X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=304134cde86262ea031de344461a4c522cae2fb7;hb=0b23947e2cdcd704d3f313b23ba271e43d097344;hp=484287ce727a84ebf1875c267e971e18f59492f9;hpb=90bd6677b1f44a0608dcccde1ff59632cc9a54a1;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 484287c..304134c 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,47 +1,58 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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.*; +import java.awt.BorderLayout; -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 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 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(); @@ -50,12 +61,13 @@ 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 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 hydrophobicityColour = new + JRadioButtonMenuItem(); protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); @@ -65,47 +77,84 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = 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 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(); - JMenuItem pdbTest = new JMenuItem(); + 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 secondaryStructure = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeatures = 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 seqLimits = 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(); + protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JMenuItem showTranslation = new JMenuItem(); + public JMenuItem featureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); + protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem(); + 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(); 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) @@ -114,16 +163,63 @@ 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); @@ -137,15 +233,105 @@ 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 + + private void jbInit() + throws Exception { - fileMenu.setMnemonic('F'); fileMenu.setText("File"); - saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save alignment to local file"); + saveAs.setText("Save As ..."); + saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. + KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false)); + saveAs.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveAs_actionPerformed(e); + } + }); closeMenuItem.setMnemonic('C'); closeMenuItem.setText("Close"); + closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_W, java.awt.event.KeyEvent.CTRL_MASK, false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -154,36 +340,38 @@ 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); - } - }); + webService.setText("Web Service"); selectAllSequenceMenuItem.setText("Select all"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() + 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 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 Sequence Selection"); + invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_I, + java.awt.event.KeyEvent.SHIFT_MASK, false)); invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -191,15 +379,9 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem_actionPerformed(e); } }); - deselectAllColumnsMenuItem.setText("Deselect all columns"); - deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deselectAllColumnsMenuItem_actionPerformed(e); - } - }); - remove2LeftMenuItem.setText("Remove sequence <- left of selected column"); + remove2LeftMenuItem.setText("Remove Left"); + remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false)); remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -207,7 +389,9 @@ public class GAlignFrame extends JInternalFrame remove2LeftMenuItem_actionPerformed(e); } }); - remove2RightMenuItem.setText("Remove sequence -> right of selected column"); + remove2RightMenuItem.setText("Remove Right"); + remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false)); remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -215,15 +399,21 @@ 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.setAccelerator(javax.swing.KeyStroke. + getKeyStroke(java.awt.event. + KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false)); + 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.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false)); removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -231,37 +421,6 @@ 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() @@ -280,7 +439,7 @@ 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) @@ -288,7 +447,7 @@ 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) @@ -296,7 +455,7 @@ 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) @@ -304,31 +463,27 @@ 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.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, 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() + 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) @@ -336,15 +491,17 @@ 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) @@ -352,14 +509,6 @@ public class GAlignFrame extends JInternalFrame neighbourTreeMenuItem_actionPerformed(e); } }); - clustalAlignMenuItem.setText("Clustal alignment"); - clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalAlignMenuItem_actionPerformed(e); - } - }); this.getContentPane().setLayout(borderLayout1); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); @@ -367,9 +516,9 @@ public class GAlignFrame extends JInternalFrame statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); statusBar.setText("Status bar"); outputTextboxMenu.setMnemonic('T'); - outputTextboxMenu.setText("Output alignment via textbox"); - 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) @@ -377,7 +526,7 @@ public class GAlignFrame extends JInternalFrame clustalColour_actionPerformed(e); } }); - zappoColour.setText("Zappo colour scheme"); + zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -385,7 +534,7 @@ 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) @@ -393,7 +542,7 @@ 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) @@ -401,7 +550,7 @@ 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) @@ -409,7 +558,7 @@ 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) @@ -417,7 +566,7 @@ 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) @@ -425,7 +574,7 @@ 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) @@ -433,7 +582,7 @@ public class GAlignFrame extends JInternalFrame buriedColour_actionPerformed(e); } }); - userDefinedColour.setText("User defined colours"); + userDefinedColour.setText("User Defined..."); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -449,7 +598,7 @@ public class GAlignFrame extends JInternalFrame PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -457,15 +606,17 @@ 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) @@ -473,17 +624,17 @@ public class GAlignFrame extends JInternalFrame njTreeBlosumMenuItem_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) @@ -491,7 +642,7 @@ 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) @@ -499,7 +650,7 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - overviewMenuItem.setText("Overview window"); + overviewMenuItem.setText("Overview Window"); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -510,6 +661,9 @@ 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) @@ -520,6 +674,8 @@ public class GAlignFrame extends JInternalFrame redoMenuItem.setEnabled(false); redoMenuItem.setMnemonic('0'); redoMenuItem.setText("Redo"); + redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false)); redoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -527,7 +683,7 @@ 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) @@ -536,7 +692,6 @@ public class GAlignFrame extends JInternalFrame } }); noColourmenuItem.setText("None"); - noColourmenuItem.setSelected(true); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -544,8 +699,7 @@ 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) @@ -553,15 +707,9 @@ 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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false)); printMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -569,7 +717,7 @@ 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() { @@ -578,7 +726,10 @@ 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) @@ -588,22 +739,23 @@ public class GAlignFrame extends JInternalFrame }); searchMenu.setText("Search"); - abovePIDThreshold.setText("Above PID threshold"); - abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { + abovePIDThreshold.setText("Above Identity Threshold"); + abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { abovePIDThreshold_actionPerformed(e); } }); - secondaryStructure.setSelected(true); - secondaryStructure.setText("Secondary Structure"); - secondaryStructure.addActionListener(new ActionListener() + showSeqFeatures.setText("Show Sequence Features"); + showSeqFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { - secondaryStructure_actionPerformed(actionEvent); + showSeqFeatures_actionPerformed(actionEvent); } }); - nucleotideColour.setText("Nucleotide colours"); + nucleotideColour.setText("Nucleotide"); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -611,8 +763,9 @@ public class GAlignFrame extends JInternalFrame nucleotideColour_actionPerformed(e); } }); - deleteGroups.setSelected(false); - deleteGroups.setText("Delete all groups"); + deleteGroups.setText("Undefine groups"); + deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false)); deleteGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -620,393 +773,898 @@ public class GAlignFrame extends JInternalFrame deleteGroups_actionPerformed(e); } }); - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(fontMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(alignMenu); - fileMenu.add(saveAlignmentMenu); - fileMenu.add(outputTextboxMenu); - fileMenu.add(htmlMenuItem); - fileMenu.add(printMenuItem); - fileMenu.addSeparator(); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.addSeparator(); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); - editMenu.add(groupsMenuItem); - 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); - fontMenu.add(fontNameMenuItem); - fontMenu.add(fontSizeMenuItem); - fontMenu.add(fontStyleMenuItem); - viewMenu.add(wrapMenuItem); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(consensusGraphMenuItem); - viewMenu.add(overviewMenuItem); - viewMenu.add(secondaryStructure); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.add(PIDColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.addSeparator(); - colourMenu.add(abovePIDThreshold); - colourMenu.add(conservationMenuItem); - calculateMenu.add(sortPairwiseMenuItem); - calculateMenu.add(sortIDMenuItem); - calculateMenu.add(sortGroupMenuItem); - calculateMenu.add(sortTreeOrderMenuItem); - calculateMenu.add(removeRedundancyMenuItem); - 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); - this.getContentPane().add(statusBar, BorderLayout.SOUTH); - } - - protected void saveAs_actionPerformed(ActionEvent e) - { - - } - - 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) - { - - } - + copy.setText("Copy"); + copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_C, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + copy.setMnemonic(KeyEvent.VK_C); - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } + 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.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); + } + }); - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + 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) + { + seqLimit_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 Associated 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 Image"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + padGapsMenuitem_actionPerformed(e); + } + }); + vamsasStore.setVisible(false); + 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); + } + }); + + + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + featureSettings_actionPerformed(e); + } + }); + fetchSequence.setText("Fetch Sequence(s)..."); + fetchSequence.