X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=a74c5e7b6a720c945886d5d2b57c275b9bd14b3f;hb=ee0fae8126d04df7909f4a2dc39d5d695b8c9853;hp=44108804e6181cfbaa00f1d856157c932a914dee;hpb=be81a18dc614d4d778017060945a10a85d5b5c24;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 4410880..a74c5e7 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -16,7 +16,6 @@ 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(); @@ -25,13 +24,9 @@ public class GAlignFrame extends JInternalFrame 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(); @@ -65,13 +60,11 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = 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(); - protected JMenuItem conservationColourIncMenuItem = new JMenuItem(); protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); @@ -80,10 +73,21 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem undoMenuItem = new JMenuItem(); protected JMenuItem redoMenuItem = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - JMenuItem noColourmenuItem = new JMenuItem(); + 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 JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + JMenuItem deleteGroups = new JMenuItem(); public GAlignFrame() { + + try { jbInit(); @@ -121,6 +125,7 @@ public class GAlignFrame extends JInternalFrame } ButtonGroup colours = new ButtonGroup(); + colours.add(noColourmenuItem); colours.add(clustalColour); colours.add(zappoColour); colours.add(taylorColour); @@ -129,10 +134,10 @@ public class GAlignFrame extends JInternalFrame colours.add(strandColour); colours.add(turnColour); colours.add(buriedColour); - colours.add(abovePIDColour); colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(nucleotideColour); } private void jbInit() throws Exception { @@ -140,15 +145,6 @@ 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() @@ -172,15 +168,7 @@ public class GAlignFrame extends JInternalFrame groupsMenuItem_actionPerformed(e); } }); - 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 +176,7 @@ 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) @@ -204,30 +192,6 @@ 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 +232,7 @@ 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) @@ -405,7 +369,6 @@ public class GAlignFrame extends JInternalFrame statusBar.setText("Status bar"); outputTextboxMenu.setMnemonic('T'); outputTextboxMenu.setText("Output alignment via textbox"); - clustalColour.setEnabled(false); clustalColour.setSelected(false); clustalColour.setText("Clustalx colours"); clustalColour.addActionListener(new java.awt.event.ActionListener() @@ -415,7 +378,6 @@ public class GAlignFrame extends JInternalFrame clustalColour_actionPerformed(e); } }); - zappoColour.setSelected(true); zappoColour.setText("Zappo colour scheme"); zappoColour.addActionListener(new java.awt.event.ActionListener() { @@ -472,15 +434,6 @@ public class GAlignFrame extends JInternalFrame buriedColour_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() { @@ -489,8 +442,7 @@ 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) @@ -498,7 +450,7 @@ 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) @@ -522,15 +474,6 @@ 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); @@ -602,6 +545,7 @@ public class GAlignFrame extends JInternalFrame } }); noColourmenuItem.setText("None"); + noColourmenuItem.setSelected(true); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -618,32 +562,95 @@ 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() + { + 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); + } + }); + secondaryStructure.setSelected(true); + secondaryStructure.setText("Secondary Structure"); + secondaryStructure.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + secondaryStructure_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); + } + }); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); alignFrameMenuBar.add(fontMenu); 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(printMenuItem); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.addSeparator(); - editMenu.add(groupsMenuItem); - editMenu.add(groupEditingMenuItem); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(selectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); - editMenu.addSeparator(); - editMenu.add(copySelectedMenuItem); - editMenu.add(moveSelectedMenuItem); - editMenu.add(deleteSelectedMenuItem); + editMenu.add(deleteGroups); + editMenu.add(groupsMenuItem); editMenu.addSeparator(); editMenu.add(deselectAllColumnsMenuItem); editMenu.add(remove2LeftMenuItem); @@ -652,16 +659,18 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(setGapCharMenuItem); + searchMenu.add(findMenuItem); fontMenu.add(fontNameMenuItem); fontMenu.add(fontSizeMenuItem); fontMenu.add(fontStyleMenuItem); - fontMenu.addSeparator(); - fontMenu.add(colourTextMenuItem); viewMenu.add(wrapMenuItem); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); viewMenu.add(consensusGraphMenuItem); viewMenu.add(overviewMenuItem); + viewMenu.add(secondaryStructure); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(zappoColour); @@ -671,15 +680,14 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(conservationColourIncMenuItem); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); 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); @@ -695,6 +703,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(avDistanceTreeBlosumMenuItem); calculateMenu.add(njTreeBlosumMenuItem); alignMenu.add(clustalAlignMenuItem); + alignMenu.add(pdbTest); this.getContentPane().add(statusBar, BorderLayout.SOUTH); } @@ -715,10 +724,6 @@ public class GAlignFrame extends JInternalFrame - protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e) - { - - } protected void closeMenuItem_actionPerformed(ActionEvent e) @@ -742,10 +747,6 @@ public class GAlignFrame extends JInternalFrame } - protected void groupEditingMenuItem_actionPerformed(ActionEvent e) - { - - } protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -762,20 +763,6 @@ public class GAlignFrame extends JInternalFrame } - protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void moveSelectedMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void copySelectedMenuItem_actionPerformed(ActionEvent e) - { - - } protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e) { @@ -965,46 +952,76 @@ public class GAlignFrame extends JInternalFrame } - protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { - } + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + + } + + protected void PIDColour_actionPerformed(ActionEvent e) + { + + } + + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + } - protected void abovePIDColour_actionPerformed(ActionEvent e) + protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) { } + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { - protected void userDefinedColour_actionPerformed(ActionEvent e) + } + + protected void conservationMenuItem_actionPerformed(ActionEvent e) { } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void pdbTest_actionPerformed(ActionEvent e) { } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void printMenuItem_actionPerformed(ActionEvent e) { } - protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { } - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void findMenuItem_actionPerformed(ActionEvent e) { } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + + protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + + } + + public void secondaryStructure_actionPerformed(ActionEvent actionEvent) { } + protected void nucleotideColour_actionPerformed(ActionEvent e) + { + + } + + protected void deleteGroups_actionPerformed(ActionEvent e) + { + + } + + }