import javax.swing.*;\r
\r
import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
\r
public class GAlignFrame\r
extends JInternalFrame\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
protected JMenu sort = new JMenu();\r
JMenu calculate = new JMenu();\r
JMenu jMenu2 = new JMenu();\r
- JMenuItem padGapsMenuitem = 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
-\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 addFromFile = new JMenuItem();\r
+ JMenuItem addFromText = new JMenuItem();\r
+ JMenuItem addFromURL = new JMenuItem();\r
+ JMenuItem exportAnnotations = new JMenuItem();\r
+ JMenuItem exportFeatures = new JMenuItem();\r
+ JMenuItem dbRefs = new JMenuItem();\r
+ protected JPanel statusPanel = new JPanel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
public GAlignFrame()\r
{\r
\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
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
\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
tabSelected();\r
}\r
});*/\r
- featureSettings.setEnabled(false);\r
featureSettings.setText("Feature Settings...");\r
featureSettings.addActionListener(new ActionListener()\r
{\r
featureSettings_actionPerformed(e);\r
}\r
});\r
- fetchSequence.setText("Fetch Sequence...");\r
+ fetchSequence.setText("Fetch Sequence(s)...");\r
fetchSequence.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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
+ 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
+ dbRefs.setText("Fetch DB Refs");\r
+ dbRefs.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ dbRefs_actionPerformed(e);\r
+ }\r
+ });\r
+ statusPanel.setLayout(gridLayout1);\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(webService);\r
+ fileMenu.add(addSequenceMenu);\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(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(padGapsMenuitem);\r
searchMenu.add(findMenuItem);\r
viewMenu.add(font);\r
+ viewMenu.add(smoothFont);\r
viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
viewMenu.add(seqLimits);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
viewMenu.addSeparator();\r
- viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(dbRefs);\r
+ viewMenu.add(fetchSeqFeatures);\r
+ viewMenu.add(showSeqFeatures);\r
viewMenu.add(featureSettings);\r
viewMenu.addSeparator();\r
viewMenu.add(overviewMenuItem);\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(PCAMenuItem);\r
calculateMenu.addSeparator();\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
+ 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
}\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
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
{\r
}\r
\r
\r
}\r
\r
- public void tabSelected()\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- public void featureSettings_actionPerformed(ActionEvent e)\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- public void fetchSequence_actionPerformed(ActionEvent e)\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
+ public void dbRefs_actionPerformed(ActionEvent e)\r
{\r
\r
}\r