X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=37073437e703b65b3b3ad4bac5f22360023122de;hb=567c2595554096f10feab130153f97286f3f7d80;hp=c99d894e9156edb217cf1e138dfa1ee713414bd8;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index c99d894..3707343 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 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -25,8 +25,9 @@ import jalview.api.SplitContainerI; import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; -import jalview.schemes.ColourSchemeProperty; +import jalview.io.FileFormats; import jalview.util.MessageManager; +import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; @@ -50,12 +51,10 @@ 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.KeyStroke; -import javax.swing.SwingUtilities; import javax.swing.event.ChangeEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; @@ -66,15 +65,13 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem closeMenuItem = new JMenuItem(); - protected JMenu colourMenu = new JMenu(); - protected JMenu webService = new JMenu(); protected JMenuItem webServiceNoServices; - public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenu sortByAnnotScore = new JMenu(); @@ -82,86 +79,57 @@ public class GAlignFrame extends JInternalFrame protected JMenu outputTextboxMenu = new JMenu(); - protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - - 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(); - - public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); protected JMenuItem undoMenuItem = new JMenuItem(); protected JMenuItem redoMenuItem = new JMenuItem(); - public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); - - public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); - - public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); - - public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); - JMenuItem copy = new JMenuItem(); JMenuItem cut = new JMenuItem(); JMenu pasteMenu = new JMenu(); - public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem applyToAllGroups; + + protected JMenu colourMenu = new JMenu(); + + protected JMenuItem textColour; - public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem conservationMenuItem; - public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + protected JMenuItem modifyConservation; - public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem abovePIDThreshold; - public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + protected JMenuItem modifyPID; - protected JMenuItem modifyConservation = new JMenuItem(); + protected JMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); protected JMenu sort = new JMenu(); - protected JMenu calculateTree = new JMenu(); + protected JMenuItem calculateTree = new JMenuItem(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); @@ -169,13 +137,15 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); - protected ButtonGroup colours = new ButtonGroup(); - protected JMenuItem showTranslation = new JMenuItem(); + protected JMenuItem showReverse = new JMenuItem(); + + protected JMenuItem showReverseComplement = new JMenuItem(); + protected JMenu showProducts = new JMenu(); - protected JMenuItem rnahelicesColour = new JMenuItem(); + protected JMenuItem runGroovy = new JMenuItem(); protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); @@ -241,10 +211,9 @@ public class GAlignFrame extends JInternalFrame setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { - JMenuItem item = new JMenuItem( - jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); + JMenuItem item = new JMenuItem(ff); item.addActionListener(new ActionListener() { @@ -262,7 +231,7 @@ public class GAlignFrame extends JInternalFrame System.err.println(e.toString()); } - if (!jalview.util.Platform.isAMac()) + if (!Platform.isAMac()) { closeMenuItem.setMnemonic('C'); outputTextboxMenu.setMnemonic('T'); @@ -273,186 +242,12 @@ public class GAlignFrame extends JInternalFrame pasteMenu.setMnemonic('P'); reload.setMnemonic('R'); } - - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); - - while (userColours.hasMoreElements()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColours.nextElement().toString()); - radioItem.setName("USER_DEFINED"); - radioItem.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) - { - if (evt.isControlDown() - || SwingUtilities.isRightMouseButton(evt)) - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JOptionPane.showInternalConfirmDialog( - jalview.gui.Desktop.desktop, - MessageManager - .getString("label.remove_from_default_list"), - MessageManager - .getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - jalview.gui.UserDefinedColours - .removeColourFromDefaults(radioItem.getText()); - colourMenu.remove(radioItem); - } - else - { - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } - } - } - }); - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.insert(radioItem, 15); - colours.add(radioItem); - } - } - 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(userDefinedColour); - 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( - Preferences.DEFAULT_COLOUR, "None")); - } - - public void setColourSelected(String defaultColour) - { - - if (defaultColour != null) - { - int index = ColourSchemeProperty - .getColourIndexFromName(defaultColour); - - switch (index) - { - case ColourSchemeProperty.CLUSTAL: - clustalColour.setSelected(true); - - break; - - case ColourSchemeProperty.BLOSUM: - BLOSUM62Colour.setSelected(true); - - break; - - case ColourSchemeProperty.PID: - PIDColour.setSelected(true); - - break; - - case ColourSchemeProperty.ZAPPO: - zappoColour.setSelected(true); - - break; - - case ColourSchemeProperty.TAYLOR: - taylorColour.setSelected(true); - break; - - case ColourSchemeProperty.HYDROPHOBIC: - hydrophobicityColour.setSelected(true); - - break; - - case ColourSchemeProperty.HELIX: - helixColour.setSelected(true); - - break; - - case ColourSchemeProperty.STRAND: - strandColour.setSelected(true); - - break; - - case ColourSchemeProperty.TURN: - turnColour.setSelected(true); - - break; - - case ColourSchemeProperty.BURIED: - buriedColour.setSelected(true); - - break; - - case ColourSchemeProperty.NUCLEOTIDE: - nucleotideColour.setSelected(true); - - 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; - - } - } - } private void jbInit() throws Exception { + initColourMenu(); + JMenuItem saveAs = new JMenuItem( MessageManager.getString("action.save_as")); ActionListener al = new ActionListener() @@ -463,6 +258,8 @@ public class GAlignFrame extends JInternalFrame saveAs_actionPerformed(e); } }; + + // FIXME getDefaultToolkit throws an exception in Headless mode KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | KeyEvent.SHIFT_MASK, false); @@ -651,7 +448,7 @@ 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() { @@ -736,26 +533,6 @@ public class GAlignFrame extends JInternalFrame PCAMenuItem_actionPerformed(e); } }); - JMenuItem averageDistanceTreeMenuItem = new JMenuItem( - MessageManager.getString("label.average_distance_identity")); - averageDistanceTreeMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); - JMenuItem neighbourTreeMenuItem = new JMenuItem( - MessageManager.getString("label.neighbour_joining_identity")); - neighbourTreeMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - neighbourTreeMenuItem_actionPerformed(e); - } - }); this.getContentPane().setLayout(new BorderLayout()); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); @@ -765,167 +542,7 @@ public class GAlignFrame extends JInternalFrame statusBar.setText(MessageManager.getString("label.status_bar")); outputTextboxMenu.setText(MessageManager .getString("label.out_to_textbox")); - clustalColour.setText(MessageManager.getString("label.clustalx")); - clustalColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setText(MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); - strandColour.setText(MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(e); - } - }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(e); - } - }); - userDefinedColour.setText(MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour - .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); - BLOSUM62Colour - .setText(MessageManager.getString("label.blosum62_score")); - BLOSUM62Colour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); - nucleotideColour.setText(MessageManager.getString("label.nucleotide")); - nucleotideColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - nucleotideColour_actionPerformed(e); - } - }); - purinePyrimidineColour.setText(MessageManager - .getString("label.purine_pyrimidine")); - purinePyrimidineColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(e); - } - }); - - RNAInteractionColour.setText("RNA Interaction type"); - RNAInteractionColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - RNAInteractionColour_actionPerformed(e); - } - }); - /* - * covariationColour.setText("Covariation"); - * covariationColour.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); } - * }); - */ - - JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem( - MessageManager.getString("label.average_distance_bloslum62")); - avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - avTreeBlosumMenuItem_actionPerformed(e); - } - }); - JMenuItem njTreeBlosumMenuItem = new JMenuItem( - MessageManager.getString("label.neighbour_blosum62")); - njTreeBlosumMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - njTreeBlosumMenuItem_actionPerformed(e); - } - }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText(MessageManager .getString("label.show_annotations")); @@ -1021,7 +638,8 @@ public class GAlignFrame extends JInternalFrame sortAnnotations_actionPerformed(); } }); - colourTextMenuItem.setText(MessageManager + colourTextMenuItem = new JCheckBoxMenuItem( + MessageManager .getString("label.colour_text")); colourTextMenuItem.addActionListener(new ActionListener() { @@ -1093,25 +711,6 @@ public class GAlignFrame extends JInternalFrame }; addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); - conservationMenuItem.setText(MessageManager - .getString("action.by_conservation")); - conservationMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(e); - } - }); - noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new ActionListener() { @@ -1164,16 +763,6 @@ public class GAlignFrame extends JInternalFrame }; addMenuActionAndAccelerator(keyStroke, findMenuItem, al); - abovePIDThreshold.setText(MessageManager - .getString("label.above_identity_threshold")); - abovePIDThreshold.