X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=7ea492f9ee4ffb07ab5f64d0f38d2c90a3c92759;hb=a9f33c53af5893a2437b2cf7a417b96862101102;hp=9260b231b758c73c82b27989efa63aed7019e440;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 9260b23..7ea492f 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,6 +1,6 @@ /* - * 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -113,6 +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(); @@ -149,8 +156,6 @@ 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 +216,22 @@ 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 +314,8 @@ 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(); @@ -413,6 +426,8 @@ 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")); @@ -483,6 +498,16 @@ 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); @@ -846,6 +871,31 @@ 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() @@ -1065,6 +1115,16 @@ 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); @@ -1360,8 +1420,8 @@ 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) { @@ -1385,6 +1445,16 @@ 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() { @@ -1403,6 +1473,29 @@ 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() @@ -1702,6 +1795,7 @@ 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); @@ -1710,7 +1804,7 @@ 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); @@ -1733,6 +1827,8 @@ 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); @@ -1740,6 +1836,7 @@ 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(); @@ -1749,6 +1846,7 @@ 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(""); @@ -1804,6 +1902,21 @@ 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) @@ -2104,6 +2217,14 @@ public class GAlignFrame extends JInternalFrame { } + protected void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + } + + /* + * protected void covariationColour_actionPerformed(ActionEvent e) { } + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { } @@ -2256,6 +2377,11 @@ public class GAlignFrame extends JInternalFrame } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + + } + public void associatedData_actionPerformed(ActionEvent e) { @@ -2266,6 +2392,11 @@ public class GAlignFrame extends JInternalFrame } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + + } + public void showAllSeqs_actionPerformed(ActionEvent e) {