X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=44cb8b7b874ef9d64321c25a5dda0e27503151b3;hb=15648da3cecbfbe809b9279d426d88d98fbbec13;hp=fa90a6e5d2d853fc3770bc207005ab88d574180b;hpb=7c1e9288401f2e32b91d46e20131b3e23769236c;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index fa90a6e..44cb8b7 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -18,7 +18,6 @@ public class GAlignFrame extends JInternalFrame protected JMenu fileMenu = new JMenu(); 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(); @@ -33,9 +32,6 @@ public class GAlignFrame extends JInternalFrame 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(); @@ -68,22 +64,35 @@ public class GAlignFrame extends JInternalFrame 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 pdbTest = new JMenuItem(); JMenuItem printMenuItem = new JMenuItem(); protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); JMenuItem findMenuItem = new JMenuItem(); JMenu searchMenu = new JMenu(); protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem secondaryStructure = 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(); @@ -133,6 +142,7 @@ public class GAlignFrame extends JInternalFrame colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(nucleotideColour); } private void jbInit() throws Exception { @@ -150,11 +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.setVisible(false); groupsMenuItem.setText("Groups"); groupsMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -163,7 +173,7 @@ public class GAlignFrame extends JInternalFrame groupsMenuItem_actionPerformed(e); } }); - selectAllSequenceMenuItem.setText("Select all sequences"); + selectAllSequenceMenuItem.setText("Select all"); selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -171,7 +181,7 @@ public class GAlignFrame extends JInternalFrame selectAllSequenceMenuItem_actionPerformed(e); } }); - deselectAllSequenceMenuItem.setText("Clear sequence selection"); + deselectAllSequenceMenuItem.setText("Clear selection"); deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -235,29 +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() @@ -495,14 +482,6 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - schemeKeyMenuItem.setText("Colour Scheme Key"); - schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - schemeKeyMenuItem_actionPerformed(e); - } - }); overviewMenuItem.setText("Overview window"); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -548,7 +527,6 @@ public class GAlignFrame extends JInternalFrame noColourmenuItem_actionPerformed(e); } }); - wrapMenuItem.setEnabled(false); wrapMenuItem.setText("Wrap alignment"); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -557,14 +535,6 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem_actionPerformed(e); } }); - pdbTest.setText("PDB Test Viewer"); - pdbTest.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pdbTest_actionPerformed(e); - } - }); printMenuItem.setText("Print"); printMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -598,19 +568,121 @@ public class GAlignFrame extends JInternalFrame abovePIDThreshold_actionPerformed(e); } }); - secondaryStructure.setSelected(true); - secondaryStructure.setText("Secondary Structure"); - secondaryStructure.addActionListener(new ActionListener() + sequenceFeatures.setText("Sequence Features"); + sequenceFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { - secondaryStructure_actionPerformed(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(searchMenu); - alignFrameMenuBar.add(fontMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); @@ -618,17 +690,24 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(saveAlignmentMenu); fileMenu.add(outputTextboxMenu); fileMenu.add(htmlMenuItem); + fileMenu.add(epsFile); + fileMenu.add(createPNG); fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); + editMenu.add(copy); + editMenu.add(jMenu1); + editMenu.add(cut); + editMenu.add(delete); + editMenu.addSeparator(); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.addSeparator(); - editMenu.add(groupsMenuItem); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(selectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); + editMenu.add(deleteGroups); + editMenu.add(groupsMenuItem); editMenu.addSeparator(); editMenu.add(deselectAllColumnsMenuItem); editMenu.add(remove2LeftMenuItem); @@ -638,9 +717,8 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeAllGapsMenuItem); editMenu.add(setGapCharMenuItem); searchMenu.add(findMenuItem); - fontMenu.add(fontNameMenuItem); - fontMenu.add(fontSizeMenuItem); - fontMenu.add(fontStyleMenuItem); + viewMenu.add(font); + viewMenu.add(fullSeqId); viewMenu.add(wrapMenuItem); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); @@ -648,7 +726,8 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(renderGapsMenuItem); viewMenu.add(consensusGraphMenuItem); viewMenu.add(overviewMenuItem); - viewMenu.add(secondaryStructure); + viewMenu.add(sequenceFeatures); + colourMenu.add(applyToAllGroups); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(zappoColour); @@ -658,14 +737,13 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); colourMenu.add(userDefinedColour); colourMenu.add(PIDColour); colourMenu.add(BLOSUM62Colour); colourMenu.addSeparator(); colourMenu.add(abovePIDThreshold); colourMenu.add(conservationMenuItem); - colourMenu.addSeparator(); - colourMenu.add(schemeKeyMenuItem); calculateMenu.add(sortPairwiseMenuItem); calculateMenu.add(sortIDMenuItem); calculateMenu.add(sortGroupMenuItem); @@ -680,8 +758,9 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(avDistanceTreeBlosumMenuItem); calculateMenu.add(njTreeBlosumMenuItem); alignMenu.add(clustalAlignMenuItem); - alignMenu.add(pdbTest); this.getContentPane().add(statusBar, BorderLayout.SOUTH); + jMenu1.add(pasteNew); + jMenu1.add(pasteThis); } protected void saveAs_actionPerformed(ActionEvent e) @@ -772,20 +851,8 @@ 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) { @@ -945,10 +1012,6 @@ public class GAlignFrame extends JInternalFrame } - protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) - { - - } protected void noColourmenuItem_actionPerformed(ActionEvent e) { @@ -960,10 +1023,6 @@ public class GAlignFrame extends JInternalFrame } - protected void pdbTest_actionPerformed(ActionEvent e) - { - - } protected void printMenuItem_actionPerformed(ActionEvent e) { @@ -985,8 +1044,72 @@ public class GAlignFrame extends JInternalFrame } - public void secondaryStructure_actionPerformed(ActionEvent actionEvent) + 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) + { + + } + + + }