/*\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 java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
+import javax.swing.event.*;\r
\r
import jalview.schemes.*;\r
import java.awt.BorderLayout;\r
\r
+\r
+\r
+\r
public class GAlignFrame\r
extends JInternalFrame\r
{\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 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 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
+ 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
public GAlignFrame()\r
{\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
+ 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
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
exportAnnotations_actionPerformed(e);\r
}\r
});\r
- dbRefs.setText("Fetch DB Refs");\r
- dbRefs.addActionListener(new ActionListener()\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
- dbRefs_actionPerformed(e);\r
+ showAllSeqs_actionPerformed(e);\r
}\r
});\r
- statusPanel.setLayout(gridLayout1);\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.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
+ 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
+\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\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(hideMenu);\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(dbRefs);\r
- viewMenu.add(fetchSeqFeatures);\r
viewMenu.add(showSeqFeatures);\r
viewMenu.add(featureSettings);\r
viewMenu.addSeparator();\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 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
+\r
+ public void tabSelectionChanged(int sel)\r
{\r
\r
}\r
\r
- public void dbRefs_actionPerformed(ActionEvent e)\r
+ public void tabbedPane_mousePressed(MouseEvent e)\r
{\r
\r
}\r