMnemonic('Z');\r
undoMenuItem.setText("Undo");\r
undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
java.awt.event.KeyEvent.VK_Z,\r
}\r
});\r
redoMenuItem.setEnabled(false);\r
- redoMenuItem.setMnemonic('0');\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
wrapMenuItem_actionPerformed(e);\r
}\r
});\r
- printMenuItem.setText("Print");\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
findMenuItem_actionPerformed(e);\r
}\r
});\r
- searchMenu.setText("Search");\r
-\r
abovePIDThreshold.setText("Above Identity Threshold");\r
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
{\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
copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
java.awt.event.KeyEvent.VK_C,\r
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- copy.setMnemonic(KeyEvent.VK_C);\r
\r
copy.addActionListener(new java.awt.event.ActionListener()\r
{\r
cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
java.awt.event.KeyEvent.VK_X,\r
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- cut.setMnemonic(KeyEvent.VK_X);\r
cut.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent 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
delete_actionPerformed(e);\r
}\r
});\r
- jMenu1.setMnemonic('V');\r
- jMenu1.setText("Paste");\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(), false));\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+ java.awt.event.KeyEvent.SHIFT_MASK, false));\r
pasteNew.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent 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
});\r
applyToAllGroups.setText("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
});\r
\r
seqLimits.setText("Show Sequence Limits");\r
- seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\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
sortByTreeMenu.setText("By Tree Order");\r
sort.setText("Sort");\r
+ sort.addMenuListener(new MenuListener()\r
+ {\r
+ public void menuSelected(MenuEvent e)\r
+ {\r
+ buildTreeMenu();\r
+ }\r
+\r
+ public void menuDeselected(MenuEvent e)\r
+ {\r
+ }\r
+\r
+ public void menuCanceled(MenuEvent e)\r
+ {\r
+ }\r
+ });\r
calculate.setText("Calculate Tree");\r
\r
- jMenu2.setText("Export");\r
+ jMenu2.setText("Export Image");\r
padGapsMenuitem.setText("Pad Gaps");\r
- padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
+ padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
padGapsMenuitem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
\r
- /* tabbedPane.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent ece)\r
- {\r
-\r
- tabSelected();\r
- }\r
- });*/\r
featureSettings.setText("Feature Settings...");\r
featureSettings.addActionListener(new ActionListener()\r
{\r
fetchSequence_actionPerformed(e);\r
}\r
});\r
- smoothFont.setText("Smooth Fonts");\r
- smoothFont.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- smoothFont_actionPerformed(e);\r
- }\r
- });\r
- smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
+\r
annotationColour.setText("By Annotation...");\r
annotationColour.addActionListener(new ActionListener()\r
{\r
annotationColour_actionPerformed(e);\r
}\r
});\r
- fetchSeqFeatures.setText("Fetch Sequence Features");\r
- fetchSeqFeatures.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fetchSeqFeatures_actionPerformed(e);\r
- }\r
- });\r
associatedData.setText("Load Features / Annotations");\r
associatedData.addActionListener(new ActionListener()\r
{\r
}\r
});\r
autoCalculate.setText("Autocalculate Consensus");\r
- autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+ autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
autoCalculate.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
exportAnnotations_actionPerformed(e);\r
}\r
});\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
+ showAllSeqs_actionPerformed(e);\r
+ }\r
+ });\r
+ showAllColumns.setText("All Columns");\r
+ showAllColumns.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showAllColumns_actionPerformed(e);\r
+ }\r
+ });\r
+ hideMenu.setText("Hide");\r
+ hideSelSequences.setText("Selected Sequences");\r
+ hideSelSequences.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSelSequences_actionPerformed(e);\r
+ }\r
+ });\r
+ hideSelColumns.setText("Selected Columns");\r
+ hideSelColumns.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSelColumns_actionPerformed(e);\r
+ }\r
+ });\r
+ hiddenMarkers.setText("Show Hidden Markers");\r
+ hiddenMarkers.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hiddenMarkers_actionPerformed(e);\r
+ }\r
+ });\r
+ invertColSel.setText("Invert Column Selection");\r
+ invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_I,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
+ | java.awt.event.KeyEvent.ALT_MASK,\r
+ false));\r
+ invertColSel.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ invertColSel_actionPerformed(e);\r
+ }\r
+ });\r
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
+ {\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
+ tabbedPane_mousePressed(e);\r
+ }\r
+ });\r
+ tabbedPane.addFocusListener(new FocusAdapter()\r
+ {\r
+ public void focusGained(FocusEvent e)\r
+ {\r
+ tabbedPane_focusGained(e);\r
+ }\r
+ });\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
+ save_actionPerformed(e);\r
+ }\r
+ });\r
+ reload.setEnabled(false);\r
+ reload.setText("Reload");\r
+ reload.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ reload_actionPerformed(e);\r
+ }\r
+ });\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
+ newView_actionPerformed(e);\r
