X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=6a91cc4e24165d9dda3402d2feaeef300e2d0297;hb=b1cf67d148cd9cca4a12d245b6dad85a0a7376c7;hp=3cb11e25845c60ce3c953f5efdb91e459754cb36;hpb=aeb0422c06425ac0c76375106ffc635d03e88b88;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 3cb11e2..6a91cc4 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,124 +1,311 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.jbgui; -import javax.swing.*; -import java.awt.event.*; import java.awt.*; +import java.awt.event.*; + +import javax.swing.*; +import javax.swing.event.*; + +import jalview.schemes.*; public class GAlignFrame extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); + protected JMenu fileMenu = new JMenu(); + protected JMenuItem closeMenuItem = new JMenuItem(); + protected JMenu editMenu = new JMenu(); + 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 webServiceNoServices; + 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(); + + public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); + protected JMenuItem sortIDMenuItem = new JMenuItem(); + + protected JMenuItem sortLengthMenuItem = new JMenuItem(); + protected JMenuItem sortGroupMenuItem = new JMenuItem(); + + protected JMenu sortByAnnotScore = new JMenu(); + protected JMenuItem removeRedundancyMenuItem = new JMenuItem(); + protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(); + protected JMenuItem PCAMenuItem = new JMenuItem(); + 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(); + + protected JMenuItem saveAs = new JMenuItem(); + protected JMenu outputTextboxMenu = new JMenu(); + protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem buriedColour = 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 JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem(); + JMenuItem htmlMenuItem = new JMenuItem(); + JMenuItem overviewMenuItem = new JMenuItem(); + protected JMenuItem undoMenuItem = new JMenuItem(); + protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + JMenuItem printMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + JMenuItem findMenuItem = new JMenuItem(); - JMenu searchMenu = new JMenu(); - protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeaturesHeight = 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(); + + JMenu pasteMenu = new JMenu(); + JMenuItem pasteNew = new JMenuItem(); + JMenuItem pasteThis = new JMenuItem(); - protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + JMenuItem createPNG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); - protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); + JMenuItem epsFile = new JMenuItem(); + JMenuItem LoadtreeMenuItem = new JMenuItem(); - JMenuItem jpred = new JMenuItem(); - protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); - JMenuItem modifyPID = new JMenuItem(); - JMenuItem modifyConservation = new JMenuItem(); + + public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + + protected JMenuItem modifyPID = new JMenuItem(); + + protected JMenuItem modifyConservation = new JMenuItem(); + protected JMenu sortByTreeMenu = new JMenu(); - public GAlignFrame() - { + protected JMenu sort = new JMenu(); + + protected JMenu calculateTree = new JMenu(); + + JMenu jMenu2 = new JMenu(); + + protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); + + protected ButtonGroup colours = new ButtonGroup(); + + JMenuItem vamsasStore = new JMenuItem(); + + protected JMenuItem showTranslation = new JMenuItem(); + + protected JMenuItem extractScores = new JMenuItem(); + + protected JMenu showProducts = new JMenu(); + + public JMenuItem featureSettings = new JMenuItem(); + + JMenuItem fetchSequence = new JMenuItem(); + + JMenuItem annotationColour = new JMenuItem(); + + JMenuItem associatedData = new JMenuItem(); + + protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); + + JMenu addSequenceMenu = new JMenu(); + + JMenuItem addFromFile = new JMenuItem(); + JMenuItem addFromText = new JMenuItem(); + + JMenuItem addFromURL = new JMenuItem(); + + JMenuItem exportAnnotations = new JMenuItem(); + + JMenuItem exportFeatures = new JMenuItem(); + + protected JPanel statusPanel = new JPanel(); + + GridLayout gridLayout1 = new GridLayout(); + + JMenu jMenu3 = new JMenu(); + + JMenuItem showAllSeqs = new JMenuItem(); + + JMenuItem showAllColumns = new JMenuItem(); + + JMenu hideMenu = new JMenu(); + + JMenuItem hideSelSequences = new JMenuItem(); + + JMenuItem hideSelColumns = new JMenuItem(); + + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + + JMenuItem invertColSel = new JMenuItem(); + + protected JTabbedPane tabbedPane = new JTabbedPane(); + + JMenuItem save = new JMenuItem(); + + protected JMenuItem reload = new JMenuItem(); + + JMenuItem newView = new JMenuItem(); + + JMenuItem textColour = new JMenuItem(); + + JMenu formatMenu = new JMenu(); + + JMenu selectMenu = new JMenu(); + + protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); + + protected JMenuItem gatherViews = new JMenuItem(); + + protected JMenuItem expandViews = new JMenuItem(); + + JMenuItem pageSetup = new JMenuItem(); + + JMenuItem alignmentProperties = new JMenuItem(); + + JMenu tooltipSettingsMenu = new JMenu(); + + private JMenuItem justifyLeftMenuItem=new JMenuItem(); + + private JMenuItem justifyRightMenuItem=new JMenuItem(); + + JMenu autoAnnMenu = new JMenu(); + protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem(); + + private JMenuItem grpsFromSelection = new JMenuItem(); + public GAlignFrame() + { try { jbInit(); setJMenuBar(alignFrameMenuBar); - JMenuItem item; // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) { - item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i)); - saveAlignmentMenu.add( item ); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - saveAs_actionPerformed(e); - } - }); + for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) + { + JMenuItem item = new JMenuItem( + jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); - item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i)); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -127,16 +314,79 @@ public class GAlignFrame extends JInternalFrame } }); - outputTextboxMenu.add( item ); + outputTextboxMenu.add(item); } - + } catch (Exception e) + { } - catch(Exception e) + + if (!new jalview.util.Platform().isAMac()) { - e.printStackTrace(); + closeMenuItem.setMnemonic('C'); + outputTextboxMenu.setMnemonic('T'); + undoMenuItem.setMnemonic('Z'); + redoMenuItem.setMnemonic('0'); + copy.setMnemonic('C'); + cut.setMnemonic('U'); + pasteMenu.setMnemonic('P'); + reload.setMnemonic('R'); } - ButtonGroup colours = new ButtonGroup(); + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( + userColours.nextElement().toString()); + radioItem.setName("USER_DEFINED"); + radioItem.