X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=de1487a6785251663546b136aee0ec0866a03565;hb=21c29b20790ac555b2e2a124a034f6c6b4486270;hp=a12a74fb3bc33a663a65ad58d348be46902809ea;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index a12a74f..de1487a 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,30 +1,52 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 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 jalview.util.MessageManager; + +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 { @@ -68,6 +90,8 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem sortIDMenuItem = new JMenuItem(); + protected JMenuItem sortLengthMenuItem = new JMenuItem(); + protected JMenuItem sortGroupMenuItem = new JMenuItem(); protected JMenu sortByAnnotScore = new JMenu(); @@ -112,6 +136,15 @@ 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(); @@ -120,6 +153,8 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); + JMenuItem htmlMenuItem = new JMenuItem(); JMenuItem overviewMenuItem = new JMenuItem(); @@ -144,7 +179,7 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); JMenuItem deleteGroups = new JMenuItem(); @@ -186,12 +221,16 @@ public class GAlignFrame extends JInternalFrame protected JMenu sort = new JMenu(); - JMenu calculate = new JMenu(); + protected JMenu calculateTree = new JMenu(); JMenu jMenu2 = new JMenu(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); JMenuItem vamsasStore = new JMenuItem(); @@ -202,16 +241,22 @@ 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(); @@ -240,6 +285,12 @@ 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(); @@ -262,6 +313,8 @@ 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(); @@ -270,6 +323,28 @@ public class GAlignFrame extends JInternalFrame JMenuItem alignmentProperties = new JMenuItem(); + JMenu tooltipSettingsMenu = new JMenu(); + + private JMenuItem justifyLeftMenuItem = new JMenuItem(); + + private JMenuItem justifyRightMenuItem = new JMenuItem(); + + JMenu autoAnnMenu = new JMenu(); + + protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); + + private JMenuItem grpsFromSelection = new JMenuItem(); + public GAlignFrame() { try @@ -326,13 +401,12 @@ 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, - "Remove from default list?", - "Remove user defined colour", + MessageManager.getString("label.remove_from_default_list"), + MessageManager.getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { @@ -377,6 +451,9 @@ 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")); @@ -393,9 +470,6 @@ public class GAlignFrame extends JInternalFrame switch (index) { - case ColourSchemeProperty.NONE: - noColourmenuItem.setSelected(true); - break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -450,10 +524,29 @@ 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); break; + case ColourSchemeProperty.NONE: + default: + noColourmenuItem.setSelected(true); + break; + } } @@ -525,6 +618,15 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem_actionPerformed(e); } }); + grpsFromSelection.setText("Make Groups for selection"); + grpsFromSelection.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + makeGrpsFromSelection_actionPerformed(e); + } + }); + remove2LeftMenuItem.setText("Remove Left"); remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit() @@ -574,6 +676,24 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem_actionPerformed(e); } }); + justifyLeftMenuItem.setText("Left Justify Alignment"); + justifyLeftMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + justifyLeftMenuItem_actionPerformed(e); + } + }); + justifyRightMenuItem.setText("Right Justify Alignment"); + justifyRightMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + justifyRightMenuItem_actionPerformed(e); + } + }); viewBoxesMenuItem.setText("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -592,6 +712,16 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); + showNonconservedMenuItem.setText("Show nonconserved"); + showNonconservedMenuItem.setState(false); + showNonconservedMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showUnconservedMenuItem_actionPerformed(e); + } + }); sortPairwiseMenuItem.setText("by Pairwise Identity"); sortPairwiseMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -609,6 +739,15 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem_actionPerformed(e); } }); + sortLengthMenuItem.setText("By Length"); + sortLengthMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sortLengthMenuItem_actionPerformed(e); + } + }); sortGroupMenuItem.setText("by Group"); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -762,6 +901,31 @@ 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() @@ -914,6 +1078,96 @@ 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); } }); + */ + showDbRefsMenuitem.setText("Show Database Refs"); + showDbRefsMenuitem.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showDbRefs_actionPerformed(e); + } + + }); + showNpFeatsMenuitem.setText("Show Non-Positional Features"); + showNpFeatsMenuitem.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showNpFeats_actionPerformed(e); + } + + }); + showGroupConservation.setText("Group Conservation"); + showGroupConservation.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showGroupConservation_actionPerformed(e); + } + + }); + + showGroupConsensus.setText("Group Consensus"); + showGroupConsensus.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showGroupConsensus_actionPerformed(e); + } + + }); + showConsensusHistogram.setText("Show Consensus Histogram"); + showConsensusHistogram.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showConsensusHistogram_actionPerformed(e); + } + + }); + showSequenceLogo.setText("Show Consensus Logo"); + showSequenceLogo.