X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=533a698749c7de93ea7707de3c1477c6fec0c59c;hb=28787d9646cca5dd77190930f59b7ff32cf995b4;hp=a89228e585d1736b9e67ee0db1a75943911cff89;hpb=be5a6a44e9eb355110f3b414d6b0fd5419f5936c;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index a89228e..533a698 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,30 +1,51 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, 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 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ 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 { @@ -114,6 +135,17 @@ public class GAlignFrame extends JInternalFrame protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); + JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); @@ -122,7 +154,7 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); @@ -147,9 +179,8 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); JMenuItem deleteGroups = new JMenuItem(); @@ -196,7 +227,9 @@ public class GAlignFrame extends JInternalFrame JMenu jMenu2 = new JMenu(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); protected ButtonGroup colours = new ButtonGroup(); @@ -209,16 +242,22 @@ 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(); @@ -236,7 +275,7 @@ public class GAlignFrame extends JInternalFrame GridLayout gridLayout1 = new GridLayout(); JMenu jMenu3 = new JMenu(); - + JMenuItem showAllSeqs = new JMenuItem(); JMenuItem showAllColumns = new JMenuItem(); @@ -247,6 +286,12 @@ public class GAlignFrame extends JInternalFrame 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(); @@ -270,7 +315,7 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); - + protected JMenuItem gatherViews = new JMenuItem(); protected JMenuItem expandViews = new JMenuItem(); @@ -278,21 +323,29 @@ public class GAlignFrame extends JInternalFrame JMenuItem pageSetup = new JMenuItem(); JMenuItem alignmentProperties = new JMenuItem(); - + JMenu tooltipSettingsMenu = new JMenu(); - private JMenuItem justifyLeftMenuItem=new JMenuItem(); + private JMenuItem justifyLeftMenuItem = new JMenuItem(); - private JMenuItem justifyRightMenuItem=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 showConsensusProfile=new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); + public GAlignFrame() { try @@ -349,8 +402,7 @@ 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, @@ -400,7 +452,10 @@ public class GAlignFrame extends JInternalFrame colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); - + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); + colours.add(tcoffeeColour); + colours.add(RNAInteractionColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); @@ -416,9 +471,6 @@ public class GAlignFrame extends JInternalFrame switch (index) { - case ColourSchemeProperty.NONE: - noColourmenuItem.setSelected(true); - break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -473,10 +525,34 @@ public class GAlignFrame extends JInternalFrame break; + case ColourSchemeProperty.TCOFFEE: + tcoffeeColour.setSelected(true); + break; + + case ColourSchemeProperty.PURINEPYRIMIDINE: + purinePyrimidineColour.setSelected(true); + + break; + + case ColourSchemeProperty.RNAINTERACTION: + RNAInteractionColour.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; + } } @@ -554,7 +630,7 @@ public class GAlignFrame extends JInternalFrame public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); - } + } }); remove2LeftMenuItem.setText("Remove Left"); @@ -607,21 +683,23 @@ public class GAlignFrame extends JInternalFrame } }); justifyLeftMenuItem.setText("Left Justify Alignment"); - justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - justifyLeftMenuItem_actionPerformed(e); - } - }); + 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); - } - }); + 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() @@ -640,15 +718,16 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - showUnconservedMenuItem.setText("Show Unconserved"); - showUnconservedMenuItem.setState(false); - showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showUnconservedMenuItem_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() @@ -667,13 +746,14 @@ public class GAlignFrame extends JInternalFrame } }); sortLengthMenuItem.setText("By Length"); - sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortLengthMenuItem_actionPerformed(e); - } - }); + 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() { @@ -732,6 +812,7 @@ public class GAlignFrame extends JInternalFrame }); this.getContentPane().setLayout(borderLayout1); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + alignFrameMenuBar.setBackground(Color.lightGray); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); @@ -827,6 +908,39 @@ 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); + } + }); + + RNAInteractionColour.setText("RNA Interaction type"); + RNAInteractionColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + RNAInteractionColour_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() @@ -979,15 +1093,12 @@ public class GAlignFrame extends JInternalFrame showSeqFeatures_actionPerformed(actionEvent); } }); -/* - * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); - showSeqFeaturesHeight.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent actionEvent) - { - showSeqFeaturesHeight_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() { @@ -996,7 +1107,7 @@ public class GAlignFrame extends JInternalFrame { showDbRefs_actionPerformed(e); } - + }); showNpFeatsMenuitem.setText("Show Non-Positional Features"); showNpFeatsMenuitem.addActionListener(new ActionListener() @@ -1006,7 +1117,7 @@ public class GAlignFrame extends JInternalFrame { showNpFeats_actionPerformed(e); } - + }); showGroupConservation.setText("Group Conservation"); showGroupConservation.addActionListener(new ActionListener() @@ -1016,7 +1127,7 @@ public class GAlignFrame extends JInternalFrame { showGroupConservation_actionPerformed(e); } - + }); showGroupConsensus.setText("Group Consensus"); @@ -1027,7 +1138,7 @@ public class GAlignFrame extends JInternalFrame { showGroupConsensus_actionPerformed(e); } - + }); showConsensusHistogram.setText("Show Consensus Histogram"); showConsensusHistogram.addActionListener(new ActionListener() @@ -1037,17 +1148,27 @@ public class GAlignFrame extends JInternalFrame { showConsensusHistogram_actionPerformed(e); } - + + }); + showSequenceLogo.setText("Show Consensus Logo"); + showSequenceLogo.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showSequenceLogo_actionPerformed(e); + } + }); - showConsensusProfile.setText("Show Consensus Logo"); - showConsensusProfile.addActionListener(new ActionListener() + normaliseSequenceLogo.setText("Normalise Consensus Logo"); + normaliseSequenceLogo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - showConsensusProfile_actionPerformed(e); + normaliseSequenceLogo_actionPerformed(e); } - + }); applyAutoAnnotationSettings.setText("Apply to all groups"); applyAutoAnnotationSettings.setState(false); @@ -1059,7 +1180,7 @@ public class GAlignFrame extends JInternalFrame { applyAutoAnnotationSettings_actionPerformed(e); } - + }); nucleotideColour.setText("Nucleotide"); @@ -1070,6 +1191,19 @@ 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() @@ -1190,6 +1324,7 @@ public class GAlignFrame extends JInternalFrame LoadtreeMenuItem_actionPerformed(e); } }); + scaleAbove.setVisible(false); scaleAbove.setText("Scale Above"); scaleAbove.addActionListener(new java.awt.event.ActionListener() @@ -1240,9 +1375,9 @@ public class GAlignFrame extends JInternalFrame { followHighlight_actionPerformed(); } - + }); - + modifyPID.setText("Modify Identity Threshold..."); modifyPID.addActionListener(new java.awt.event.ActionListener() { @@ -1336,7 +1471,7 @@ public class GAlignFrame extends JInternalFrame } }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based - // score extraction + // score extraction showProducts.setText("Get Cross References"); /* * showProducts.addActionListener(new ActionListener() { @@ -1344,8 +1479,8 @@ 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) { @@ -1369,6 +1504,16 @@ 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() { @@ -1387,6 +1532,31 @@ 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() @@ -1431,6 +1601,7 @@ public class GAlignFrame extends JInternalFrame 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) @@ -1439,6 +1610,7 @@ public class GAlignFrame extends JInternalFrame } }); showAllColumns.setText("All Columns"); + showAllColumns.setToolTipText("Ctrl+H toggles column visiblity."); showAllColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1448,6 +1620,7 @@ public class GAlignFrame extends JInternalFrame }); hideMenu.setText("Hide"); hideSelSequences.setText("Selected Sequences"); + hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity."); hideSelSequences.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1456,6 +1629,7 @@ public class GAlignFrame extends JInternalFrame } }); hideSelColumns.setText("Selected Columns"); + hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity."); hideSelColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1463,6 +1637,34 @@ public class GAlignFrame extends JInternalFrame 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() { @@ -1637,9 +1839,10 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeRedundancyMenuItem); editMenu.addSeparator(); // dont add these yet in the CVS build - they cannot be undone! - editMenu.add(justifyLeftMenuItem); - editMenu.add(justifyRightMenuItem); - editMenu.addSeparator(); + // 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); @@ -1652,16 +1855,17 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(annotationPanelMenuItem); autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); - autoAnnMenu.add(showConsensusProfile); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normaliseSequenceLogo); autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); - //viewMenu.add(showSeqFeaturesHeight); - - viewMenu.add(featureSettings); + // viewMenu.add(showSeqFeaturesHeight); + + viewMenu.add(openFeatureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); viewMenu.add(tooltipSettingsMenu); @@ -1684,6 +1888,10 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + colourMenu.add(RNAInteractionColour); + // colourMenu.add(covariationColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1691,6 +1899,7 @@ 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(); @@ -1700,6 +1909,7 @@ 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(""); @@ -1726,8 +1936,12 @@ public class GAlignFrame extends JInternalFrame 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); @@ -1742,7 +1956,7 @@ public class GAlignFrame extends JInternalFrame formatMenu.add(colourTextMenuItem); formatMenu.add(renderGapsMenuItem); formatMenu.add(centreColumnLabelsMenuItem); - formatMenu.add(showUnconservedMenuItem); + formatMenu.add(showNonconservedMenuItem); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem); @@ -1751,85 +1965,119 @@ 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) + { + // 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 showConsensusProfile_actionPerformed(ActionEvent e) + 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) @@ -2033,6 +2281,19 @@ public class GAlignFrame extends JInternalFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + protected void RNAInteractionColour_actionPerformed(ActionEvent e) + { + } + + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -2116,6 +2377,33 @@ 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) @@ -2185,6 +2473,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -2195,6 +2488,11 @@ public class GAlignFrame extends JInternalFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) {