X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=5a0357e23d7353d2c2b6899ddab60ef01b43690a;hb=628a03775931b98995f07682b1cbc3b9d09f3e73;hp=cbed306cf60efeef08d9da32398591659f4f7959;hpb=f333a271f26f2f930bf24cb3daeb5d18d02a6cb8;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index cbed306..5a0357e 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,51 +1,54 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * - * AM Waterhouse - *******************/ - + * 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 +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 fontMenu = new JMenu(); protected JMenu viewMenu = new JMenu(); protected JMenu colourMenu = new JMenu(); protected JMenu calculateMenu = new JMenu(); - protected JMenu alignMenu = new JMenu(); - protected JMenuItem groupsMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem(); + protected JMenu webService = new JMenu(); + protected JMenuItem webServiceNoServices; protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem invertSequenceMenuItem = new JMenuItem(); - protected JMenuItem deleteSelectedMenuItem = new JMenuItem(); - protected JMenuItem moveSelectedMenuItem = new JMenuItem(); - protected JMenuItem copySelectedMenuItem = new JMenuItem(); - protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem(); protected JMenuItem remove2LeftMenuItem = new JMenuItem(); protected JMenuItem remove2RightMenuItem = new JMenuItem(); protected JMenuItem removeGappedColumnMenuItem = new JMenuItem(); protected JMenuItem removeAllGapsMenuItem = new JMenuItem(); - protected JMenuItem setGapCharMenuItem = new JMenuItem(); - protected JMenuItem fontNameMenuItem = new JMenuItem(); - protected JMenuItem fontSizeMenuItem = new JMenuItem(); - protected JMenuItem fontStyleMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); protected JMenuItem sortIDMenuItem = new JMenuItem(); protected JMenuItem sortGroupMenuItem = new JMenuItem(); - protected JMenuItem sortTreeOrderMenuItem = new JMenuItem(); protected JMenuItem removeRedundancyMenuItem = new JMenuItem(); protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(); protected JMenuItem PCAMenuItem = new JMenuItem(); @@ -54,59 +57,82 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem clustalAlignMenuItem = new JMenuItem(); BorderLayout borderLayout1 = new BorderLayout(); public JLabel statusBar = new JLabel(); - protected JMenu saveAlignmentMenu = new JMenu(); + protected JMenuItem saveAlignmentMenu = 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 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 abovePIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); - protected JMenuItem conservationColourIncMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); - JMenuItem schemeKeyMenuItem = new JMenuItem(); JMenuItem overviewMenuItem = new JMenuItem(); protected JMenuItem undoMenuItem = new JMenuItem(); protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - JMenuItem noColourmenuItem = new JMenuItem(); - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); - JMenuItem pdbTest = new JMenuItem(); + public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + 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(); + public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + JMenuItem deleteGroups = new JMenuItem(); + JMenuItem delete = new JMenuItem(); + JMenuItem copy = new JMenuItem(); + JMenuItem cut = new JMenuItem(); + JMenu jMenu1 = new JMenu(); + JMenuItem pasteNew = new JMenuItem(); + JMenuItem pasteThis = new JMenuItem(); + public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + JMenuItem createPNG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); + public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem(); + JMenuItem epsFile = new JMenuItem(); + JMenuItem LoadtreeMenuItem = 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(); + protected JMenu sort = new JMenu(); + JMenu calculate = new JMenu(); + JMenu jMenu2 = new JMenu(); + JMenuItem padGapsMenuitem = new JMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem(); + protected JTabbedPane tabbedPane = new JTabbedPane(); + protected JMenuItem featureSettings = 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); - } - }); - - item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i)); + for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) + { + JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats. + elementAt( + i)); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -115,16 +141,64 @@ public class GAlignFrame extends JInternalFrame } }); - outputTextboxMenu.add( item ); + outputTextboxMenu.add(item); } - } - catch(Exception e) + catch (Exception e) { - e.printStackTrace(); } - 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); colours.add(taylorColour); @@ -133,17 +207,107 @@ public class GAlignFrame extends JInternalFrame colours.add(strandColour); colours.add(turnColour); colours.add(buriedColour); - colours.add(abovePIDColour); colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(nucleotideColour); + + 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 + + private void jbInit() + throws Exception { fileMenu.setMnemonic('F'); fileMenu.setText("File"); saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save alignment to local file"); + saveAlignmentMenu.setText("Save As"); + saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false)); + saveAlignmentMenu.