+ }\r
+ });\r
+ tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
+ +\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
+ textColour_actionPerformed(e);\r
+ }\r
+ });\r
+ formatMenu.setText("Format");\r
+ selectMenu.setText("Select");\r
+ idRightAlign.setText("Right Align Sequence Id");\r
+ idRightAlign.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ idRightAlign_actionPerformed(e);\r
+ }\r
+ });\r
+ gatherViews.setEnabled(false);\r
+ gatherViews.setText("Gather Views");\r
+ gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_G, 0, false));\r
+ gatherViews.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ gatherViews_actionPerformed(e);\r
+ }\r
+ });\r
+ expandViews.setEnabled(false);\r
+ expandViews.setText("Expand Views");\r
+ expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_X, 0, false));\r
+ expandViews.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ expandViews_actionPerformed(e);\r
+ }\r
+ });\r
+ pageSetup.setText("Page Setup ...");\r
+ pageSetup.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pageSetup_actionPerformed(e);\r
+ }\r
+ });\r
+\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(webService);\r
- fileMenu.add(addSequenceMenu);\r
fileMenu.add(fetchSequence);\r
+ fileMenu.add(addSequenceMenu);\r
+ fileMenu.add(reload);\r
fileMenu.addSeparator();\r
fileMenu.add(vamsasStore);\r
- fileMenu.add(saveAlignmentMenu);\r
- fileMenu.add(jMenu2);\r
+ fileMenu.add(save);\r
+ fileMenu.add(saveAs);\r
fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(pageSetup);\r
fileMenu.add(printMenuItem);\r
fileMenu.addSeparator();\r
+ fileMenu.add(jMenu2);\r
fileMenu.add(exportFeatures);\r
fileMenu.add(exportAnnotations);\r
fileMenu.add(LoadtreeMenuItem);\r
editMenu.add(redoMenuItem);\r
editMenu.add(cut);\r
editMenu.add(copy);\r
- editMenu.add(jMenu1);\r
+ editMenu.add(pasteMenu);\r
editMenu.add(delete);\r
editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeRedundancyMenuItem);\r
editMenu.addSeparator();\r
editMenu.add(padGapsMenuitem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.add(smoothFont);\r
+ viewMenu.add(newView);\r
+ viewMenu.add(expandViews);\r
+ viewMenu.add(gatherViews);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(jMenu3);\r
+ viewMenu.add(hideMenu);\r
viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(seqLimits);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
viewMenu.addSeparator();\r
- viewMenu.add(fetchSeqFeatures);\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
calculateMenu.addSeparator();\r
calculateMenu.add(showTranslation);\r
calculateMenu.add(autoCalculate);\r
- webServiceNoServices=new JMenuItem("<No Services>");\r
+ webServiceNoServices = new JMenuItem("<No Services>");\r
webService.add(webServiceNoServices);\r
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
- jMenu1.add(pasteNew);\r
- jMenu1.add(pasteThis);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
sort.add(sortIDMenuItem);\r
sort.add(sortGroupMenuItem);\r
sort.add(sortPairwiseMenuItem);\r
+ sort.add(sortByTreeMenu);\r
calculate.add(averageDistanceTreeMenuItem);\r
calculate.add(neighbourTreeMenuItem);\r
calculate.add(avDistanceTreeBlosumMenuItem);\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
+ formatMenu.add(font);\r
+ formatMenu.addSeparator();\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(idRightAlign);\r
+ formatMenu.add(hiddenMarkers);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(deleteGroups);\r
}\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
+ protected void closeMenuItem_actionPerformed(boolean b)\r
{\r
}\r
\r
\r
}\r
\r
-\r
public void createEPS(java.io.File f)\r
{\r
}\r
{\r
}\r
\r
-\r
-\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
{\r
}\r
\r
-\r
public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
\r
\r
}\r
\r
- public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+ public void associatedData_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- public void associatedData_actionPerformed(ActionEvent e)\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- public void autoCalculate_actionPerformed(ActionEvent e)\r
+ public void showAllSeqs_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void showAllColumns_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void hideSelSequences_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void hideSelColumns_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void findPdbId_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void enterPdbId_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void pdbFile_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void invertColSel_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void tabSelectionChanged(int sel)\r
+ {\r
+\r
+ }\r
+\r
+ public void tabbedPane_mousePressed(MouseEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void tabbedPane_focusGained(FocusEvent e)\r
+ {\r
+ requestFocus();\r
+ }\r
+\r
+ public void save_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void reload_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void newView_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void textColour_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void idRightAlign_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void expandViews_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void gatherViews_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void buildTreeMenu()\r
+ {\r
+\r
+ }\r
+\r
+ public void pageSetup_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff