From b5699e7d9cc2045f623609948ee10a736256abc4 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 13 Dec 2016 10:46:04 +0000 Subject: [PATCH] JAL-2361 adding items to applet colour menus, TCoffee colour to desktop popup menu, extracted PopupMenu.buildColourMenu() --- resources/lang/Messages.properties | 3 +- resources/lang/Messages_es.properties | 3 +- src/jalview/appletgui/APopupMenu.java | 24 ++++- src/jalview/appletgui/AlignFrame.java | 3 +- src/jalview/gui/PopupMenu.java | 180 ++++++++++++++++++++------------- src/jalview/jbgui/GAlignFrame.java | 5 +- 6 files changed, 136 insertions(+), 82 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 74bb2d1..2a69f14 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -210,7 +210,7 @@ label.hide_all = Hide all label.add_reference_annotations = Add reference annotations label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).
Accepts regular expressions - search Help for 'regex' for details. label.colour_text = Colour Text -label.show_non_conversed = Show nonconserved +label.show_non_conserved = Show nonconserved label.overview_window = Overview Window label.none = None label.above_identity_threshold = Above Identity Threshold @@ -669,7 +669,6 @@ action.set_text_colour = Text Colour... label.structure = Structure label.show_pdbstruct_dialog = 3D Structure Data... label.view_rna_structure = VARNA 2D Structure -label.above_identity_percentage = Above % Identity label.create_sequence_details_report_annotation_for = Annotation for {0} label.sequence_details_for = Sequence Details for {0} label.sequence_name = Sequence Name diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 8da7dcb..9756ab4 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -199,7 +199,7 @@ label.average_distance_bloslum62 = Distancia Media Usando BLOSUM62 label.neighbour_blosum62 = Neighbour Joining usando BLOSUM62 label.show_annotations = Mostrar anotaciones label.colour_text = Color del texto -label.show_non_conversed = Mostrar no conservadas +label.show_non_conserved = Mostrar no conservadas label.overview_window = Ventana resumen label.none = Ninguno label.above_identity_threshold = Por encima del umbral de identidad @@ -621,7 +621,6 @@ label.from_file = desde fichero label.enter_pdb_id = Introducir PDB Id label.text_colour = Color del texto label.structure = Estructura -label.above_identity_percentage = Sobre % identidad label.create_sequence_details_report_annotation_for = Anotación para {0} label.sequence_details_for = Detalles de la secuencia para {0} label.sequence_name = Nombre de la secuencia diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 9080cdd..39c6a8b 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -45,6 +45,7 @@ import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; @@ -113,6 +114,8 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem nucleotideMenuItem = new MenuItem(); + MenuItem purinePyrimidineMenuItem = new MenuItem(); + Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); @@ -563,6 +566,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { nucleotideMenuItem_actionPerformed(); } + else if (source == purinePyrimidineMenuItem) + { + purinePyrimidineColour_actionPerformed(); + } else if (source == userDefinedColour) { @@ -894,6 +901,9 @@ public class APopupMenu extends java.awt.PopupMenu implements nucleotideMenuItem.setLabel(MessageManager .getString("label.nucleotide")); nucleotideMenuItem.addActionListener(this); + purinePyrimidineMenuItem.setLabel(MessageManager + .getString("label.purine_pyrimidine")); + purinePyrimidineMenuItem.addActionListener(this); conservationMenuItem.addItemListener(this); abovePIDColour.addItemListener(this); colourMenu.setLabel(MessageManager.getString("label.group_colour")); @@ -904,7 +914,7 @@ public class APopupMenu extends java.awt.PopupMenu implements sequenceDetails.addActionListener(this); selSeqDetails.addActionListener(this); displayNonconserved.setLabel(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconserved.setState(false); displayNonconserved.addItemListener(this); showText.setLabel(MessageManager.getString("action.text")); @@ -948,6 +958,7 @@ public class APopupMenu extends java.awt.PopupMenu implements colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); + colourMenu.add(purinePyrimidineMenuItem); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(abovePIDColour); @@ -976,7 +987,7 @@ public class APopupMenu extends java.awt.PopupMenu implements buriedColour.setLabel(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(this); abovePIDColour.setLabel(MessageManager - .getString("label.above_identity_percentage")); + .getString("label.above_identity_threshold")); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); @@ -984,7 +995,8 @@ public class APopupMenu extends java.awt.PopupMenu implements PIDColour.setLabel(MessageManager .getString("label.percentage_identity")); PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62"); + BLOSUM62Colour.setLabel(MessageManager + .getString("label.blosum62_score")); BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel(MessageManager .getString("label.conservation")); @@ -1089,6 +1101,12 @@ public class APopupMenu extends java.awt.PopupMenu implements refresh(); } + public void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + protected void abovePIDColour_itemStateChanged() { SequenceGroup sg = getGroup(); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index f830fe6..14b3e6a 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -296,6 +296,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { RNAHelixColour.setEnabled(false); purinePyrimidineColour.setEnabled(false); + nucleotideColour.setEnabled(false); } // Some