X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=4a7c3f07eaf4257cceb1ee19b75709ff0d3e365b;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=2325de1dd37e5eee4fe55d4d5659bd191509a0b6;hpb=aff93619ba53584f9b01970832558331951d9dbf;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 2325de1..4a7c3f0 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,20 +1,19 @@ /* - * 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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. * - * 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 + * 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 . */ package jalview.jbgui; @@ -114,6 +113,13 @@ 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(); + JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); @@ -122,7 +128,7 @@ 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 +153,8 @@ 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 +201,9 @@ 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(); @@ -215,10 +222,16 @@ public class GAlignFrame extends JInternalFrame 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 +249,7 @@ public class GAlignFrame extends JInternalFrame GridLayout gridLayout1 = new GridLayout(); JMenu jMenu3 = new JMenu(); - + JMenuItem showAllSeqs = new JMenuItem(); JMenuItem showAllColumns = new JMenuItem(); @@ -276,7 +289,7 @@ 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(); @@ -284,21 +297,27 @@ 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 showSequenceLogo=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 applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); + public GAlignFrame() { try @@ -355,8 +374,7 @@ 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, @@ -406,6 +424,8 @@ public class GAlignFrame extends JInternalFrame colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); @@ -422,9 +442,6 @@ public class GAlignFrame extends JInternalFrame switch (index) { - case ColourSchemeProperty.NONE: - noColourmenuItem.setSelected(true); - break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -479,10 +496,25 @@ public class GAlignFrame extends JInternalFrame 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; + } } @@ -560,7 +592,7 @@ public class GAlignFrame extends JInternalFrame public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); - } + } }); remove2LeftMenuItem.setText("Remove Left"); @@ -613,21 +645,23 @@ 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() @@ -646,15 +680,16 @@ 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() @@ -673,13 +708,14 @@ 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() { @@ -833,6 +869,31 @@ 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() @@ -985,15 +1046,12 @@ 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() { @@ -1002,7 +1060,7 @@ public class GAlignFrame extends JInternalFrame { showDbRefs_actionPerformed(e); } - + }); showNpFeatsMenuitem.setText("Show Non-Positional Features"); showNpFeatsMenuitem.addActionListener(new ActionListener() @@ -1012,7 +1070,7 @@ public class GAlignFrame extends JInternalFrame { showNpFeats_actionPerformed(e); } - + }); showGroupConservation.setText("Group Conservation"); showGroupConservation.addActionListener(new ActionListener() @@ -1022,7 +1080,7 @@ public class GAlignFrame extends JInternalFrame { showGroupConservation_actionPerformed(e); } - + }); showGroupConsensus.setText("Group Consensus"); @@ -1033,7 +1091,7 @@ public class GAlignFrame extends JInternalFrame { showGroupConsensus_actionPerformed(e); } - + }); showConsensusHistogram.setText("Show Consensus Histogram"); showConsensusHistogram.addActionListener(new ActionListener() @@ -1043,7 +1101,7 @@ public class GAlignFrame extends JInternalFrame { showConsensusHistogram_actionPerformed(e); } - + }); showSequenceLogo.setText("Show Consensus Logo"); showSequenceLogo.addActionListener(new ActionListener() @@ -1053,7 +1111,7 @@ public class GAlignFrame extends JInternalFrame { showSequenceLogo_actionPerformed(e); } - + }); applyAutoAnnotationSettings.setText("Apply to all groups"); applyAutoAnnotationSettings.setState(false); @@ -1065,7 +1123,7 @@ public class GAlignFrame extends JInternalFrame { applyAutoAnnotationSettings_actionPerformed(e); } - + }); nucleotideColour.setText("Nucleotide"); @@ -1246,9 +1304,9 @@ public class GAlignFrame extends JInternalFrame { followHighlight_actionPerformed(); } - + }); - + modifyPID.setText("Modify Identity Threshold..."); modifyPID.addActionListener(new java.awt.event.ActionListener() { @@ -1342,7 +1400,7 @@ 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() { @@ -1375,6 +1433,16 @@ 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() { @@ -1393,6 +1461,29 @@ 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() @@ -1482,7 +1573,7 @@ public class GAlignFrame extends JInternalFrame } }); // TODO: should be hidden if no selection exists. - hideAllButSelection.setText("All but Selected Rregion (Shift+Ctrl+H)"); + hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)"); hideAllButSelection.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1491,7 +1582,8 @@ public class GAlignFrame extends JInternalFrame } }); showAllhidden.setText("All Sequences and Columns"); - showAllhidden.setToolTipText("H toggles visibility of hidden or selected regions."); + showAllhidden + .setToolTipText("H toggles visibility of hidden or selected regions."); showAllhidden.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1697,8 +1789,8 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); - //viewMenu.add(showSeqFeaturesHeight); - + // viewMenu.add(showSeqFeaturesHeight); + viewMenu.add(featureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); @@ -1722,6 +1814,8 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1729,6 +1823,7 @@ 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(); @@ -1738,6 +1833,7 @@ 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(""); @@ -1769,7 +1865,7 @@ public class GAlignFrame extends JInternalFrame hideMenu.add(hideSelSequences); hideMenu.add(hideAllSelection); hideMenu.add(hideAllButSelection); - + formatMenu.add(font); formatMenu.addSeparator(); formatMenu.add(wrapMenuItem); @@ -1784,7 +1880,7 @@ 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); @@ -1793,103 +1889,112 @@ 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 showAllhidden_actionPerformed(ActionEvent e) + 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) @@ -2093,6 +2198,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -2245,6 +2358,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -2255,6 +2373,11 @@ public class GAlignFrame extends JInternalFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) {