X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=5a0357e23d7353d2c2b6899ddab60ef01b43690a;hb=628a03775931b98995f07682b1cbc3b9d09f3e73;hp=7d931cf4bfa8ffc3740808ff9b88c807295db74d;hpb=58e98265790efe8b1fece777a33842063ec1e808;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 7d931cf..5a0357e 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,21 +1,32 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * - * AM Waterhouse - *******************/ - + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.jbgui; -import javax.swing.*; -import java.awt.event.*; import java.awt.*; +import java.awt.event.*; +import javax.swing.*; +import javax.swing.event.*; -import jalview.gui.Preferences; -import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.*; -public class GAlignFrame extends JInternalFrame +public class GAlignFrame + extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenu fileMenu = new JMenu(); @@ -25,6 +36,7 @@ public class GAlignFrame extends JInternalFrame 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(); @@ -32,8 +44,8 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem remove2RightMenuItem = new JMenuItem(); protected JMenuItem removeGappedColumnMenuItem = new JMenuItem(); protected JMenuItem removeAllGapsMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); protected JMenuItem sortIDMenuItem = new JMenuItem(); protected JMenuItem sortGroupMenuItem = new JMenuItem(); @@ -45,12 +57,13 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem clustalAlignMenuItem = new JMenuItem(); BorderLayout borderLayout1 = new BorderLayout(); public JLabel statusBar = new JLabel(); - protected JMenu saveAlignmentMenu = new JMenu(); + protected JMenuItem saveAlignmentMenu = new JMenuItem(); protected JMenu outputTextboxMenu = new JMenu(); protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem hydrophobicityColour = new + JRadioButtonMenuItem(); protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); @@ -60,21 +73,21 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); JMenuItem overviewMenuItem = new JMenuItem(); protected JMenuItem undoMenuItem = new JMenuItem(); protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); JMenuItem printMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); JMenuItem findMenuItem = new JMenuItem(); JMenu searchMenu = new JMenu(); - protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem(); protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); JMenuItem deleteGroups = new JMenuItem(); JMenuItem delete = new JMenuItem(); @@ -83,60 +96,30 @@ public class GAlignFrame extends JInternalFrame JMenu jMenu1 = new JMenu(); JMenuItem pasteNew = new JMenuItem(); JMenuItem pasteThis = new JMenuItem(); - protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); JMenuItem createPNG = new JMenuItem(); protected JMenuItem font = new JMenuItem(); - protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem(); JMenuItem epsFile = new JMenuItem(); JMenuItem LoadtreeMenuItem = new JMenuItem(); - JMenuItem jpred = new JMenuItem(); - protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); - JMenuItem modifyPID = new JMenuItem(); - JMenuItem modifyConservation = new JMenuItem(); + public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); protected JMenu sortByTreeMenu = new JMenu(); - JMenu jMenu2 = new JMenu(); - JMenu sort = new JMenu(); + protected JMenu sort = new JMenu(); JMenu calculate = new JMenu(); - JMenuItem msaAlignMenuItem = new JMenuItem(); + JMenu jMenu2 = new JMenu(); + JMenuItem padGapsMenuitem = new JMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem(); + protected JTabbedPane tabbedPane = new JTabbedPane(); + protected JMenuItem featureSettings = new JMenuItem(); + public GAlignFrame() { - ButtonGroup colours = new ButtonGroup(); - 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); - - noColourmenuItem.setSelected(true); - String defaultColour = Preferences.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.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break; - case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break; - case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break; - case ColourSchemeProperty.TURN : turnColour.setSelected(true); break; - case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break; - case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break; - case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break; - } - } try @@ -144,44 +127,187 @@ public class GAlignFrame extends JInternalFrame jbInit(); setJMenuBar(alignFrameMenuBar); - JMenuItem item; // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) { - item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i)); - saveAlignmentMenu.add( item ); + for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) + { + JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats. + elementAt( + i)); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - saveAs_actionPerformed(e); + outputText_actionPerformed(e); } }); - item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i)); - item.addActionListener(new java.awt.event.ActionListener() + outputTextboxMenu.add(item); + } + } + catch (Exception e) + { + } + + + 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 e) + public void actionPerformed(ActionEvent evt) { - outputText_actionPerformed(e); + userDefinedColour_actionPerformed(evt); } }); - - outputTextboxMenu.add( item ); + colourMenu.insert(radioItem, 15); + colours.add(radioItem); } - } - catch(Exception e) + 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); + + setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); + + + } + + public void setColourSelected(String defaultColour) + { + + if (defaultColour != null) { - e.printStackTrace(); + int index = ColourSchemeProperty.getColourIndexFromName(defaultColour); + + switch (index) + { + case ColourSchemeProperty.NONE: + noColourmenuItem.setSelected(true); + break; + case ColourSchemeProperty.CLUSTAL: + clustalColour.setSelected(true); + + break; + + case ColourSchemeProperty.BLOSUM: + BLOSUM62Colour.setSelected(true); + + break; + + case ColourSchemeProperty.PID: + PIDColour.setSelected(true); + + break; + + case ColourSchemeProperty.ZAPPO: + zappoColour.setSelected(true); + + break; + + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; + + case ColourSchemeProperty.HYDROPHOBIC: + hydrophobicityColour.setSelected(true); + + break; + + case ColourSchemeProperty.HELIX: + helixColour.setSelected(true); + + break; + + case ColourSchemeProperty.STRAND: + strandColour.setSelected(true); + + break; + + case ColourSchemeProperty.TURN: + turnColour.setSelected(true); + + break; + + case ColourSchemeProperty.BURIED: + buriedColour.setSelected(true); + + break; + + case ColourSchemeProperty.NUCLEOTIDE: + nucleotideColour.setSelected(true); + + break; + + case ColourSchemeProperty.USER_DEFINED: + userDefinedColour.setSelected(true); + + break; + } } } - private void jbInit() throws Exception + + private void jbInit() + throws Exception { fileMenu.setMnemonic('F'); fileMenu.setText("File"); saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save"); + saveAlignmentMenu.setText("Save As"); + saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false)); + saveAlignmentMenu.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + saveAlignmentMenu_actionPerformed(e); + } + }); closeMenuItem.setMnemonic('C'); closeMenuItem.setText("Close"); closeMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -198,8 +324,10 @@ public class GAlignFrame extends JInternalFrame 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() + java.awt.event.KeyEvent.VK_A, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + selectAllSequenceMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { @@ -208,9 +336,10 @@ public class GAlignFrame extends JInternalFrame }); 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() + getKeyStroke( + java.awt.event.KeyEvent.VK_ESCAPE, 0, false)); + deselectAllSequenceMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { @@ -242,7 +371,8 @@ public class GAlignFrame extends JInternalFrame } }); removeGappedColumnMenuItem.setText("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() + removeGappedColumnMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { @@ -275,7 +405,7 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - sortPairwiseMenuItem.setText("Pairwise Identity"); + sortPairwiseMenuItem.setText("by Pairwise Identity"); sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -283,7 +413,7 @@ public class GAlignFrame extends JInternalFrame sortPairwiseMenuItem_actionPerformed(e); } }); - sortIDMenuItem.setText("ID"); + sortIDMenuItem.setText("by ID"); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -291,7 +421,7 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem_actionPerformed(e); } }); - sortGroupMenuItem.setText("Group"); + sortGroupMenuItem.setText("by Group"); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -300,7 +430,8 @@ public class GAlignFrame extends JInternalFrame } }); removeRedundancyMenuItem.setText("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() + removeRedundancyMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { @@ -308,14 +439,15 @@ public class GAlignFrame extends JInternalFrame } }); pairwiseAlignmentMenuItem.setText("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() + pairwiseAlignmentMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { pairwiseAlignmentMenuItem_actionPerformed(e); } }); - PCAMenuItem.setText("Principal Component Analysis..."); + PCAMenuItem.setText("Principal Component Analysis"); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -323,15 +455,17 @@ public class GAlignFrame extends JInternalFrame PCAMenuItem_actionPerformed(e); } }); - averageDistanceTreeMenuItem.setText("Average Distance Using % Identity..."); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() + averageDistanceTreeMenuItem.setText( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { averageDistanceTreeMenuItem_actionPerformed(e); } }); - neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity..."); + neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity"); neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -339,16 +473,23 @@ public class GAlignFrame extends JInternalFrame neighbourTreeMenuItem_actionPerformed(e); } }); - clustalAlignMenuItem.setText("Clustal Alignment..."); - clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() + this.getContentPane().setLayout(borderLayout1); + alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + alignFrameMenuBar.addAncestorListener(new AncestorListener() { - public void actionPerformed(ActionEvent e) + public void ancestorAdded(AncestorEvent event) + { + alignFrameMenuBar_ancestorAdded(event); + } + + public void ancestorRemoved(AncestorEvent event) + { + } + + public