X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=62165cdef1a950763e4b4b8c9f5ffe14e278da48;hb=ed581b841fe9361bfe80bb006df190a29df264fb;hp=294596ce1ce2cbc445503a40a683c8dd98d2cd2a;hpb=36c0eac11fb0d0ac6df2d971fabf524325db5e97;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 294596c..62165cd 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,23 +21,22 @@ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.analysis.GeneticCodeI; +import jalview.analysis.GeneticCodes; import jalview.api.SplitContainerI; import jalview.bin.Cache; -import jalview.gui.Desktop; -import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; -import jalview.gui.UserDefinedColours; -import jalview.io.FileFormat; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.UserColourScheme; +import jalview.hmmer.HmmerCommand; +import jalview.io.FileFormatException; +import jalview.io.FileFormats; +import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; import jalview.util.Platform; 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; @@ -45,6 +44,7 @@ import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.io.IOException; import java.util.HashMap; import java.util.Map; @@ -66,16 +66,14 @@ import javax.swing.event.MenuListener; public class GAlignFrame extends JInternalFrame { - protected static final String USER_DEFINED_COLOUR_SCHEME = "USER_DEFINED"; - protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenuItem closeMenuItem = new JMenuItem(); - protected JMenu colourMenu = new JMenu(); - protected JMenu webService = new JMenu(); + protected JMenu hmmerMenu = new JMenu(); + protected JMenuItem webServiceNoServices; protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); @@ -84,44 +82,10 @@ public class GAlignFrame extends JInternalFrame protected JMenu sortByAnnotScore = new JMenu(); - public JLabel statusBar = new JLabel(); + protected JLabel statusBar = new JLabel(); protected JMenu outputTextboxMenu = new JMenu(); - protected JRadioButtonMenuItem textColour; - - protected JRadioButtonMenuItem clustalColour; - - protected JRadioButtonMenuItem zappoColour; - - protected JRadioButtonMenuItem taylorColour; - - protected JRadioButtonMenuItem hydrophobicityColour; - - protected JRadioButtonMenuItem helixColour; - - protected JRadioButtonMenuItem strandColour; - - protected JRadioButtonMenuItem turnColour; - - protected JRadioButtonMenuItem buriedColour; - - protected JRadioButtonMenuItem userDefinedColour; - - protected JRadioButtonMenuItem PIDColour; - - protected JRadioButtonMenuItem BLOSUM62Colour; - - protected JRadioButtonMenuItem nucleotideColour; - - protected JRadioButtonMenuItem purinePyrimidineColour; - - protected JRadioButtonMenuItem RNAInteractionColour; - - // protected JRadioButtonMenuItem covariationColour; - - protected JRadioButtonMenuItem tcoffeeColour; - protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); @@ -132,16 +96,10 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem; - - JRadioButtonMenuItem noColourmenuItem; - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem abovePIDThreshold; - public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); JMenuItem copy = new JMenuItem(); @@ -150,8 +108,6 @@ public class GAlignFrame extends JInternalFrame JMenu pasteMenu = new JMenu(); - protected JCheckBoxMenuItem applyToAllGroups; - protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); @@ -160,17 +116,27 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); - protected JMenuItem modifyPID; + protected JCheckBoxMenuItem applyToAllGroups; + + protected JMenu colourMenu = new JMenu(); + + protected JMenuItem textColour; + + protected JCheckBoxMenuItem conservationMenuItem; protected JMenuItem modifyConservation; - protected JMenuItem annotationColour; + protected JCheckBoxMenuItem abovePIDThreshold; + + protected JMenuItem modifyPID; + + protected JRadioButtonMenuItem 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(); @@ -178,9 +144,7 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); - protected ButtonGroup colours = new ButtonGroup(); - - protected JMenuItem showTranslation = new JMenuItem(); + protected JMenu showTranslation = new JMenu(); protected JMenuItem showReverse = new JMenuItem(); @@ -190,7 +154,7 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem runGroovy = new JMenuItem(); - protected JMenuItem rnahelicesColour; + protected JMenuItem loadVcf; protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); @@ -238,13 +202,19 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private SequenceAnnotationOrder annotationSortOrder; private boolean showAutoCalculatedAbove = false; - private Map accelerators = new HashMap(); + private Map accelerators = new HashMap<>(); private SplitContainerI splitFrame; @@ -256,7 +226,7 @@ public class GAlignFrame extends JInternalFrame setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); @@ -287,206 +257,12 @@ public class GAlignFrame extends JInternalFrame pasteMenu.setMnemonic('P'); reload.setMnemonic('R'); } - - // Map userColourSchemes = UserDefinedColours - // .getUserColourSchemes(); - // if (userColourSchemes != null) - // { - // int insertionPoint = findUserDefinedColourPosition(); - // for (String userColour : userColourSchemes.keySet()) - // { - // final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - // userColour); - // radioItem.setName(USER_DEFINED_COLOUR_SCHEME); - // radioItem.addMouseListener(new MouseAdapter() - // { - // @Override - // public void mousePressed(MouseEvent evt) - // { - // if (evt.isPopupTrigger()) // Mac - // { - // offerRemoval(); - // } - // } - // - // @Override - // public void mouseReleased(MouseEvent evt) - // { - // if (evt.isPopupTrigger()) // Windows - // { - // offerRemoval(); - // } - // } - // - // void offerRemoval() - // { - // radioItem.removeActionListener(radioItem.getActionListeners()[0]); - // - // int option = JvOptionPane.showInternalConfirmDialog( - // Desktop.desktop, MessageManager - // .getString("label.remove_from_default_list"), - // MessageManager - // .getString("label.remove_user_defined_colour"), - // JvOptionPane.YES_NO_OPTION); - // if (option == JvOptionPane.YES_OPTION) - // { - // 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, insertionPoint); - // insertionPoint++; - // colours.add(radioItem); - // } - // } - // - // /* - // * add colours to a ButtonGroup to make their - // * selection mutually exclusive - // */ - // 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(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(); - buildColourMenu(); - + JMenuItem saveAs = new JMenuItem( MessageManager.getString("action.save_as")); ActionListener al = new ActionListener() @@ -497,16 +273,17 @@ 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); + KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); addMenuActionAndAccelerator(keyStroke, saveAs, al); - + closeMenuItem.setText(MessageManager.getString("action.close")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -516,7 +293,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); - + JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); JMenu annotationsMenu = new JMenu( @@ -526,10 +303,13 @@ public class GAlignFrame extends JInternalFrame JMenu calculateMenu = new JMenu( MessageManager.getString("action.calculate")); webService.setText(MessageManager.getString("action.web_service")); + + initHMMERMenu(); + JMenuItem selectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.select_all")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -539,7 +319,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); - + JMenuItem deselectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.deselect_all")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); @@ -552,11 +332,11 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); - + JMenuItem invertSequenceMenuItem = new JMenuItem( MessageManager.getString("action.invert_sequence_selection")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -566,7 +346,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); - + JMenuItem grpsFromSelection = new JMenuItem( MessageManager.getString("action.make_groups_selection")); grpsFromSelection.addActionListener(new ActionListener() @@ -579,8 +359,8 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem expandAlignment = new JMenuItem( MessageManager.getString("action.view_flanking_regions")); - expandAlignment.setToolTipText(MessageManager - .getString("label.view_flanking_regions")); + expandAlignment.setToolTipText( + MessageManager.getString("label.view_flanking_regions")); expandAlignment.addActionListener(new ActionListener() { @Override @@ -591,8 +371,8 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem remove2LeftMenuItem = new JMenuItem( MessageManager.getString("action.remove_left")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -602,11 +382,11 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); - + JMenuItem remove2RightMenuItem = new JMenuItem( MessageManager.getString("action.remove_right")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -616,11 +396,11 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); - + JMenuItem removeGappedColumnMenuItem = new JMenuItem( MessageManager.getString("action.remove_empty_columns")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -630,12 +410,13 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); - + JMenuItem removeAllGapsMenuItem = new JMenuItem( MessageManager.getString("action.remove_all_gaps")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); al = new ActionListener() { @Override @@ -645,7 +426,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); - + JMenuItem justifyLeftMenuItem = new JMenuItem( MessageManager.getString("action.left_justify_alignment")); justifyLeftMenuItem.addActionListener(new ActionListener() @@ -686,8 +467,8 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem_actionPerformed(e); } }); - showNonconservedMenuItem.setText(MessageManager - .getString("label.show_non_conversed")); + showNonconservedMenuItem + .setText(MessageManager.getString("label.show_non_conserved")); showNonconservedMenuItem.setState(false); showNonconservedMenuItem.addActionListener(new ActionListener() { @@ -737,11 +518,11 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); - + JMenuItem removeRedundancyMenuItem = new JMenuItem( MessageManager.getString("action.remove_redundancy")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -752,82 +533,57 @@ public class GAlignFrame extends JInternalFrame }; addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); - JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( - MessageManager.getString("action.pairwise_alignment")); - pairwiseAlignmentMenuItem.addActionListener(new ActionListener() + JMenuItem filterByEValue = new JMenuItem( + MessageManager.getString("action.filter_by_evalue")); + filterByEValue.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - pairwiseAlignmentMenuItem_actionPerformed(e); - } - }); - JMenuItem PCAMenuItem = new JMenuItem( - MessageManager.getString("label.principal_component_analysis")); - PCAMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - PCAMenuItem_actionPerformed(e); + filterByEValue_actionPerformed(); } + }); - JMenuItem averageDistanceTreeMenuItem = new JMenuItem( - MessageManager.getString("label.average_distance_identity")); - averageDistanceTreeMenuItem.addActionListener(new ActionListener() + + JMenuItem filterByScore = new JMenuItem( + MessageManager.getString("action.filter_by_score")); + filterByScore.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - averageDistanceTreeMenuItem_actionPerformed(e); + filterByScore_actionPerformed(); } + }); - JMenuItem neighbourTreeMenuItem = new JMenuItem( - MessageManager.getString("label.neighbour_joining_identity")); - neighbourTreeMenuItem.addActionListener(new ActionListener() + + JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( + MessageManager.getString("action.pairwise_alignment")); + pairwiseAlignmentMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - neighbourTreeMenuItem_actionPerformed(e); + pairwiseAlignmentMenuItem_actionPerformed(e); } }); - + this.getContentPane().setLayout(new BorderLayout()); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); statusBar.setText(MessageManager.getString("label.status_bar")); - outputTextboxMenu.setText(MessageManager - .getString("label.out_to_textbox")); + + outputTextboxMenu + .setText(MessageManager.getString("label.out_to_textbox")); - 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")); - annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS", - true)); + annotationPanelMenuItem + .setText(MessageManager.getString("label.show_annotations")); + annotationPanelMenuItem + .setState(Cache.getDefault("SHOW_ANNOTATIONS", true)); annotationPanelMenuItem.addActionListener(new ActionListener() { @Override @@ -836,8 +592,8 @@ public class GAlignFrame extends JInternalFrame annotationPanelMenuItem_actionPerformed(e); } }); - showAllAlAnnotations.setText(MessageManager - .getString("label.show_all_al_annotations")); + showAllAlAnnotations.setText( + MessageManager.getString("label.show_all_al_annotations")); final boolean isAnnotationPanelShown = annotationPanelMenuItem .getState(); showAllAlAnnotations.setEnabled(isAnnotationPanelShown); @@ -849,8 +605,8 @@ public class GAlignFrame extends JInternalFrame showAllAnnotations_actionPerformed(false, true); } }); - hideAllAlAnnotations.setText(MessageManager - .getString("label.hide_all_al_annotations")); + hideAllAlAnnotations.setText( + MessageManager.getString("label.hide_all_al_annotations")); hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); hideAllAlAnnotations.addActionListener(new ActionListener() { @@ -860,8 +616,8 @@ public class GAlignFrame extends JInternalFrame hideAllAnnotations_actionPerformed(false, true); } }); - showAllSeqAnnotations.setText(MessageManager - .getString("label.show_all_seq_annotations")); + showAllSeqAnnotations.setText( + MessageManager.getString("label.show_all_seq_annotations")); showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); showAllSeqAnnotations.addActionListener(new ActionListener() { @@ -871,8 +627,8 @@ public class GAlignFrame extends JInternalFrame showAllAnnotations_actionPerformed(true, false); } }); - hideAllSeqAnnotations.setText(MessageManager - .getString("label.hide_all_seq_annotations")); + hideAllSeqAnnotations.setText( + MessageManager.getString("label.hide_all_seq_annotations")); hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); hideAllSeqAnnotations.addActionListener(new ActionListener() { @@ -890,8 +646,9 @@ public class GAlignFrame extends JInternalFrame final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem( MessageManager.getString("label.sort_annotations_by_label")); - sortAnnBySequence - .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + + sortAnnBySequence.setSelected( + sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); sortAnnBySequence.addActionListener(new ActionListener() { @Override @@ -899,13 +656,14 @@ public class GAlignFrame extends JInternalFrame { boolean newState = sortAnnBySequence.getState(); sortAnnByLabel.setSelected(false); - setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL - : SequenceAnnotationOrder.NONE); + setAnnotationSortOrder( + newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL + : SequenceAnnotationOrder.NONE); sortAnnotations_actionPerformed(); } }); - sortAnnByLabel - .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + sortAnnByLabel.setSelected( + sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); sortAnnByLabel.addActionListener(new ActionListener() { @Override @@ -913,14 +671,14 @@ public class GAlignFrame extends JInternalFrame { boolean newState = sortAnnByLabel.getState(); sortAnnBySequence.setSelected(false); - setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE - : SequenceAnnotationOrder.NONE); + setAnnotationSortOrder( + newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE + : SequenceAnnotationOrder.NONE); sortAnnotations_actionPerformed(); } }); colourTextMenuItem = new JCheckBoxMenuItem( - MessageManager - .getString("label.colour_text")); + MessageManager.getString("label.colour_text")); colourTextMenuItem.addActionListener(new ActionListener() { @Override @@ -929,7 +687,7 @@ public class GAlignFrame extends JInternalFrame colourTextMenuItem_actionPerformed(e); } }); - + JMenuItem htmlMenuItem = new JMenuItem( MessageManager.getString("label.html")); htmlMenuItem.addActionListener(new ActionListener() @@ -940,7 +698,7 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); - + JMenuItem createBioJS = new JMenuItem( MessageManager.getString("label.biojs_html_export")); createBioJS.addActionListener(new java.awt.event.ActionListener() @@ -951,7 +709,7 @@ public class GAlignFrame extends JInternalFrame bioJSMenuItem_actionPerformed(e); } }); - + JMenuItem overviewMenuItem = new JMenuItem( MessageManager.getString("label.overview_window")); overviewMenuItem.addActionListener(new ActionListener() @@ -962,11 +720,11 @@ public class GAlignFrame extends JInternalFrame overviewMenuItem_actionPerformed(e); } }); - + undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -976,11 +734,11 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); - + redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -990,7 +748,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); - + wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new ActionListener() { @@ -1000,11 +758,11 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem_actionPerformed(e); } }); - + JMenuItem printMenuItem = new JMenuItem( MessageManager.getString("action.print")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -1014,7 +772,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, printMenuItem, al); - + renderGapsMenuItem .setText(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); @@ -1026,11 +784,11 @@ public class GAlignFrame extends JInternalFrame renderGapsMenuItem_actionPerformed(e); } }); - + JMenuItem findMenuItem = new JMenuItem( MessageManager.getString("action.find")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.find_tip"))); al = new ActionListener() @@ -1043,8 +801,9 @@ public class GAlignFrame extends JInternalFrame }; addMenuActionAndAccelerator(keyStroke, findMenuItem, al); - showSeqFeatures.setText(MessageManager - .getString("label.show_sequence_features")); + showSeqFeatures.setText( + MessageManager.getString("label.show_sequence_features")); + showSeqFeatures.addActionListener(new ActionListener() { @Override @@ -1059,93 +818,93 @@ public class GAlignFrame extends JInternalFrame * void actionPerformed(ActionEvent actionEvent) { * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); */ - showDbRefsMenuitem.setText(MessageManager - .getString("label.show_database_refs")); + showDbRefsMenuitem + .setText(MessageManager.getString("label.show_database_refs")); showDbRefsMenuitem.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showDbRefs_actionPerformed(e); } - + }); - showNpFeatsMenuitem.setText(MessageManager - .getString("label.show_non_positional_features")); + showNpFeatsMenuitem.setText( + MessageManager.getString("label.show_non_positional_features")); showNpFeatsMenuitem.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showNpFeats_actionPerformed(e); } - + }); - showGroupConservation.setText(MessageManager - .getString("label.group_conservation")); + showGroupConservation + .setText(MessageManager.getString("label.group_conservation")); showGroupConservation.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showGroupConservation_actionPerformed(e); } - + }); - showGroupConsensus.setText(MessageManager - .getString("label.group_consensus")); + showGroupConsensus + .setText(MessageManager.getString("label.group_consensus")); showGroupConsensus.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showGroupConsensus_actionPerformed(e); } - + }); - showConsensusHistogram.setText(MessageManager - .getString("label.show_consensus_histogram")); + showConsensusHistogram.setText( + MessageManager.getString("label.show_consensus_histogram")); showConsensusHistogram.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showConsensusHistogram_actionPerformed(e); } - + }); - showSequenceLogo.setText(MessageManager - .getString("label.show_consensus_logo")); + showSequenceLogo + .setText(MessageManager.getString("label.show_consensus_logo")); showSequenceLogo.