X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=44cb8b7b874ef9d64321c25a5dda0e27503151b3;hb=71154bd332b2c1487a0bd67e5afbeb0a25423a28;hp=20df46f031f0b7cec6dc9cc5ac87f78e186f5c53;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 20df46f..44cb8b7 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -11,38 +11,27 @@ package jalview.jbgui; import javax.swing.*; import java.awt.event.*; import java.awt.*; -import javax.swing.event.*; - public class GAlignFrame extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenu fileMenu = new JMenu(); - protected JMenuItem saveAsPostscriptMenuItem = new JMenuItem(); protected JMenuItem closeMenuItem = new JMenuItem(); protected JMenu editMenu = new JMenu(); - protected JMenu fontMenu = new JMenu(); protected JMenu viewMenu = new JMenu(); protected JMenu colourMenu = new JMenu(); protected JMenu calculateMenu = new JMenu(); protected JMenu alignMenu = new JMenu(); protected JMenuItem groupsMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem(); protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem invertSequenceMenuItem = new JMenuItem(); - protected JMenuItem deleteSelectedMenuItem = new JMenuItem(); - protected JMenuItem moveSelectedMenuItem = new JMenuItem(); - protected JMenuItem copySelectedMenuItem = new JMenuItem(); protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem(); protected JMenuItem remove2LeftMenuItem = new JMenuItem(); protected JMenuItem remove2RightMenuItem = new JMenuItem(); protected JMenuItem removeGappedColumnMenuItem = new JMenuItem(); protected JMenuItem removeAllGapsMenuItem = new JMenuItem(); protected JMenuItem setGapCharMenuItem = new JMenuItem(); - protected JMenuItem fontNameMenuItem = new JMenuItem(); - protected JMenuItem fontSizeMenuItem = new JMenuItem(); - protected JMenuItem fontStyleMenuItem = new JMenuItem(); protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); @@ -67,20 +56,43 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem conservationColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); - JMenuItem conservationColourIncMenuItem = new JMenuItem(); protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); - JMenuItem schemeKeyMenuItem = new JMenuItem(); + JMenuItem overviewMenuItem = new JMenuItem(); + protected JMenuItem undoMenuItem = new JMenuItem(); + protected JMenuItem redoMenuItem = new JMenuItem(); + protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + JMenuItem printMenuItem = new JMenuItem(); + protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + JMenuItem findMenuItem = new JMenuItem(); + JMenu searchMenu = new JMenu(); + protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + JMenuItem deleteGroups = new JMenuItem(); + JMenuItem delete = new JMenuItem(); + JMenuItem copy = new JMenuItem(); + JMenuItem cut = new JMenuItem(); + JMenu jMenu1 = new JMenu(); + JMenuItem pasteNew = new JMenuItem(); + JMenuItem pasteThis = new JMenuItem(); + protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + JMenuItem createPNG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); + protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem(); + JMenuItem epsFile = new JMenuItem(); public GAlignFrame() { + + try { jbInit(); @@ -118,6 +130,7 @@ public class GAlignFrame extends JInternalFrame } ButtonGroup colours = new ButtonGroup(); + colours.add(noColourmenuItem); colours.add(clustalColour); colours.add(zappoColour); colours.add(taylorColour); @@ -126,11 +139,10 @@ public class GAlignFrame extends JInternalFrame colours.add(strandColour); colours.add(turnColour); colours.add(buriedColour); - colours.add(conservationColour); - colours.add(abovePIDColour); colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(nucleotideColour); } private void jbInit() throws Exception { @@ -138,15 +150,6 @@ public class GAlignFrame extends JInternalFrame fileMenu.setText("File"); saveAlignmentMenu.setMnemonic('L'); saveAlignmentMenu.setText("Save alignment to local file"); - saveAsPostscriptMenuItem.setMnemonic('P'); - saveAsPostscriptMenuItem.setText("Save alignment as postscript"); - saveAsPostscriptMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - saveAsPostscriptMenuItem_actionPerformed(e); - } - }); closeMenuItem.setMnemonic('C'); closeMenuItem.setText("Close"); closeMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -157,12 +160,11 @@ public class GAlignFrame extends JInternalFrame } }); editMenu.setText("Edit"); - fontMenu.setText("Font"); viewMenu.setText("View"); colourMenu.setText("Colour"); calculateMenu.setText("Calculate"); alignMenu.setText("Web Service"); - groupsMenuItem.setEnabled(false); + groupsMenuItem.setVisible(false); groupsMenuItem.setText("Groups"); groupsMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -171,16 +173,7 @@ public class GAlignFrame extends JInternalFrame groupsMenuItem_actionPerformed(e); } }); - groupEditingMenuItem.setEnabled(false); - groupEditingMenuItem.setText("Group editing mode"); - groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupEditingMenuItem_actionPerformed(e); - } - }); - selectAllSequenceMenuItem.setText("Select all sequences"); + selectAllSequenceMenuItem.setText("Select all"); selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -188,7 +181,7 @@ public class GAlignFrame extends JInternalFrame selectAllSequenceMenuItem_actionPerformed(e); } }); - deselectAllSequenceMenuItem.setText("Deselect all sequences"); + deselectAllSequenceMenuItem.setText("Clear selection"); deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -204,30 +197,6 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem_actionPerformed(e); } }); - deleteSelectedMenuItem.setText("Delete selected sequences"); - deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSelectedMenuItem_actionPerformed(e); - } - }); - moveSelectedMenuItem.setText("Move selected sequences to new alignment"); - moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveSelectedMenuItem_actionPerformed(e); - } - }); - copySelectedMenuItem.setText("Copy selected sequences to new alignment"); - copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copySelectedMenuItem_actionPerformed(e); - } - }); deselectAllColumnsMenuItem.setText("Deselect all columns"); deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -268,7 +237,7 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem_actionPerformed(e); } }); - setGapCharMenuItem.setText("Set gap character to \"-\""); + setGapCharMenuItem.setText("Set gap character to \".\""); setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -276,29 +245,6 @@ public class GAlignFrame extends JInternalFrame setGapCharMenuItem_actionPerformed(e); } }); - fontNameMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontNameMenuItem_actionPerformed(e); - } - }); - fontSizeMenuItem.setText("10"); - fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontSizeMenuItem_actionPerformed(e); - } - }); - fontStyleMenuItem.setText("Plain"); - fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontStyleMenuItem_actionPerformed(e); - } - }); viewBoxesMenuItem.setText("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -414,7 +360,6 @@ public class GAlignFrame extends JInternalFrame clustalColour_actionPerformed(e); } }); - zappoColour.setSelected(true); zappoColour.setText("Zappo colour scheme"); zappoColour.addActionListener(new java.awt.event.ActionListener() { @@ -471,24 +416,6 @@ public class GAlignFrame extends JInternalFrame buriedColour_actionPerformed(e); } }); - conservationColour.setEnabled(false); - conservationColour.setText("By conservation"); - conservationColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationColour_actionPerformed(e); - } - }); - abovePIDColour.setEnabled(false); - abovePIDColour.setText("Above PID threshold only"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(e); - } - }); userDefinedColour.setText("User defined colours"); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { @@ -497,8 +424,7 @@ public class GAlignFrame extends JInternalFrame userDefinedColour_actionPerformed(e); } }); - PIDColour.setEnabled(false); - PIDColour.setText("By PID"); + PIDColour.setText("Percentage Identity"); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -506,7 +432,7 @@ public class GAlignFrame extends JInternalFrame PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("By BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62 score"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -530,15 +456,6 @@ public class GAlignFrame extends JInternalFrame njTreeBlosumMenuItem_actionPerformed(e); } }); - conservationColourIncMenuItem.setEnabled(false); - conservationColourIncMenuItem.setText("Conservation Colour Increment"); - conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationColourIncMenuItem_actionPerformed(e); - } - }); consensusGraphMenuItem.setActionCommand(""); consensusGraphMenuItem.setText("Consensus graph"); consensusGraphMenuItem.setState(true); @@ -565,37 +482,232 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - schemeKeyMenuItem.setText("Colour Scheme Key"); - schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener() + overviewMenuItem.setText("Overview window"); + overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - schemeKeyMenuItem_actionPerformed(e); + overviewMenuItem_actionPerformed(e); + } + }); + undoMenuItem.setEnabled(false); + undoMenuItem.setMnemonic('Z'); + undoMenuItem.setText("Undo"); + undoMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + undoMenuItem_actionPerformed(e); + } + }); + redoMenuItem.setEnabled(false); + redoMenuItem.setMnemonic('0'); + redoMenuItem.setText("Redo"); + redoMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + redoMenuItem_actionPerformed(e); + } + }); + conservationMenuItem.setText("By conservation"); + conservationMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(e); + } + }); + noColourmenuItem.setText("None"); + noColourmenuItem.setSelected(true); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + noColourmenuItem_actionPerformed(e); + } + }); + wrapMenuItem.setText("Wrap alignment"); + wrapMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + wrapMenuItem_actionPerformed(e); + } + }); + printMenuItem.setText("Print"); + printMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + printMenuItem_actionPerformed(e); + } + }); + renderGapsMenuItem.setText("Render gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + renderGapsMenuItem_actionPerformed(e); + } + }); + findMenuItem.setText("Find"); + findMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + findMenuItem_actionPerformed(e); + } + }); + searchMenu.setText("Search"); + + abovePIDThreshold.setText("Above PID threshold"); + abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + abovePIDThreshold_actionPerformed(e); + } + }); + sequenceFeatures.setText("Sequence Features"); + sequenceFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + sequenceFeatures_actionPerformed(actionEvent); + } + }); + nucleotideColour.setText("Nucleotide colours"); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideColour_actionPerformed(e); + } + }); + deleteGroups.setSelected(false); + deleteGroups.setText("Delete all groups"); + deleteGroups.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + deleteGroups_actionPerformed(e); + } + }); + copy.setText("Copy"); + copy.setMnemonic(KeyEvent.VK_C); + + copy.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(e); + } + }); + cut.setText("Cut"); + cut.setMnemonic(KeyEvent.VK_X); + cut.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(e); + } + }); + delete.setText("Delete"); + delete.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + delete_actionPerformed(e); + } + }); + jMenu1.setMnemonic('V'); + jMenu1.setText("Paste"); + pasteNew.setText("to new alignment"); + pasteNew.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pasteNew_actionPerformed(e); + } + }); + pasteThis.setText("add to this alignment"); + pasteThis.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pasteThis_actionPerformed(e); + } + }); + applyToAllGroups.setText("Apply colour to all groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + applyToAllGroups_actionPerformed(e); + } + }); + createPNG.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createPNG_actionPerformed(e); + } + }); + createPNG.setActionCommand("Save as PNG Image"); + createPNG.setText("Save as PNG Image"); + font.setText("Change Font"); + font.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + font_actionPerformed(e); + } + }); + fullSeqId.setText("Show full sequence id"); + fullSeqId.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fullSeqId_actionPerformed(e); + } + }); + epsFile.setText("Save as EPS file"); + epsFile.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + epsFile_actionPerformed(e); } }); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(fontMenu); + alignFrameMenuBar.add(searchMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(alignMenu); fileMenu.add(saveAlignmentMenu); - fileMenu.add(saveAsPostscriptMenuItem); fileMenu.add(outputTextboxMenu); fileMenu.add(htmlMenuItem); + fileMenu.add(epsFile); + fileMenu.add(createPNG); + fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); - editMenu.add(groupsMenuItem); - editMenu.add(groupEditingMenuItem); + editMenu.add(copy); + editMenu.add(jMenu1); + editMenu.add(cut); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(selectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); - editMenu.addSeparator(); - editMenu.add(deleteSelectedMenuItem); - editMenu.add(moveSelectedMenuItem); - editMenu.add(copySelectedMenuItem); + editMenu.add(deleteGroups); + editMenu.add(groupsMenuItem); editMenu.addSeparator(); editMenu.add(deselectAllColumnsMenuItem); editMenu.add(remove2LeftMenuItem); @@ -604,14 +716,19 