X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=b523763b3ff023681b0a53c04faa5879752ede66;hb=a3e8ea093f8e93e6ebaf6faa7a44615fdf75b020;hp=af7766a8ca5dd3c889081cea16ca208f95f39d07;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index af7766a..b523763 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 @@ -17,13 +17,35 @@ */ package jalview.jbgui; -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; -import javax.swing.event.*; - -import jalview.schemes.*; +import jalview.schemes.ColourSchemeProperty; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.GridLayout; +import java.awt.Toolkit; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; + +import javax.swing.BorderFactory; +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JMenu; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JTabbedPane; +import javax.swing.SwingUtilities; +import javax.swing.event.ChangeEvent; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; public class GAlignFrame extends JInternalFrame { @@ -113,6 +135,15 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); + JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); @@ -149,8 +180,6 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); - JMenuItem deleteGroups = new JMenuItem(); JMenuItem delete = new JMenuItem(); @@ -211,16 +240,22 @@ public class GAlignFrame extends JInternalFrame protected JMenu showProducts = new JMenu(); - public JMenuItem featureSettings = new JMenuItem(); + public JMenuItem openFeatureSettings = 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(); @@ -303,6 +338,8 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); @@ -363,8 +400,7 @@ public class GAlignFrame extends JInternalFrame if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - radioItem - .removeActionListener(radioItem.getActionListeners()[0]); + radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, @@ -414,6 +450,9 @@ public class GAlignFrame extends JInternalFrame colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); + colours.add(tcoffeeColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); @@ -484,6 +523,20 @@ public class GAlignFrame extends JInternalFrame break; + case ColourSchemeProperty.TCOFFEE: + tcoffeeColour.setSelected(true); + break; + + case ColourSchemeProperty.PURINEPYRIMIDINE: + purinePyrimidineColour.setSelected(true); + + break; + /* + * case ColourSchemeProperty.COVARIATION: + * covariationColour.setSelected(true); + * + * break; + */ case ColourSchemeProperty.USER_DEFINED: userDefinedColour.setSelected(true); @@ -492,7 +545,7 @@ public class GAlignFrame extends JInternalFrame default: noColourmenuItem.setSelected(true); break; - + } } @@ -847,6 +900,31 @@ public class GAlignFrame extends JInternalFrame 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() @@ -1066,6 +1144,16 @@ public class GAlignFrame extends JInternalFrame } }); + normaliseSequenceLogo.setText("Normalise Consensus Logo"); + normaliseSequenceLogo.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + normaliseSequenceLogo_actionPerformed(e); + } + + }); applyAutoAnnotationSettings.setText("Apply to all groups"); applyAutoAnnotationSettings.setState(false); applyAutoAnnotationSettings.setVisible(true); @@ -1087,6 +1175,19 @@ public class GAlignFrame extends JInternalFrame nucleotideColour_actionPerformed(e); } }); + + tcoffeeColour.setText("T-Coffee scores"); + tcoffeeColour.setEnabled(false); + tcoffeeColour.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + tcoffeeColorScheme_actionPerformed(e); + } + }); + deleteGroups.setText("Undefine groups"); deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit() @@ -1207,6 +1308,7 @@ public class GAlignFrame extends JInternalFrame LoadtreeMenuItem_actionPerformed(e); } }); + scaleAbove.setVisible(false); scaleAbove.setText("Scale Above"); scaleAbove.addActionListener(new java.awt.event.ActionListener() @@ -1361,8 +1463,8 @@ public class GAlignFrame extends JInternalFrame * public void actionPerformed(ActionEvent e) { * showProducts_actionPerformed(e); } }); */ - featureSettings.setText("Feature Settings..."); - featureSettings.addActionListener(new ActionListener() + openFeatureSettings.setText("Feature Settings..."); + openFeatureSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { @@ -1386,6 +1488,16 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -1404,6 +1516,31 @@ public class GAlignFrame extends JInternalFrame autoCalculate_actionPerformed(e); } }); + sortByTree.setText("Sort Alignment With New Tree"); + sortByTree + .setToolTipText("Enable this to automatically sort
the alignment when you open
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("When selected, selections in this view will mirror
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() @@ -1703,6 +1840,7 @@ public class GAlignFrame extends JInternalFrame autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normaliseSequenceLogo); autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); @@ -1711,7 +1849,7 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(showSeqFeatures); // viewMenu.add(showSeqFeaturesHeight); - viewMenu.add(featureSettings); + viewMenu.add(openFeatureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); viewMenu.add(tooltipSettingsMenu); @@ -1734,6 +1872,9 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + // colourMenu.add(covariationColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1741,6 +1882,7 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(rnahelicesColour); calculateMenu.add(sort); calculateMenu.add(calculateTree); calculateMenu.addSeparator(); @@ -1750,6 +1892,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(showTranslation); calculateMenu.add(showProducts); calculateMenu.add(autoCalculate); + calculateMenu.add(sortByTree); calculateMenu.addSeparator(); calculateMenu.add(extractScores); webServiceNoServices = new JMenuItem(""); @@ -1805,6 +1948,22 @@ public class GAlignFrame extends JInternalFrame 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 normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + } protected void showAllhidden_actionPerformed(ActionEvent e) @@ -2105,6 +2264,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -2188,6 +2355,33 @@ public class GAlignFrame extends JInternalFrame protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + + } + + /** + * Template method to handle the 'load T-Coffee scores' menu event. + *

+ * Subclasses override this method to provide a custom action. + * + * @param event + * The raised event + */ + protected void loadScores_actionPerformed(ActionEvent event) + { + + } + + /** + * Template method to handle the 'Color T-Coffee scores' menu event. + *

+ * Subclasses override this method to provide a custom action. + * + * @param event + * The raised event + */ + protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) + { + } protected void jpred_actionPerformed(ActionEvent e) @@ -2257,6 +2451,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -2267,6 +2466,11 @@ public class GAlignFrame extends JInternalFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) {