From 21f3d4f639e1234ab4504d6f4df59f139588569c Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 28 Apr 2005 15:42:34 +0000 Subject: [PATCH] Label changes as AF recommended --- src/jalview/jbgui/GAlignFrame.java | 254 +++++++++++++++++------------------- 1 file changed, 119 insertions(+), 135 deletions(-) diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 3cb11e2..f94ef41 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,16 +21,14 @@ public class GAlignFrame extends JInternalFrame protected JMenu viewMenu = new JMenu(); protected JMenu colourMenu = new JMenu(); protected JMenu calculateMenu = new JMenu(); - protected JMenu alignMenu = new JMenu(); + protected JMenu webService = new JMenu(); protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem invertSequenceMenuItem = 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 JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); @@ -42,7 +40,6 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem(); protected JMenuItem neighbourTreeMenuItem = new JMenuItem(); protected JMenuItem clustalAlignMenuItem = new JMenuItem(); - protected JMenuItem msaAlignMenuItem = new JMenuItem(); BorderLayout borderLayout1 = new BorderLayout(); public JLabel statusBar = new JLabel(); protected JMenu saveAlignmentMenu = new JMenu(); @@ -96,6 +93,10 @@ public class GAlignFrame extends JInternalFrame JMenuItem modifyPID = new JMenuItem(); JMenuItem modifyConservation = new JMenuItem(); protected JMenu sortByTreeMenu = new JMenu(); + JMenu jMenu2 = new JMenu(); + JMenu sort = new JMenu(); + JMenu calculate = new JMenu(); + JMenuItem preferences = new JMenuItem(); public GAlignFrame() { @@ -156,7 +157,7 @@ public class GAlignFrame extends JInternalFrame fileMenu.setMnemonic('F'); fileMenu.setText("File"); saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save alignment to local file"); + saveAlignmentMenu.setText("Save"); closeMenuItem.setMnemonic('C'); closeMenuItem.setText("Close"); closeMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -170,8 +171,10 @@ public class GAlignFrame extends JInternalFrame viewMenu.setText("View"); colourMenu.setText("Colour"); calculateMenu.setText("Calculate"); - alignMenu.setText("Web Service"); + webService.setText("Web Service"); selectAllSequenceMenuItem.setText("Select all"); + selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false)); selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -179,7 +182,10 @@ public class GAlignFrame extends JInternalFrame selectAllSequenceMenuItem_actionPerformed(e); } }); - deselectAllSequenceMenuItem.setText("Clear selection"); + deselectAllSequenceMenuItem.setText("Deselect All"); + deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke. + getKeyStroke(java.awt.event. + KeyEvent.VK_ESCAPE, 0, false)); deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -187,7 +193,7 @@ public class GAlignFrame extends JInternalFrame deselectAllSequenceMenuItem_actionPerformed(e); } }); - invertSequenceMenuItem.setText("Invert sequence selection"); + invertSequenceMenuItem.setText("Invert Selection"); invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -195,15 +201,7 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem_actionPerformed(e); } }); - deselectAllColumnsMenuItem.setText("Deselect all columns"); - deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deselectAllColumnsMenuItem_actionPerformed(e); - } - }); - remove2LeftMenuItem.setText("Remove sequence <- left of selected column"); + remove2LeftMenuItem.setText("Remove Left"); remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -211,7 +209,7 @@ public class GAlignFrame extends JInternalFrame remove2LeftMenuItem_actionPerformed(e); } }); - remove2RightMenuItem.setText("Remove sequence -> right of selected column"); + remove2RightMenuItem.setText("Remove Right"); remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -219,7 +217,7 @@ public class GAlignFrame extends JInternalFrame remove2RightMenuItem_actionPerformed(e); } }); - removeGappedColumnMenuItem.setText("Remove gapped columns"); + removeGappedColumnMenuItem.setText("Remove Empty Columns"); removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -227,7 +225,7 @@ public class GAlignFrame extends JInternalFrame removeGappedColumnMenuItem_actionPerformed(e); } }); - removeAllGapsMenuItem.setText("Remove all gaps"); + removeAllGapsMenuItem.setText("Remove All Gaps"); removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -235,14 +233,6 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem_actionPerformed(e); } }); - setGapCharMenuItem.setText("Set gap character to \".