import javax.swing.*;\r
\r
import jalview.schemes.*;\r
+import java.awt.BorderLayout;\r
\r
public class GAlignFrame\r
extends JInternalFrame\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
+ 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 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 jMenu4 = new JMenu();\r
+ JMenuItem hideSelSequences = new JMenuItem();\r
+ JMenuItem hideSelColumns = new JMenuItem();\r
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
+ JMenuItem invertColSel = new JMenuItem();\r
+\r
public GAlignFrame()\r
{\r
\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.WRITEABLE_FORMATS[i] );\r
+\r
item.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.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
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(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
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
+ jMenu4.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.setState(true);\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.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ invertColSel_actionPerformed(e);\r
+ }\r
+ });\r
+\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(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
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
viewMenu.add(font);\r
viewMenu.add(smoothFont);\r
viewMenu.addSeparator();\r
+ viewMenu.add(jMenu3);\r
+ viewMenu.add(jMenu4);\r
+ viewMenu.add(hiddenMarkers);\r
+ viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
viewMenu.add(seqLimits);\r
viewMenu.add(scaleAbove);\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
colourMenu.add(nucleotideColour);\r
colourMenu.add(userDefinedColour);\r
colourMenu.addSeparator();\r
- colourMenu.add(annotationColour);\r
colourMenu.add(conservationMenuItem);\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(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
+ jMenu3.add(showAllColumns);\r
+ jMenu3.add(showAllSeqs);\r
+ jMenu4.add(hideSelColumns);\r
+ jMenu4.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
- public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+\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
git://source.jalview.org / jalview.git / blobdiff