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + if (evt.isControlDown() + || SwingUtilities.isRightMouseButton(evt)) + { + radioItem + .removeActionListener(radioItem.getActionListeners()[0]); + + int option = JOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, + "Remove from default list?", + "Remove user defined colour", + JOptionPane.YES_NO_OPTION); + if (option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours + .removeColourFromDefaults(radioItem.getText()); + colourMenu.remove(radioItem); + } + else + { + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + } + } + } + }); + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.insert(radioItem, 15); + colours.add(radioItem); + } + } colours.add(noColourmenuItem); colours.add(clustalColour); colours.add(zappoColour); @@ -150,652 +400,1282 @@ public class GAlignFrame extends JInternalFrame colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); + + setColourSelected(jalview.bin.Cache + .getDefault("DEFAULT_COLOUR", "None")); + } + + public void setColourSelected(String defaultColour) + { + + if (defaultColour != null) + { + int index = ColourSchemeProperty + .getColourIndexFromName(defaultColour); + + switch (index) + { + case ColourSchemeProperty.NONE: + noColourmenuItem.setSelected(true); + break; + case ColourSchemeProperty.CLUSTAL: + clustalColour.setSelected(true); + + break; + + case ColourSchemeProperty.BLOSUM: + BLOSUM62Colour.setSelected(true); + + break; + + case ColourSchemeProperty.PID: + PIDColour.setSelected(true); + + break; + + case ColourSchemeProperty.ZAPPO: + zappoColour.setSelected(true); + + break; + + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; + + case ColourSchemeProperty.HYDROPHOBIC: + hydrophobicityColour.setSelected(true); + + break; + + case ColourSchemeProperty.HELIX: + helixColour.setSelected(true); + + break; + + case ColourSchemeProperty.STRAND: + strandColour.setSelected(true); + + break; + + case ColourSchemeProperty.TURN: + turnColour.setSelected(true); + + break; + + case ColourSchemeProperty.BURIED: + buriedColour.setSelected(true); + + break; + + case ColourSchemeProperty.NUCLEOTIDE: + nucleotideColour.setSelected(true); + + break; + + case ColourSchemeProperty.USER_DEFINED: + userDefinedColour.setSelected(true); + + break; + } + } + + } + private void jbInit() throws Exception { - fileMenu.setMnemonic('F'); fileMenu.setText("File"); - saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save alignment to local file"); - closeMenuItem.setMnemonic('C'); + saveAs.setText("Save As..."); + saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.SHIFT_MASK, false)); + saveAs.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveAs_actionPerformed(e); + } + }); closeMenuItem.setText("Close"); + closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - closeMenuItem_actionPerformed(e); + closeMenuItem_actionPerformed(false); + } + }); + editMenu.setText("Edit"); + viewMenu.setText("View"); + colourMenu.setText("Colour"); + calculateMenu.setText("Calculate"); + webService.setText("Web Service"); + selectAllSequenceMenuItem.setText("Select All"); + selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke + .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false)); + selectAllSequenceMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + selectAllSequenceMenuItem_actionPerformed(e); + } + }); + 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) + { + deselectAllSequenceMenuItem_actionPerformed(e); + } + }); + invertSequenceMenuItem.setText("Invert Sequence Selection"); + invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke + .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false)); + invertSequenceMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertSequenceMenuItem_actionPerformed(e); + } + }); + grpsFromSelection.setText("Make Groups for selection"); + grpsFromSelection.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + makeGrpsFromSelection_actionPerformed(e); + } + }); + + remove2LeftMenuItem.setText("Remove Left"); + remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + remove2LeftMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + remove2LeftMenuItem_actionPerformed(e); + } + }); + remove2RightMenuItem.setText("Remove Right"); + remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + remove2RightMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + remove2RightMenuItem_actionPerformed(e); + } + }); + removeGappedColumnMenuItem.setText("Remove Empty Columns"); + removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke + .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false)); + removeGappedColumnMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + removeGappedColumnMenuItem_actionPerformed(e); + } + }); + removeAllGapsMenuItem.setText("Remove All Gaps"); + removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke + .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.SHIFT_MASK, false)); + removeAllGapsMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + removeAllGapsMenuItem_actionPerformed(e); + } + }); + justifyLeftMenuItem.setText("Left Justify Alignment"); + justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + justifyLeftMenuItem_actionPerformed(e); + } + }); + justifyRightMenuItem.setText("Right Justify Alignment"); + justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + justifyRightMenuItem_actionPerformed(e); + } + }); + viewBoxesMenuItem.setText("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + viewBoxesMenuItem_actionPerformed(e); + } + }); + viewTextMenuItem.setText("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + viewTextMenuItem_actionPerformed(e); + } + }); + showUnconservedMenuItem.setText("Show Unconserved"); + showUnconservedMenuItem.setState(false); + showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showUnconservedMenuItem_actionPerformed(e); + } + }); + sortPairwiseMenuItem.setText("by Pairwise Identity"); + sortPairwiseMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortPairwiseMenuItem_actionPerformed(e); + } + }); + sortIDMenuItem.setText("by ID"); + sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortIDMenuItem_actionPerformed(e); + } + }); + sortLengthMenuItem.setText("By Length"); + sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortLengthMenuItem_actionPerformed(e); + } + }); + sortGroupMenuItem.setText("by Group"); + sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortGroupMenuItem_actionPerformed(e); + } + }); + removeRedundancyMenuItem.setText("Remove Redundancy..."); + removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke + .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false)); + removeRedundancyMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + removeRedundancyMenuItem_actionPerformed(e); + } + }); + pairwiseAlignmentMenuItem.setText("Pairwise Alignments..."); + pairwiseAlignmentMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pairwiseAlignmentMenuItem_actionPerformed(e); + } + }); + PCAMenuItem.setText("Principal Component Analysis"); + PCAMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + PCAMenuItem_actionPerformed(e); + } + }); + averageDistanceTreeMenuItem + .setText("Average Distance Using % Identity"); + averageDistanceTreeMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + averageDistanceTreeMenuItem_actionPerformed(e); + } + }); + neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + neighbourTreeMenuItem_actionPerformed(e); + } + }); + this.getContentPane().setLayout(borderLayout1); + alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); + statusBar.setText("Status bar"); + outputTextboxMenu.setText("Output to Textbox"); + clustalColour.setText("Clustalx"); + + clustalColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + clustalColour_actionPerformed(e); + } + }); + zappoColour.setText("Zappo"); + zappoColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + zappoColour_actionPerformed(e); } }); - editMenu.setText("Edit"); - viewMenu.setText("View"); - colourMenu.setText("Colour"); - calculateMenu.setText("Calculate"); - alignMenu.setText("Web Service"); - selectAllSequenceMenuItem.setText("Select all"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() + taylorColour.setText("Taylor"); + taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - selectAllSequenceMenuItem_actionPerformed(e); + taylorColour_actionPerformed(e); } }); - deselectAllSequenceMenuItem.setText("Clear selection"); - deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() + hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(e); + } + }); + helixColour.setText("Helix Propensity"); + helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - deselectAllSequenceMenuItem_actionPerformed(e); + helixColour_actionPerformed(e); } }); - invertSequenceMenuItem.setText("Invert sequence selection"); - invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() + strandColour.setText("Strand Propensity"); + strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - invertSequenceMenuItem_actionPerformed(e); + strandColour_actionPerformed(e); } }); - deselectAllColumnsMenuItem.setText("Deselect all columns"); - deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener() + turnColour.setText("Turn Propensity"); + turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - deselectAllColumnsMenuItem_actionPerformed(e); + turnColour_actionPerformed(e); } }); - remove2LeftMenuItem.setText("Remove sequence <- left of selected column"); - remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() + buriedColour.setText("Buried Index"); + buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - remove2LeftMenuItem_actionPerformed(e); + buriedColour_actionPerformed(e); } }); - remove2RightMenuItem.setText("Remove sequence -> right of selected column"); - remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() + userDefinedColour.setText("User Defined..."); + userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - remove2RightMenuItem_actionPerformed(e); + userDefinedColour_actionPerformed(e); } }); - removeGappedColumnMenuItem.setText("Remove gapped columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() + PIDColour.setText("Percentage Identity"); + PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - removeGappedColumnMenuItem_actionPerformed(e); + PIDColour_actionPerformed(e); } }); - removeAllGapsMenuItem.setText("Remove all gaps"); - removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() + BLOSUM62Colour.setText("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - removeAllGapsMenuItem_actionPerformed(e); + BLOSUM62Colour_actionPerformed(e); } }); - setGapCharMenuItem.setText("Set gap character to \".\""); - setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener() + avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + avTreeBlosumMenuItem_actionPerformed(e); + } + }); + njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62"); + njTreeBlosumMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + njTreeBlosumMenuItem_actionPerformed(e); + } + }); + annotationPanelMenuItem.setActionCommand(""); + annotationPanelMenuItem.setText("Show Annotations"); + annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault( + "SHOW_ANNOTATIONS", true)); + annotationPanelMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotationPanelMenuItem_actionPerformed(e); + } + }); + colourTextMenuItem.setText("Colour Text"); + colourTextMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + colourTextMenuItem_actionPerformed(e); + } + }); + htmlMenuItem.setText("HTML"); + htmlMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - setGapCharMenuItem_actionPerformed(e); + htmlMenuItem_actionPerformed(e); } }); - viewBoxesMenuItem.setText("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() + overviewMenuItem.setText("Overview Window"); + overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - viewBoxesMenuItem_actionPerformed(e); + overviewMenuItem_actionPerformed(e); } }); - viewTextMenuItem.setText("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() + undoMenuItem.setEnabled(false); + undoMenuItem.setText("Undo"); + undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + undoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - viewTextMenuItem_actionPerformed(e); + undoMenuItem_actionPerformed(e); } }); - sortPairwiseMenuItem.setText("Sort by pairwise identity"); - sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() + redoMenuItem.setEnabled(false); + redoMenuItem.setText("Redo"); + redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + redoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - sortPairwiseMenuItem_actionPerformed(e); + redoMenuItem_actionPerformed(e); } }); - sortIDMenuItem.setText("Sort by ID"); - sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() + conservationMenuItem.setText("By Conservation"); + conservationMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(e); + } + }); + noColourmenuItem.setText("None"); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - sortIDMenuItem_actionPerformed(e); + noColourmenuItem_actionPerformed(e); } }); - sortGroupMenuItem.setText("Sort by group"); - sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + wrapMenuItem.setText("Wrap"); + wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - sortGroupMenuItem_actionPerformed(e); + wrapMenuItem_actionPerformed(e); } }); - removeRedundancyMenuItem.setText("Remove redundancy"); - removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() + printMenuItem.setText("Print ..."); + printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + printMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - removeRedundancyMenuItem_actionPerformed(e); + printMenuItem_actionPerformed(e); } }); - pairwiseAlignmentMenuItem.setText("Pairwise alignments"); - pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() + renderGapsMenuItem.setText("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + renderGapsMenuItem_actionPerformed(e); + } + }); + findMenuItem.setText("Find..."); + findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + findMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - pairwiseAlignmentMenuItem_actionPerformed(e); + findMenuItem_actionPerformed(e); } }); - PCAMenuItem.setText("Principal component analysis"); - PCAMenuItem.addActionListener(new java.awt.event.ActionListener() + abovePIDThreshold.setText("Above Identity Threshold"); + abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - PCAMenuItem_actionPerformed(e); + abovePIDThreshold_actionPerformed(e); + } + }); + showSeqFeatures.setText("Show Sequence Features"); + showSeqFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + showSeqFeatures_actionPerformed(actionEvent); } }); - averageDistanceTreeMenuItem.setText("Average distance tree using PID"); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() +/* + * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); + showSeqFeaturesHeight.