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(setGapCharMenuItem); - fontMenu.add(fontNameMenuItem); - fontMenu.add(fontSizeMenuItem); - fontMenu.add(fontStyleMenuItem); - fontMenu.addSeparator(); - fontMenu.add(colourTextMenuItem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.add(fullSeqId); + viewMenu.add(wrapMenuItem); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); viewMenu.add(consensusGraphMenuItem); + viewMenu.add(overviewMenuItem); + viewMenu.add(sequenceFeatures); + colourMenu.add(applyToAllGroups); + colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(zappoColour); colourMenu.add(taylorColour); @@ -620,16 +737,13 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationColour); - colourMenu.add(conservationColourIncMenuItem); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); colourMenu.add(PIDColour); colourMenu.add(BLOSUM62Colour); colourMenu.addSeparator(); - colourMenu.add(schemeKeyMenuItem); + colourMenu.add(abovePIDThreshold); + colourMenu.add(conservationMenuItem); calculateMenu.add(sortPairwiseMenuItem); calculateMenu.add(sortIDMenuItem); calculateMenu.add(sortGroupMenuItem); @@ -645,6 +759,8 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(njTreeBlosumMenuItem); alignMenu.add(clustalAlignMenuItem); this.getContentPane().add(statusBar, BorderLayout.SOUTH); + jMenu1.add(pasteNew); + jMenu1.add(pasteThis); } protected void saveAs_actionPerformed(ActionEvent e) @@ -664,10 +780,6 @@ public class GAlignFrame extends JInternalFrame - protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e) - { - - } protected void closeMenuItem_actionPerformed(ActionEvent e) @@ -675,46 +787,39 @@ public class GAlignFrame extends JInternalFrame } - protected void groupsMenuItem_actionPerformed(ActionEvent e) + protected void redoMenuItem_actionPerformed(ActionEvent e) { } - protected void groupEditingMenuItem_actionPerformed(ActionEvent e) + protected void undoMenuItem_actionPerformed(ActionEvent e) { } - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + protected void groupsMenuItem_actionPerformed(ActionEvent e) { } - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e) + protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { } - protected void moveSelectedMenuItem_actionPerformed(ActionEvent e) + protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { } - protected void copySelectedMenuItem_actionPerformed(ActionEvent e) + protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) { } + protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e) { @@ -746,21 +851,15 @@ public class GAlignFrame extends JInternalFrame } - protected void fontNameMenuItem_actionPerformed(ActionEvent e) - { - } - protected void fontSizeMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void fontStyleMenuItem_actionPerformed(ActionEvent e) + protected void wrapMenuItem_actionPerformed(ActionEvent e) { } + protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -771,6 +870,7 @@ public class GAlignFrame extends JInternalFrame } + protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -783,10 +883,10 @@ public class GAlignFrame extends JInternalFrame } + protected void overviewMenuItem_actionPerformed(ActionEvent e) + { - - - + } protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -895,41 +995,121 @@ public class GAlignFrame extends JInternalFrame } - protected void conservationColour_actionPerformed(ActionEvent e) + + + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + + } + + protected void PIDColour_actionPerformed(ActionEvent e) { } - protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + { - } + } - protected void abovePIDColour_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { - protected void userDefinedColour_actionPerformed(ActionEvent e) + } + + + protected void printMenuItem_actionPerformed(ActionEvent e) { } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void findMenuItem_actionPerformed(ActionEvent e) { } - protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) + + protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + + } + + public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + { + + } + + protected void nucleotideColour_actionPerformed(ActionEvent e) + { + + } + + protected void deleteGroups_actionPerformed(ActionEvent e) + { + + } + + protected void copy_actionPerformed(ActionEvent e) + { + + } + + + protected void cut_actionPerformed(ActionEvent e) { } + protected void delete_actionPerformed(ActionEvent e) + { + + } + + protected void pasteNew_actionPerformed(ActionEvent e) + { + + } + + protected void pasteThis_actionPerformed(ActionEvent e) + { + + } + + protected void applyToAllGroups_actionPerformed(ActionEvent e) + { + + } + + protected void createPNG_actionPerformed(ActionEvent e) + { + + } + + protected void font_actionPerformed(ActionEvent e) + { + + } + + protected void fullSeqId_actionPerformed(ActionEvent e) + { + + } + + protected void epsFile_actionPerformed(ActionEvent e) + { + + } + + + }