JVMS send keyevents to Top frame or lowest panel, // Havent worked out why yet. So add to both this frame and seqCanvas for @@ -3436,7 +3437,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.colour_text")); colourTextMenuItem.addItemListener(this); displayNonconservedMenuItem.setLabel(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconservedMenuItem.addItemListener(this); wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 0166e75..838b534 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -52,6 +52,7 @@ import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; @@ -119,9 +120,13 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem RNAInteractionColour; JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); @@ -149,8 +154,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -239,23 +242,6 @@ public class PopupMenu extends JPopupMenu this.ap = ap; sequence = seq; - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(purinePyrimidineColour); - colours.add(RNAInteractionColour); - for (String ff : FileFormat.getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); @@ -526,6 +512,10 @@ public class PopupMenu extends JPopupMenu { purinePyrimidineColour.setSelected(true); } + else if (sg.cs instanceof NucleotideColourScheme) + { + nucleotideColour.setSelected(true); + } /* * else if (sg.cs instanceof CovariationColourScheme) { @@ -1121,9 +1111,9 @@ public class PopupMenu extends JPopupMenu outline_actionPerformed(); } }); - nucleotideMenuItem + nucleotideColour .setText(MessageManager.getString("label.nucleotide")); - nucleotideMenuItem.addActionListener(new ActionListener() + nucleotideColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1162,7 +1152,7 @@ public class PopupMenu extends JPopupMenu } }); displayNonconserved.setText(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1338,47 +1328,9 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); sequenceMenu.add(makeReferenceSeq); - colourMenu.add(textColour); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideMenuItem); - if (ap.getAlignment().isNucleotide()) - { - colourMenu.add(purinePyrimidineColour); - } - SortedMap userColourSchemes = UserDefinedColours - .getUserColourSchemes(); - if (userColourSchemes != null) - { - for (String userColour : userColourSchemes.keySet()) - { - JMenuItem item = new JMenuItem(userColour); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.add(item); - } - } - colourMenu.add(userDefinedColour); + buildColourMenu(); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -1482,7 +1434,7 @@ public class PopupMenu extends JPopupMenu } }); abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); + .getString("label.above_identity_threshold")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1533,6 +1485,16 @@ public class PopupMenu extends JPopupMenu } }); + tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + tcoffeeColorScheme_actionPerformed(); + } + }); + /* * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { @@ -1540,19 +1502,89 @@ public class PopupMenu extends JPopupMenu */ conservationMenuItem.setText(MessageManager - .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); + .getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); } }); } /** + * Adds items to the group colour sub-menu + */ + protected void buildColourMenu() + { + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + colourMenu.add(tcoffeeColour); + + SortedMap userColourSchemes = UserDefinedColours + .getUserColourSchemes(); + if (userColourSchemes != null) + { + for (String userColour : userColourSchemes.keySet()) + { + JMenuItem item = new JMenuItem(userColour); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + colourMenu.add(userDefinedColour); + + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + + /* + * add some of these items to a ButtonGroup so their + * selection is mutually exclusive + */ + ButtonGroup colours = new ButtonGroup(); + colours.add(noColourmenuItem); + colours.add(clustalColour); + colours.add(BLOSUM62Colour); + colours.add(PIDColour); + colours.add(zappoColour); + colours.add(taylorColour); + colours.add(hydrophobicityColour); + colours.add(helixColour); + colours.add(strandColour); + colours.add(turnColour); + colours.add(buriedColour); + colours.add(purinePyrimidineColour); + colours.add(tcoffeeColour); + colours.add(nucleotideColour); + colours.add(userDefinedColour); + colours.add(abovePIDColour); + // colours.add(RNAInteractionColour); + + } + + /** * Check for any annotations on the underlying dataset sequences (for the * current selection group) which are not 'on the alignment'.If any are found, * enable the option to add them to the alignment. The criteria for 'on the @@ -1838,6 +1870,12 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void tcoffeeColorScheme_actionPerformed() + { + getGroup().cs = new TCoffeeColourScheme(getGroup()); + refresh(); + } + /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 294596c..088ddfa 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -687,7 +687,7 @@ public class GAlignFrame extends JInternalFrame } }); showNonconservedMenuItem.setText(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); showNonconservedMenuItem.setState(false); showNonconservedMenuItem.addActionListener(new ActionListener() { @@ -2471,8 +2471,7 @@ public class GAlignFrame extends JInternalFrame */ conservationMenuItem = new JCheckBoxMenuItem( - MessageManager - .getString("action.by_conservation")); + MessageManager.getString("action.by_conservation")); conservationMenuItem.addActionListener(new ActionListener() { @Override -- 1.7.10.2