/*\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) 2006 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 javax.swing.*;\r
import javax.swing.event.*;\r
\r
-import jalview.gui.*;\r
import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
+\r
+\r
+\r
\r
public class GAlignFrame\r
extends JInternalFrame\r
protected JMenu colourMenu = new JMenu();\r
protected JMenu calculateMenu = new JMenu();\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 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 findMenuItem = new JMenuItem();\r
JMenu searchMenu = new JMenu();\r
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem sequenceFeatures = 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
public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
JMenuItem createPNG = new JMenuItem();\r
protected JMenuItem font = new JMenuItem();\r
- public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
JMenuItem epsFile = new JMenuItem();\r
JMenuItem LoadtreeMenuItem = new JMenuItem();\r
- JMenuItem jnet = new JMenuItem();\r
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
- JMenuItem modifyPID = new JMenuItem();\r
- JMenuItem modifyConservation = new JMenuItem();\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
- JMenuItem msaAlignMenuItem = new JMenuItem();\r
JMenu jMenu2 = new JMenu();\r
- JMenuItem padGapsMenuitem = new JMenuItem();\r
- JMenuItem ClustalRealign = new JMenuItem();\r
-\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
+ protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\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
public GAlignFrame()\r
{\r
- ButtonGroup colours = new ButtonGroup();\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.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ }\r
+\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(BLOSUM62Colour);\r
colours.add(nucleotideColour);\r
\r
- noColourmenuItem.setSelected(true);\r
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
\r
- String defaultColour = Preferences.defaultColour;\r
+\r
+ }\r
+\r
+ public void setColourSelected(String defaultColour)\r
+ {\r
\r
if (defaultColour != null)\r
{\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
\r
break;\r
\r
+ case ColourSchemeProperty.TAYLOR:\r
+ taylorColour.setSelected(true);\r
+ break;\r
+\r
case ColourSchemeProperty.HYDROPHOBIC:\r
hydrophobicityColour.setSelected(true);\r
\r
}\r
}\r
\r
- try\r
- {\r
- jbInit();\r
- setJMenuBar(alignFrameMenuBar);\r
-\r
- JMenuItem item;\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
- {\r
- item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
- elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\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 As");\r
- saveAlignmentMenu.addActionListener(new ActionListener()\r
+ saveAs.setText("Save As ...");\r
+ saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_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, java.awt.event.KeyEvent.CTRL_MASK, false));\r
closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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
+ java.awt.event.KeyEvent.SHIFT_MASK, 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, java.awt.event.KeyEvent.CTRL_MASK, 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, java.awt.event.KeyEvent.CTRL_MASK, 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, java.awt.event.KeyEvent.CTRL_MASK, 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_G, java.awt.event.KeyEvent.CTRL_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_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
ActionListener()\r
{\r
neighbourTreeMenuItem_actionPerformed(e);\r
}\r
});\r
- clustalAlignMenuItem.setText("Clustal Alignment");\r
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalAlignMenuItem_actionPerformed(e);\r
- }\r
- });\r
this.getContentPane().setLayout(borderLayout1);\r
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
- {\r
- public void ancestorAdded(AncestorEvent event)\r
- {\r
- alignFrameMenuBar_ancestorAdded(event);\r
- }\r
-\r
- public void ancestorRemoved(AncestorEvent event)\r
- {\r
- }\r
-\r
- public void ancestorMoved(AncestorEvent event)\r
- {\r
- }\r
- });\r
statusBar.setBackground(Color.white);\r
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
});\r
annotationPanelMenuItem.setActionCommand("");\r
annotationPanelMenuItem.setText("Show Annotations");\r
- annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\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
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, java.awt.event.KeyEvent.CTRL_MASK, false));\r
redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
printMenuItem.setText("Print");\r
+ printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
abovePIDThreshold_actionPerformed(e);\r
}\r
});\r
- sequenceFeatures.setText("Sequence Features");\r
- sequenceFeatures.addActionListener(new ActionListener()\r
+ showSeqFeatures.setText("Show Sequence Features");\r
+ showSeqFeatures.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent actionEvent)\r
{\r
- sequenceFeatures_actionPerformed(actionEvent);\r
+ showSeqFeatures_actionPerformed(actionEvent);\r
}\r
});\r
nucleotideColour.setText("Nucleotide");\r
}\r
});\r
deleteGroups.setText("Undefine groups");\r
+ deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+ event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));\r
deleteGroups.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
font_actionPerformed(e);\r
}\r
});\r
- fullSeqId.setText("Show Full Sequence ID");\r
- fullSeqId.setState(true);\r
- fullSeqId.addActionListener(new java.awt.event.ActionListener()\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
- fullSeqId_actionPerformed(e);\r
+ seqLimit_actionPerformed(e);\r
}\r
});\r
epsFile.setText("EPS");\r
}\r
});\r
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
- LoadtreeMenuItem.setText("Load Assocated Tree");\r
+ LoadtreeMenuItem.setText("Load Associated Tree");\r
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
LoadtreeMenuItem_actionPerformed(e);\r
}\r
});\r
- jnet.setText("JNet");\r
- jnet.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- jpred_actionPerformed(e);\r
- }\r
- });\r
scaleAbove.setVisible(false);\r
scaleAbove.setText("Scale Above");\r
scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
sortByTreeMenu.setText("By Tree Order");\r
sort.setText("Sort");\r
calculate.setText("Calculate Tree");\r
- msaAlignMenuItem.setText("Muscle Alignment");\r
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\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
+ padGapsMenuitem_actionPerformed(e);\r
+ }\r
+ });\r
+ vamsasStore.setVisible(false);\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- msaAlignMenuItem_actionPerformed(e);\r
+ vamsasStore_actionPerformed(e);\r
}\r
});\r
- jMenu2.setText("Export");\r
- padGapsMenuitem.setText("Pad Gaps");\r
- padGapsMenuitem.addActionListener(new ActionListener()\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- padGapsMenuitem_actionPerformed(e);\r
+ showTranslation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ featureSettings_actionPerformed(e);\r
+ }\r
+ });\r
+ fetchSequence.setText("Fetch Sequence(s)...");\r
+ fetchSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\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
+\r
+ annotationColour.setText("By Annotation...");\r
+ annotationColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ annotationColour_actionPerformed(e);\r
+ }\r
+ });\r
+ associatedData.setText("Load Features / Annotations");\r
+ associatedData.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ associatedData_actionPerformed(e);\r
+ }\r
+ });\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
+ autoCalculate_actionPerformed(e);\r
+ }\r
+ });\r
+ addSequenceMenu.setText("Add Sequences");\r
+ addFromFile.setText("From File");\r
+ addFromFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addFromFile_actionPerformed(e);\r
+ }\r
+ });\r
+ addFromText.setText("From Textbox");\r
+ addFromText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addFromText_actionPerformed(e);\r
+ }\r
+ });\r
+ addFromURL.setText("From URL");\r
+ addFromURL.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addFromURL_actionPerformed(e);\r
+ }\r
+ });\r
+ exportFeatures.setText("Export Features...");\r
+ exportFeatures.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ exportFeatures_actionPerformed(e);\r
+ }\r
+ });\r
+ exportAnnotations.setText("Export Annotations...");\r
+ exportAnnotations.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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("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, java.awt.event.KeyEvent.CTRL_MASK, 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
- ClustalRealign.setText("Clustal Realign");\r
- ClustalRealign.addActionListener(new ActionListener()\r
+ save.setText("Save");\r
+ save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+ KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
+ save.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- ClustalRealign_actionPerformed(e);\r
+ save_actionPerformed(e);\r
}\r
});\r
+\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\r
alignFrameMenuBar.add(viewMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
- fileMenu.add(saveAlignmentMenu);\r
- fileMenu.add(jMenu2);\r
+ alignFrameMenuBar.add(webService);\r
+ fileMenu.add(addSequenceMenu);\r
+ fileMenu.add(fetchSequence);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(vamsasStore);\r
+ fileMenu.add(save);\r
+ fileMenu.add(saveAs);\r
fileMenu.add(outputTextboxMenu);\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(selectAllSequenceMenuItem);\r
editMenu.add(deselectAllSequenceMenuItem);\r
editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(invertColSel);\r
editMenu.add(deleteGroups);\r
editMenu.addSeparator();\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(padGapsMenuitem);\r
searchMenu.add(findMenuItem);\r
viewMenu.add(font);\r
+ viewMenu.add(smoothFont);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(jMenu3);\r
+ viewMenu.add(hideMenu);\r
+ viewMenu.add(hiddenMarkers);\r
viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
- viewMenu.add(fullSeqId);\r
+ viewMenu.add(seqLimits);\r
viewMenu.add(scaleAbove);\r
viewMenu.add(scaleLeft);\r
viewMenu.add(scaleRight);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.add(sequenceFeatures);\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(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(webService);\r
- webService.add(clustalAlignMenuItem);\r
- webService.add(msaAlignMenuItem);\r
- webService.add(jnet);\r
- webService.add(ClustalRealign);\r
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
- jMenu1.add(pasteNew);\r
+ calculateMenu.add(showTranslation);\r
+ calculateMenu.add(autoCalculate);\r
+ webServiceNoServices=new JMenuItem("<No Services>");\r
+ webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
jMenu1.add(pasteThis);\r
sort.add(sortIDMenuItem);\r
sort.add(sortGroupMenuItem);\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
}\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
+ public void addFromFile_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void addFromText_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void addFromURL_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void exportFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void exportAnnotations_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
}\r
{\r
}\r
\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
}\r
{\r
}\r
\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
{\r
}\r
\r
{\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
+ public void seqDBRef_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+\r
public void createEPS(java.io.File f)\r
{\r
}\r
{\r
}\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
+\r
+\r
+ protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
- protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void padGapsMenuitem_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
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void smoothFont_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+ public void annotationColour_actionPerformed(ActionEvent e)\r
{\r
+\r
+ }\r
+\r
+\r
+ public void associatedData_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\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
git://source.jalview.org / jalview.git / blobdiff