\""); - setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - setGapCharMenuItem_actionPerformed(e); - } - }); viewBoxesMenuItem.setText("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -261,7 +251,7 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - sortPairwiseMenuItem.setText("Sort by pairwise identity"); + sortPairwiseMenuItem.setText("Pairwise Identity"); sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -269,7 +259,7 @@ public class GAlignFrame extends JInternalFrame sortPairwiseMenuItem_actionPerformed(e); } }); - sortIDMenuItem.setText("Sort by ID"); + sortIDMenuItem.setText("ID"); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -277,7 +267,7 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem_actionPerformed(e); } }); - sortGroupMenuItem.setText("Sort by group"); + sortGroupMenuItem.setText("Group"); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -285,7 +275,7 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); - removeRedundancyMenuItem.setText("Remove redundancy"); + removeRedundancyMenuItem.setText("Remove Redundancy..."); removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -293,7 +283,7 @@ public class GAlignFrame extends JInternalFrame removeRedundancyMenuItem_actionPerformed(e); } }); - pairwiseAlignmentMenuItem.setText("Pairwise alignments"); + pairwiseAlignmentMenuItem.setText("Pairwise Alignments..."); pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -301,7 +291,7 @@ public class GAlignFrame extends JInternalFrame pairwiseAlignmentMenuItem_actionPerformed(e); } }); - PCAMenuItem.setText("Principal component analysis"); + PCAMenuItem.setText("Principal Component Analysis..."); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -309,7 +299,7 @@ public class GAlignFrame extends JInternalFrame PCAMenuItem_actionPerformed(e); } }); - averageDistanceTreeMenuItem.setText("Average distance tree using PID"); + averageDistanceTreeMenuItem.setText("Average Distance Using % Identity..."); averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -317,7 +307,7 @@ public class GAlignFrame extends JInternalFrame averageDistanceTreeMenuItem_actionPerformed(e); } }); - neighbourTreeMenuItem.setText("Neighbour joining tree using PID"); + neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity..."); neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -325,7 +315,7 @@ public class GAlignFrame extends JInternalFrame neighbourTreeMenuItem_actionPerformed(e); } }); - clustalAlignMenuItem.setText("Clustal alignment"); + clustalAlignMenuItem.setText("Clustal Alignment..."); clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -333,14 +323,6 @@ public class GAlignFrame extends JInternalFrame clustalAlignMenuItem_actionPerformed(e); } }); - msaAlignMenuItem.setText("Muscle alignment"); - msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - msaAlignMenuItem_actionPerformed(e); - } - }); this.getContentPane().setLayout(borderLayout1); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); @@ -348,9 +330,9 @@ public class GAlignFrame extends JInternalFrame statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); statusBar.setText("Status bar"); outputTextboxMenu.setMnemonic('T'); - outputTextboxMenu.setText("Output alignment via textbox"); + outputTextboxMenu.setText("Output to Textbox"); clustalColour.setSelected(false); - clustalColour.setText("Clustalx colours"); + clustalColour.setText("Clustalx"); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -358,7 +340,7 @@ public class GAlignFrame extends JInternalFrame clustalColour_actionPerformed(e); } }); - zappoColour.setText("Zappo colour scheme"); + zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -366,7 +348,7 @@ public class GAlignFrame extends JInternalFrame zappoColour_actionPerformed(e); } }); - taylorColour.setText("Taylor colour scheme"); + taylorColour.setText("Taylor"); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -374,7 +356,7 @@ public class GAlignFrame extends JInternalFrame taylorColour_actionPerformed(e); } }); - hydrophobicityColour.setText("By hydrophobicity"); + hydrophobicityColour.setText("Hydrophobicity"); hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -382,7 +364,7 @@ public class GAlignFrame extends JInternalFrame hydrophobicityColour_actionPerformed(e); } }); - helixColour.setText("Helix propensity"); + helixColour.setText("Helix Propensity"); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -390,7 +372,7 @@ public class GAlignFrame extends JInternalFrame helixColour_actionPerformed(e); } }); - strandColour.setText("Strand propensity"); + strandColour.setText("Strand Propensity"); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -398,7 +380,7 @@ public class GAlignFrame extends JInternalFrame strandColour_actionPerformed(e); } }); - turnColour.setText("Turn propensity"); + turnColour.setText("Turn Propensity"); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -406,7 +388,7 @@ public class GAlignFrame extends JInternalFrame turnColour_actionPerformed(e); } }); - buriedColour.setText("Buried index"); + buriedColour.setText("Buried Index"); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -414,7 +396,7 @@ public class GAlignFrame extends JInternalFrame buriedColour_actionPerformed(e); } }); - userDefinedColour.setText("User defined colours"); + userDefinedColour.setText("User Defined..."); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -430,7 +412,7 @@ public class GAlignFrame extends JInternalFrame PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -438,7 +420,7 @@ public class GAlignFrame extends JInternalFrame BLOSUM62Colour_actionPerformed(e); } }); - avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62"); + avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62..."); avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -446,7 +428,7 @@ public class GAlignFrame extends JInternalFrame avTreeBlosumMenuItem_actionPerformed(e); } }); - njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62"); + njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62..."); njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -455,7 +437,7 @@ public class GAlignFrame extends JInternalFrame } }); annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setText("Annotation Panel"); + annotationPanelMenuItem.setText("Show Annotations"); annotationPanelMenuItem.setState(true); annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -464,7 +446,7 @@ public class GAlignFrame extends JInternalFrame annotationPanelMenuItem_actionPerformed(e); } }); - colourTextMenuItem.setText("Colour text"); + colourTextMenuItem.setText("Colour Text"); colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -472,7 +454,7 @@ public class GAlignFrame extends JInternalFrame colourTextMenuItem_actionPerformed(e); } }); - htmlMenuItem.setText("Output as HTML"); + htmlMenuItem.setText("HTML"); htmlMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -480,7 +462,7 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - overviewMenuItem.setText("Overview window"); + overviewMenuItem.setText("Overview Window..."); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -491,6 +473,8 @@ public class GAlignFrame extends JInternalFrame undoMenuItem.setEnabled(false); undoMenuItem.setMnemonic('Z'); undoMenuItem.setText("Undo"); + undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false)); undoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -508,7 +492,7 @@ public class GAlignFrame extends JInternalFrame redoMenuItem_actionPerformed(e); } }); - conservationMenuItem.setText("By conservation"); + conservationMenuItem.setText("By Conservation"); conservationMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -525,7 +509,7 @@ public class GAlignFrame extends JInternalFrame noColourmenuItem_actionPerformed(e); } }); - wrapMenuItem.setText("Wrap alignment"); + wrapMenuItem.setText("Wrap"); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -541,7 +525,7 @@ public class GAlignFrame extends JInternalFrame printMenuItem_actionPerformed(e); } }); - renderGapsMenuItem.setText("Render gaps"); + renderGapsMenuItem.setText("Show Gaps"); renderGapsMenuItem.setState(true); renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -550,7 +534,9 @@ public class GAlignFrame extends JInternalFrame renderGapsMenuItem_actionPerformed(e); } }); - findMenuItem.setText("Find"); + findMenuItem.setText("Find..."); + findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false)); findMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -560,7 +546,7 @@ public class GAlignFrame extends JInternalFrame }); searchMenu.setText("Search"); - abovePIDThreshold.setText("Above PID threshold"); + abovePIDThreshold.setText("Above Identity threshold"); abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { abovePIDThreshold_actionPerformed(e); @@ -574,7 +560,7 @@ public class GAlignFrame extends JInternalFrame sequenceFeatures_actionPerformed(actionEvent); } }); - nucleotideColour.setText("Nucleotide colours"); + nucleotideColour.setText("Nucleotide"); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -583,7 +569,7 @@ public class GAlignFrame extends JInternalFrame } }); deleteGroups.setSelected(false); - deleteGroups.setText("Delete all groups"); + deleteGroups.setText("Undefine groups"); deleteGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -592,6 +578,8 @@ public class GAlignFrame extends JInternalFrame } }); copy.setText("Copy"); + copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. + KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false)); copy.setMnemonic(KeyEvent.VK_C); copy.addActionListener(new java.awt.event.ActionListener() @@ -602,6 +590,8 @@ public class GAlignFrame extends JInternalFrame } }); cut.setText("Cut"); + cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. + KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false)); cut.setMnemonic(KeyEvent.VK_X); cut.addActionListener(new java.awt.event.ActionListener() { @@ -621,6 +611,8 @@ public class GAlignFrame extends JInternalFrame jMenu1.setMnemonic('V'); jMenu1.setText("Paste"); pasteNew.setText("to new alignment"); + pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. + KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -636,7 +628,7 @@ public class GAlignFrame extends JInternalFrame pasteThis_actionPerformed(e); } }); - applyToAllGroups.setText("Apply colour to all groups"); + applyToAllGroups.setText("Apply Colour To All Groups"); applyToAllGroups.setState(true); applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { @@ -653,8 +645,8 @@ public class GAlignFrame extends JInternalFrame } }); createPNG.setActionCommand("Save as PNG Image"); - createPNG.setText("Save as PNG Image"); - font.setText("Change Font"); + createPNG.setText("PNG"); + font.setText("Font..."); font.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -662,7 +654,7 @@ public class GAlignFrame extends JInternalFrame font_actionPerformed(e); } }); - fullSeqId.setText("Show full sequence id"); + fullSeqId.setText("Show Full Sequence ID"); fullSeqId.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -670,7 +662,7 @@ public class GAlignFrame extends JInternalFrame fullSeqId_actionPerformed(e); } }); - epsFile.setText("Save as EPS file"); + epsFile.setText("EPS"); epsFile.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -679,14 +671,14 @@ public class GAlignFrame extends JInternalFrame } }); LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); - LoadtreeMenuItem.setText("Load assocated tree"); + LoadtreeMenuItem.setText("Load Assocated Tree"); LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { LoadtreeMenuItem_actionPerformed(e); } }); - jpred.setText("JPred"); + jpred.setText("JPred..."); jpred.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -695,7 +687,7 @@ public class GAlignFrame extends JInternalFrame } }); scaleAbove.setVisible(false); - scaleAbove.setText("Scale above alignment"); + scaleAbove.setText("Scale Above"); scaleAbove.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -705,7 +697,7 @@ public class GAlignFrame extends JInternalFrame }); scaleLeft.setVisible(false); scaleLeft.setSelected(true); - scaleLeft.setText("Scale left of sequence"); + scaleLeft.setText("Scale Left"); scaleLeft.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -715,7 +707,7 @@ public class GAlignFrame extends JInternalFrame }); scaleRight.setVisible(false); scaleRight.setSelected(true); - scaleRight.setText("Scale right of sequence"); + scaleRight.setText("Scale Right"); scaleRight.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -723,7 +715,7 @@ public class GAlignFrame extends JInternalFrame scaleRight_actionPerformed(e); } }); - modifyPID.setText("Modify PID Threshold"); + modifyPID.setText("Modify Identity Threshold..."); modifyPID.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -731,7 +723,7 @@ public class GAlignFrame extends JInternalFrame modifyPID_actionPerformed(e); } }); - modifyConservation.setText("Modify Conservation Threshold"); + modifyConservation.setText("Modify Conservation Threshold..."); modifyConservation.