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveAlignmentMenu_actionPerformed(e); + } + }); closeMenuItem.setMnemonic('C'); closeMenuItem.setText("Close"); closeMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -154,44 +318,35 @@ public class GAlignFrame extends JInternalFrame } }); editMenu.setText("Edit"); - fontMenu.setText("Font"); viewMenu.setText("View"); colourMenu.setText("Colour"); calculateMenu.setText("Calculate"); - alignMenu.setText("Web Service"); - groupsMenuItem.setText("Groups"); - groupsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupsMenuItem_actionPerformed(e); - } - }); - groupEditingMenuItem.setText("Group editing mode"); - groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupEditingMenuItem_actionPerformed(e); - } - }); - selectAllSequenceMenuItem.setText("Select all sequences"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() + 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("Clear sequence selection"); - deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() + 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.setText("Invert Selection"); invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -199,39 +354,7 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem_actionPerformed(e); } }); - deleteSelectedMenuItem.setText("Delete selected sequences"); - deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSelectedMenuItem_actionPerformed(e); - } - }); - moveSelectedMenuItem.setText("Move selected sequences to new alignment"); - moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveSelectedMenuItem_actionPerformed(e); - } - }); - copySelectedMenuItem.setText("Copy selected sequences to new alignment"); - copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copySelectedMenuItem_actionPerformed(e); - } - }); - deselectAllColumnsMenuItem.setText("Deselect all columns"); - deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - 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) @@ -239,7 +362,7 @@ 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) @@ -247,15 +370,16 @@ public class GAlignFrame extends JInternalFrame remove2RightMenuItem_actionPerformed(e); } }); - removeGappedColumnMenuItem.setText("Remove gapped columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() + removeGappedColumnMenuItem.setText("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { 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) @@ -263,37 +387,6 @@ 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); - } - }); - fontNameMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontNameMenuItem_actionPerformed(e); - } - }); - fontSizeMenuItem.setText("10"); - fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontSizeMenuItem_actionPerformed(e); - } - }); - fontStyleMenuItem.setText("Plain"); - fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - fontStyleMenuItem_actionPerformed(e); - } - }); viewBoxesMenuItem.setText("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -312,7 +405,7 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - sortPairwiseMenuItem.setText("Sort by pairwise identity"); + sortPairwiseMenuItem.setText("by Pairwise Identity"); sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -320,7 +413,7 @@ public class GAlignFrame extends JInternalFrame sortPairwiseMenuItem_actionPerformed(e); } }); - sortIDMenuItem.setText("Sort by ID"); + sortIDMenuItem.setText("by ID"); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -328,7 +421,7 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem_actionPerformed(e); } }); - sortGroupMenuItem.setText("Sort by group"); + sortGroupMenuItem.setText("by Group"); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -336,31 +429,25 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); - sortTreeOrderMenuItem.setText("Sort by tree order"); - sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortTreeOrderMenuItem_actionPerformed(e); - } - }); - removeRedundancyMenuItem.setText("Remove redundancy"); - removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() + removeRedundancyMenuItem.setText("Remove Redundancy..."); + 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() + 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.setText("Principal Component Analysis"); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -368,15 +455,17 @@ public class GAlignFrame extends JInternalFrame PCAMenuItem_actionPerformed(e); } }); - averageDistanceTreeMenuItem.setText("Average distance tree using PID"); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() + 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 tree using PID"); + neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity"); neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -384,25 +473,31 @@ public class GAlignFrame extends JInternalFrame neighbourTreeMenuItem_actionPerformed(e); } }); - clustalAlignMenuItem.setText("Clustal alignment"); - clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() + this.getContentPane().setLayout(borderLayout1); + alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + alignFrameMenuBar.addAncestorListener(new AncestorListener() { - public void actionPerformed(ActionEvent e) + public void ancestorAdded(AncestorEvent event) + { + alignFrameMenuBar_ancestorAdded(event); + } + + public void ancestorRemoved(AncestorEvent event) + { + } + + public void ancestorMoved(AncestorEvent event) { - clustalAlignMenuItem_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.setEnabled(false); - clustalColour.setSelected(false); - clustalColour.setText("Clustalx colours"); + outputTextboxMenu.setText("Output to Textbox"); + clustalColour.setText("Clustalx"); + clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -410,8 +505,7 @@ public class GAlignFrame extends JInternalFrame clustalColour_actionPerformed(e); } }); - zappoColour.setSelected(true); - zappoColour.setText("Zappo colour scheme"); + zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -419,7 +513,7 @@ 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) @@ -427,7 +521,7 @@ 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) @@ -435,7 +529,7 @@ 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) @@ -443,7 +537,7 @@ 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) @@ -451,7 +545,7 @@ 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) @@ -459,7 +553,7 @@ 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) @@ -467,16 +561,7 @@ public class GAlignFrame extends JInternalFrame