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchSequence_actionPerformed(e); + } + }); + smoothFont.setText("Smooth Fonts"); + smoothFont.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + smoothFont_actionPerformed(e); + } + }); + + annotationColour.setText("By Annotation..."); + annotationColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(e); + } + }); + associatedData.setText("Load Features / Annotations"); + associatedData.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + associatedData_actionPerformed(e); + } + }); + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + autoCalculate_actionPerformed(e); + } + }); + addSequenceMenu.setText("Add Sequences"); + addFromFile.setText("From File"); + addFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromFile_actionPerformed(e); + } + }); + addFromText.setText("From Textbox"); + addFromText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromText_actionPerformed(e); + } + }); + addFromURL.setText("From URL"); + addFromURL.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromURL_actionPerformed(e); + } + }); + exportFeatures.setText("Export Features..."); + exportFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + exportFeatures_actionPerformed(e); + } + }); + exportAnnotations.setText("Export Annotations..."); + exportAnnotations.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + exportAnnotations_actionPerformed(e); + } + }); + statusPanel.setLayout(gridLayout1); + jMenu3.setText("Show"); + showAllSeqs.setText("All Sequences"); + showAllSeqs.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllSeqs_actionPerformed(e); + } + }); + showAllColumns.setText("All Columns"); + showAllColumns.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllColumns_actionPerformed(e); + } + }); + hideMenu.setText("Hide"); + hideSelSequences.setText("Selected Sequences"); + hideSelSequences.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSelSequences_actionPerformed(e); + } + }); + hideSelColumns.setText("Selected Columns"); + hideSelColumns.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSelColumns_actionPerformed(e); + } + }); + hiddenMarkers.setText("Hidden Markers"); + hiddenMarkers.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hiddenMarkers_actionPerformed(e); + } + }); + invertColSel.setText("Invert Column Selection"); + invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false)); + invertColSel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertColSel_actionPerformed(e); + } + }); + 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, java.awt.event.KeyEvent.CTRL_MASK, false)); + save.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + save_actionPerformed(e); + } + }); + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(addSequenceMenu); + fileMenu.add(fetchSequence); + fileMenu.addSeparator(); + fileMenu.add(vamsasStore); + fileMenu.add(save); + fileMenu.add(saveAs); + fileMenu.add(outputTextboxMenu); + 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(undoMenuItem); + editMenu.add(redoMenuItem); + 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(invertColSel); + editMenu.add(deleteGroups); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + editMenu.addSeparator(); + editMenu.add(padGapsMenuitem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.add(smoothFont); + viewMenu.addSeparator(); + viewMenu.add(jMenu3); + viewMenu.add(hideMenu); + viewMenu.add(hiddenMarkers); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(seqLimits); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.add(viewBoxesMenuItem); + viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + 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); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.addSeparator(); + calculateMenu.add(showTranslation); + calculateMenu.add(autoCalculate); + webServiceNoServices=new JMenuItem(""); + webService.add(webServiceNoServices);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); + 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); + } + + protected void outputText_actionPerformed(ActionEvent e) + { + } + + public void addFromFile_actionPerformed(ActionEvent e) { } - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) + public void addFromText_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 closeMenuItem_actionPerformed(ActionEvent e) + { } - protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + protected void redoMenuItem_actionPerformed(ActionEvent e) { + } + protected void undoMenuItem_actionPerformed(ActionEvent e) + { } - protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { + } + protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + { } - protected void setGapCharMenuItem_actionPerformed(ActionEvent e) + protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) { + } + protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) + { } + protected void remove2RightMenuItem_actionPerformed(ActionEvent e) + { + } - protected void fontNameMenuItem_actionPerformed(ActionEvent e) + protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { + } + protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + { } - protected void fontSizeMenuItem_actionPerformed(ActionEvent e) + protected void wrapMenuItem_actionPerformed(ActionEvent e) { + } + protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) + { } - protected void fontStyleMenuItem_actionPerformed(ActionEvent e) + protected void viewTextMenuItem_actionPerformed(ActionEvent e) { + } + protected void colourTextMenuItem_actionPerformed(ActionEvent e) + { } - protected void wrapMenuItem_actionPerformed(ActionEvent e) + protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { + } + protected void overviewMenuItem_actionPerformed(ActionEvent e) + { } + protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + { + } - protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) + protected void sortIDMenuItem_actionPerformed(ActionEvent e) { + } + protected void sortGroupMenuItem_actionPerformed(ActionEvent e) + { } - protected void