void ancestorMoved(AncestorEvent event) { - clustalAlignMenuItem_actionPerformed(e); } }); - this.getContentPane().setLayout(borderLayout1); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); @@ -444,15 +585,17 @@ public class GAlignFrame extends JInternalFrame BLOSUM62Colour_actionPerformed(e); } }); - avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62..."); - avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() + avDistanceTreeBlosumMenuItem.setText( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event. + ActionListener() { public void actionPerformed(ActionEvent e) { avTreeBlosumMenuItem_actionPerformed(e); } }); - njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62..."); + njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62"); njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -462,7 +605,7 @@ public class GAlignFrame extends JInternalFrame }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText("Show Annotations"); - annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation ); + annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true)); annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -486,7 +629,7 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - overviewMenuItem.setText("Overview Window..."); + overviewMenuItem.setText("Overview Window"); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -497,8 +640,9 @@ public class GAlignFrame extends JInternalFrame undoMenuItem.setEnabled(false); undoMenuItem.setMnemonic('Z'); undoMenuItem.setText("Undo"); - undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + undoMenuItem.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) @@ -558,8 +702,9 @@ public class GAlignFrame extends JInternalFrame } }); findMenuItem.setText("Find..."); - findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + 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) @@ -569,9 +714,11 @@ public class GAlignFrame extends JInternalFrame }); searchMenu.setText("Search"); - abovePIDThreshold.setText("Above Identity threshold"); - abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { + abovePIDThreshold.setText("Above Identity Threshold"); + abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { abovePIDThreshold_actionPerformed(e); } }); @@ -600,8 +747,9 @@ public class GAlignFrame extends JInternalFrame } }); copy.setText("Copy"); - copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_C, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); copy.setMnemonic(KeyEvent.VK_C); copy.addActionListener(new java.awt.event.ActionListener() @@ -612,8 +760,9 @@ public class GAlignFrame extends JInternalFrame } }); cut.setText("Cut"); - cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_X, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); cut.setMnemonic(KeyEvent.VK_X); cut.addActionListener(new java.awt.event.ActionListener() { @@ -632,9 +781,10 @@ public class GAlignFrame extends JInternalFrame }); jMenu1.setMnemonic('V'); jMenu1.setText("Paste"); - pasteNew.setText("to new alignment"); - pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. - KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + pasteNew.setText("To New Alignment"); + pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_V, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -642,7 +792,7 @@ public class GAlignFrame extends JInternalFrame pasteNew_actionPerformed(e); } }); - pasteThis.setText("add to this alignment"); + pasteThis.setText("Add To This Alignment"); pasteThis.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -663,10 +813,10 @@ public class GAlignFrame extends JInternalFrame { public void actionPerformed(ActionEvent e) { - createPNG_actionPerformed(e); + createPNG(null); } }); - createPNG.setActionCommand("Save as PNG Image"); + createPNG.setActionCommand("Save As PNG Image"); createPNG.setText("PNG"); font.setText("Font..."); font.addActionListener(new java.awt.event.ActionListener() @@ -677,6 +827,7 @@ public class GAlignFrame extends JInternalFrame } }); fullSeqId.setText("Show Full Sequence ID"); + fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true)); fullSeqId.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -689,23 +840,16 @@ public class GAlignFrame extends JInternalFrame { public void actionPerformed(ActionEvent e) { - epsFile_actionPerformed(e); + createEPS(null); } }); LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); LoadtreeMenuItem.setText("Load Assocated Tree"); - LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) - { - LoadtreeMenuItem_actionPerformed(e); - } - }); - jpred.setText("JPred..."); - jpred.addActionListener(new java.awt.event.ActionListener() + LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - jpred_actionPerformed(e); + LoadtreeMenuItem_actionPerformed(e); } }); scaleAbove.setVisible(false); @@ -753,14 +897,51 @@ public class GAlignFrame extends JInternalFrame modifyConservation_actionPerformed(e); } }); - sortByTreeMenu.setText("Tree Order"); - jMenu2.setText("Save as"); + sortByTreeMenu.setText("By Tree Order"); sort.setText("Sort"); calculate.setText("Calculate Tree"); - msaAlignMenuItem.setText("Muscle Alignment..."); - msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - msaAlignMenuItem_actionPerformed(e); + + jMenu2.setText("Export"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + padGapsMenuitem_actionPerformed(e); + } + }); + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + vamsasStore_actionPerformed(e); + } + }); + showTranslation.setText("Translate cDNA"); + showTranslation.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(e); + } + }); + + tabbedPane.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent ece) + { + + tabSelected(); + } + }); + featureSettings.setEnabled(false); + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + featureSettings_actionPerformed(e); } }); alignFrameMenuBar.add(fileMenu); @@ -769,6 +950,8 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(vamsasStore); fileMenu.add(saveAlignmentMenu); fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); @@ -783,6 +966,7 @@ public class GAlignFrame extends JInternalFrame editMenu.add(copy); editMenu.add(jMenu1); editMenu.add(delete); + editMenu.addSeparator(); editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); @@ -793,26 +977,29 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(removeRedundancyMenuItem); + editMenu.addSeparator(); + editMenu.add(padGapsMenuitem); searchMenu.add(findMenuItem); viewMenu.add(font); - viewMenu.add(fullSeqId); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); + viewMenu.add(fullSeqId); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); - viewMenu.addSeparator(); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); - colourMenu.add(noColourmenuItem); colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); colourMenu.add(PIDColour); @@ -836,385 +1023,335 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); - calculateMenu.add(webService); - webService.add(clustalAlignMenuItem); - webService.add(jpred); - webService.add(msaAlignMenuItem); + calculateMenu.add(showTranslation); + webServiceNoServices=new JMenuItem(""); + webService.add(webServiceNoServices); this.getContentPane().add(statusBar, BorderLayout.SOUTH); + this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); jMenu1.add(pasteNew); jMenu1.add(pasteThis); - jMenu2.add(htmlMenuItem); - jMenu2.add(epsFile); - jMenu2.add(createPNG); sort.add(sortIDMenuItem); sort.add(sortGroupMenuItem); - sort.add(sortByTreeMenu); sort.add(sortPairwiseMenuItem); calculate.add(averageDistanceTreeMenuItem); calculate.add(neighbourTreeMenuItem); calculate.add(avDistanceTreeBlosumMenuItem); calculate.add(njTreeBlosumMenuItem); - } - - protected void saveAs_actionPerformed(ActionEvent e) - { - + jMenu2.add(htmlMenuItem); + jMenu2.add(epsFile); + jMenu2.add(createPNG); } protected void outputText_actionPerformed(ActionEvent e) { - } protected void htmlMenuItem_actionPerformed(ActionEvent e) { - } - protected void closeMenuItem_actionPerformed(ActionEvent e) { - } protected void redoMenuItem_actionPerformed(ActionEvent e) { - } protected void undoMenuItem_actionPerformed(ActionEvent e) { - } - protected void 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 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 clustalAlignMenuItem_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 noColourmenuItem_actionPerformed(ActionEvent e) { - } - protected void conservationMenuItem_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) { - + protected void abovePIDThreshold_actionPerformed(ActionEvent e) + { } public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) { - } protected void nucleotideColour_actionPerformed(ActionEvent e) { - } protected void deleteGroups_actionPerformed(ActionEvent e) { - } - protected void copy_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) { - } - protected void createPNG_actionPerformed(ActionEvent e) + public void createPNG(java.io.File f) { - } protected void font_actionPerformed(ActionEvent e) { - } protected void fullSeqId_actionPerformed(ActionEvent e) { + } + + public void createEPS(java.io.File f) + { + } + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + { } - protected void epsFile_actionPerformed(ActionEvent e) + protected void jpred_actionPerformed(ActionEvent e) { + } + protected void scaleAbove_actionPerformed(ActionEvent e) + { } - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + protected void scaleLeft_actionPerformed(ActionEvent e) + { + } + protected void scaleRight_actionPerformed(ActionEvent e) + { } - protected void jpred_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed(ActionEvent e) { + } + protected void modifyConservation_actionPerformed(ActionEvent e) + { } - protected void scaleAbove_actionPerformed(ActionEvent e) + protected void preferences_actionPerformed(ActionEvent e) { + } + protected void msaAlignMenuItem_actionPerformed(ActionEvent e) + { } - protected void scaleLeft_actionPerformed(ActionEvent e) + protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) { + } + protected void saveAlignmentMenu_actionPerformed(ActionEvent e) + { } - protected void scaleRight_actionPerformed(ActionEvent e) + protected void padGapsMenuitem_actionPerformed(ActionEvent e) { + } + protected void ClustalRealign_actionPerformed(ActionEvent e) + { } - protected void modifyPID_actionPerformed(ActionEvent e) + public void vamsasStore_actionPerformed(ActionEvent e) { } - protected void modifyConservation_actionPerformed(ActionEvent e) + public void vamsasLoad_actionPerformed(ActionEvent e) { } - protected void preferences_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(ActionEvent e) { } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) { + public void tabSelected() + { } + public void featureSettings_actionPerformed(ActionEvent e) + { + + } }