X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d9c87cb45ac63f17af70782d33f37a0f120919ed;hb=7498f96b78e7d8f3d2f015343b0948810668c0e9;hp=dba77dd2f09eb25c6ef8daf5b1d164721735cfee;hpb=eaf9092bfa74b5162589c8775f68a19dd79dbb1d;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index dba77dd..d9c87cb 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,8 +21,10 @@ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.api.SplitContainerI; import jalview.bin.Cache; import jalview.gui.JvSwingUtils; +import jalview.gui.Preferences; import jalview.schemes.ColourSchemeProperty; import jalview.util.MessageManager; @@ -34,8 +36,11 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; +import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.util.HashMap; +import java.util.Map; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; @@ -49,6 +54,7 @@ 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; @@ -213,6 +219,10 @@ public class GAlignFrame extends JInternalFrame JMenuItem createPNG = new JMenuItem(); + JMenuItem createBioJS = new JMenuItem(); + + JMenuItem createSVG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); @@ -263,6 +273,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem annotationColour = new JMenuItem(); + JMenuItem annotationColumn = new JMenuItem(); + protected JMenuItem rnahelicesColour = new JMenuItem(); JMenuItem associatedData = new JMenuItem(); @@ -289,7 +301,7 @@ public class GAlignFrame extends JInternalFrame GridLayout gridLayout1 = new GridLayout(); - JMenu jMenu3 = new JMenu(); + JMenu showMenu = new JMenu(); JMenuItem showAllSeqs = new JMenuItem(); @@ -315,6 +327,8 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem hideAllAlAnnotations = new JMenuItem(); + protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(); @@ -333,7 +347,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem textColour = new JMenuItem(); - JMenu formatMenu = new JMenu(); + protected JMenu formatMenu = new JMenu(); JMenu selectMenu = new JMenu(); @@ -371,9 +385,9 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem showAutoFirst = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem showAutoLast = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); @@ -381,6 +395,10 @@ public class GAlignFrame extends JInternalFrame private boolean showAutoCalculatedAbove = false; + private Map accelerators = new HashMap(); + + private SplitContainerI splitFrame; + public GAlignFrame() { try @@ -394,7 +412,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -498,9 +516,8 @@ public class GAlignFrame extends JInternalFrame // colours.add(covariationColour); colours.add(tcoffeeColour); colours.add(RNAInteractionColour); - setColourSelected(jalview.bin.Cache - .getDefault("DEFAULT_COLOUR", "None")); - + setColourSelected(jalview.bin.Cache.getDefault( + Preferences.DEFAULT_COLOUR, "None")); } public void setColourSelected(String defaultColour) @@ -603,81 +620,85 @@ public class GAlignFrame extends JInternalFrame private void jbInit() throws Exception { fileMenu.setText(MessageManager.getString("action.file")); + saveAs.setText(MessageManager.getString("action.save_as") + "..."); - saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask() - | java.awt.event.KeyEvent.SHIFT_MASK, false)); - saveAs.addActionListener(new ActionListener() + ActionListener al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { saveAs_actionPerformed(e); } - }); + }; + KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.SHIFT_MASK, false); + addMenuActionAndAccelerator(keyStroke, saveAs, al); + closeMenuItem.setText(MessageManager.getString("action.close")); - closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - closeMenuItem.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { closeMenuItem_actionPerformed(false); } - }); + }; + addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); + editMenu.setText(MessageManager.getString("action.edit")); viewMenu.setText(MessageManager.getString("action.view")); annotationsMenu.setText(MessageManager.getString("action.annotations")); colourMenu.setText(MessageManager.getString("action.colour")); calculateMenu.setText(MessageManager.getString("action.calculate")); webService.setText(MessageManager.getString("action.web_service")); + selectAllSequenceMenuItem.setText(MessageManager .getString("action.select_all")); - selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke - .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false)); - selectAllSequenceMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - selectAllSequenceMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + selectAllSequenceMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); + deselectAllSequenceMenuItem.setText(MessageManager .getString("action.deselect_all")); - deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke - .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false)); - deselectAllSequenceMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - deselectAllSequenceMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + deselectAllSequenceMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); + invertSequenceMenuItem.setText(MessageManager .getString("action.invert_sequence_selection")); - invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke - .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false)); - invertSequenceMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - invertSequenceMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + invertSequenceMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); + grpsFromSelection.setText(MessageManager .getString("action.make_groups_selection")); - grpsFromSelection.addActionListener(new java.awt.event.ActionListener() + grpsFromSelection.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -689,7 +710,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.view_flanking_regions")); expandAlignment.setToolTipText(MessageManager .getString("label.view_flanking_regions")); - expandAlignment.addActionListener(new java.awt.event.ActionListener() + expandAlignment.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -699,86 +720,84 @@ public class GAlignFrame extends JInternalFrame }); remove2LeftMenuItem.setText(MessageManager .getString("action.remove_left")); - remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - remove2LeftMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - remove2LeftMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + remove2LeftMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); + remove2RightMenuItem.setText(MessageManager .getString("action.remove_right")); - remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - remove2RightMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - remove2RightMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + remove2RightMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); + removeGappedColumnMenuItem.setText(MessageManager .getString("action.remove_empty_columns")); - removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke - .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false)); - removeGappedColumnMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - removeGappedColumnMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + removeGappedColumnMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); + removeAllGapsMenuItem.setText(MessageManager .getString("action.remove_all_gaps")); - removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke - .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask() - | java.awt.event.KeyEvent.SHIFT_MASK, false)); - removeAllGapsMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - removeAllGapsMenuItem_actionPerformed(e); - } - }); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.SHIFT_MASK, false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + removeAllGapsMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); + justifyLeftMenuItem.setText(MessageManager .getString("action.left_justify_alignment")); - justifyLeftMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - justifyLeftMenuItem_actionPerformed(e); - } - }); + justifyLeftMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + justifyLeftMenuItem_actionPerformed(e); + } + }); justifyRightMenuItem.setText(MessageManager .getString("action.right_justify_alignment")); - justifyRightMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - justifyRightMenuItem_actionPerformed(e); - } - }); + justifyRightMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + justifyRightMenuItem_actionPerformed(e); + } + }); viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() + viewBoxesMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -788,7 +807,7 @@ public class GAlignFrame extends JInternalFrame }); viewTextMenuItem.setText(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); - viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() + viewTextMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -799,28 +818,26 @@ public class GAlignFrame extends JInternalFrame showNonconservedMenuItem.setText(MessageManager .getString("label.show_non_conversed")); showNonconservedMenuItem.setState(false); - showNonconservedMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - showUnconservedMenuItem_actionPerformed(e); - } - }); + showNonconservedMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showUnconservedMenuItem_actionPerformed(e); + } + }); sortPairwiseMenuItem.setText(MessageManager .getString("action.by_pairwise_id")); - sortPairwiseMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sortPairwiseMenuItem_actionPerformed(e); - } - }); + sortPairwiseMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortPairwiseMenuItem_actionPerformed(e); + } + }); sortIDMenuItem.setText(MessageManager.getString("action.by_id")); - sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() + sortIDMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -830,17 +847,16 @@ public class GAlignFrame extends JInternalFrame }); sortLengthMenuItem .setText(MessageManager.getString("action.by_length")); - sortLengthMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sortLengthMenuItem_actionPerformed(e); - } - }); + sortLengthMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortLengthMenuItem_actionPerformed(e); + } + }); sortGroupMenuItem.setText(MessageManager.getString("action.by_group")); - sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + sortGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -848,34 +864,34 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); - removeRedundancyMenuItem.setText(MessageManager - .getString("action.remove_redundancy").concat("...")); - removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke - .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask(), false)); - removeRedundancyMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - removeRedundancyMenuItem_actionPerformed(e); - } - }); + + removeRedundancyMenuItem.setText(MessageManager.getString( + "action.remove_redundancy").concat("...")