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -739,44 +731,52 @@ public class GAlignFrame extends JInternalFrame modifyConservation_actionPerformed(e); } }); - sortByTreeMenu.setText("Sort by tree order"); + sortByTreeMenu.setText("Tree Order"); + jMenu2.setText("Save as"); + sort.setText("Sort"); + calculate.setText("Calculate Tree"); + preferences.setText("Preferences..."); + preferences.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + preferences_actionPerformed(e); + } + }); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(alignMenu); fileMenu.add(saveAlignmentMenu); + fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); - fileMenu.add(htmlMenuItem); - fileMenu.add(epsFile); - fileMenu.add(createPNG); fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(LoadtreeMenuItem); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); editMenu.add(copy); editMenu.add(jMenu1); - editMenu.add(cut); editMenu.add(delete); editMenu.addSeparator(); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.addSeparator(); - editMenu.add(deselectAllSequenceMenuItem); editMenu.add(selectAllSequenceMenuItem); + editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); editMenu.add(deleteGroups); editMenu.addSeparator(); - editMenu.add(deselectAllColumnsMenuItem); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); - editMenu.addSeparator(); editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); - editMenu.add(setGapCharMenuItem); + editMenu.add(removeRedundancyMenuItem); + editMenu.addSeparator(); + editMenu.add(preferences); + searchMenu.add(findMenuItem); viewMenu.add(font); viewMenu.add(fullSeqId); @@ -791,11 +791,15 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.add(overviewMenuItem); viewMenu.add(sequenceFeatures); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); colourMenu.add(noColourmenuItem); + colourMenu.addSeparator(); colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); colourMenu.add(zappoColour); colourMenu.add(taylorColour); colourMenu.add(hydrophobicityColour); @@ -805,32 +809,34 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(userDefinedColour); - colourMenu.add(PIDColour); - colourMenu.add(BLOSUM62Colour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); - calculateMenu.add(sortPairwiseMenuItem); - calculateMenu.add(sortIDMenuItem); - calculateMenu.add(sortGroupMenuItem); - calculateMenu.add(sortByTreeMenu); - calculateMenu.add(removeRedundancyMenuItem); + calculateMenu.add(sort); + calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); - calculateMenu.add(averageDistanceTreeMenuItem); - calculateMenu.add(neighbourTreeMenuItem); - calculateMenu.add(avDistanceTreeBlosumMenuItem); - calculateMenu.add(njTreeBlosumMenuItem); - alignMenu.add(clustalAlignMenuItem); - alignMenu.add(msaAlignMenuItem); - alignMenu.add(jpred); + calculateMenu.add(webService); + webService.add(clustalAlignMenuItem); + webService.add(jpred); this.getContentPane().add(statusBar, BorderLayout.SOUTH); jMenu1.add(pasteNew); jMenu1.add(pasteThis); + jMenu2.add(htmlMenuItem); + jMenu2.add(epsFile); + jMenu2.add(createPNG); + sort.add(sortIDMenuItem); + sort.add(sortGroupMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); } protected void saveAs_actionPerformed(ActionEvent e) @@ -849,9 +855,6 @@ public class GAlignFrame extends JInternalFrame } - - - protected void closeMenuItem_actionPerformed(ActionEvent e) { @@ -868,8 +871,6 @@ public class GAlignFrame extends JInternalFrame } - - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -885,12 +886,6 @@ public class GAlignFrame extends JInternalFrame } - - protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e) - { - - } - protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -911,14 +906,6 @@ public class GAlignFrame extends JInternalFrame } - protected void setGapCharMenuItem_actionPerformed(ActionEvent e) - { - - } - - - - protected void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -942,8 +929,6 @@ public class GAlignFrame extends JInternalFrame } - - protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { @@ -1013,10 +998,7 @@ public class GAlignFrame extends JInternalFrame } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) - { - } protected void clustalColour_actionPerformed(ActionEvent e) @@ -1209,7 +1191,9 @@ public class GAlignFrame extends JInternalFrame } + protected void preferences_actionPerformed(ActionEvent e) + { + } - -} +} \ No newline at end of file -- 1.7.10.2