buriedColour_actionPerformed(e); } }); - abovePIDColour.setEnabled(false); - abovePIDColour.setText("Above PID threshold only"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(e); - } - }); - userDefinedColour.setText("User defined colours"); + userDefinedColour.setText("User Defined..."); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -484,8 +569,7 @@ public class GAlignFrame extends JInternalFrame userDefinedColour_actionPerformed(e); } }); - PIDColour.setEnabled(false); - PIDColour.setText("By PID"); + PIDColour.setText("Percentage Identity"); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -493,7 +577,7 @@ public class GAlignFrame extends JInternalFrame PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("By BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -501,15 +585,17 @@ public class GAlignFrame extends JInternalFrame BLOSUM62Colour_actionPerformed(e); } }); - avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62"); - avDistanceTreeBlosumMenuItem.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 tree using BLOSUM62"); + njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62"); njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -517,26 +603,17 @@ public class GAlignFrame extends JInternalFrame njTreeBlosumMenuItem_actionPerformed(e); } }); - conservationColourIncMenuItem.setEnabled(false); - conservationColourIncMenuItem.setText("Conservation Colour Increment"); - conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationColourIncMenuItem_actionPerformed(e); - } - }); - consensusGraphMenuItem.setActionCommand(""); - consensusGraphMenuItem.setText("Consensus graph"); - consensusGraphMenuItem.setState(true); - consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener() + 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) { - consensusGraphMenuItem_actionPerformed(e); + annotationPanelMenuItem_actionPerformed(e); } }); - colourTextMenuItem.setText("Colour text"); + colourTextMenuItem.setText("Colour Text"); colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -544,7 +621,7 @@ 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) @@ -552,15 +629,7 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - schemeKeyMenuItem.setText("Colour Scheme Key"); - schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - schemeKeyMenuItem_actionPerformed(e); - } - }); - overviewMenuItem.setText("Overview window"); + overviewMenuItem.setText("Overview Window"); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -571,6 +640,9 @@ 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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); undoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -588,7 +660,7 @@ 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) @@ -604,8 +676,7 @@ public class GAlignFrame extends JInternalFrame noColourmenuItem_actionPerformed(e); } }); - wrapMenuItem.setEnabled(false); - wrapMenuItem.setText("Wrap alignment"); + wrapMenuItem.setText("Wrap"); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -613,14 +684,6 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem_actionPerformed(e); } }); - pdbTest.setText("PDB Test Viewer"); - pdbTest.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pdbTest_actionPerformed(e); - } - }); printMenuItem.setText("Print"); printMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -629,7 +692,7 @@ 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() { @@ -638,7 +701,10 @@ 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, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); findMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -647,55 +713,296 @@ public class GAlignFrame extends JInternalFrame } }); searchMenu.setText("Search"); + + abovePIDThreshold.setText("Above Identity Threshold"); + abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + abovePIDThreshold_actionPerformed(e); + } + }); + sequenceFeatures.setText("Sequence Features"); + sequenceFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + sequenceFeatures_actionPerformed(actionEvent); + } + }); + nucleotideColour.setText("Nucleotide"); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideColour_actionPerformed(e); + } + }); + deleteGroups.setText("Undefine groups"); + deleteGroups.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + deleteGroups_actionPerformed(e); + } + }); + copy.setText("Copy"); + copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_C, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + copy.setMnemonic(KeyEvent.VK_C); + + copy.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(e); + } + }); + cut.setText("Cut"); + cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_X, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + cut.setMnemonic(KeyEvent.VK_X); + cut.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(e); + } + }); + delete.setText("Delete"); + delete.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + delete_actionPerformed(e); + } + }); + jMenu1.setMnemonic('V'); + jMenu1.setText("Paste"); + pasteNew.setText("To New Alignment"); + pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_V, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + pasteNew.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pasteNew_actionPerformed(e); + } + }); + pasteThis.setText("Add To This Alignment"); + pasteThis.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pasteThis_actionPerformed(e); + } + }); + applyToAllGroups.setText("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + applyToAllGroups_actionPerformed(e); + } + }); + createPNG.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createPNG(null); + } + }); + createPNG.setActionCommand("Save As PNG Image"); + createPNG.setText("PNG"); + font.setText("Font..."); + font.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + font_actionPerformed(e); + } + }); + fullSeqId.setText("Show Full Sequence ID"); + fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true)); + fullSeqId.