import javax.swing.*;\r
import javax.swing.event.*;\r
\r
-import jalview.gui.*;\r
import jalview.schemes.*;\r
\r
public class GAlignFrame\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
public JCheckBoxMenuItem fullSeqId = 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 ButtonGroup colours = new ButtonGroup();\r
+ JMenuItem vamsasStore = new JMenuItem();\r
+ protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+ protected JTabbedPane tabbedPane = new JTabbedPane();\r
+ protected JMenuItem featureSettings = new JMenuItem();\r
\r
public GAlignFrame()\r
{\r
- ButtonGroup colours = new ButtonGroup();\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
+ {\r
+ JMenuItem 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
+ }\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
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
{\r
public void actionPerformed(ActionEvent e)\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
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
}\r
});\r
fullSeqId.setText("Show Full Sequence ID");\r
- fullSeqId.setState(true);\r
+ fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));\r
fullSeqId.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.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.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
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showTranslation_actionPerformed(e);\r
}\r
});\r
- ClustalRealign.setText("Clustal Realign");\r
- ClustalRealign.addActionListener(new ActionListener()\r
+\r
+ tabbedPane.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent ece)\r
+ {\r
+\r
+ tabSelected();\r
+ }\r
+ });\r
+ featureSettings.setEnabled(false);\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- ClustalRealign_actionPerformed(e);\r
+ featureSettings_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(vamsasStore);\r
fileMenu.add(saveAlignmentMenu);\r
fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
viewMenu.addSeparator();\r
viewMenu.add(overviewMenuItem);\r
colourMenu.add(applyToAllGroups);\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
+ 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
protected void ClustalRealign_actionPerformed(ActionEvent e)\r
{\r
}\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void tabSelected()\r
+ {\r
+\r
+ }\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff