-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.jbgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import jalview.schemes.*;\r
-import java.awt.BorderLayout;\r
-\r
-public class GAlignFrame\r
- extends JInternalFrame\r
-{\r
- protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
- protected JMenu fileMenu = new JMenu();\r
- protected JMenuItem closeMenuItem = new JMenuItem();\r
- protected JMenu editMenu = new JMenu();\r
- protected JMenu viewMenu = new JMenu();\r
- protected JMenu colourMenu = new JMenu();\r
- protected JMenu calculateMenu = new JMenu();\r
- protected JMenu webService = new JMenu();\r
- protected JMenuItem webServiceNoServices;\r
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
- protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
- protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
- protected JMenuItem sortIDMenuItem = new JMenuItem();\r
- protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
- protected JMenuItem PCAMenuItem = new JMenuItem();\r
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public JLabel statusBar = new JLabel();\r
- protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
- protected JMenu outputTextboxMenu = new JMenu();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new\r
- JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
- JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem htmlMenuItem = new JMenuItem();\r
- JMenuItem overviewMenuItem = new JMenuItem();\r
- protected JMenuItem undoMenuItem = new JMenuItem();\r
- protected JMenuItem redoMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem printMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem findMenuItem = new JMenuItem();\r
- JMenu searchMenu = new JMenu();\r
- public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
- JMenuItem deleteGroups = new JMenuItem();\r
- JMenuItem delete = new JMenuItem();\r
- JMenuItem copy = new JMenuItem();\r
- JMenuItem cut = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenuItem pasteNew = new JMenuItem();\r
- JMenuItem pasteThis = new JMenuItem();\r
- public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
- JMenuItem createPNG = new JMenuItem();\r
- protected JMenuItem font = new JMenuItem();\r
- public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
- JMenuItem epsFile = new JMenuItem();\r
- JMenuItem LoadtreeMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
- protected JMenuItem modifyPID = new JMenuItem();\r
- protected JMenuItem modifyConservation = new JMenuItem();\r
- protected JMenu sortByTreeMenu = new JMenu();\r
- protected JMenu sort = new JMenu();\r
- JMenu calculate = new JMenu();\r
- JMenu jMenu2 = new JMenu();\r
- protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
- protected ButtonGroup colours = new ButtonGroup();\r
- JMenuItem vamsasStore = new JMenuItem();\r
- protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
- public JMenuItem featureSettings = new JMenuItem();\r
- JMenuItem fetchSequence = new JMenuItem();\r
- protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
- JMenuItem annotationColour = new JMenuItem();\r
- JMenuItem associatedData = new JMenuItem();\r
- protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
- JMenu addSequenceMenu = new JMenu();\r
- JMenuItem addFromFile = new JMenuItem();\r
- JMenuItem addFromText = new JMenuItem();\r
- JMenuItem addFromURL = new JMenuItem();\r
- JMenuItem exportAnnotations = new JMenuItem();\r
- JMenuItem exportFeatures = new JMenuItem();\r
- protected JPanel statusPanel = new JPanel();\r
- GridLayout gridLayout1 = new GridLayout();\r
- public GAlignFrame()\r
- {\r
-\r
-\r
- try\r
- {\r
- jbInit();\r
- setJMenuBar(alignFrameMenuBar);\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
- {\r
- JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
- elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- }\r
-\r
-\r
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
- {\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
- getUserColourSchemes().keys();\r
-\r
- while (userColours.hasMoreElements())\r
- {\r
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
- nextElement().toString());\r
- radioItem.setName("USER_DEFINED");\r
- radioItem.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
- {\r
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
-\r
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
- "Remove from default list?",\r
- "Remove user defined colour",\r
- JOptionPane.YES_NO_OPTION);\r
- if(option == JOptionPane.YES_OPTION)\r
- {\r
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
- colourMenu.remove(radioItem);\r
- }\r
- else\r
- radioItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- }\r
- }\r
- });\r
- radioItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- colourMenu.insert(radioItem, 15);\r
- colours.add(radioItem);\r
- }\r
- }\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(nucleotideColour);\r
-\r
- setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
-\r
-\r
- }\r
-\r
- public void setColourSelected(String defaultColour)\r
- {\r
-\r
- if (defaultColour != null)\r
- {\r
- int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
-\r
- switch (index)\r
- {\r
- case ColourSchemeProperty.NONE:\r
- noColourmenuItem.setSelected(true);\r
- break;\r
- case ColourSchemeProperty.CLUSTAL:\r
- clustalColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.BLOSUM:\r
- BLOSUM62Colour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.PID:\r
- PIDColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.ZAPPO:\r
- zappoColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.TAYLOR:\r
- taylorColour.setSelected(true);\r
- break;\r
-\r
- case ColourSchemeProperty.HYDROPHOBIC:\r
- hydrophobicityColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.HELIX:\r
- helixColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.STRAND:\r
- strandColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.TURN:\r
- turnColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.BURIED:\r
- buriedColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.NUCLEOTIDE:\r
- nucleotideColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.USER_DEFINED:\r
- userDefinedColour.setSelected(true);\r
-\r
- break;\r
- }\r
- }\r
-\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- fileMenu.setMnemonic('F');\r
- fileMenu.setText("File");\r
- saveAlignmentMenu.setMnemonic('L');\r
- saveAlignmentMenu.setText("Save As");\r
- saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
- awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
- saveAlignmentMenu.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAlignmentMenu_actionPerformed(e);\r
- }\r
- });\r
- closeMenuItem.setMnemonic('C');\r
- closeMenuItem.setText("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- viewMenu.setText("View");\r
- colourMenu.setText("Colour");\r
- calculateMenu.setText("Calculate");\r
- webService.setText("Web Service");\r
- selectAllSequenceMenuItem.setText("Select all");\r
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_A,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setText("Deselect All");\r
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
- getKeyStroke(\r
- java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setText("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setText("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setText("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setText("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewBoxesMenuItem.setText("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewBoxesMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewTextMenuItem.setText("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- viewTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortPairwiseMenuItem.setText("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setText("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setText("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setText("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setText("Principal Component Analysis");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setText(\r
- "Average Distance Using % Identity");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(borderLayout1);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setMnemonic('T');\r
- outputTextboxMenu.setText("Output to Textbox");\r
- clustalColour.setText("Clustalx");\r
-\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setText("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setText("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setText(\r
- "Average Distance Using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
- ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setText("Show Annotations");\r
- annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
- annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotationPanelMenuItem_actionPerformed(e);\r
- }\r
- });\r
- colourTextMenuItem.setText("Colour Text");\r
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- colourTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- htmlMenuItem.setText("HTML");\r
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- htmlMenuItem_actionPerformed(e);\r
- }\r
- });\r
- overviewMenuItem.setText("Overview Window");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setMnemonic('Z');\r
- undoMenuItem.setText("Undo");\r
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_Z,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setMnemonic('0');\r
- redoMenuItem.setText("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setText("By Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setText("Wrap");\r
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- wrapMenuItem_actionPerformed(e);\r
- }\r
- });\r
- printMenuItem.setText("Print");\r
- printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- printMenuItem_actionPerformed(e);\r
- }\r
- });\r
- renderGapsMenuItem.setText("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- renderGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- findMenuItem.setText("Find...");\r
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_F,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
- searchMenu.setText("Search");\r
-\r
- abovePIDThreshold.setText("Above Identity Threshold");\r
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDThreshold_actionPerformed(e);\r
- }\r
- });\r
- showSeqFeatures.setText("Show Sequence Features");\r
- showSeqFeatures.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- showSeqFeatures_actionPerformed(actionEvent);\r
- }\r
- });\r
- nucleotideColour.setText("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
- deleteGroups.setText("Undefine groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
- copy.setText("Copy");\r
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_C,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- copy.setMnemonic(KeyEvent.VK_C);\r
-\r
- copy.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
- cut.setText("Cut");\r
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_X,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- cut.setMnemonic(KeyEvent.VK_X);\r
- cut.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
- delete.setText("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- jMenu1.setMnemonic('V');\r
- jMenu1.setText("Paste");\r
- pasteNew.setText("To New Alignment");\r
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_V,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- pasteNew.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
- pasteThis.setText("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
- applyToAllGroups.setText("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- applyToAllGroups_actionPerformed(e);\r
- }\r
- });\r
- createPNG.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createPNG(null);\r
- }\r
- });\r
- createPNG.setActionCommand("Save As PNG Image");\r
- createPNG.setText("PNG");\r
- font.setText("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- font_actionPerformed(e);\r
- }\r
- });\r
-\r
- seqLimits.setText("Show Sequence Limits");\r
- seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
- seqLimits.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- seqLimit_actionPerformed(e);\r
- }\r
- });\r
- epsFile.setText("EPS");\r
- epsFile.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createEPS(null);\r
- }\r
- });\r
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
- LoadtreeMenuItem.setText("Load Associated Tree");\r
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- LoadtreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- scaleAbove.setVisible(false);\r
- scaleAbove.setText("Scale Above");\r
- scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- scaleAbove_actionPerformed(e);\r
- }\r
- });\r
- scaleLeft.setVisible(false);\r
- scaleLeft.setSelected(true);\r
- scaleLeft.setText("Scale Left");\r
- scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- scaleLeft_actionPerformed(e);\r
- }\r
- });\r
- scaleRight.setVisible(false);\r
- scaleRight.setSelected(true);\r
- scaleRight.setText("Scale Right");\r
- scaleRight.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- scaleRight_actionPerformed(e);\r
- }\r
- });\r
- modifyPID.setText("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
- modifyConservation.setText("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
- sortByTreeMenu.setText("By Tree Order");\r
- sort.setText("Sort");\r
- calculate.setText("Calculate Tree");\r
-\r
- jMenu2.setText("Export");\r
- padGapsMenuitem.setText("Pad Gaps");\r
- padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
- padGapsMenuitem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- padGapsMenuitem_actionPerformed(e);\r
- }\r
- });\r
- vamsasStore.setVisible(false);\r
- vamsasStore.setText("VAMSAS store");\r
- vamsasStore.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- vamsasStore_actionPerformed(e);\r
- }\r
- });\r
- showTranslation.setText("Translate cDNA");\r
- showTranslation.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showTranslation_actionPerformed(e);\r
- }\r
- });\r
-\r
- /* tabbedPane.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent ece)\r
- {\r
-\r
- tabSelected();\r
- }\r
- });*/\r
- featureSettings.setText("Feature Settings...");\r
- featureSettings.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- featureSettings_actionPerformed(e);\r
- }\r
- });\r
- fetchSequence.setText("Fetch Sequence(s)...");\r
- fetchSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fetchSequence_actionPerformed(e);\r
- }\r
- });\r
- smoothFont.setText("Smooth Fonts");\r
- smoothFont.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- smoothFont_actionPerformed(e);\r
- }\r
- });\r
- smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
- annotationColour.setText("By Annotation...");\r
- annotationColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotationColour_actionPerformed(e);\r
- }\r
- });\r
- associatedData.setText("Load Features / Annotations");\r
- associatedData.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- associatedData_actionPerformed(e);\r
- }\r
- });\r
- autoCalculate.setText("Autocalculate Consensus");\r
- autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
- autoCalculate.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- autoCalculate_actionPerformed(e);\r
- }\r
- });\r
- addSequenceMenu.setText("Add Sequences");\r
- addFromFile.setText("From File");\r
- addFromFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addFromFile_actionPerformed(e);\r
- }\r
- });\r
- addFromText.setText("From Textbox");\r
- addFromText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addFromText_actionPerformed(e);\r
- }\r
- });\r
- addFromURL.setText("From URL");\r
- addFromURL.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addFromURL_actionPerformed(e);\r
- }\r
- });\r
- exportFeatures.setText("Export Features...");\r
- exportFeatures.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- exportFeatures_actionPerformed(e);\r
- }\r
- });\r
- exportAnnotations.setText("Export Annotations...");\r
- exportAnnotations.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- exportAnnotations_actionPerformed(e);\r
- }\r
- });\r
- statusPanel.setLayout(gridLayout1);\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(webService);\r
- fileMenu.add(addSequenceMenu);\r
- fileMenu.add(fetchSequence);\r
- fileMenu.addSeparator();\r
- fileMenu.add(vamsasStore);\r
- fileMenu.add(saveAlignmentMenu);\r
- fileMenu.add(jMenu2);\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(printMenuItem);\r
- fileMenu.addSeparator();\r
- fileMenu.add(exportFeatures);\r
- fileMenu.add(exportAnnotations);\r
- fileMenu.add(LoadtreeMenuItem);\r
- fileMenu.add(associatedData);\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(jMenu1);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(padGapsMenuitem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.add(smoothFont);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(seqLimits);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
- viewMenu.add(showSeqFeatures);\r
- viewMenu.add(featureSettings);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- colourMenu.add(annotationColour);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(showTranslation);\r
- calculateMenu.add(autoCalculate);\r
- webServiceNoServices=new JMenuItem("<No Services>");\r
- webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
- jMenu1.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- jMenu2.add(htmlMenuItem);\r
- jMenu2.add(epsFile);\r
- jMenu2.add(createPNG);\r
- addSequenceMenu.add(addFromFile);\r
- addSequenceMenu.add(addFromText);\r
- addSequenceMenu.add(addFromURL);\r
- this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
- statusPanel.add(statusBar, null);\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- public void addFromFile_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void addFromText_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void addFromURL_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void exportFeatures_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void exportAnnotations_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