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showSequenceLogo_actionPerformed(e); } - + }); - normaliseSequenceLogo.setText(MessageManager - .getString("label.norm_consensus_logo")); + normaliseSequenceLogo + .setText(MessageManager.getString("label.norm_consensus_logo")); normaliseSequenceLogo.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { normaliseSequenceLogo_actionPerformed(e); } - + }); - applyAutoAnnotationSettings.setText(MessageManager - .getString("label.apply_all_groups")); + applyAutoAnnotationSettings + .setText(MessageManager.getString("label.apply_all_groups")); applyAutoAnnotationSettings.setState(false); applyAutoAnnotationSettings.setVisible(true); applyAutoAnnotationSettings.addActionListener(new ActionListener() @@ -1156,7 +915,7 @@ public class GAlignFrame extends JInternalFrame applyAutoAnnotationSettings_actionPerformed(e); } }); - + ButtonGroup buttonGroup = new ButtonGroup(); final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( MessageManager.getString("label.show_first")); @@ -1164,8 +923,8 @@ public class GAlignFrame extends JInternalFrame MessageManager.getString("label.show_last")); buttonGroup.add(showAutoFirst); buttonGroup.add(showAutoLast); - final boolean autoFirst = Cache.getDefault( - Preferences.SHOW_AUTOCALC_ABOVE, false); + final boolean autoFirst = Cache + .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); showAutoFirst.setSelected(autoFirst); setShowAutoCalculatedAbove(autoFirst); showAutoFirst.addActionListener(new ActionListener() @@ -1187,11 +946,11 @@ public class GAlignFrame extends JInternalFrame sortAnnotations_actionPerformed(); } }); - + JMenuItem deleteGroups = new JMenuItem( MessageManager.getString("action.undefine_groups")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -1201,7 +960,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, deleteGroups, al); - + JMenuItem annotationColumn = new JMenuItem( MessageManager.getString("action.select_by_annotation")); annotationColumn.addActionListener(new ActionListener() @@ -1212,11 +971,11 @@ public class GAlignFrame extends JInternalFrame annotationColumn_actionPerformed(e); } }); - + JMenuItem createGroup = new JMenuItem( - MessageManager.getString("action.create_groups")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + MessageManager.getString("action.create_group")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -1226,12 +985,13 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, createGroup, al); - + JMenuItem unGroup = new JMenuItem( MessageManager.getString("action.remove_group")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); al = new ActionListener() { @Override @@ -1241,10 +1001,10 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, unGroup, al); - + copy.setText(MessageManager.getString("action.copy")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @@ -1255,10 +1015,10 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, copy, al); - + cut.setText(MessageManager.getString("action.cut")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -1268,7 +1028,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, cut, al); - + JMenuItem delete = new JMenuItem( MessageManager.getString("action.delete")); delete.addActionListener(new ActionListener() @@ -1279,37 +1039,52 @@ public class GAlignFrame extends JInternalFrame delete_actionPerformed(e); } }); - + pasteMenu.setText(MessageManager.getString("action.paste")); JMenuItem pasteNew = new JMenuItem( MessageManager.getString("label.to_new_alignment")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.SHIFT_MASK, false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - pasteNew_actionPerformed(e); + try + { + pasteNew_actionPerformed(e); + } catch (IOException | InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } } }; addMenuActionAndAccelerator(keyStroke, pasteNew, al); - + JMenuItem pasteThis = new JMenuItem( MessageManager.getString("label.to_this_alignment")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - pasteThis_actionPerformed(e); + try + { + pasteThis_actionPerformed(e); + } catch (IOException | InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } } }; addMenuActionAndAccelerator(keyStroke, pasteThis, al); - + JMenuItem createPNG = new JMenuItem("PNG"); createPNG.addActionListener(new ActionListener() { @@ -1319,9 +1094,8 @@ public class GAlignFrame extends JInternalFrame createPNG(null); } }); - createPNG.setActionCommand(MessageManager - .getString("label.save_png_image")); - + createPNG.setActionCommand( + MessageManager.getString("label.save_png_image")); JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); font.addActionListener(new ActionListener() { @@ -1331,8 +1105,8 @@ public class GAlignFrame extends JInternalFrame font_actionPerformed(e); } }); - seqLimits.setText(MessageManager - .getString("label.show_sequence_limits")); + seqLimits.setText( + MessageManager.getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new ActionListener() { @@ -1351,7 +1125,7 @@ public class GAlignFrame extends JInternalFrame createEPS(null); } }); - + JMenuItem createSVG = new JMenuItem("SVG"); createSVG.addActionListener(new ActionListener() { @@ -1361,11 +1135,11 @@ public class GAlignFrame extends JInternalFrame createSVG(null); } }); - + JMenuItem loadTreeMenuItem = new JMenuItem( MessageManager.getString("label.load_associated_tree")); - loadTreeMenuItem.setActionCommand(MessageManager - .getString("label.load_tree_for_sequence_set")); + loadTreeMenuItem.setActionCommand( + MessageManager.getString("label.load_tree_for_sequence_set")); loadTreeMenuItem.addActionListener(new ActionListener() { @Override @@ -1374,7 +1148,7 @@ public class GAlignFrame extends JInternalFrame loadTreeMenuItem_actionPerformed(e); } }); - + scaleAbove.setVisible(false); scaleAbove.setText(MessageManager.getString("action.scale_above")); scaleAbove.addActionListener(new ActionListener() @@ -1409,8 +1183,8 @@ public class GAlignFrame extends JInternalFrame }); centreColumnLabelsMenuItem.setVisible(true); centreColumnLabelsMenuItem.setState(false); - centreColumnLabelsMenuItem.setText(MessageManager - .getString("label.centre_column_labels")); + centreColumnLabelsMenuItem.setText( + MessageManager.getString("label.centre_column_labels")); centreColumnLabelsMenuItem.addActionListener(new ActionListener() { @Override @@ -1421,19 +1195,19 @@ public class GAlignFrame extends JInternalFrame }); followHighlightMenuItem.setVisible(true); followHighlightMenuItem.setState(true); - followHighlightMenuItem.setText(MessageManager - .getString("label.automatic_scrolling")); + followHighlightMenuItem + .setText(MessageManager.getString("label.automatic_scrolling")); followHighlightMenuItem.