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 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
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
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
protected ButtonGroup colours = new ButtonGroup();\r
+ JMenuItem vamsasStore = new JMenuItem();\r
+ protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+ //protected JTabbedPane tabbedPane = new JTabbedPane();\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
public GAlignFrame()\r
{\r
\r
\r
while (userColours.hasMoreElements())\r
{\r
- JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\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
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
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
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");\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
- msaAlignMenuItem_actionPerformed(e);\r
+ padGapsMenuitem_actionPerformed(e);\r
}\r
});\r
- jMenu2.setText("Export");\r
- padGapsMenuitem.setText("Pad Gaps");\r
- padGapsMenuitem.addActionListener(new ActionListener()\r
+ vamsasStore.setVisible(false);\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- padGapsMenuitem_actionPerformed(e);\r
+ vamsasStore_actionPerformed(e);\r
}\r
});\r
- ClustalRealign.setText("Clustal Realign");\r
- ClustalRealign.addActionListener(new ActionListener()\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- ClustalRealign_actionPerformed(e);\r
+ showTranslation_actionPerformed(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
+ 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
+ smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\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
+ 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
+ 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
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(viewMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(webService);\r
+ fileMenu.add(fetchSequence);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(vamsasStore);\r
fileMenu.add(saveAlignmentMenu);\r
fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
fileMenu.add(printMenuItem);\r
fileMenu.addSeparator();\r
fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.add(associatedData);\r
fileMenu.addSeparator();\r
fileMenu.add(closeMenuItem);\r
editMenu.add(undoMenuItem);\r
editMenu.add(padGapsMenuitem);\r
searchMenu.add(findMenuItem);\r
viewMenu.add(font);\r
+ viewMenu.add(smoothFont);\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(fetchSeqFeatures);\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
+ calculateMenu.add(showTranslation);\r
+ calculateMenu.add(autoCalculate);\r
+ webServiceNoServices=new JMenuItem("<No Services>");\r
+ webService.add(webServiceNoServices);\r
this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ // this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
jMenu1.add(pasteNew);\r
jMenu1.add(pasteThis);\r
sort.add(sortIDMenuItem);\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 saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
+\r
+ }\r
+\r
+ public void smoothFont_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void annotationColour_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void fetchSeqFeatures_actionPerformed(ActionEvent e)\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
git://source.jalview.org / jalview.git / blobdiff