- {\r
- }\r
-\r
- protected void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- public void createPNG(java.io.File f)\r
- {\r
- }\r
-\r
- protected void font_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void seqLimit_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- public void seqDBRef_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- public void createEPS(java.io.File f)\r
- {\r
- }\r
-\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void jpred_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
-\r
-\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
-\r
- public void vamsasStore_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void vamsasLoad_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void showTranslation_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void featureSettings_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void fetchSequence_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void smoothFont_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void annotationColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- public void associatedData_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- public void autoCalculate_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.schemes.*;
+
+public class GAlignFrame extends JInternalFrame
+{
+ protected JMenuBar alignFrameMenuBar = new JMenuBar();
+
+ protected JMenu fileMenu = new JMenu();
+
+ protected JMenuItem closeMenuItem = new JMenuItem();
+
+ protected JMenu editMenu = new JMenu();
+
+ protected JMenu viewMenu = new JMenu();
+
+ protected JMenu colourMenu = new JMenu();
+
+ protected JMenu calculateMenu = new JMenu();
+
+ protected JMenu webService = new JMenu();
+
+ protected JMenuItem webServiceNoServices;
+
+ protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+
+ protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+
+ protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+
+ protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+
+ protected JMenuItem remove2RightMenuItem = new JMenuItem();
+
+ protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+
+ protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+
+ protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
+
+ protected JMenuItem sortIDMenuItem = new JMenuItem();
+
+ protected JMenuItem sortLengthMenuItem = new JMenuItem();
+
+ protected JMenuItem sortGroupMenuItem = new JMenuItem();
+
+ protected JMenu sortByAnnotScore = new JMenu();
+
+ protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
+
+ protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
+
+ protected JMenuItem PCAMenuItem = new JMenuItem();
+
+ protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
+
+ protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ public JLabel statusBar = new JLabel();
+
+ protected JMenuItem saveAs = new JMenuItem();
+
+ protected JMenu outputTextboxMenu = new JMenu();
+
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem();
+
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
+
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+
+ JMenuItem htmlMenuItem = new JMenuItem();
+
+ JMenuItem overviewMenuItem = new JMenuItem();
+
+ protected JMenuItem undoMenuItem = new JMenuItem();
+
+ protected JMenuItem redoMenuItem = new JMenuItem();
+
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
+ JMenuItem printMenuItem = new JMenuItem();
+
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
+ JMenuItem findMenuItem = new JMenuItem();
+
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
+
+ JMenuItem deleteGroups = new JMenuItem();
+
+ JMenuItem delete = new JMenuItem();
+
+ JMenuItem copy = new JMenuItem();
+
+ JMenuItem cut = new JMenuItem();
+
+ JMenu pasteMenu = 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();
+
+ protected JMenu calculateTree = new JMenu();
+
+ JMenu jMenu2 = new JMenu();
+
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
+
+ protected ButtonGroup colours = new ButtonGroup();
+
+ JMenuItem vamsasStore = new JMenuItem();
+
+ protected JMenuItem showTranslation = new JMenuItem();
+
+ protected JMenuItem extractScores = new JMenuItem();
+
+ protected JMenu showProducts = new JMenu();
+
+ public JMenuItem featureSettings = new JMenuItem();
+
+ JMenuItem fetchSequence = new JMenuItem();
+
+ JMenuItem annotationColour = new JMenuItem();
+
+ protected JMenuItem rnahelicesColour = new JMenuItem();
+
+ JMenuItem associatedData = new JMenuItem();
+
+ protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem listenToViewSelections = 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();
+
+ JMenuItem hideAllButSelection = new JMenuItem();
+
+ JMenuItem hideAllSelection = new JMenuItem();
+
+ JMenuItem showAllhidden = new JMenuItem();
+
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+
+ JMenuItem invertColSel = new JMenuItem();
+
+ protected JTabbedPane tabbedPane = new JTabbedPane();
+
+ JMenuItem save = new JMenuItem();
+
+ protected JMenuItem reload = new JMenuItem();
+
+ JMenuItem newView = new JMenuItem();
+
+ JMenuItem textColour = new JMenuItem();
+
+ JMenu formatMenu = new JMenu();
+
+ JMenu selectMenu = new JMenu();
+
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
+
+ protected JMenuItem gatherViews = new JMenuItem();
+
+ protected JMenuItem expandViews = new JMenuItem();
+
+ JMenuItem pageSetup = new JMenuItem();
+
+ JMenuItem alignmentProperties = new JMenuItem();
+
+ JMenu tooltipSettingsMenu = new JMenu();
+
+ private JMenuItem justifyLeftMenuItem = new JMenuItem();
+
+ private JMenuItem justifyRightMenuItem = new JMenuItem();
+
+ JMenu autoAnnMenu = new JMenu();
+
+ protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+
+ private JMenuItem grpsFromSelection = new JMenuItem();
+
+ public GAlignFrame()
+ {
+ try
+ {
+ jbInit();
+ setJMenuBar(alignFrameMenuBar);
+
+ // dynamically fill save as menu with available formats
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem(
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputTextboxMenu.add(item);