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { followHighlight_actionPerformed(); } - + }); - + sortByTreeMenu .setText(MessageManager.getString("action.by_tree_order")); sort.setText(MessageManager.getString("action.sort")); @@ -1442,35 +1216,35 @@ public class GAlignFrame extends JInternalFrame @Override public void menuSelected(MenuEvent e) { - buildTreeMenu(); + buildTreeSortMenu(); } - + @Override public void menuDeselected(MenuEvent e) { } - + @Override public void menuCanceled(MenuEvent e) { } }); - sortByAnnotScore.setText(MessageManager - .getString("label.sort_by_score")); + sortByAnnotScore + .setText(MessageManager.getString("label.sort_by_score")); sort.add(sortByAnnotScore); sort.addMenuListener(new javax.swing.event.MenuListener() { - + @Override public void menuCanceled(MenuEvent e) { } - + @Override public void menuDeselected(MenuEvent e) { } - + @Override public void menuSelected(MenuEvent e) { @@ -1480,11 +1254,11 @@ public class GAlignFrame extends JInternalFrame sortByAnnotScore.setVisible(false); calculateTree - .setText(MessageManager.getString("action.calculate_tree")); + .setText(MessageManager.getString("action.calculate_tree_pca")); padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); - padGapsMenuitem.setState(jalview.bin.Cache - .getDefault("PAD_GAPS", false)); + padGapsMenuitem + .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { @Override @@ -1504,16 +1278,33 @@ public class GAlignFrame extends JInternalFrame vamsasStore_actionPerformed(e); } }); + + /* + * Translate as cDNA with sub-menu of translation tables + */ showTranslation.setText(MessageManager .getString("label.translate_cDNA")); - showTranslation.addActionListener(new ActionListener() + boolean first = true; + for (final GeneticCodeI table : GeneticCodes.getInstance() + .getCodeTables()) { - @Override - public void actionPerformed(ActionEvent e) + JMenuItem item = new JMenuItem(table.getId() + " " + table.getName()); + showTranslation.add(item); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(table); + } + }); + if (first) { - showTranslation_actionPerformed(e); + showTranslation.addSeparator(); } - }); + first = false; + } + showReverse.setText(MessageManager.getString("label.reverse")); showReverse.addActionListener(new ActionListener() { @@ -1523,8 +1314,8 @@ public class GAlignFrame extends JInternalFrame showReverse_actionPerformed(false); } }); - showReverseComplement.setText(MessageManager - .getString("label.reverse_complement")); + showReverseComplement + .setText(MessageManager.getString("label.reverse_complement")); showReverseComplement.addActionListener(new ActionListener() { @Override @@ -1533,7 +1324,7 @@ public class GAlignFrame extends JInternalFrame showReverse_actionPerformed(true); } }); - + JMenuItem extractScores = new JMenuItem( MessageManager.getString("label.extract_scores")); extractScores.addActionListener(new ActionListener() @@ -1546,13 +1337,13 @@ public class GAlignFrame extends JInternalFrame }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction - + // 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.setToolTipText( + MessageManager.getString("label.run_groovy_tip")); runGroovy.addActionListener(new ActionListener() { @Override @@ -1561,7 +1352,7 @@ public class GAlignFrame extends JInternalFrame runGroovy_actionPerformed(); } }); - + JMenuItem openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() @@ -1582,7 +1373,7 @@ public class GAlignFrame extends JInternalFrame fetchSequence_actionPerformed(e); } }); - + JMenuItem associatedData = new JMenuItem( MessageManager.getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() @@ -1590,13 +1381,30 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - associatedData_actionPerformed(e); + try + { + associatedData_actionPerformed(e); + } catch (IOException | InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } } }); - autoCalculate.setText(MessageManager - .getString("label.autocalculate_consensus")); - autoCalculate.setState(jalview.bin.Cache.getDefault( - "AUTO_CALC_CONSENSUS", true)); + loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file")); + loadVcf.setToolTipText(MessageManager.getString("label.load_vcf")); + loadVcf.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + loadVcf_actionPerformed(); + } + }); + autoCalculate.setText( + MessageManager.getString("label.autocalculate_consensus")); + autoCalculate.setState( + jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { @Override @@ -1605,12 +1413,10 @@ public class GAlignFrame extends JInternalFrame autoCalculate_actionPerformed(e); } }); - sortByTree.setText(MessageManager - .getString("label.sort_alignment_new_tree")); - sortByTree - .setToolTipText("" - + MessageManager - .getString("label.enable_automatically_sort_alignment_when_open_new_tree")); + sortByTree.setText( + MessageManager.getString("label.sort_alignment_new_tree")); + sortByTree.setToolTipText("" + MessageManager.getString( + "label.enable_automatically_sort_alignment_when_open_new_tree")); sortByTree .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() @@ -1622,12 +1428,11 @@ public class GAlignFrame extends JInternalFrame } }); - listenToViewSelections.setText(MessageManager - .getString("label.listen_for_selections")); + listenToViewSelections.setText( + MessageManager.getString("label.listen_for_selections")); listenToViewSelections - .setToolTipText("" - + MessageManager - .getString("label.selections_mirror_selections_made_same_sequences_other_views")); + .setToolTipText("" + MessageManager.getString( + "label.selections_mirror_selections_made_same_sequences_other_views")); listenToViewSelections.setState(false); listenToViewSelections.addActionListener(new ActionListener() { @@ -1637,7 +1442,7 @@ public class GAlignFrame extends JInternalFrame listenToViewSelections_actionPerformed(e); } }); - + JMenu addSequenceMenu = new JMenu( MessageManager.getString("label.add_sequences")); JMenuItem addFromFile = new JMenuItem( @@ -1693,8 +1498,8 @@ public class GAlignFrame extends JInternalFrame statusPanel.setLayout(new GridLayout()); JMenuItem showAllSeqs = new JMenuItem( MessageManager.getString("label.all_sequences")); - showAllSeqs.setToolTipText(MessageManager - .getString("label.toggle_sequence_visibility")); + showAllSeqs.setToolTipText( + MessageManager.getString("label.toggle_sequence_visibility")); showAllSeqs.addActionListener(new ActionListener() { @Override @@ -1705,8 +1510,8 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem showAllColumns = new JMenuItem( MessageManager.getString("label.all_columns")); - showAllColumns.setToolTipText(MessageManager - .getString("label.toggle_columns_visibility")); + showAllColumns.setToolTipText( + MessageManager.getString("label.toggle_columns_visibility")); showAllColumns.addActionListener(new ActionListener() { @Override @@ -1718,8 +1523,8 @@ public class GAlignFrame extends JInternalFrame JMenu hideMenu = new JMenu(MessageManager.getString("action.hide")); JMenuItem