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + showSequenceLogo_actionPerformed(e); + } + + }); + 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); + applyAutoAnnotationSettings.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + applyAutoAnnotationSettings_actionPerformed(e); + } + + }); + nucleotideColour.setText("Nucleotide"); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { @@ -922,6 +1176,19 @@ 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() @@ -1042,6 +1309,7 @@ public class GAlignFrame extends JInternalFrame LoadtreeMenuItem_actionPerformed(e); } }); + scaleAbove.setVisible(false); scaleAbove.setText("Scale Above"); scaleAbove.addActionListener(new java.awt.event.ActionListener() @@ -1082,6 +1350,18 @@ public class GAlignFrame extends JInternalFrame centreColumnLabels_actionPerformed(e); } }); + followHighlightMenuItem.setVisible(true); + followHighlightMenuItem.setState(true); + followHighlightMenuItem.setText("Automatic Scrolling"); + followHighlightMenuItem.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + followHighlight_actionPerformed(); + } + + }); modifyPID.setText("Modify Identity Threshold..."); modifyPID.addActionListener(new java.awt.event.ActionListener() @@ -1137,7 +1417,7 @@ public class GAlignFrame extends JInternalFrame }); sortByAnnotScore.setVisible(false); - calculate.setText("Calculate Tree"); + calculateTree.setText("Calculate Tree"); jMenu2.setText("Export Image"); padGapsMenuitem.setText("Pad Gaps"); @@ -1176,7 +1456,7 @@ 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() { @@ -1184,8 +1464,8 @@ 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) { @@ -1209,6 +1489,16 @@ 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() { @@ -1227,6 +1517,31 @@ 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() @@ -1271,6 +1586,7 @@ 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) @@ -1279,6 +1595,7 @@ 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) @@ -1288,6 +1605,7 @@ 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) @@ -1296,6 +1614,7 @@ 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) @@ -1303,6 +1622,34 @@ 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() { @@ -1435,7 +1782,8 @@ public class GAlignFrame extends JInternalFrame alignmentProperties(); } }); - + tooltipSettingsMenu.setText("Sequence ID Tooltip"); + autoAnnMenu.setText("Autocalculated Annotation"); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); @@ -1475,6 +1823,11 @@ public class GAlignFrame extends JInternalFrame editMenu.add(removeAllGapsMenuItem); editMenu.add(removeRedundancyMenuItem); editMenu.addSeparator(); + // dont add these yet in the CVS build - they cannot be undone! + // Excluded from Jalview 2.5 release - undo needs to be implemented. + // editMenu.add(justifyLeftMenuItem); + // editMenu.add(justifyRightMenuItem); + // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); viewMenu.add(newView); viewMenu.add(expandViews); @@ -1483,10 +1836,24 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(jMenu3); viewMenu.add(hideMenu); viewMenu.addSeparator(); + viewMenu.add(followHighlightMenuItem); viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normaliseSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); - viewMenu.add(featureSettings); + // viewMenu.add(showSeqFeaturesHeight); + + viewMenu.add(openFeatureSettings); + tooltipSettingsMenu.add(showDbRefsMenuitem); + tooltipSettingsMenu.add(showNpFeatsMenuitem); + viewMenu.add(tooltipSettingsMenu); viewMenu.addSeparator(); viewMenu.add(alignmentProperties); viewMenu.addSeparator(); @@ -1506,6 +1873,9 @@ 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); @@ -1513,8 +1883,9 @@ public class GAlignFrame extends JInternalFrame colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(rnahelicesColour); calculateMenu.add(sort); - calculateMenu.add(calculate); + calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); @@ -1522,6 +1893,7 @@ 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(""); @@ -1529,13 +1901,14 @@ public class GAlignFrame extends JInternalFrame pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); sort.add(sortByTreeMenu); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); + calculateTree.add(averageDistanceTreeMenuItem); + calculateTree.add(neighbourTreeMenuItem); + calculateTree.add(avDistanceTreeBlosumMenuItem); + calculateTree.add(njTreeBlosumMenuItem); jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); @@ -1547,8 +1920,12 @@ 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); @@ -1563,6 +1940,7 @@ public class GAlignFrame extends JInternalFrame formatMenu.add(colourTextMenuItem); formatMenu.add(renderGapsMenuItem); formatMenu.add(centreColumnLabelsMenuItem); + formatMenu.add(showNonconservedMenuItem); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem); @@ -1570,6 +1948,120 @@ public class GAlignFrame extends JInternalFrame selectMenu.add(invertSequenceMenuItem); selectMenu.add(invertColSel); selectMenu.add(deleteGroups); + selectMenu.add(grpsFromSelection); + // TODO - determine if the listenToViewSelections button is needed : see bug + // JAL-574 + // selectMenu.addSeparator(); + // selectMenu.add(listenToViewSelections); + } + + protected void 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 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) @@ -1693,6 +2185,10 @@ public class GAlignFrame extends JInternalFrame { } + protected void sortLengthMenuItem_actionPerformed(ActionEvent e) + { + } + protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { } @@ -1769,6 +2265,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -1852,6 +2356,33 @@ 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) @@ -1921,6 +2452,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -1931,6 +2467,11 @@ public class GAlignFrame extends JInternalFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) {