+ }
+ } catch (Exception e)
+ {
+ }
+
+ if (!new jalview.util.Platform().isAMac())
+ {
+ closeMenuItem.setMnemonic('C');
+ outputTextboxMenu.setMnemonic('T');
+ undoMenuItem.setMnemonic('Z');
+ redoMenuItem.setMnemonic('0');
+ copy.setMnemonic('C');
+ cut.setMnemonic('U');
+ pasteMenu.setMnemonic('P');
+ reload.setMnemonic('R');
+ }
+
+ 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);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+ colours.add(nucleotideColour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
+
+ 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.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.PURINEPYRIMIDINE:
+ purinePyrimidineColour.setSelected(true);
+
+ break;
+ /*
+ * case ColourSchemeProperty.COVARIATION:
+ * covariationColour.setSelected(true);
+ *
+ * break;
+ */
+ case ColourSchemeProperty.USER_DEFINED:
+ userDefinedColour.setSelected(true);
+
+ break;
+ case ColourSchemeProperty.NONE:
+ default:
+ noColourmenuItem.setSelected(true);
+ break;
+
+ }
+ }
+
+ }
+
+ private void jbInit() throws Exception
+ {
+ fileMenu.setText("File");
+ saveAs.setText("Save As...");
+ saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ saveAs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveAs_actionPerformed(e);
+ }
+ });
+ closeMenuItem.setText("Close");
+ closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ closeMenuItem_actionPerformed(false);
+ }
+ });
+ editMenu.setText("Edit");
+ viewMenu.setText("View");
+ colourMenu.setText("Colour");
+ calculateMenu.setText("Calculate");
+ webService.setText("Web Service");
+ selectAllSequenceMenuItem.setText("Select All");
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ selectAllSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ deselectAllSequenceMenuItem.setText("Deselect All");
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+ deselectAllSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ invertSequenceMenuItem.setText("Invert Sequence Selection");
+ invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ invertSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ grpsFromSelection.setText("Make Groups for selection");
+ grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ makeGrpsFromSelection_actionPerformed(e);
+ }
+ });
+
+ remove2LeftMenuItem.setText("Remove Left");
+ remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ remove2LeftMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(e);
+ }
+ });
+ remove2RightMenuItem.setText("Remove Right");
+ remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ remove2RightMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ });
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");
+ removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ removeGappedColumnMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeGappedColumnMenuItem_actionPerformed(e);
+ }
+ });
+ removeAllGapsMenuItem.setText("Remove All Gaps");
+ removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ removeAllGapsMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeAllGapsMenuItem_actionPerformed(e);
+ }
+ });
+ justifyLeftMenuItem.setText("Left Justify Alignment");
+ justifyLeftMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
+ });
+ justifyRightMenuItem.setText("Right Justify Alignment");
+ justifyRightMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
+ });
+ viewBoxesMenuItem.setText("Boxes");
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewBoxesMenuItem_actionPerformed(e);
+ }
+ });
+ viewTextMenuItem.setText("Text");
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewTextMenuItem_actionPerformed(e);
+ }
+ });
+ showNonconservedMenuItem.setText("Show nonconserved");
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
+ sortPairwiseMenuItem.setText("by Pairwise Identity");
+ sortPairwiseMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
+ sortIDMenuItem.setText("by ID");
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortIDMenuItem_actionPerformed(e);
+ }
+ });
+ sortLengthMenuItem.setText("By Length");
+ sortLengthMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortLengthMenuItem_actionPerformed(e);
+ }
+ });
+ sortGroupMenuItem.setText("by Group");
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortGroupMenuItem_actionPerformed(e);
+ }
+ });
+ removeRedundancyMenuItem.setText("Remove Redundancy...");
+ removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ removeRedundancyMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ });
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
+ PCAMenuItem.setText("Principal Component Analysis");
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PCAMenuItem_actionPerformed(e);
+ }
+ });
+ averageDistanceTreeMenuItem
+ .setText("Average Distance Using % Identity");
+ averageDistanceTreeMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_actionPerformed(e);
+ }
+ });
+ this.getContentPane().setLayout(borderLayout1);
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
+ statusBar.setText("Status bar");
+ outputTextboxMenu.setText("Output to Textbox");
+ clustalColour.setText("Clustalx");
+
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed(e);
+ }
+ });
+ zappoColour.setText("Zappo");
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed(e);
+ }
+ });
+ taylorColour.setText("Taylor");
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed(e);
+ }
+ });
+ hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
+ helixColour.setText("Helix Propensity");
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed(e);
+ }
+ });
+ strandColour.setText("Strand Propensity");
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed(e);
+ }
+ });
+ turnColour.setText("Turn Propensity");
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed(e);
+ }
+ });
+ buriedColour.setText("Buried Index");
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed(e);
+ }
+ });
+ userDefinedColour.setText("User Defined...");
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour.setText("Percentage Identity");
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed(e);