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fullSeqId_actionPerformed(e); + } + }); + epsFile.setText("EPS"); + epsFile.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createEPS(null); + } + }); + LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); + LoadtreeMenuItem.setText("Load Assocated Tree"); + LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + LoadtreeMenuItem_actionPerformed(e); + } + }); + scaleAbove.setVisible(false); + scaleAbove.setText("Scale Above"); + scaleAbove.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + scaleAbove_actionPerformed(e); + } + }); + scaleLeft.setVisible(false); + scaleLeft.setSelected(true); + scaleLeft.setText("Scale Left"); + scaleLeft.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + scaleLeft_actionPerformed(e); + } + }); + scaleRight.setVisible(false); + scaleRight.setSelected(true); + scaleRight.setText("Scale Right"); + scaleRight.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + scaleRight_actionPerformed(e); + } + }); + modifyPID.setText("Modify Identity Threshold..."); + modifyPID.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + modifyPID_actionPerformed(e); + } + }); + 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"); + calculate.setText("Calculate Tree"); + + jMenu2.setText("Export"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + padGapsMenuitem_actionPerformed(e); + } + }); + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + vamsasStore_actionPerformed(e); + } + }); + showTranslation.setText("Translate cDNA"); + showTranslation.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(e); + } + }); + + tabbedPane.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent ece) + { + + tabSelected(); + } + }); + featureSettings.setEnabled(false); + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + featureSettings_actionPerformed(e); + } + }); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(fontMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(alignMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(vamsasStore); fileMenu.add(saveAlignmentMenu); + fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); - fileMenu.add(htmlMenuItem); fileMenu.add(printMenuItem); fileMenu.addSeparator(); + fileMenu.add(LoadtreeMenuItem); + fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); - editMenu.addSeparator(); - editMenu.add(groupsMenuItem); - editMenu.add(groupEditingMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(jMenu1); + editMenu.add(delete); editMenu.addSeparator(); editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); + editMenu.add(deleteGroups); editMenu.addSeparator(); - editMenu.add(copySelectedMenuItem); - editMenu.add(moveSelectedMenuItem); - editMenu.add(deleteSelectedMenuItem); - 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(padGapsMenuitem); searchMenu.add(findMenuItem); - fontMenu.add(fontNameMenuItem); - fontMenu.add(fontSizeMenuItem); - fontMenu.add(fontStyleMenuItem); + viewMenu.add(font); + viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); + viewMenu.add(fullSeqId); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); - viewMenu.add(consensusGraphMenuItem); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); colourMenu.add(zappoColour); colourMenu.add(taylorColour); colourMenu.add(hydrophobicityColour); @@ -703,357 +1010,348 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); - colourMenu.add(conservationColourIncMenuItem); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(PIDColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.addSeparator(); - colourMenu.add(schemeKeyMenuItem); - calculateMenu.add(sortPairwiseMenuItem); - calculateMenu.add(sortIDMenuItem); - calculateMenu.add(sortGroupMenuItem); - calculateMenu.add(sortTreeOrderMenuItem); - calculateMenu.add(removeRedundancyMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + 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(pdbTest); + calculateMenu.add(showTranslation); + webServiceNoServices=new JMenuItem(""); + webService.add(webServiceNoServices); this.getContentPane().add(statusBar, BorderLayout.SOUTH); - } - - protected void saveAs_actionPerformed(ActionEvent e) - { - + this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); + jMenu1.add(pasteNew); + jMenu1.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + jMenu2.add(htmlMenuItem); + jMenu2.add(epsFile); + jMenu2.add(createPNG); } protected void outputText_actionPerformed(ActionEvent e) { - } protected void htmlMenuItem_actionPerformed(ActionEvent e) { - } - - - - protected void closeMenuItem_actionPerformed(ActionEvent e) { - } protected void redoMenuItem_actionPerformed(ActionEvent e) { - } protected void undoMenuItem_actionPerformed(ActionEvent e) { - } - - protected void groupsMenuItem_actionPerformed(ActionEvent e) + protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - } - protected void groupEditingMenuItem_actionPerformed(ActionEvent e) + protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - } - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) { - } - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) { - } - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) + protected void remove2RightMenuItem_actionPerformed(ActionEvent e) { - } - protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e) + protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { - } - protected void moveSelectedMenuItem_actionPerformed(ActionEvent e) + protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { - } - protected void copySelectedMenuItem_actionPerformed(ActionEvent e) + protected void wrapMenuItem_actionPerformed(ActionEvent e) { - } - protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e) + protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) { - } - protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) + protected void viewTextMenuItem_actionPerformed(ActionEvent e) { - } - protected void remove2RightMenuItem_actionPerformed(ActionEvent