hideSelSequences = new JMenuItem( MessageManager.getString("label.selected_sequences")); - hideSelSequences.setToolTipText(MessageManager - .getString("label.toggle_sequence_visibility")); + hideSelSequences.setToolTipText( + MessageManager.getString("label.toggle_sequence_visibility")); hideSelSequences.addActionListener(new ActionListener() { @Override @@ -1730,8 +1535,8 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem hideSelColumns = new JMenuItem( MessageManager.getString("label.selected_columns")); - hideSelColumns.setToolTipText(MessageManager - .getString("label.toggle_columns_visibility")); + hideSelColumns.setToolTipText( + MessageManager.getString("label.toggle_columns_visibility")); hideSelColumns.addActionListener(new ActionListener() { @Override @@ -1773,8 +1578,8 @@ public class GAlignFrame extends JInternalFrame showAllhidden_actionPerformed(e); } }); - hiddenMarkers.setText(MessageManager - .getString("action.show_hidden_markers")); + hiddenMarkers.setText( + MessageManager.getString("action.show_hidden_markers")); hiddenMarkers.addActionListener(new ActionListener() { @Override @@ -1783,12 +1588,13 @@ public class GAlignFrame extends JInternalFrame hiddenMarkers_actionPerformed(e); } }); - + JMenuItem invertColSel = new JMenuItem( MessageManager.getString("action.invert_column_selection")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask() - | KeyEvent.ALT_MASK, false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, + false); al = new ActionListener() { @Override @@ -1798,7 +1604,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, invertColSel, al); - + showComplementMenuItem.setVisible(false); showComplementMenuItem.addActionListener(new ActionListener() { @@ -1808,7 +1614,7 @@ public class GAlignFrame extends JInternalFrame showComplement_actionPerformed(showComplementMenuItem.getState()); } }); - + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { @Override @@ -1829,7 +1635,7 @@ public class GAlignFrame extends JInternalFrame tabbedPane_mousePressed(e); } } - + @Override public void mouseReleased(MouseEvent e) { @@ -1847,10 +1653,10 @@ public class GAlignFrame extends JInternalFrame tabbedPane_focusGained(e); } }); - + JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -1860,7 +1666,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, save, al); - + reload.setEnabled(false); reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() @@ -1871,11 +1677,11 @@ public class GAlignFrame extends JInternalFrame reload_actionPerformed(e); } }); - + JMenuItem newView = new JMenuItem( MessageManager.getString("action.new_view")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); al = new ActionListener() { @Override @@ -1885,15 +1691,16 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, newView, al); - + tabbedPane.setToolTipText("" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + ""); - + formatMenu.setText(MessageManager.getString("action.format")); JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); - idRightAlign.setText(MessageManager - .getString("label.right_align_sequence_id")); + + idRightAlign.setText( + MessageManager.getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() { @Override @@ -1902,7 +1709,7 @@ public class GAlignFrame extends JInternalFrame idRightAlign_actionPerformed(e); } }); - + gatherViews.setEnabled(false); gatherViews.setText(MessageManager.getString("action.gather_views")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); @@ -1915,7 +1722,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, gatherViews, al); - + expandViews.setEnabled(false); expandViews.setText(MessageManager.getString("action.expand_views")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); @@ -1928,7 +1735,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, expandViews, al); - + JMenuItem pageSetup = new JMenuItem( MessageManager.getString("action.page_setup")); pageSetup.addActionListener(new ActionListener() @@ -1951,8 +1758,20 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem selectHighlighted = new JMenuItem( MessageManager.getString("action.select_highlighted_columns")); - selectHighlighted.setToolTipText(MessageManager - .getString("tooltip.select_highlighted_columns")); + selectHighlighted.setToolTipText( + MessageManager.getString("tooltip.select_highlighted_columns")); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + selectHighlightedColumns_actionPerformed(actionEvent); + } + }; + JMenuItem Filter = new JMenuItem( + MessageManager.getString("action.select_highlighted_columns")); + selectHighlighted.setToolTipText( + MessageManager.getString("tooltip.select_highlighted_columns")); al = new ActionListener() { @Override @@ -1966,7 +1785,7 @@ public class GAlignFrame extends JInternalFrame MessageManager.getString("label.sequence_id_tooltip")); JMenu autoAnnMenu = new JMenu( MessageManager.getString("label.autocalculated_annotation")); - + JMenu exportImageMenu = new JMenu( MessageManager.getString("label.export_image")); JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); @@ -1979,7 +1798,8 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); - + alignFrameMenuBar.add(hmmerMenu); + fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); fileMenu.add(reload); @@ -1996,9 +1816,10 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(exportAnnotations); fileMenu.add(loadTreeMenuItem); fileMenu.add(associatedData); + fileMenu.add(loadVcf); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); - + pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); editMenu.add(undoMenuItem); @@ -2020,7 +1841,10 @@ public class GAlignFrame extends JInternalFrame // editMenu.add(justifyRightMenuItem); // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); - + editMenu.addSeparator(); + editMenu.add(filterByEValue); + editMenu.add(filterByScore); + showMenu.add(showAllColumns); showMenu.add(showAllSeqs); showMenu.add(showAllhidden); @@ -2048,7 +1872,7 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(alignmentProperties); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); - + annotationsMenu.add(annotationPanelMenuItem); annotationsMenu.addSeparator(); annotationsMenu.add(showAllAlAnnotations); @@ -2071,7 +1895,6 @@ public class GAlignFrame extends JInternalFrame autoAnnMenu.add(showGroupConsensus); annotationsMenu.add(autoAnnMenu); - sort.add(sortIDMenuItem); sort.add(sortLengthMenuItem); sort.add(sortGroupMenuItem); @@ -2081,7 +1904,6 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); calculateMenu.add(showReverse); @@ -2094,7 +1916,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(extractScores); calculateMenu.addSeparator(); calculateMenu.add(runGroovy); - + webServiceNoServices = new JMenuItem( MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); @@ -2109,7 +1931,7 @@ 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); - + formatMenu.add(font); formatMenu.addSeparator(); formatMenu.add(wrapMenuItem); @@ -2144,351 +1966,210 @@ public class GAlignFrame extends JInternalFrame } /** - * Rebuilds the Colour menu, including any user-defined colours which have - * been loaded either on startup or during the session + * Constructs the entries on the HMMER menu */ - public void buildColourMenu() - { - colourMenu.removeAll(); - colours = new ButtonGroup(); - - 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); - - /* - * add any user-defined colours - */ - Map userColourSchemes = UserDefinedColours - .getUserColourSchemes(); - if (userColourSchemes != null) - { - for (String userColour : userColourSchemes.keySet()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColour); - radioItem.setName(USER_DEFINED_COLOUR_SCHEME); - radioItem.