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + showSeqFeaturesHeight_actionPerformed(actionEvent); + } + }); */ + showDbRefsMenuitem.setText("Show Database Refs"); + showDbRefsMenuitem.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - averageDistanceTreeMenuItem_actionPerformed(e); + showDbRefs_actionPerformed(e); } + }); - neighbourTreeMenuItem.setText("Neighbour joining tree using PID"); - neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() + showNpFeatsMenuitem.setText("Show Non-Positional Features"); + showNpFeatsMenuitem.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - neighbourTreeMenuItem_actionPerformed(e); + showNpFeats_actionPerformed(e); } + }); - clustalAlignMenuItem.setText("Clustal alignment"); - clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() + showGroupConservation.setText("Group Conservation"); + showGroupConservation.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - clustalAlignMenuItem_actionPerformed(e); + showGroupConservation_actionPerformed(e); } + }); - msaAlignMenuItem.setText("Muscle alignment"); - msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() + + showGroupConsensus.setText("Group Consensus"); + showGroupConsensus.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - msaAlignMenuItem_actionPerformed(e); + showGroupConsensus_actionPerformed(e); } + }); - this.getContentPane().setLayout(borderLayout1); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); - statusBar.setText("Status bar"); - outputTextboxMenu.setMnemonic('T'); - outputTextboxMenu.setText("Output alignment via textbox"); - clustalColour.setSelected(false); - clustalColour.setText("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() + showConsensusHistogram.setText("Show Consensus Histogram"); + showConsensusHistogram.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(e); + showConsensusHistogram_actionPerformed(e); } + }); - zappoColour.setText("Zappo colour scheme"); - zappoColour.addActionListener(new java.awt.event.ActionListener() + showSequenceLogo.setText("Show Consensus Logo"); + showSequenceLogo.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(e); + showSequenceLogo_actionPerformed(e); } + }); - taylorColour.setText("Taylor colour scheme"); - taylorColour.addActionListener(new java.awt.event.ActionListener() + applyAutoAnnotationSettings.setText("Apply to all groups"); + applyAutoAnnotationSettings.setState(false); + applyAutoAnnotationSettings.setVisible(true); + applyAutoAnnotationSettings.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(e); + applyAutoAnnotationSettings_actionPerformed(e); } + }); - hydrophobicityColour.setText("By hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() + + nucleotideColour.setText("Nucleotide"); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - hydrophobicityColour_actionPerformed(e); + nucleotideColour_actionPerformed(e); } }); - helixColour.setText("Helix propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() + deleteGroups.setText("Undefine groups"); + deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + deleteGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(e); + deleteGroups_actionPerformed(e); } }); - strandColour.setText("Strand propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() + copy.setText("Copy"); + copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + + copy.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(e); + copy_actionPerformed(e); } }); - turnColour.setText("Turn propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() + cut.setText("Cut"); + cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + cut.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(e); + cut_actionPerformed(e); } }); - buriedColour.setText("Buried index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() + delete.setText("Delete"); + delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false)); + delete.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(e); + delete_actionPerformed(e); } }); - userDefinedColour.setText("User defined colours"); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + pasteMenu.setText("Paste"); + pasteNew.setText("To New Alignment"); + pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.SHIFT_MASK, false)); + pasteNew.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); + pasteNew_actionPerformed(e); } }); - PIDColour.setText("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() + pasteThis.setText("Add To This Alignment"); + pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + pasteThis.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(e); + pasteThis_actionPerformed(e); } }); - BLOSUM62Colour.setText("BLOSUM62 score"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + applyToAllGroups.setText("Apply Colour To All Groups"); + applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(e); + applyToAllGroups_actionPerformed(e); + } + }); + createPNG.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createPNG(null); } }); - avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() + createPNG.setActionCommand("Save As PNG Image"); + createPNG.setText("PNG"); + font.setText("Font..."); + font.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - avTreeBlosumMenuItem_actionPerformed(e); + font_actionPerformed(e); } }); - njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() + + seqLimits.setText("Show Sequence Limits"); + seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); + seqLimits.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - njTreeBlosumMenuItem_actionPerformed(e); + seqLimit_actionPerformed(e); } }); - annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setText("Annotation Panel"); - annotationPanelMenuItem.setState(true); - annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() + epsFile.setText("EPS"); + epsFile.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - annotationPanelMenuItem_actionPerformed(e); + createEPS(null); } }); - colourTextMenuItem.setText("Colour text"); - colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() + LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); + LoadtreeMenuItem.setText("Load Associated Tree"); + LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - colourTextMenuItem_actionPerformed(e); + LoadtreeMenuItem_actionPerformed(e); } }); - htmlMenuItem.setText("Output as HTML"); - htmlMenuItem.addActionListener(new java.awt.event.ActionListener() + scaleAbove.setVisible(false); + scaleAbove.setText("Scale Above"); + scaleAbove.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - htmlMenuItem_actionPerformed(e); + scaleAbove_actionPerformed(e); } }); - overviewMenuItem.setText("Overview window"); - overviewMenuItem.addActionListener(new java.awt.event.ActionListener() + scaleLeft.setVisible(false); + scaleLeft.setSelected(true); + scaleLeft.setText("Scale Left"); + scaleLeft.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - overviewMenuItem_actionPerformed(e); + scaleLeft_actionPerformed(e); } }); - undoMenuItem.setEnabled(false); - undoMenuItem.setMnemonic('Z'); - undoMenuItem.setText("Undo"); - undoMenuItem.addActionListener(new java.awt.event.ActionListener() + scaleRight.setVisible(false); + scaleRight.setSelected(true); + scaleRight.setText("Scale Right"); + scaleRight.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - undoMenuItem_actionPerformed(e); + scaleRight_actionPerformed(e); } }); - redoMenuItem.setEnabled(false); - redoMenuItem.setMnemonic('0'); - redoMenuItem.setText("Redo"); - redoMenuItem.addActionListener(new java.awt.event.ActionListener() + centreColumnLabelsMenuItem.setVisible(true); + centreColumnLabelsMenuItem.setState(false); + centreColumnLabelsMenuItem.setText("Centre Column Labels"); + centreColumnLabelsMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + centreColumnLabels_actionPerformed(e); + } + }); + followHighlightMenuItem.setVisible(true); + followHighlightMenuItem.setState(true); + followHighlightMenuItem.setText("Automatic Scrolling"); + followHighlightMenuItem.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { - redoMenuItem_actionPerformed(e); + followHighlight_actionPerformed(); } + }); - conservationMenuItem.setText("By conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() + + modifyPID.setText("Modify Identity Threshold..."); + modifyPID.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(e); + modifyPID_actionPerformed(e); } }); - noColourmenuItem.setText("None"); - noColourmenuItem.setSelected(true); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + modifyConservation.setText("Modify Conservation Threshold..."); + modifyConservation + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + modifyConservation_actionPerformed(e); + } + }); + sortByTreeMenu.setText("By Tree Order"); + sort.setText("Sort"); + sort.addMenuListener(new MenuListener() + { + public void menuSelected(MenuEvent e) + { + buildTreeMenu(); + } + + public void menuDeselected(MenuEvent e) + { + } + + public void menuCanceled(MenuEvent e) + { + } + }); + sortByAnnotScore.setText("by Score"); + sort.add(sortByAnnotScore); + sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() + { + + public void menuCanceled(MenuEvent e) + { + } + + public void menuDeselected(MenuEvent e) + { + } + + public void menuSelected(MenuEvent e) + { + buildSortByAnnotationScoresMenu(); + } + }); + sortByAnnotScore.setVisible(false); + + calculateTree.setText("Calculate Tree"); + + jMenu2.setText("Export Image"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.setState(jalview.bin.Cache + .getDefault("PAD_GAPS", false)); + padGapsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); + padGapsMenuitem_actionPerformed(e); } }); - wrapMenuItem.setText("Wrap alignment"); - wrapMenuItem.addActionListener(new java.awt.event.ActionListener() + vamsasStore.setVisible(false); + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - wrapMenuItem_actionPerformed(e); + vamsasStore_actionPerformed(e); } }); - printMenuItem.setText("Print"); - printMenuItem.addActionListener(new java.awt.event.ActionListener() + showTranslation.setText("Translate cDNA"); + showTranslation.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - printMenuItem_actionPerformed(e); + showTranslation_actionPerformed(e); } }); - renderGapsMenuItem.setText("Render gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() + extractScores.setText("Extract Scores..."); + extractScores.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - renderGapsMenuItem_actionPerformed(e); + extractScores_actionPerformed(e); } }); - findMenuItem.setText("Find"); - findMenuItem.addActionListener(new java.awt.event.ActionListener() + extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based + // score extraction + showProducts.setText("Get Cross References"); + /* + * showProducts.addActionListener(new ActionListener() { + * + * public void actionPerformed(ActionEvent e) { + * showProducts_actionPerformed(e); } }); + */ + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - findMenuItem_actionPerformed(e); + featureSettings_actionPerformed(e); + } + }); + fetchSequence.setText("Fetch Sequence(s)..."); + fetchSequence.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchSequence_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); + annotationColour.setText("By Annotation..."); + annotationColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(e); } }); - sequenceFeatures.setText("Sequence Features"); - sequenceFeatures.addActionListener(new ActionListener() + associatedData.setText("Load Features / Annotations"); + associatedData.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent actionEvent) + public void actionPerformed(ActionEvent e) { - sequenceFeatures_actionPerformed(actionEvent); + associatedData_actionPerformed(e); } }); - nucleotideColour.setText("Nucleotide colours"); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState(jalview.bin.Cache.getDefault( + "AUTO_CALC_CONSENSUS", true)); + autoCalculate.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - nucleotideColour_actionPerformed(e); + autoCalculate_actionPerformed(e); } }); - deleteGroups.setSelected(false); - deleteGroups.setText("Delete all groups"); - deleteGroups.addActionListener(new java.awt.event.ActionListener() + addSequenceMenu.setText("Add Sequences"); + addFromFile.setText("From File"); + addFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - deleteGroups_actionPerformed(e); + addFromFile_actionPerformed(e); } }); - copy.setText("Copy"); - copy.setMnemonic(KeyEvent.VK_C); - - copy.addActionListener(new java.awt.event.ActionListener() + addFromText.setText("From Textbox"); + addFromText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); + addFromText_actionPerformed(e); } }); - cut.setText("Cut"); - cut.setMnemonic(KeyEvent.VK_X); - cut.addActionListener(new java.awt.event.ActionListener() + addFromURL.setText("From URL"); + addFromURL.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); + addFromURL_actionPerformed(e); } }); - delete.setText("Delete"); - delete.addActionListener(new java.awt.event.ActionListener() + exportFeatures.setText("Export Features..."); + exportFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); + exportFeatures_actionPerformed(e); } }); - jMenu1.setMnemonic('V'); - jMenu1.setText("Paste"); - pasteNew.setText("to new alignment"); - pasteNew.addActionListener(new java.awt.event.ActionListener() + exportAnnotations.setText("Export Annotations..."); + exportAnnotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - pasteNew_actionPerformed(e); + exportAnnotations_actionPerformed(e); } }); - pasteThis.setText("add to this alignment"); - pasteThis.addActionListener(new java.awt.event.ActionListener() + statusPanel.setLayout(gridLayout1); + jMenu3.setText("Show"); + showAllSeqs.setText("All Sequences"); + showAllSeqs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - pasteThis_actionPerformed(e); + showAllSeqs_actionPerformed(e); } }); - applyToAllGroups.setText("Apply colour to all groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addActionListener(new java.awt.event.ActionListener() + showAllColumns.setText("All Columns"); + showAllColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - applyToAllGroups_actionPerformed(e); + showAllColumns_actionPerformed(e); } }); - createPNG.addActionListener(new java.awt.event.ActionListener() + hideMenu.setText("Hide"); + hideSelSequences.setText("Selected Sequences"); + hideSelSequences.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - createPNG_actionPerformed(e); + hideSelSequences_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() + hideSelColumns.setText("Selected Columns"); + hideSelColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - font_actionPerformed(e); + hideSelColumns_actionPerformed(e); } }); - fullSeqId.setText("Show full sequence id"); - fullSeqId.addActionListener(new java.awt.event.ActionListener() + hiddenMarkers.setText("Show Hidden Markers"); + hiddenMarkers.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - fullSeqId_actionPerformed(e); + hiddenMarkers_actionPerformed(e); } }); - epsFile.setText("Save as EPS file"); - epsFile.addActionListener(new java.awt.event.ActionListener() + invertColSel.setText("Invert Column Selection"); + invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.ALT_MASK, false)); + invertColSel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - epsFile_actionPerformed(e); + invertColSel_actionPerformed(e); } }); - LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); - LoadtreeMenuItem.setText("Load assocated tree"); - LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + JTabbedPane pane = (JTabbedPane) evt.getSource(); + int sel = pane.getSelectedIndex(); + tabSelectionChanged(sel); + } + }); + tabbedPane.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent e) + { + tabbedPane_mousePressed(e); + } + }); + tabbedPane.addFocusListener(new FocusAdapter() + { + public void focusGained(FocusEvent e) + { + tabbedPane_focusGained(e); + } + }); + save.setText("Save"); + save.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + save.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + save_actionPerformed(e); + } + }); + reload.setEnabled(false); + reload.setText("Reload"); + reload.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + reload_actionPerformed(e); + } + }); + newView.setText("New View"); + newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit() + .getMenuShortcutKeyMask(), false)); + newView.addActionListener(new ActionListener() + { public void actionPerformed(ActionEvent e) { - LoadtreeMenuItem_actionPerformed(e); + newView_actionPerformed(e); } }); - jpred.setText("JPred"); - jpred.addActionListener(new java.awt.event.ActionListener() + tabbedPane.setToolTipText(" Right-click to rename tab" + + "
Press X to eXpand tabs, G to reGroup."); + textColour.setText("Colour Text ..."); + textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - jpred_actionPerformed(e); + textColour_actionPerformed(e); } }); - scaleAbove.setVisible(false); - scaleAbove.setText("Scale above alignment"); - scaleAbove.addActionListener(new java.awt.event.ActionListener() + formatMenu.setText("Format"); + selectMenu.setText("Select"); + idRightAlign.setText("Right Align Sequence Id"); + idRightAlign.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - scaleAbove_actionPerformed(e); + idRightAlign_actionPerformed(e); } }); - scaleLeft.setVisible(false); - scaleLeft.setSelected(true); - scaleLeft.setText("Scale left of sequence"); - scaleLeft.addActionListener(new java.awt.event.ActionListener() + gatherViews.setEnabled(false); + gatherViews.setText("Gather Views"); + gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_G, 0, false)); + gatherViews.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - scaleLeft_actionPerformed(e); + gatherViews_actionPerformed(e); } }); - scaleRight.setVisible(false); - scaleRight.setSelected(true); - scaleRight.setText("Scale right of sequence"); - scaleRight.addActionListener(new java.awt.event.ActionListener() + expandViews.setEnabled(false); + expandViews.setText("Expand Views"); + expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_X, 0, false)); + expandViews.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - scaleRight_actionPerformed(e); + expandViews_actionPerformed(e); } }); - modifyPID.setText("Modify PID Threshold"); - modifyPID.addActionListener(new java.awt.event.ActionListener() + pageSetup.setText("Page Setup ..."); + pageSetup.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - modifyPID_actionPerformed(e); + pageSetup_actionPerformed(e); } }); - modifyConservation.setText("Modify Conservation Threshold"); - modifyConservation.addActionListener(new java.awt.event.ActionListener() + alignmentProperties.setText("Alignment Properties..."); + alignmentProperties.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent actionEvent) { - modifyConservation_actionPerformed(e); + alignmentProperties(); } }); - sortByTreeMenu.setText("Sort by tree order"); + tooltipSettingsMenu.setText("Sequence ID Tooltip"); + autoAnnMenu.setText("Autocalculated Annotation"); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(selectMenu); alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(alignMenu); - fileMenu.add(saveAlignmentMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(fetchSequence); + fileMenu.add(addSequenceMenu); + fileMenu.add(reload); + fileMenu.addSeparator(); + fileMenu.add(vamsasStore); + fileMenu.add(save); + fileMenu.add(saveAs); fileMenu.add(outputTextboxMenu); - fileMenu.add(htmlMenuItem); - fileMenu.add(epsFile); - fileMenu.add(createPNG); + fileMenu.add(pageSetup); fileMenu.add(printMenuItem); fileMenu.addSeparator(); + fileMenu.add(jMenu2); + fileMenu.add(exportFeatures); + fileMenu.add(exportAnnotations); fileMenu.add(LoadtreeMenuItem); + fileMenu.add(associatedData); 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.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); editMenu.addSeparator(); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(selectAllSequenceMenuItem); - 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); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.add(fullSeqId); + editMenu.add(removeRedundancyMenuItem); + editMenu.addSeparator(); + // dont add these yet in the CVS build - they cannot be undone! + editMenu.add(justifyLeftMenuItem); + editMenu.add(justifyRightMenuItem); + editMenu.addSeparator(); + editMenu.add(padGapsMenuitem); + viewMenu.add(newView); + viewMenu.add(expandViews); + viewMenu.add(gatherViews); viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); + viewMenu.add(jMenu3); + viewMenu.add(hideMenu); viewMenu.addSeparator(); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); + viewMenu.add(followHighlightMenuItem); viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + //viewMenu.add(showSeqFeaturesHeight); + + viewMenu.add(featureSettings); + tooltipSettingsMenu.add(showDbRefsMenuitem); + tooltipSettingsMenu.add(showNpFeatsMenuitem); + viewMenu.add(tooltipSettingsMenu); + viewMenu.addSeparator(); + viewMenu.add(alignmentProperties); + viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); - viewMenu.add(sequenceFeatures); colourMenu.add(applyToAllGroups); + colourMenu.add(textColour); + colourMenu.addSeparator(); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); colourMenu.add(zappoColour); colourMenu.add(taylorColour); colourMenu.add(hydrophobicityColour); @@ -805,411 +1685,623 @@ 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); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculateTree); 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); - this.getContentPane().add(statusBar, BorderLayout.SOUTH); - jMenu1.add(pasteNew); - jMenu1.add(pasteThis); + calculateMenu.add(showTranslation); + calculateMenu.add(showProducts); + calculateMenu.add(autoCalculate); + calculateMenu.addSeparator(); + calculateMenu.add(extractScores); + webServiceNoServices = new JMenuItem(""); + webService.add(webServiceNoServices); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + sort.add(sortByTreeMenu); + calculateTree.add(averageDistanceTreeMenuItem); + calculateTree.add(neighbourTreeMenuItem); + calculateTree.add(avDistanceTreeBlosumMenuItem); + calculateTree.add(njTreeBlosumMenuItem); + jMenu2.add(htmlMenuItem); + jMenu2.add(epsFile); + jMenu2.add(createPNG); + addSequenceMenu.add(addFromFile); + addSequenceMenu.add(addFromText); + addSequenceMenu.add(addFromURL); + this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); + statusPanel.add(statusBar, null); + this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); + jMenu3.add(showAllColumns); + jMenu3.add(showAllSeqs); + hideMenu.add(hideSelColumns); + hideMenu.add(hideSelSequences); + formatMenu.add(font); + formatMenu.addSeparator(); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(seqLimits); + formatMenu.add(idRightAlign); + formatMenu.add(hiddenMarkers); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + formatMenu.add(centreColumnLabelsMenuItem); + formatMenu.add(showUnconservedMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); + selectMenu.add(grpsFromSelection); } - protected void saveAs_actionPerformed(ActionEvent e) + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { - + // TODO Auto-generated method stub + } - protected void outputText_actionPerformed(ActionEvent e) + protected void showConsensusHistogram_actionPerformed(ActionEvent e) { + // TODO Auto-generated method stub + + } + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + } - protected void htmlMenuItem_actionPerformed(ActionEvent e) + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { + // TODO Auto-generated method stub + + } + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + } + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + protected void showSeqFeaturesHeight_actionPerformed( + ActionEvent actionEvent) + { + // TODO Auto-generated method stub + + } + protected void justifyRightMenuItem_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } - protected void closeMenuItem_actionPerformed(ActionEvent e) + protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { + // TODO Auto-generated method stub + + } + protected void followHighlight_actionPerformed() + { + // TODO Auto-generated method stub + } - protected void redoMenuItem_actionPerformed(ActionEvent e) + protected void showNpFeats_actionPerformed(ActionEvent e) { + // TODO Auto-generated method stub + + } + protected void showDbRefs_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + } - protected void undoMenuItem_actionPerformed(ActionEvent e) + protected void centreColumnLabels_actionPerformed(ActionEvent e) { + } + protected void showProducts_actionPerformed(ActionEvent e) + { } + protected void buildSortByAnnotationScoresMenu() + { + } + protected void extractScores_actionPerformed(ActionEvent e) + { + } + protected void outputText_actionPerformed(ActionEvent e) + { + } - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void addFromFile_actionPerformed(ActionEvent e) { } - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void addFromText_actionPerformed(ActionEvent e) { } - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) + public void addFromURL_actionPerformed(ActionEvent e) { } - - protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e) + public void exportFeatures_actionPerformed(ActionEvent e) { } - protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) + public void exportAnnotations_actionPerformed(ActionEvent e) { } - protected void remove2RightMenuItem_actionPerformed(ActionEvent e) + protected void htmlMenuItem_actionPerformed(ActionEvent e) { - } - protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + protected void closeMenuItem_actionPerformed(boolean b) { + } + protected void redoMenuItem_actionPerformed(ActionEvent e) + { } - protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + protected void undoMenuItem_actionPerformed(ActionEvent e) { + } + protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + { } - protected void setGapCharMenuItem_actionPerformed(ActionEvent e) + protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { + } + protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) + { } + protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) + { + } + protected void remove2RightMenuItem_actionPerformed(ActionEvent e) + { + } + protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + { + } + protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + { + } protected void wrapMenuItem_actionPerformed(ActionEvent e) { - } - protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) { - } protected void viewTextMenuItem_actionPerformed(ActionEvent e) { - } - protected void colourTextMenuItem_actionPerformed(ActionEvent e) { - } - - protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - } protected void overviewMenuItem_actionPerformed(ActionEvent e) { - } protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { - } protected void sortIDMenuItem_actionPerformed(ActionEvent e) { + } + protected void sortLengthMenuItem_actionPerformed(ActionEvent e) + { } protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { - } - protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { - } protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { - } protected void PCAMenuItem_actionPerformed(ActionEvent e) { - } protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { - } protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { + } + protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + { } + protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + { + } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed(ActionEvent e) { + } + protected void zappoColour_actionPerformed(ActionEvent e) + { } - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed(ActionEvent e) { + } + protected void hydrophobicityColour_actionPerformed(ActionEvent e) + { } + protected void helixColour_actionPerformed(ActionEvent e) + { + } + protected void strandColour_actionPerformed(ActionEvent e) + { + } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed(ActionEvent e) { + } + protected void buriedColour_actionPerformed(ActionEvent e) + { } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) + protected void userDefinedColour_actionPerformed(ActionEvent e) { + } + protected void PIDColour_actionPerformed(ActionEvent e) + { } + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + } - protected void clustalColour_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed(ActionEvent e) { + } + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { } - protected void zappoColour_actionPerformed(ActionEvent e) + protected void printMenuItem_actionPerformed(ActionEvent e) { + } + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { } - protected void taylorColour_actionPerformed(ActionEvent e) + protected void findMenuItem_actionPerformed(ActionEvent e) { + } + protected void abovePIDThreshold_actionPerformed(ActionEvent e) + { } + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) + { + } - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void nucleotideColour_actionPerformed(ActionEvent e) { + } + protected void deleteGroups_actionPerformed(ActionEvent e) + { } - protected void helixColour_actionPerformed(ActionEvent e) + protected void copy_actionPerformed(ActionEvent e) + { + } + + protected void cut_actionPerformed(ActionEvent e) { + } + protected void delete_actionPerformed(ActionEvent e) + { } - protected void strandColour_actionPerformed(ActionEvent e) + protected void pasteNew_actionPerformed(ActionEvent e) { + } + protected void pasteThis_actionPerformed(ActionEvent e) + { } - protected void turnColour_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed(ActionEvent e) { + } + public void createPNG(java.io.File f) + { } - protected void buriedColour_actionPerformed(ActionEvent e) + protected void font_actionPerformed(ActionEvent e) { + } + protected void seqLimit_actionPerformed(ActionEvent e) + { } + public void seqDBRef_actionPerformed(ActionEvent e) + { + } - protected void userDefinedColour_actionPerformed(ActionEvent e) + public void createEPS(java.io.File f) { + } + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + { } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void jpred_actionPerformed(ActionEvent e) { + } + protected void scaleAbove_actionPerformed(ActionEvent e) + { } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void scaleLeft_actionPerformed(ActionEvent e) + { + } + + protected void scaleRight_actionPerformed(ActionEvent e) { + } + protected void modifyPID_actionPerformed(ActionEvent e) + { } + protected void modifyConservation_actionPerformed(ActionEvent e) + { + } - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void saveAs_actionPerformed(ActionEvent e) { + } + protected void padGapsMenuitem_actionPerformed(ActionEvent e) + { } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + public void vamsasStore_actionPerformed(ActionEvent e) { } + public void vamsasLoad_actionPerformed(ActionEvent e) + { - protected void printMenuItem_actionPerformed(ActionEvent e) + } + + public void showTranslation_actionPerformed(ActionEvent e) { } - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + public void featureSettings_actionPerformed(ActionEvent e) { } - protected void findMenuItem_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed(ActionEvent e) { } + public void smoothFont_actionPerformed(ActionEvent e) + { + + } - protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + public void annotationColour_actionPerformed(ActionEvent e) + { } - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + public void associatedData_actionPerformed(ActionEvent e) { } - protected void nucleotideColour_actionPerformed(ActionEvent e) + public void autoCalculate_actionPerformed(ActionEvent e) { } - protected void deleteGroups_actionPerformed(ActionEvent e) + public void showAllSeqs_actionPerformed(ActionEvent e) { } - protected void copy_actionPerformed(ActionEvent e) + public void showAllColumns_actionPerformed(ActionEvent e) { } + public void hideSelSequences_actionPerformed(ActionEvent e) + { - protected void cut_actionPerformed(ActionEvent e) + } + + public void hideSelColumns_actionPerformed(ActionEvent e) { } - protected void delete_actionPerformed(ActionEvent e) + public void hiddenMarkers_actionPerformed(ActionEvent e) { } - protected void pasteNew_actionPerformed(ActionEvent e) + public void findPdbId_actionPerformed(ActionEvent e) { } - protected void pasteThis_actionPerformed(ActionEvent e) + public void enterPdbId_actionPerformed(ActionEvent e) { } - protected void applyToAllGroups_actionPerformed(ActionEvent e) + public void pdbFile_actionPerformed(ActionEvent e) { } - protected void createPNG_actionPerformed(ActionEvent e) + public void invertColSel_actionPerformed(ActionEvent e) { } - protected void font_actionPerformed(ActionEvent e) + public void tabSelectionChanged(int sel) { } - protected void fullSeqId_actionPerformed(ActionEvent e) + public void tabbedPane_mousePressed(MouseEvent e) { } - protected void epsFile_actionPerformed(ActionEvent e) + public void tabbedPane_focusGained(FocusEvent e) + { + requestFocus(); + } + + public void save_actionPerformed(ActionEvent e) { } - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + public void reload_actionPerformed(ActionEvent e) + { } - protected void jpred_actionPerformed(ActionEvent e) + public void newView_actionPerformed(ActionEvent e) { } - protected void scaleAbove_actionPerformed(ActionEvent e) + public void textColour_actionPerformed(ActionEvent e) { } - protected void scaleLeft_actionPerformed(ActionEvent e) + public void idRightAlign_actionPerformed(ActionEvent e) { } - protected void scaleRight_actionPerformed(ActionEvent e) + public void expandViews_actionPerformed(ActionEvent e) { } - protected void modifyPID_actionPerformed(ActionEvent e) + public void gatherViews_actionPerformed(ActionEvent e) { } - protected void modifyConservation_actionPerformed(ActionEvent e) + public void buildTreeMenu() { } + public void pageSetup_actionPerformed(ActionEvent e) + { + } + public void alignmentProperties() + { + } }