+ }
+ });
+ BLOSUM62Colour.setText("BLOSUM62 Score");
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed(e);
+ }
+ });
+ nucleotideColour.setText("Nucleotide");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(e); } });
+ */
+
+ avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
+ njTreeBlosumMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ annotationPanelMenuItem.setActionCommand("");
+ annotationPanelMenuItem.setText("Show Annotations");
+ annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+ "SHOW_ANNOTATIONS", true));
+ annotationPanelMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ colourTextMenuItem.setText("Colour Text");
+ colourTextMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
+ htmlMenuItem.setText("HTML");
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ htmlMenuItem_actionPerformed(e);
+ }
+ });
+ overviewMenuItem.setText("Overview Window");
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ overviewMenuItem_actionPerformed(e);
+ }
+ });
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ undoMenuItem_actionPerformed(e);
+ }
+ });
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
+ redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ redoMenuItem_actionPerformed(e);
+ }
+ });
+ conservationMenuItem.setText("By Conservation");
+ conservationMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
+ noColourmenuItem.setText("None");
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed(e);
+ }
+ });
+ wrapMenuItem.setText("Wrap");
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ wrapMenuItem_actionPerformed(e);
+ }
+ });
+ printMenuItem.setText("Print ...");
+ printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ printMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ printMenuItem_actionPerformed(e);
+ }
+ });
+ renderGapsMenuItem.setText("Show Gaps");
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ renderGapsMenuItem_actionPerformed(e);
+ }
+ });
+ findMenuItem.setText("Find...");
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ findMenuItem_actionPerformed(e);
+ }
+ });
+ abovePIDThreshold.setText("Above Identity Threshold");
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed(e);
+ }
+ });
+ showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ showSeqFeatures_actionPerformed(actionEvent);
+ }
+ });
+ /*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+ * void actionPerformed(ActionEvent actionEvent) {
+ * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+ */
+ showDbRefsMenuitem.setText("Show Database Refs");
+ showDbRefsMenuitem.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showDbRefs_actionPerformed(e);
+ }
+
+ });
+ showNpFeatsMenuitem.setText("Show Non-Positional Features");
+ showNpFeatsMenuitem.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showNpFeats_actionPerformed(e);
+ }
+
+ });
+ showGroupConservation.setText("Group Conservation");
+ showGroupConservation.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConservation_actionPerformed(e);
+ }
+
+ });
+
+ showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConsensus_actionPerformed(e);
+ }
+
+ });
+ showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+
+ });
+
+ nucleotideColour.setText("Nucleotide");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+ deleteGroups.setText("Undefine groups");
+ deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ deleteGroups.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteGroups_actionPerformed(e);
+ }
+ });
+ copy.setText("Copy");
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+
+ copy.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(e);
+ }
+ });
+ cut.setText("Cut");
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ cut.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed(e);
+ }
+ });
+ delete.setText("Delete");
+ delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
+ delete.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ delete_actionPerformed(e);
+ }
+ });
+ pasteMenu.setText("Paste");
+ pasteNew.setText("To New Alignment");
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ pasteNew.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteNew_actionPerformed(e);
+ }
+ });
+ pasteThis.setText("Add To This Alignment");
+ pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ pasteThis.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ 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);
+ }
+ });
+
+ 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);
+ }
+ });
+ centreColumnLabelsMenuItem.setVisible(true);
+ centreColumnLabelsMenuItem.setState(false);
+ centreColumnLabelsMenuItem.setText("Centre Column Labels");
+ centreColumnLabelsMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
+ followHighlightMenuItem.setVisible(true);
+ followHighlightMenuItem.setState(true);
+ followHighlightMenuItem.setText("Automatic Scrolling");
+ followHighlightMenuItem.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ followHighlight_actionPerformed();
+ }
+
+ });
+
+ 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");
+ sort.addMenuListener(new MenuListener()
+ {
+ public void menuSelected(MenuEvent e)
+ {
+ buildTreeMenu();
+ }
+
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+ sortByAnnotScore.setText("by Score");
+ sort.add(sortByAnnotScore);
+ sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+ {
+
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ public void menuSelected(MenuEvent e)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ });
+ sortByAnnotScore.setVisible(false);
+
+ calculateTree.setText("Calculate Tree");
+
+ jMenu2.setText("Export Image");
+ padGapsMenuitem.setText("Pad Gaps");
+ padGapsMenuitem.setState(jalview.bin.Cache
+ .getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ 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);
+ }
+ });
+ extractScores.setText("Extract Scores...");
+ extractScores.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ extractScores_actionPerformed(e);
+ }
+ });
+ extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