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + removeRedundancyMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); + pairwiseAlignmentMenuItem.setText(MessageManager .getString("action.pairwise_alignment")); - pairwiseAlignmentMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - pairwiseAlignmentMenuItem_actionPerformed(e); - } - }); + pairwiseAlignmentMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + pairwiseAlignmentMenuItem_actionPerformed(e); + } + }); PCAMenuItem.setText(MessageManager .getString("label.principal_component_analysis")); - PCAMenuItem.addActionListener(new java.awt.event.ActionListener() + PCAMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -885,26 +901,24 @@ public class GAlignFrame extends JInternalFrame }); averageDistanceTreeMenuItem.setText(MessageManager .getString("label.average_distance_identity")); - averageDistanceTreeMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); + averageDistanceTreeMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + averageDistanceTreeMenuItem_actionPerformed(e); + } + }); neighbourTreeMenuItem.setText(MessageManager .getString("label.neighbour_joining_identity")); - neighbourTreeMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - neighbourTreeMenuItem_actionPerformed(e); - } - }); + neighbourTreeMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + neighbourTreeMenuItem_actionPerformed(e); + } + }); this.getContentPane().setLayout(borderLayout1); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); @@ -915,7 +929,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.out_to_textbox")); clustalColour.setText(MessageManager.getString("label.clustalx")); - clustalColour.addActionListener(new java.awt.event.ActionListener() + clustalColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -924,7 +938,7 @@ public class GAlignFrame extends JInternalFrame } }); zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() + zappoColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -933,7 +947,7 @@ public class GAlignFrame extends JInternalFrame } }); taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() + taylorColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -943,17 +957,16 @@ public class GAlignFrame extends JInternalFrame }); hydrophobicityColour.setText(MessageManager .getString("label.hydrophobicity")); - hydrophobicityColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); + hydrophobicityColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(e); + } + }); helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new java.awt.event.ActionListener() + helixColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -963,7 +976,7 @@ public class GAlignFrame extends JInternalFrame }); strandColour.setText(MessageManager .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() + strandColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -972,7 +985,7 @@ public class GAlignFrame extends JInternalFrame } }); turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() + turnColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -981,7 +994,7 @@ public class GAlignFrame extends JInternalFrame } }); buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() + buriedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -991,7 +1004,7 @@ public class GAlignFrame extends JInternalFrame }); userDefinedColour.setText(MessageManager .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + userDefinedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1001,7 +1014,7 @@ public class GAlignFrame extends JInternalFrame }); PIDColour .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() + PIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1011,7 +1024,7 @@ public class GAlignFrame extends JInternalFrame }); BLOSUM62Colour .setText(MessageManager.getString("label.blosum62_score")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + BLOSUM62Colour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1020,7 +1033,7 @@ public class GAlignFrame extends JInternalFrame } }); nucleotideColour.setText(MessageManager.getString("label.nucleotide")); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() + nucleotideColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1031,55 +1044,51 @@ public class GAlignFrame extends JInternalFrame purinePyrimidineColour.setText(MessageManager .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(e); - } - }); + purinePyrimidineColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(e); + } + }); RNAInteractionColour.setText("RNA Interaction type"); - RNAInteractionColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - RNAInteractionColour_actionPerformed(e); - } - }); + RNAInteractionColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + RNAInteractionColour_actionPerformed(e); + } + }); /* * covariationColour.setText("Covariation"); - * covariationColour.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * covariationColour_actionPerformed(e); } }); + * covariationColour.addActionListener(new ActionListener() { public void + * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); } + * }); */ avDistanceTreeBlosumMenuItem.setText(MessageManager .getString("label.average_distance_bloslum62")); - avDistanceTreeBlosumMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - avTreeBlosumMenuItem_actionPerformed(e); - } - }); + avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + avTreeBlosumMenuItem_actionPerformed(e); + } + }); njTreeBlosumMenuItem.setText(MessageManager .getString("label.neighbour_blosum62")); - njTreeBlosumMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - njTreeBlosumMenuItem_actionPerformed(e); - } - }); + njTreeBlosumMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + njTreeBlosumMenuItem_actionPerformed(e); + } + }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText(MessageManager .getString("label.show_annotations")); @@ -1139,15 +1148,20 @@ public class GAlignFrame extends JInternalFrame hideAllAnnotations_actionPerformed(true, false); } }); + SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder + .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); sortAnnBySequence.setText(MessageManager .getString("label.sort_annotations_by_sequence")); + sortAnnBySequence + .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); sortAnnBySequence.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { boolean newState = sortAnnBySequence.getState(); - sortAnnByLabel.setState(false); + sortAnnByLabel.setSelected(false); setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL : SequenceAnnotationOrder.NONE); sortAnnotations_actionPerformed(); @@ -1155,13 +1169,15 @@ public class GAlignFrame extends JInternalFrame }); sortAnnByLabel.setText(MessageManager .getString("label.sort_annotations_by_label")); + sortAnnByLabel + .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); sortAnnByLabel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { boolean newState = sortAnnByLabel.getState(); - sortAnnBySequence.setState(false); + sortAnnBySequence.setSelected(false); setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE : SequenceAnnotationOrder.NONE); sortAnnotations_actionPerformed(); @@ -1169,17 +1185,16 @@ public class GAlignFrame extends JInternalFrame }); colourTextMenuItem.setText(MessageManager .getString("label.colour_text")); - colourTextMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - colourTextMenuItem_actionPerformed(e); - } - }); + colourTextMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + colourTextMenuItem_actionPerformed(e); + } + }); htmlMenuItem.setText(MessageManager.getString("label.html")); - htmlMenuItem.addActionListener(new java.awt.event.ActionListener() + htmlMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1187,9 +1202,22 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); + + // TODO uncomment when supported by MassageManager + // createBioJS.setText(MessageManager.getString("label.biojs_html_export")); + createBioJS.setText("BioJS"); + createBioJS.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + bioJSMenuItem_actionPerformed(e); + } + }); + overviewMenuItem.setText(MessageManager .getString("label.overview_window")); - overviewMenuItem.addActionListener(new java.awt.event.ActionListener() + overviewMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1197,45 +1225,47 @@ public class GAlignFrame extends JInternalFrame overviewMenuItem_actionPerformed(e); } }); + undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); - undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - undoMenuItem.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { undoMenuItem_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); + redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); - redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - redoMenuItem.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { redoMenuItem_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); + conservationMenuItem.setText(MessageManager .getString("action.by_conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(e); - } - }); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(e); + } + }); noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + noColourmenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1244,7 +1274,7 @@ public class GAlignFrame extends JInternalFrame } }); wrapMenuItem.setText(MessageManager.getString("label.wrap")); - wrapMenuItem.addActionListener(new java.awt.event.ActionListener() + wrapMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1252,47 +1282,50 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem_actionPerformed(e); } }); + printMenuItem.setText(MessageManager.getString("action.print") + "..."); - printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - printMenuItem.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { printMenuItem_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, printMenuItem, al); + renderGapsMenuItem .setText(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); - renderGapsMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - renderGapsMenuItem_actionPerformed(e); - } - }); + renderGapsMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + renderGapsMenuItem_actionPerformed(e); + } + }); + findMenuItem.setText(MessageManager.getString("action.find")); - findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.find_tip"))); - findMenuItem.addActionListener(new java.awt.event.ActionListener() + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { findMenuItem_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, findMenuItem, al); + abovePIDThreshold.setText(MessageManager .getString("label.above_identity_threshold")); - abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() + abovePIDThreshold.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1414,35 +1447,35 @@ public class GAlignFrame extends JInternalFrame } }); + ButtonGroup buttonGroup = new ButtonGroup(); + buttonGroup.add(showAutoFirst); + buttonGroup.add(showAutoLast); showAutoFirst.setText(MessageManager.getString("label.show_first")); - showAutoFirst.setState(Cache.getDefault("SHOW_AUTOCALC_ABOVE", false)); + showAutoFirst.setSelected(Cache.getDefault( + Preferences.SHOW_AUTOCALC_ABOVE, false)); showAutoFirst.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - boolean sortFirst = showAutoFirst.getState(); - setShowAutoCalculatedAbove(sortFirst); - showAutoLast.setState(!sortFirst); + setShowAutoCalculatedAbove(showAutoFirst.isSelected()); sortAnnotations_actionPerformed(); } }); showAutoLast.setText(MessageManager.getString("label.show_last")); - showAutoLast.setState(!showAutoFirst.getState()); + showAutoLast.setSelected(!showAutoFirst.isSelected()); showAutoLast.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - boolean sortLast = showAutoLast.getState(); - setShowAutoCalculatedAbove(!sortLast); - showAutoFirst.setState(!sortLast); + setShowAutoCalculatedAbove(!showAutoLast.isSelected()); sortAnnotations_actionPerformed(); } }); nucleotideColour.setText(MessageManager.getString("label.nucleotide")); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() + nucleotideColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1465,69 +1498,74 @@ public class GAlignFrame extends JInternalFrame deleteGroups .setText(MessageManager.getString("action.undefine_groups")); - deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - deleteGroups.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { deleteGroups_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, deleteGroups, al); + createGroup.setText(MessageManager.getString("action.create_groups")); - createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - createGroup.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { createGroup_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, createGroup, al); + unGroup.setText(MessageManager.getString("action.remove_group")); - unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask() - | java.awt.event.KeyEvent.SHIFT_MASK, false)); - unGroup.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.SHIFT_MASK, false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { unGroup_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, unGroup, al); + copy.setText(MessageManager.getString("action.copy")); - copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); - copy.addActionListener(new java.awt.event.ActionListener() + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, copy, al); + cut.setText(MessageManager.getString("action.cut")); - cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - cut.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, cut, al); + delete.setText(MessageManager.getString("action.delete")); - delete.addActionListener(new java.awt.event.ActionListener() + delete.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1535,35 +1573,38 @@ public class GAlignFrame extends JInternalFrame delete_actionPerformed(e); } }); + pasteMenu.setText(MessageManager.getString("action.paste")); pasteNew.setText(MessageManager.getString("label.to_new_alignment")); - pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask() - | java.awt.event.KeyEvent.SHIFT_MASK, false)); - pasteNew.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.SHIFT_MASK, false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pasteNew_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, pasteNew, al); + pasteThis.setText(MessageManager.getString("label.to_this_alignment")); - pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - pasteThis.addActionListener(new java.awt.event.ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pasteThis_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, pasteThis, al); + applyToAllGroups.setText(MessageManager .getString("label.apply_colour_to_all_groups")); - applyToAllGroups.addActionListener(new java.awt.event.ActionListener() + applyToAllGroups.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1571,7 +1612,7 @@ public class GAlignFrame extends JInternalFrame applyToAllGroups_actionPerformed(e); } }); - createPNG.addActionListener(new java.awt.event.ActionListener() + createPNG.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1582,8 +1623,9 @@ public class GAlignFrame extends JInternalFrame createPNG.setActionCommand(MessageManager .getString("label.save_png_image")); createPNG.setText("PNG"); + font.setText(MessageManager.getString("action.font")); - font.addActionListener(new java.awt.event.ActionListener() + font.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1591,11 +1633,10 @@ public class GAlignFrame extends JInternalFrame font_actionPerformed(e); } }); - seqLimits.setText(MessageManager .getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); - seqLimits.addActionListener(new java.awt.event.ActionListener() + seqLimits.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1604,7 +1645,7 @@ public class GAlignFrame extends JInternalFrame } }); epsFile.setText("EPS"); - epsFile.addActionListener(new java.awt.event.ActionListener() + epsFile.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1612,11 +1653,22 @@ public class GAlignFrame extends JInternalFrame createEPS(null); } }); + + createSVG.setText("SVG"); + createSVG.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createSVG(null); + } + }); + LoadtreeMenuItem.setActionCommand(MessageManager .getString("label.load_tree_for_sequence_set")); LoadtreeMenuItem.setText(MessageManager .getString("label.load_associated_tree")); - LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() + LoadtreeMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1627,7 +1679,7 @@ public class GAlignFrame extends JInternalFrame scaleAbove.setVisible(false); scaleAbove.setText(MessageManager.getString("action.scale_above")); - scaleAbove.addActionListener(new java.awt.event.ActionListener() + scaleAbove.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1638,7 +1690,7 @@ public class GAlignFrame extends JInternalFrame scaleLeft.setVisible(false); scaleLeft.setSelected(true); scaleLeft.setText(MessageManager.getString("action.scale_left")); - scaleLeft.addActionListener(new java.awt.event.ActionListener() + scaleLeft.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1649,7 +1701,7 @@ public class GAlignFrame extends JInternalFrame scaleRight.setVisible(false); scaleRight.setSelected(true); scaleRight.setText(MessageManager.getString("action.scale_right")); - scaleRight.addActionListener(new java.awt.event.ActionListener() + scaleRight.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1661,15 +1713,14 @@ public class GAlignFrame extends JInternalFrame centreColumnLabelsMenuItem.setState(false); centreColumnLabelsMenuItem.setText(MessageManager .getString("label.centre_column_labels")); - centreColumnLabelsMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - centreColumnLabels_actionPerformed(e); - } - }); + centreColumnLabelsMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + centreColumnLabels_actionPerformed(e); + } + }); followHighlightMenuItem.setVisible(true); followHighlightMenuItem.setState(true); followHighlightMenuItem.setText(MessageManager @@ -1687,7 +1738,7 @@ public class GAlignFrame extends JInternalFrame modifyPID.setText(MessageManager .getString("label.modify_identity_thereshold")); - modifyPID.addActionListener(new java.awt.event.ActionListener() + modifyPID.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1697,15 +1748,14 @@ public class GAlignFrame extends JInternalFrame }); modifyConservation.setText(MessageManager .getString("label.modify_conservation_thereshold")); - modifyConservation - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - modifyConservation_actionPerformed(e); - } - }); + 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")); @@ -1730,7 +1780,7 @@ public class GAlignFrame extends JInternalFrame sortByAnnotScore.setText(MessageManager .getString("label.sort_by_score")); sort.add(sortByAnnotScore); - sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() + sort.addMenuListener(new javax.swing.event.MenuListener() { @Override @@ -1786,6 +1836,7 @@ public class GAlignFrame extends JInternalFrame showTranslation_actionPerformed(e); } }); + extractScores.setText(MessageManager.getString("label.extract_scores") + "..."); extractScores.addActionListener(new ActionListener() @@ -1796,15 +1847,11 @@ public class GAlignFrame extends JInternalFrame extractScores_actionPerformed(e); } }); - extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based - // score extraction + 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")); - /* - * showProducts.addActionListener(new ActionListener() { - * - * public void actionPerformed(ActionEvent e) { - * showProducts_actionPerformed(e); } }); - */ openFeatureSettings.setText(MessageManager .getString("label.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() @@ -1837,6 +1884,17 @@ public class GAlignFrame extends JInternalFrame } }); + annotationColumn.setText(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() @@ -1953,7 +2011,7 @@ public class GAlignFrame extends JInternalFrame } }); statusPanel.setLayout(gridLayout1); - jMenu3.setText(MessageManager.getString("action.show")); + showMenu.setText(MessageManager.getString("action.show")); showAllSeqs.setText(MessageManager.getString("label.all_sequences")); showAllSeqs.setToolTipText(MessageManager .getString("label.toggle_sequence_visibility")); @@ -2044,20 +2102,32 @@ public class GAlignFrame extends JInternalFrame hiddenMarkers_actionPerformed(e); } }); + invertColSel.setText(MessageManager .getString("action.invert_column_selection")); - invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask() - | java.awt.event.KeyEvent.ALT_MASK, false)); - invertColSel.addActionListener(new ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() + | KeyEvent.ALT_MASK, false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { invertColSel_actionPerformed(e); } + }; + addMenuActionAndAccelerator(keyStroke, invertColSel, al); + + showComplementMenuItem.setVisible(false); + showComplementMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showComplement_actionPerformed(showComplementMenuItem.getState()); + } }); + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { @Override @@ -2084,18 +2154,20 @@ public class GAlignFrame extends JInternalFrame tabbedPane_focusGained(e); } }); + save.setText(MessageManager.getString("action.save")); - save.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - save.addActionListener(new ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { save_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, save, al); + reload.setEnabled(false); reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() @@ -2106,18 +2178,20 @@ public class GAlignFrame extends JInternalFrame reload_actionPerformed(e); } }); + newView.setText(MessageManager.getString("action.new_view")); - newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit() - .getMenuShortcutKeyMask(), false)); - newView.addActionListener(new ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask(), false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { newView_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, newView, al); + tabbedPane.setToolTipText("" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + ""); @@ -2143,30 +2217,33 @@ public class GAlignFrame extends JInternalFrame idRightAlign_actionPerformed(e); } }); + gatherViews.setEnabled(false); gatherViews.setText(MessageManager.getString("action.gather_views")); - gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_G, 0, false)); - gatherViews.addActionListener(new ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { gatherViews_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, gatherViews, al); + expandViews.setEnabled(false); expandViews.setText(MessageManager.getString("action.expand_views")); - expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_X, 0, false)); - expandViews.addActionListener(new ActionListener() + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); + al = new ActionListener() { @Override public void actionPerformed(ActionEvent e) { expandViews_actionPerformed(e); } - }); + }; + addMenuActionAndAccelerator(keyStroke, expandViews, al); + pageSetup .setText(MessageManager.getString("action.page_setup") + "..."); pageSetup.addActionListener(new ActionListener() @@ -2241,8 +2318,9 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(expandViews); viewMenu.add(gatherViews); viewMenu.addSeparator(); - viewMenu.add(jMenu3); + viewMenu.add(showMenu); viewMenu.add(hideMenu); + viewMenu.add(showComplementMenuItem); viewMenu.addSeparator(); viewMenu.add(followHighlightMenuItem); annotationsMenu.add(annotationPanelMenuItem); @@ -2330,15 +2408,17 @@ public class GAlignFrame extends JInternalFrame jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); + jMenu2.add(createBioJS); + jMenu2.add(createSVG); addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); addSequenceMenu.add(addFromURL); this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); statusPanel.add(statusBar, null); this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); - jMenu3.add(showAllColumns); - jMenu3.add(showAllSeqs); - jMenu3.add(showAllhidden); + showMenu.add(showAllColumns); + showMenu.add(showAllSeqs); + showMenu.add(showAllhidden); hideMenu.add(hideSelColumns); hideMenu.add(hideSelSequences); hideMenu.add(hideAllSelection); @@ -2369,6 +2449,7 @@ public class GAlignFrame extends JInternalFrame selectMenu.add(unGroup); selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); + selectMenu.add(annotationColumn); calculateMenu.add(expandAlignment); // TODO - determine if the listenToViewSelections button is needed : see bug // JAL-574 @@ -2377,6 +2458,22 @@ public class GAlignFrame extends JInternalFrame } /** + * 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. + * + * @param keyStroke + * @param menuItem + * @param actionListener + */ + protected void addMenuActionAndAccelerator(KeyStroke keyStroke, + JMenuItem menuItem, ActionListener actionListener) + { + menuItem.setAccelerator(keyStroke); + accelerators.put(keyStroke, menuItem); + menuItem.addActionListener(actionListener); + } + + /** * Action on clicking sort annotations by type. * * @param sortOrder @@ -2542,10 +2639,6 @@ public class GAlignFrame extends JInternalFrame { } - protected void showProducts_actionPerformed(ActionEvent e) - { - } - protected void buildSortByAnnotationScoresMenu() { } @@ -2587,6 +2680,11 @@ public class GAlignFrame extends JInternalFrame { } + protected void bioJSMenuItem_actionPerformed(ActionEvent e) + { + + } + protected void closeMenuItem_actionPerformed(boolean b) { } @@ -2840,6 +2938,10 @@ public class GAlignFrame extends JInternalFrame { } + public void createSVG(java.io.File f) + { + + } protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { @@ -2938,6 +3040,11 @@ public class GAlignFrame extends JInternalFrame } + public void annotationColumn_actionPerformed(ActionEvent e) + { + + } + public void rnahelicesColour_actionPerformed(ActionEvent e) { @@ -3093,4 +3200,50 @@ public class GAlignFrame extends JInternalFrame { this.annotationSortOrder = annotationSortOrder; } + + public Map getAccelerators() + { + return this.accelerators; + } + + /** + * Returns the selected index of the tabbed pane, or -1 if none selected + * (including the case where the tabbed pane has not been made visible). + * + * @return + */ + public int getTabIndex() + { + return tabbedPane.getSelectedIndex(); + } + + public JPanel getStatusPanel() + { + return statusPanel; + } + + /** + * Sets a reference to the containing split frame. Also makes the 'toggle + * split view' menu item visible and checked. + * + * @param sf + */ + public void setSplitFrame(SplitContainerI sf) + { + this.splitFrame = sf; + if (sf != null) + { + this.showComplementMenuItem.setVisible(true); + this.showComplementMenuItem.setState(true); + } + } + + public SplitContainerI getSplitViewContainer() + { + return this.splitFrame; + } + + protected void showComplement_actionPerformed(boolean state) + { + } }