viewTextMenuItem_actionPerformed(ActionEvent e) + protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { + } + protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + { } + protected void PCAMenuItem_actionPerformed(ActionEvent e) + { + } - protected void colourTextMenuItem_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 consensusGraphMenuItem_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed(ActionEvent e) { + } + protected void zappoColour_actionPerformed(ActionEvent e) + { } - protected void overviewMenuItem_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed(ActionEvent e) { + } + protected void hydrophobicityColour_actionPerformed(ActionEvent e) + { } - protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed(ActionEvent e) { + } + protected void strandColour_actionPerformed(ActionEvent e) + { } - protected void sortIDMenuItem_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed(ActionEvent e) { + } + protected void buriedColour_actionPerformed(ActionEvent e) + { } - protected void sortGroupMenuItem_actionPerformed(ActionEvent e) + protected void userDefinedColour_actionPerformed(ActionEvent e) { + } + protected void PIDColour_actionPerformed(ActionEvent e) + { } - protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e) + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { + } + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { } - protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed(ActionEvent e) { + } + protected void printMenuItem_actionPerformed(ActionEvent e) + { } - protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { + } + protected void findMenuItem_actionPerformed(ActionEvent e) + { } - protected void PCAMenuItem_actionPerformed(ActionEvent e) + protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + } + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) + { } - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + protected void nucleotideColour_actionPerformed(ActionEvent e) { + } + protected void deleteGroups_actionPerformed(ActionEvent e) + { } - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + protected void copy_actionPerformed(ActionEvent e) { + } + protected void cut_actionPerformed(ActionEvent e) + { } + protected void delete_actionPerformed(ActionEvent e) + { + } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void pasteNew_actionPerformed(ActionEvent e) { + } + protected void pasteThis_actionPerformed(ActionEvent e) + { } - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed(ActionEvent e) { + } + public void createPNG(java.io.File f) + { } + protected void font_actionPerformed(ActionEvent e) + { + } + protected void seqLimit_actionPerformed(ActionEvent e) + { + } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) + public void seqDBRef_actionPerformed(ActionEvent e) { } + public void createEPS(java.io.File f) + { + } + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + { + } - protected void clustalColour_actionPerformed(ActionEvent e) + protected void jpred_actionPerformed(ActionEvent e) { + } + protected void scaleAbove_actionPerformed(ActionEvent e) + { } - protected void zappoColour_actionPerformed(ActionEvent e) + protected void scaleLeft_actionPerformed(ActionEvent e) { + } + protected void scaleRight_actionPerformed(ActionEvent e) + { } - protected void taylorColour_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed(ActionEvent e) { + } + protected void modifyConservation_actionPerformed(ActionEvent e) + { } - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + + protected void saveAs_actionPerformed(ActionEvent e) { + } + protected void padGapsMenuitem_actionPerformed(ActionEvent e) + { } - protected void helixColour_actionPerformed(ActionEvent e) + + public void vamsasStore_actionPerformed(ActionEvent e) { } - protected void strandColour_actionPerformed(ActionEvent e) + public void vamsasLoad_actionPerformed(ActionEvent e) { } - protected void turnColour_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(ActionEvent e) { } - protected void buriedColour_actionPerformed(ActionEvent e) + public void featureSettings_actionPerformed(ActionEvent e) { } + public void fetchSequence_actionPerformed(ActionEvent e) + { + } - protected void userDefinedColour_actionPerformed(ActionEvent e) + public void smoothFont_actionPerformed(ActionEvent e) { } - protected void PIDColour_actionPerformed(ActionEvent e) + public void annotationColour_actionPerformed(ActionEvent e) { } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + + public void associatedData_actionPerformed(ActionEvent e) { } + public void autoCalculate_actionPerformed(ActionEvent e) + { - protected void noColourmenuItem_actionPerformed(ActionEvent e) + } + + public void showAllSeqs_actionPerformed(ActionEvent e) { } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + public void showAllColumns_actionPerformed(ActionEvent e) { } - protected void pdbTest_actionPerformed(ActionEvent e) + public void hideSelSequences_actionPerformed(ActionEvent e) { } - protected void printMenuItem_actionPerformed(ActionEvent e) + public void hideSelColumns_actionPerformed(ActionEvent e) { } - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + public void hiddenMarkers_actionPerformed(ActionEvent e) { } - protected void findMenuItem_actionPerformed(ActionEvent e) + public void findPdbId_actionPerformed(ActionEvent e) { } + public void enterPdbId_actionPerformed(ActionEvent e) + { + + } - protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + public void pdbFile_actionPerformed(ActionEvent e) + { } - public void secondaryStructure_actionPerformed(ActionEvent actionEvent) + public void invertColSel_actionPerformed(ActionEvent e) { } - protected void nucleotideColour_actionPerformed(ActionEvent e) + public void tabSelectionChanged(int sel) { } - protected void deleteGroups_actionPerformed(ActionEvent e) + public void tabbedPane_mousePressed(MouseEvent e) { } + public void tabbedPane_focusGained(FocusEvent e) + { + requestFocus(); + } + + public void save_actionPerformed(ActionEvent e) + { + } }