+ // score extraction
+ showProducts.setText("Get Cross References");
+ /*
+ * showProducts.addActionListener(new ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * showProducts_actionPerformed(e); } });
+ */
+ featureSettings.setText("Feature Settings...");
+ featureSettings.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ featureSettings_actionPerformed(e);
+ }
+ });
+ fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
+ }
+ });
+
+ annotationColour.setText("By Annotation...");
+ annotationColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed(e);
+ }
+ });
+
+ rnahelicesColour.setText("By RNA helices");
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_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);
+ }
+ });
+ sortByTree.setText("Sort Alignment With New Tree");
+ sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
+ sortByTree.setState(jalview.bin.Cache.getDefault(
+ "SORT_BY_TREE", false));
+ sortByTree.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortByTreeOption_actionPerformed(e);
+ }
+ });
+
+ listenToViewSelections.setText("Listen for selections");
+ listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
+ listenToViewSelections.setState(false);
+ listenToViewSelections.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ listenToViewSelections_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.setToolTipText("Shift+H toggles sequence visiblity.");
+ showAllSeqs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllSeqs_actionPerformed(e);
+ }
+ });
+ showAllColumns.setText("All Columns");
+ showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
+ showAllColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllColumns_actionPerformed(e);
+ }
+ });
+ hideMenu.setText("Hide");
+ hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
+ hideSelSequences.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelSequences_actionPerformed(e);
+ }
+ });
+ hideSelColumns.setText("Selected Columns");
+ hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
+ hideSelColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelColumns_actionPerformed(e);
+ }
+ });
+ hideAllSelection.setText("Selected Region");
+ hideAllSelection.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllSelection_actionPerformed(e);
+ }
+ });
+ // TODO: should be hidden if no selection exists.
+ hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
+ hideAllButSelection.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllButSelection_actionPerformed(e);
+ }
+ });
+ showAllhidden.setText("All Sequences and Columns");
+ showAllhidden
+ .setToolTipText("H toggles visibility of hidden or selected regions.");
+ showAllhidden.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllhidden_actionPerformed(e);
+ }
+ });
+
+ hiddenMarkers.setText("Show 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, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.ALT_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, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ save.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ save_actionPerformed(e);
+ }
+ });
+ reload.setEnabled(false);
+ reload.setText("Reload");
+ reload.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ reload_actionPerformed(e);
+ }
+ });
+ newView.setText("New View");
+ newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+ newView.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed(e);
+ }
+ });
+ tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
+ + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+ textColour.setText("Colour Text ...");
+ textColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed(e);
+ }
+ });
+ formatMenu.setText("Format");
+ selectMenu.setText("Select");
+ idRightAlign.setText("Right Align Sequence Id");
+ idRightAlign.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ idRightAlign_actionPerformed(e);
+ }
+ });
+ gatherViews.setEnabled(false);
+ gatherViews.setText("Gather Views");
+ gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_G, 0, false));
+ gatherViews.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed(e);
+ }
+ });
+ expandViews.setEnabled(false);
+ expandViews.setText("Expand Views");
+ expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_X, 0, false));
+ expandViews.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed(e);
+ }
+ });
+ pageSetup.setText("Page Setup ...");
+ pageSetup.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pageSetup_actionPerformed(e);
+ }
+ });
+ alignmentProperties.setText("Alignment Properties...");
+ alignmentProperties.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alignmentProperties();
+ }
+ });
+ tooltipSettingsMenu.setText("Sequence ID Tooltip");
+ autoAnnMenu.setText("Autocalculated Annotation");
+ alignFrameMenuBar.add(fileMenu);
+ alignFrameMenuBar.add(editMenu);
+ alignFrameMenuBar.add(selectMenu);
+ alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(formatMenu);
+ alignFrameMenuBar.add(colourMenu);
+ alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(webService);
+ fileMenu.add(fetchSequence);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(reload);
+ fileMenu.addSeparator();
+ fileMenu.add(vamsasStore);
+ fileMenu.add(save);
+ fileMenu.add(saveAs);
+ fileMenu.add(outputTextboxMenu);
+ fileMenu.add(pageSetup);
+ fileMenu.add(printMenuItem);
+ fileMenu.addSeparator();
+ fileMenu.add(jMenu2);
+ fileMenu.add(exportFeatures);
+ fileMenu.add(exportAnnotations);
+ fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(associatedData);
+ fileMenu.addSeparator();
+ fileMenu.add(closeMenuItem);
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.add(cut);
+ editMenu.add(copy);
+ editMenu.add(pasteMenu);
+ editMenu.add(delete);
+ editMenu.addSeparator();
+ editMenu.add(remove2LeftMenuItem);
+ editMenu.add(remove2RightMenuItem);
+ editMenu.add(removeGappedColumnMenuItem);
+ editMenu.add(removeAllGapsMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+ editMenu.addSeparator();
+ // dont add these yet in the CVS build - they cannot be undone!