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Mac - { - offerRemoval(); - } - } - - @Override - public void mouseReleased(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Windows - { - offerRemoval(); - } - } - - void offerRemoval() - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JvOptionPane.showInternalConfirmDialog( - Desktop.desktop, MessageManager - .getString("label.remove_from_default_list"), - MessageManager - .getString("label.remove_user_defined_colour"), - JvOptionPane.YES_NO_OPTION); - if (option == JvOptionPane.YES_OPTION) - { - 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.add(radioItem); - colours.add(radioItem); - } - } - - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - colourMenu.add(annotationColour); - colourMenu.add(rnahelicesColour); - + protected void initHMMERMenu() + { /* - * add colours to a ButtonGroup to make their - * selection mutually exclusive + * hmmbuild */ - 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(Cache.getDefault(Preferences.DEFAULT_COLOUR, "None")); - - } - - /** - * 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(); - } - }); - - textColour = new JRadioButtonMenuItem( - MessageManager.getString("action.set_text_colour")); - textColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - textColour_actionPerformed(); - } - }); - clustalColour = new JRadioButtonMenuItem( - MessageManager.getString("label.clustalx")); - clustalColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(); - } - }); - zappoColour = new JRadioButtonMenuItem( - MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new ActionListener() + JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild")); + JMenuItem hmmBuildSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmBuildSettings.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(); + hmmBuild_actionPerformed(false); } }); - taylorColour = new JRadioButtonMenuItem( - MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new ActionListener() + JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmbuild")); + hmmBuildRun.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(); + hmmBuild_actionPerformed(true); } }); - hydrophobicityColour = new JRadioButtonMenuItem( - MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); - helixColour = new JRadioButtonMenuItem( - MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(); - } - }); - strandColour = new JRadioButtonMenuItem( - MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new ActionListener() + hmmBuild.add(hmmBuildRun); + hmmBuild.add(hmmBuildSettings); + + /* + * hmmalign + */ + JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign")); + JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmalign")); + hmmAlignRun.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(); + hmmAlign_actionPerformed(true); } }); - turnColour = new JRadioButtonMenuItem( - MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new ActionListener() + JMenuItem hmmAlignSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmAlignSettings.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(); + hmmAlign_actionPerformed(false); } }); - buriedColour = new JRadioButtonMenuItem( - MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new ActionListener() + hmmAlign.add(hmmAlignRun); + hmmAlign.add(hmmAlignSettings); + + /* + * hmmsearch + */ + JMenu hmmSearch = new JMenu( + MessageManager.getString("label.hmmsearch")); + JMenuItem hmmSearchSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmSearchSettings.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(); + hmmSearch_actionPerformed(false); } }); - userDefinedColour = new JRadioButtonMenuItem( - MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new ActionListener() + JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmsearch")); + hmmSearchRun.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); + hmmSearch_actionPerformed(true); } }); - PIDColour = new JRadioButtonMenuItem( - MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new ActionListener() + JMenuItem addDatabase = new JMenuItem( + MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(); + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } } }); - BLOSUM62Colour = new JRadioButtonMenuItem( - MessageManager.getString("label.blosum62_score")); - BLOSUM62Colour.addActionListener(new ActionListener() + hmmSearch.add(hmmSearchRun); + hmmSearch.add(hmmSearchSettings); + // hmmSearch.add(addDatabase); + + /* + * jackhmmer + */ + JMenu jackhmmer = new JMenu( + MessageManager.getString("label.jackhmmer")); + JMenuItem jackhmmerSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + jackhmmerSettings.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(); + jackhmmer_actionPerformed(false); } }); - nucleotideColour = new JRadioButtonMenuItem( - MessageManager.getString("label.nucleotide")); - nucleotideColour.addActionListener(new ActionListener() + JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "jackhmmer")); + jackhmmerRun.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - nucleotideColour_actionPerformed(); + jackhmmer_actionPerformed(true); } + }); - purinePyrimidineColour = new JRadioButtonMenuItem( - MessageManager.getString("label.purine_pyrimidine")); - purinePyrimidineColour.addActionListener(new ActionListener() + /* + JMenuItem addDatabase = new JMenuItem( + MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - purinePyrimidineColour_actionPerformed(); + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } } }); + */ + jackhmmer.add(jackhmmerRun); + jackhmmer.add(jackhmmerSettings); + // hmmSearch.add(addDatabase); - tcoffeeColour = new JRadioButtonMenuItem( - MessageManager.getString("label.tcoffee_scores")); - tcoffeeColour.setEnabled(false); - tcoffeeColour.addActionListener(new ActionListener() - { + /* + * top level menu + */ + hmmerMenu.setText(MessageManager.getString("action.hmmer")); + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + hmmerMenu.add(hmmBuild); + hmmerMenu.add(hmmAlign); + hmmerMenu.add(hmmSearch); + hmmerMenu.add(jackhmmer); + } + + protected void loadVcf_actionPerformed() + { + } + + /** + * 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) { - tcoffeeColorScheme_actionPerformed(); + applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); } }); - RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type"); - RNAInteractionColour.addActionListener(new ActionListener() + textColour = new JMenuItem( + MessageManager.getString("label.text_colour")); + textColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - RNAInteractionColour_actionPerformed(); + textColour_actionPerformed(); } }); - /* - * covariationColour = new JRadioButtonMenuItem("Covariation"); - * covariationColour.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); } - * }); - */ conservationMenuItem = new JCheckBoxMenuItem( - MessageManager - .getString("action.by_conservation")); + MessageManager.getString("action.by_conservation")); conservationMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(); - } - }); - noColourmenuItem = new JRadioButtonMenuItem( - MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(); + conservationMenuItem_actionPerformed( + conservationMenuItem.isSelected()); } }); @@ -2499,7 +2180,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - abovePIDThreshold_actionPerformed(); + abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); } }); modifyPID = new JMenuItem( @@ -2512,8 +2193,7 @@ public class GAlignFrame extends JInternalFrame modifyPID_actionPerformed(); } }); - modifyConservation = new JMenuItem( - MessageManager + modifyConservation = new JMenuItem(MessageManager .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(new ActionListener() { @@ -2524,8 +2204,9 @@ public class GAlignFrame extends JInternalFrame } }); - annotationColour = new JMenuItem( + annotationColour = new JRadioButtonMenuItem( MessageManager.getString("action.by_annotation")); + annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); annotationColour.addActionListener(new ActionListener() { @Override @@ -2534,17 +2215,6 @@ public class GAlignFrame extends JInternalFrame annotationColour_actionPerformed(); } }); - - rnahelicesColour = new JMenuItem( - MessageManager.getString("action.by_rna_helixes")); - rnahelicesColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - rnahelicesColour_actionPerformed(); - } - }); } protected void selectHighlightedColumns_actionPerformed( @@ -2882,147 +2552,90 @@ public class GAlignFrame extends JInternalFrame { } - protected void PCAMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - } - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed(boolean selected) { } - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void clustalColour_actionPerformed() - { - } - - protected void zappoColour_actionPerformed() - { - } - - protected void taylorColour_actionPerformed() - { - } - - protected void hydrophobicityColour_actionPerformed() - { - } - - protected void helixColour_actionPerformed() - { - } - - protected void strandColour_actionPerformed() - { - } - - protected void turnColour_actionPerformed() - { - } - - protected void buriedColour_actionPerformed() - { - } - - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - } - - protected void PIDColour_actionPerformed() - { - } - - protected void BLOSUM62Colour_actionPerformed() - { - } - - protected void purinePyrimidineColour_actionPerformed() + protected void printMenuItem_actionPerformed(ActionEvent e) { } - protected void RNAInteractionColour_actionPerformed() + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { } - /* - * protected void covariationColour_actionPerformed() { } - */ - - protected void noColourmenuItem_actionPerformed() + protected void findMenuItem_actionPerformed(ActionEvent e) { } - protected void conservationMenuItem_actionPerformed() + protected void abovePIDThreshold_actionPerformed(boolean selected) { } - protected void printMenuItem_actionPerformed(ActionEvent e) + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + protected void deleteGroups_actionPerformed(ActionEvent e) { } - protected void findMenuItem_actionPerformed(ActionEvent e) + protected void createGroup_actionPerformed(ActionEvent e) { } - protected void abovePIDThreshold_actionPerformed() + protected void unGroup_actionPerformed(ActionEvent e) { } - public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) + protected void copy_actionPerformed(ActionEvent e) { } - protected void nucleotideColour_actionPerformed() + protected void cut_actionPerformed(ActionEvent e) { } - protected void deleteGroups_actionPerformed(ActionEvent e) + protected void delete_actionPerformed(ActionEvent e) { } - protected void createGroup_actionPerformed(ActionEvent e) + protected void pasteNew_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { } - protected void unGroup_actionPerformed(ActionEvent e) + protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { } - protected void copy_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed(boolean selected) { } - protected void cut_actionPerformed(ActionEvent e) + protected void hmmBuild_actionPerformed(boolean withDefaults) { } - protected void delete_actionPerformed(ActionEvent e) + protected void hmmSearch_actionPerformed(boolean withDefaults) { } - protected void pasteNew_actionPerformed(ActionEvent e) + protected void jackhmmer_actionPerformed(boolean b) { } - protected void pasteThis_actionPerformed(ActionEvent e) + protected void addDatabase_actionPerformed() + throws FileFormatException, IOException { } - protected void applyToAllGroups_actionPerformed() + protected void hmmAlign_actionPerformed(boolean withDefaults) { } @@ -3070,25 +2683,23 @@ 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. - */ - protected void tcoffeeColorScheme_actionPerformed() + protected void jpred_actionPerformed(ActionEvent e) { + } + protected void scaleAbove_actionPerformed(ActionEvent e) + { } - protected void jpred_actionPerformed(ActionEvent e) + protected void scaleLeft_actionPerformed(ActionEvent e) { } - protected void scaleAbove_actionPerformed(ActionEvent e) + protected void filterByEValue_actionPerformed() { } - protected void scaleLeft_actionPerformed(ActionEvent e) + protected void filterByScore_actionPerformed() { } @@ -3122,7 +2733,7 @@ public class GAlignFrame extends JInternalFrame } - public void showTranslation_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(GeneticCodeI codeTable) { } @@ -3150,12 +2761,8 @@ public class GAlignFrame extends JInternalFrame { } - public void rnahelicesColour_actionPerformed() - { - - } - public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { } @@ -3265,7 +2872,7 @@ public class GAlignFrame extends JInternalFrame } - public void buildTreeMenu() + public void buildTreeSortMenu() { }