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - abovePIDThreshold_actionPerformed(e); - } - }); showSeqFeatures.setText(MessageManager .getString("label.show_sequence_features")); showSeqFeatures.addActionListener(new ActionListener() @@ -1319,28 +908,6 @@ public class GAlignFrame extends JInternalFrame } }); - nucleotideColour.setText(MessageManager.getString("label.nucleotide")); - nucleotideColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - nucleotideColour_actionPerformed(e); - } - }); - - tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores")); - tcoffeeColour.setEnabled(false); - tcoffeeColour.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - tcoffeeColorScheme_actionPerformed(e); - } - }); - JMenuItem deleteGroups = new JMenuItem( MessageManager.getString("action.undefine_groups")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit @@ -1355,8 +922,19 @@ public class GAlignFrame extends JInternalFrame }; addMenuActionAndAccelerator(keyStroke, deleteGroups, al); + JMenuItem annotationColumn = new JMenuItem( + MessageManager.getString("action.select_by_annotation")); + annotationColumn.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + annotationColumn_actionPerformed(e); + } + }); + JMenuItem createGroup = new JMenuItem( - MessageManager.getString("action.create_groups")); + MessageManager.getString("action.create_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() @@ -1452,16 +1030,6 @@ public class GAlignFrame extends JInternalFrame }; addMenuActionAndAccelerator(keyStroke, pasteThis, al); - applyToAllGroups.setText(MessageManager - .getString("label.apply_colour_to_all_groups")); - applyToAllGroups.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - applyToAllGroups_actionPerformed(e); - } - }); JMenuItem createPNG = new JMenuItem("PNG"); createPNG.addActionListener(new ActionListener() { @@ -1586,26 +1154,6 @@ public class GAlignFrame extends JInternalFrame }); - JMenuItem modifyPID = new JMenuItem( - MessageManager.getString("label.modify_identity_thereshold")); - modifyPID.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - modifyPID_actionPerformed(e); - } - }); - modifyConservation.setText(MessageManager - .getString("label.modify_conservation_thereshold")); - modifyConservation.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - modifyConservation_actionPerformed(e); - } - }); sortByTreeMenu .setText(MessageManager.getString("action.by_tree_order")); sort.setText(MessageManager.getString("action.sort")); @@ -1614,7 +1162,7 @@ public class GAlignFrame extends JInternalFrame @Override public void menuSelected(MenuEvent e) { - buildTreeMenu(); + buildTreeSortMenu(); } @Override @@ -1651,8 +1199,8 @@ public class GAlignFrame extends JInternalFrame }); sortByAnnotScore.setVisible(false); - calculateTree - .setText(MessageManager.getString("action.calculate_tree")); + calculateTree.setText(MessageManager + .getString("action.calculate_tree_pca")); padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); padGapsMenuitem.setState(jalview.bin.Cache @@ -1676,14 +1224,33 @@ public class GAlignFrame extends JInternalFrame vamsasStore_actionPerformed(e); } }); - showTranslation.setText(MessageManager - .getString("label.translate_cDNA")); - showTranslation.addActionListener(new ActionListener() + showTranslation.setText(MessageManager + .getString("label.translate_cDNA")); + showTranslation.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(e); + } + }); + showReverse.setText(MessageManager.getString("label.reverse")); + showReverse.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showReverse_actionPerformed(false); + } + }); + showReverseComplement.setText(MessageManager + .getString("label.reverse_complement")); + showReverseComplement.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showTranslation_actionPerformed(e); + showReverse_actionPerformed(true); } }); @@ -1703,6 +1270,18 @@ public class GAlignFrame extends JInternalFrame // for show products actions see AlignFrame.canShowProducts showProducts.setText(MessageManager.getString("label.get_cross_refs")); + runGroovy.setText(MessageManager.getString("label.run_groovy")); + runGroovy.setToolTipText(MessageManager + .getString("label.run_groovy_tip")); + runGroovy.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + runGroovy_actionPerformed(); + } + }); + JMenuItem openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() @@ -1724,39 +1303,6 @@ public class GAlignFrame extends JInternalFrame } }); - JMenuItem annotationColour = new JMenuItem( - MessageManager.getString("action.by_annotation")); - annotationColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - annotationColour_actionPerformed(e); - } - }); - - JMenuItem annotationColumn = new JMenuItem( - MessageManager.getString("action.select_by_annotation")); - annotationColumn.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - annotationColumn_actionPerformed(e); - } - }); - - rnahelicesColour.setText(MessageManager - .getString("action.by_rna_helixes")); - rnahelicesColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - rnahelicesColour_actionPerformed(e); - } - }); - JMenuItem associatedData = new JMenuItem( MessageManager.getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() @@ -1998,7 +1544,19 @@ public class GAlignFrame extends JInternalFrame @Override public void mousePressed(MouseEvent e) { - tabbedPane_mousePressed(e); + if (e.isPopupTrigger()) // Mac + { + tabbedPane_mousePressed(e); + } + } + + @Override + public void mouseReleased(MouseEvent e) + { + if (e.isPopupTrigger()) // Windows + { + tabbedPane_mousePressed(e); + } } }); tabbedPane.addFocusListener(new FocusAdapter() @@ -2051,18 +1609,10 @@ public class GAlignFrame extends JInternalFrame tabbedPane.setToolTipText("" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + ""); - JMenuItem textColour = new JMenuItem( - MessageManager.getString("action.set_text_colour")); - textColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - textColour_actionPerformed(e); - } - }); + formatMenu.setText(MessageManager.getString("action.format")); JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); + idRightAlign.setText(MessageManager .getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() @@ -2120,6 +1670,19 @@ public class GAlignFrame extends JInternalFrame alignmentProperties(); } }); + JMenuItem selectHighlighted = new JMenuItem( + MessageManager.getString("action.select_highlighted_columns")); + selectHighlighted.setToolTipText(MessageManager + .getString("tooltip.select_highlighted_columns")); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + selectHighlightedColumns_actionPerformed(actionEvent); + } + }; + selectHighlighted.addActionListener(al); JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); JMenu autoAnnMenu = new JMenu( @@ -2137,6 +1700,7 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); + fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); fileMenu.add(reload); @@ -2155,6 +1719,9 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(associatedData); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); + + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.add(cut); @@ -2175,6 +1742,13 @@ public class GAlignFrame extends JInternalFrame // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); + showMenu.add(showAllColumns); + showMenu.add(showAllSeqs); + showMenu.add(showAllhidden); + hideMenu.add(hideSelColumns); + hideMenu.add(hideSelSequences); + hideMenu.add(hideAllSelection); + hideMenu.add(hideAllButSelection); viewMenu.add(newView); viewMenu.add(expandViews); viewMenu.add(gatherViews); @@ -2218,55 +1792,33 @@ public class GAlignFrame extends JInternalFrame autoAnnMenu.add(showGroupConsensus); annotationsMenu.add(autoAnnMenu); - colourMenu.add(applyToAllGroups); - colourMenu.add(textColour); - colourMenu.addSeparator(); - 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(RNAInteractionColour); - // colourMenu.add(covariationColour); - colourMenu.add(tcoffeeColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - colourMenu.add(annotationColour); - colourMenu.add(rnahelicesColour); + + sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + sort.add(sortByTreeMenu); calculateMenu.add(sort); calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); + // calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); + calculateMenu.add(showReverse); + calculateMenu.add(showReverseComplement); calculateMenu.add(showProducts); calculateMenu.add(autoCalculate); calculateMenu.add(sortByTree); calculateMenu.addSeparator(); + calculateMenu.add(expandAlignment); calculateMenu.add(extractScores); + calculateMenu.addSeparator(); + calculateMenu.add(runGroovy); + webServiceNoServices = new JMenuItem( MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); - pasteMenu.add(pasteNew); - pasteMenu.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortLengthMenuItem); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - sort.add(sortByTreeMenu); exportImageMenu.add(htmlMenuItem); exportImageMenu.add(epsFile); exportImageMenu.add(createPNG); @@ -2278,13 +1830,6 @@ public class GAlignFrame extends JInternalFrame this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); statusPanel.add(statusBar, null); this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); - showMenu.add(showAllColumns); - showMenu.add(showAllSeqs); - showMenu.add(showAllhidden); - hideMenu.add(hideSelColumns); - hideMenu.add(hideSelSequences); - hideMenu.add(hideAllSelection); - hideMenu.add(hideAllButSelection); formatMenu.add(font); formatMenu.addSeparator(); @@ -2312,13 +1857,129 @@ public class GAlignFrame extends JInternalFrame selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); selectMenu.add(annotationColumn); - calculateMenu.add(expandAlignment); + selectMenu.add(selectHighlighted); // TODO - determine if the listenToViewSelections button is needed : see bug // JAL-574 // selectMenu.addSeparator(); // selectMenu.add(listenToViewSelections); } + protected void configureSelectMenu() + { + // TODO Auto-generated method stub + + } + + /** + * Constructs the entries on the Colour menu (but does not add them to the + * menu). + */ + protected void initColourMenu() + { + applyToAllGroups = new JCheckBoxMenuItem( + MessageManager.getString("label.apply_colour_to_all_groups")); + applyToAllGroups.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); + } + }); + + textColour = new JMenuItem( + MessageManager.getString("label.text_colour")); + textColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + + conservationMenuItem = new JCheckBoxMenuItem( + MessageManager.getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(conservationMenuItem + .isSelected()); + } + }); + + abovePIDThreshold = new JCheckBoxMenuItem( + MessageManager.getString("label.above_identity_threshold")); + abovePIDThreshold.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); + } + }); + modifyPID = new JMenuItem( + MessageManager.getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyPID_actionPerformed(); + } + }); + modifyConservation = new JMenuItem( + MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyConservation_actionPerformed(); + } + }); + + annotationColour = new JMenuItem( + MessageManager.getString("action.by_annotation")); + annotationColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(); + } + }); + } + + protected void selectHighlightedColumns_actionPerformed( + ActionEvent actionEvent) + { + // TODO Auto-generated method stub + + } + + /** + * Generate the reverse sequence (or reverse complement if the flag is true) + * and add it to the alignment + * + * @param complement + */ + protected void showReverse_actionPerformed(boolean complement) + { + } + + /** + * Try to run script in a Groovy console, having first ensured that this + * alignframe is set as currentAlignFrame in Desktop + */ + protected void runGroovy_actionPerformed() + { + + } + /** * Adds the given action listener and key accelerator to the given menu item. * Also saves in a lookup table to support lookup of action by key stroke. @@ -2460,13 +2121,6 @@ public class GAlignFrame extends JInternalFrame } - protected void showSeqFeaturesHeight_actionPerformed( - ActionEvent actionEvent) - { - // TODO Auto-generated method stub - - } - protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub @@ -2639,83 +2293,11 @@ public class GAlignFrame extends JInternalFrame { } - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - } - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void clustalColour_actionPerformed(ActionEvent e) - { - } - - protected void zappoColour_actionPerformed(ActionEvent e) - { - } - - protected void taylorColour_actionPerformed(ActionEvent e) - { - } - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) - { - } - - protected void helixColour_actionPerformed(ActionEvent e) - { - } - - protected void strandColour_actionPerformed(ActionEvent e) - { - } - - protected void turnColour_actionPerformed(ActionEvent e) - { - } - - protected void buriedColour_actionPerformed(ActionEvent e) - { - } - - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - } - - protected void PIDColour_actionPerformed(ActionEvent e) - { - } - - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - } - - protected void purinePyrimidineColour_actionPerformed(ActionEvent e) - { - } - - protected void RNAInteractionColour_actionPerformed(ActionEvent e) - { - } - - /* - * protected void covariationColour_actionPerformed(ActionEvent e) { } - */ - - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - } - - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed(boolean selected) { } @@ -2731,7 +2313,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void abovePIDThreshold_actionPerformed(ActionEvent e) + protected void abovePIDThreshold_actionPerformed(boolean selected) { } @@ -2739,10 +2321,6 @@ public class GAlignFrame extends JInternalFrame { } - protected void nucleotideColour_actionPerformed(ActionEvent e) - { - } - protected void deleteGroups_actionPerformed(ActionEvent e) { } @@ -2775,7 +2353,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void applyToAllGroups_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed(boolean selected) { } @@ -2823,19 +2401,6 @@ public class GAlignFrame extends JInternalFrame } - /** - * 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) { } @@ -2852,11 +2417,11 @@ public class GAlignFrame extends JInternalFrame { } - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { } - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { } @@ -2898,19 +2463,12 @@ public class GAlignFrame extends JInternalFrame } - public void annotationColour_actionPerformed(ActionEvent e) + public void annotationColour_actionPerformed() { - } public void annotationColumn_actionPerformed(ActionEvent e) { - - } - - public void rnahelicesColour_actionPerformed(ActionEvent e) - { - } public void associatedData_actionPerformed(ActionEvent e) @@ -3003,7 +2561,7 @@ public class GAlignFrame extends JInternalFrame } - public void textColour_actionPerformed(ActionEvent e) + public void textColour_actionPerformed() { } @@ -3023,7 +2581,7 @@ public class GAlignFrame extends JInternalFrame } - public void buildTreeMenu() + public void buildTreeSortMenu() { } @@ -3107,7 +2665,7 @@ public class GAlignFrame extends JInternalFrame return this.splitFrame; } - protected void showComplement_actionPerformed(boolean state) + protected void showComplement_actionPerformed(boolean complement) { } }