+ // Excluded from Jalview 2.5 release - undo needs to be implemented.
+ // editMenu.add(justifyLeftMenuItem);
+ // editMenu.add(justifyRightMenuItem);
+ // editMenu.addSeparator();
+ editMenu.add(padGapsMenuitem);
+ viewMenu.add(newView);
+ viewMenu.add(expandViews);
+ viewMenu.add(gatherViews);
+ viewMenu.addSeparator();
+ viewMenu.add(jMenu3);
+ viewMenu.add(hideMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(followHighlightMenuItem);
+ viewMenu.add(annotationPanelMenuItem);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ // viewMenu.add(showSeqFeaturesHeight);
+
+ viewMenu.add(featureSettings);
+ tooltipSettingsMenu.add(showDbRefsMenuitem);
+ tooltipSettingsMenu.add(showNpFeatsMenuitem);
+ viewMenu.add(tooltipSettingsMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
+ viewMenu.addSeparator();
+ viewMenu.add(overviewMenuItem);
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(covariationColour);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+ colourMenu.add(rnahelicesColour);
+ calculateMenu.add(sort);
+ calculateMenu.add(calculateTree);
+ calculateMenu.addSeparator();
+ calculateMenu.add(pairwiseAlignmentMenuItem);
+ calculateMenu.add(PCAMenuItem);
+ calculateMenu.addSeparator();
+ calculateMenu.add(showTranslation);
+ calculateMenu.add(showProducts);
+ calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
+ calculateMenu.addSeparator();
+ calculateMenu.add(extractScores);
+ webServiceNoServices = new JMenuItem("<No Services>");
+ webService.add(webServiceNoServices);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
+ sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
+ calculateTree.add(averageDistanceTreeMenuItem);
+ calculateTree.add(neighbourTreeMenuItem);
+ calculateTree.add(avDistanceTreeBlosumMenuItem);
+ calculateTree.add(njTreeBlosumMenuItem);
+ jMenu2.add(htmlMenuItem);
+ jMenu2.add(epsFile);
+ jMenu2.add(createPNG);
+ addSequenceMenu.add(addFromFile);
+ addSequenceMenu.add(addFromText);
+ addSequenceMenu.add(addFromURL);
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+ jMenu3.add(showAllColumns);
+ jMenu3.add(showAllSeqs);
+ jMenu3.add(showAllhidden);
+ hideMenu.add(hideSelColumns);
+ hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+
+ formatMenu.add(font);
+ formatMenu.addSeparator();
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(seqLimits);
+ formatMenu.add(idRightAlign);
+ formatMenu.add(hiddenMarkers);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelsMenuItem);
+ formatMenu.add(showNonconservedMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(grpsFromSelection);
+ // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
+ //selectMenu.addSeparator();
+ //selectMenu.add(listenToViewSelections);
+ }
+
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSeqFeaturesHeight_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void followHighlight_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showNpFeats_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void showProducts_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void buildSortByAnnotationScoresMenu()
+ {
+ }
+
+ protected void extractScores_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void closeMenuItem_actionPerformed(boolean b)
+ {
+ }
+
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void clustalColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void taylorColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void strandColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void turnColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ }
+
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+ {
+ }
+
+ protected void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void pasteThis_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)
+ {
+ }
+
+ public void seqDBRef_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void createEPS(java.io.File f)
+ {
+ }
+
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void jpred_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void saveAs_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ public void vamsasStore_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void findPdbId_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void enterPdbId_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void invertColSel_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void tabSelectionChanged(int sel)
+ {
+
+ }
+
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
+
+ }
+
+ public void tabbedPane_focusGained(FocusEvent e)
+ {
+ requestFocus();
+ }
+
+ public void save_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void reload_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void newView_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void textColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void expandViews_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void gatherViews_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void buildTreeMenu()
+ {
+
+ }
+
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void alignmentProperties()
+ {
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff