X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d9c87cb45ac63f17af70782d33f37a0f120919ed;hb=7498f96b78e7d8f3d2f015343b0948810668c0e9;hp=6f963a52844860d3269cad90dcf300b76d884137;hpb=541c8e105bb5073795321ddc386f9b9f9f3ccdff;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6f963a5..d9c87cb 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,6 +21,7 @@ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.api.SplitContainerI; import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; @@ -218,6 +219,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem createPNG = new JMenuItem(); + JMenuItem createBioJS = new JMenuItem(); + JMenuItem createSVG = new JMenuItem(); protected JMenuItem font = new JMenuItem(); @@ -258,8 +261,6 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem showTranslation = new JMenuItem(); - protected JMenu cdna = new JMenu(); - protected JMenuItem extractScores = new JMenuItem(); protected JMenuItem expandAlignment = new JMenuItem(); @@ -272,6 +273,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem annotationColour = new JMenuItem(); + JMenuItem annotationColumn = new JMenuItem(); + protected JMenuItem rnahelicesColour = new JMenuItem(); JMenuItem associatedData = new JMenuItem(); @@ -298,7 +301,7 @@ public class GAlignFrame extends JInternalFrame GridLayout gridLayout1 = new GridLayout(); - JMenu jMenu3 = new JMenu(); + JMenu showMenu = new JMenu(); JMenuItem showAllSeqs = new JMenuItem(); @@ -324,6 +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(); @@ -342,7 +347,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem textColour = new JMenuItem(); - JMenu formatMenu = new JMenu(); + protected JMenu formatMenu = new JMenu(); JMenu selectMenu = new JMenu(); @@ -390,7 +395,9 @@ public class GAlignFrame extends JInternalFrame private boolean showAutoCalculatedAbove = false; - private Map accelerators = new HashMap(); + private Map accelerators = new HashMap(); + + private SplitContainerI splitFrame; public GAlignFrame() { @@ -509,9 +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) @@ -1196,6 +1202,19 @@ 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 ActionListener() @@ -1614,7 +1633,6 @@ 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)); @@ -1819,54 +1837,6 @@ public class GAlignFrame extends JInternalFrame } }); - /* - * cDNA menu options - */ - cdna.setText(MessageManager.getString("label.cdna")); - // link to available cDNA - JMenuItem linkCdna = new JMenuItem( - MessageManager.getString("label.link_cdna")); - linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.link_cdna_tip"))); - linkCdna.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - linkCdna_actionPerformed(); - } - }); - cdna.add(linkCdna); - // align linked cDNA - JMenuItem alignCdna = new JMenuItem( - MessageManager.getString("label.align_cdna")); - alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.align_cdna_tip"))); - alignCdna.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - alignCdna_actionPerformed(); - } - }); - cdna.add(alignCdna); - - // view alignment as cDNA (when known) - JMenuItem viewAsCdna = new JMenuItem( - MessageManager.getString("label.view_as_cdna")); - viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.view_as_cdna_tip"))); - viewAsCdna.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - viewAsCdna_actionPerformed(); - } - }); - cdna.add(viewAsCdna); - extractScores.setText(MessageManager.getString("label.extract_scores") + "..."); extractScores.addActionListener(new ActionListener() @@ -1914,6 +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() @@ -2030,7 +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")); @@ -2137,6 +2118,16 @@ public class GAlignFrame extends JInternalFrame }; 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 @@ -2327,8 +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); @@ -2398,7 +2390,6 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); - calculateMenu.add(cdna); calculateMenu.add(showProducts); calculateMenu.add(autoCalculate); calculateMenu.add(sortByTree); @@ -2417,6 +2408,7 @@ 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); @@ -2424,9 +2416,9 @@ 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); - 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); @@ -2457,6 +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 @@ -2476,22 +2469,10 @@ public class GAlignFrame extends JInternalFrame JMenuItem menuItem, ActionListener actionListener) { menuItem.setAccelerator(keyStroke); - accelerators.put(keyStroke, actionListener); + accelerators.put(keyStroke, menuItem); menuItem.addActionListener(actionListener); } - protected void viewAsCdna_actionPerformed() - { - } - - protected void alignCdna_actionPerformed() - { - } - - protected void linkCdna_actionPerformed() - { - } - /** * Action on clicking sort annotations by type. * @@ -2699,6 +2680,11 @@ public class GAlignFrame extends JInternalFrame { } + protected void bioJSMenuItem_actionPerformed(ActionEvent e) + { + + } + protected void closeMenuItem_actionPerformed(boolean b) { } @@ -3054,6 +3040,11 @@ public class GAlignFrame extends JInternalFrame } + public void annotationColumn_actionPerformed(ActionEvent e) + { + + } + public void rnahelicesColour_actionPerformed(ActionEvent e) { @@ -3210,8 +3201,49 @@ public class GAlignFrame extends JInternalFrame this.annotationSortOrder = annotationSortOrder; } - public Map getAccelerators() + 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) + { + } }