e) + protected void colourTextMenuItem_actionPerformed(ActionEvent e) { - } - protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - } - protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + protected void overviewMenuItem_actionPerformed(ActionEvent e) { - } - protected void setGapCharMenuItem_actionPerformed(ActionEvent e) + protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { - } - - protected void fontNameMenuItem_actionPerformed(ActionEvent e) + protected void sortIDMenuItem_actionPerformed(ActionEvent e) { - } - protected void fontSizeMenuItem_actionPerformed(ActionEvent e) + protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { - } - protected void fontStyleMenuItem_actionPerformed(ActionEvent e) + protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { - } - protected void wrapMenuItem_actionPerformed(ActionEvent e) + protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { - } - - protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) + protected void PCAMenuItem_actionPerformed(ActionEvent e) { - } - protected void viewTextMenuItem_actionPerformed(ActionEvent e) + protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { - } - - protected void colourTextMenuItem_actionPerformed(ActionEvent e) + protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { - } - - - protected void consensusGraphMenuItem_actionPerformed(ActionEvent e) + protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - } - protected void overviewMenuItem_actionPerformed(ActionEvent e) + protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - } - protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) { - } - protected void sortIDMenuItem_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed(ActionEvent e) { - } - protected void sortGroupMenuItem_actionPerformed(ActionEvent e) + protected void zappoColour_actionPerformed(ActionEvent e) { - } - protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed(ActionEvent e) { - } - protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + protected void hydrophobicityColour_actionPerformed(ActionEvent e) { - } - protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed(ActionEvent e) { - } - protected void PCAMenuItem_actionPerformed(ActionEvent e) + protected void strandColour_actionPerformed(ActionEvent e) { - } - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed(ActionEvent e) { - } - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + protected void buriedColour_actionPerformed(ActionEvent e) { - } - - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void userDefinedColour_actionPerformed(ActionEvent e) { - } - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void PIDColour_actionPerformed(ActionEvent e) { - } - - - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - } - - - - protected void clustalColour_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed(ActionEvent e) { - } - protected void zappoColour_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed(ActionEvent e) { - } - protected void taylorColour_actionPerformed(ActionEvent e) + protected void printMenuItem_actionPerformed(ActionEvent e) { + } + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { } + protected void findMenuItem_actionPerformed(ActionEvent e) + { + } - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + } + public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + { } - protected void helixColour_actionPerformed(ActionEvent e) + protected void nucleotideColour_actionPerformed(ActionEvent e) { + } + protected void deleteGroups_actionPerformed(ActionEvent e) + { } - protected void strandColour_actionPerformed(ActionEvent e) + protected void copy_actionPerformed(ActionEvent e) { + } + protected void cut_actionPerformed(ActionEvent e) + { } - protected void turnColour_actionPerformed(ActionEvent e) + protected void delete_actionPerformed(ActionEvent e) { + } + protected void pasteNew_actionPerformed(ActionEvent e) + { } - protected void buriedColour_actionPerformed(ActionEvent e) + protected void pasteThis_actionPerformed(ActionEvent e) { + } + protected void applyToAllGroups_actionPerformed(ActionEvent e) + { } + public void createPNG(java.io.File f) + { + } - protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { + protected void font_actionPerformed(ActionEvent e) + { + } - } + protected void fullSeqId_actionPerformed(ActionEvent e) + { + } + public void createEPS(java.io.File f) + { + } - protected void abovePIDColour_actionPerformed(ActionEvent e) + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + } + protected void jpred_actionPerformed(ActionEvent e) + { } + protected void scaleAbove_actionPerformed(ActionEvent e) + { + } - protected void userDefinedColour_actionPerformed(ActionEvent e) + protected void scaleLeft_actionPerformed(ActionEvent e) { + } + protected void scaleRight_actionPerformed(ActionEvent e) + { } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed(ActionEvent e) { + } + protected void modifyConservation_actionPerformed(ActionEvent e) + { } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void preferences_actionPerformed(ActionEvent e) { + } + protected void msaAlignMenuItem_actionPerformed(ActionEvent e) + { } - protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) + protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) { + } + protected void saveAlignmentMenu_actionPerformed(ActionEvent e) + { } - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void padGapsMenuitem_actionPerformed(ActionEvent e) { + } + protected void ClustalRealign_actionPerformed(ActionEvent e) + { } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + public void vamsasStore_actionPerformed(ActionEvent e) { } - protected void pdbTest_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 tabSelected() { } - protected void findMenuItem_actionPerformed(ActionEvent e) + public void featureSettings_actionPerformed(ActionEvent e) { } - }