X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;fp=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=c228c9098f14590044c4a8c584acb4ad2b6c3e54;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=075b490f4673b1a91beae7d1fb0f770d2bbe1900;hpb=9e31a59b947882325ffe614bd71fb732d7952a23;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 075b490..c228c90 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -27,6 +27,8 @@ import jalview.api.SplitContainerI; import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; +import jalview.hmmer.HmmerCommand; +import jalview.io.FileFormatException; import jalview.io.FileFormats; import jalview.schemes.ResidueColourScheme; import jalview.util.MessageManager; @@ -42,6 +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; @@ -69,6 +72,8 @@ public class GAlignFrame extends JInternalFrame protected JMenu webService = new JMenu(); + protected JMenu hmmerMenu = new JMenu(); + protected JMenuItem webServiceNoServices; protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); @@ -197,6 +202,12 @@ 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; @@ -251,7 +262,7 @@ public class GAlignFrame extends JInternalFrame private void jbInit() throws Exception { initColourMenu(); - + JMenuItem saveAs = new JMenuItem( MessageManager.getString("action.save_as")); ActionListener al = new ActionListener() @@ -262,14 +273,14 @@ public class GAlignFrame extends JInternalFrame saveAs_actionPerformed(e); } }; - + // FIXME getDefaultToolkit throws an exception in Headless mode 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, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); @@ -282,7 +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( @@ -292,6 +303,9 @@ 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, @@ -305,7 +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); @@ -318,7 +332,7 @@ 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, @@ -332,7 +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() @@ -368,7 +382,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); - + JMenuItem remove2RightMenuItem = new JMenuItem( MessageManager.getString("action.remove_right")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, @@ -382,7 +396,7 @@ 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, @@ -396,7 +410,7 @@ 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, @@ -412,7 +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() @@ -504,7 +518,7 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem_actionPerformed(e); } }); - + JMenuItem removeRedundancyMenuItem = new JMenuItem( MessageManager.getString("action.remove_redundancy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, @@ -518,7 +532,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); - + JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( MessageManager.getString("action.pairwise_alignment")); pairwiseAlignmentMenuItem.addActionListener(new ActionListener() @@ -529,16 +543,18 @@ public class GAlignFrame extends JInternalFrame 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")); + annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem .setText(MessageManager.getString("label.show_annotations")); @@ -606,6 +622,7 @@ 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.addActionListener(new ActionListener() @@ -646,7 +663,7 @@ public class GAlignFrame extends JInternalFrame colourTextMenuItem_actionPerformed(e); } }); - + JMenuItem htmlMenuItem = new JMenuItem( MessageManager.getString("label.html")); htmlMenuItem.addActionListener(new ActionListener() @@ -657,7 +674,7 @@ 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() @@ -668,7 +685,7 @@ public class GAlignFrame extends JInternalFrame bioJSMenuItem_actionPerformed(e); } }); - + JMenuItem overviewMenuItem = new JMenuItem( MessageManager.getString("label.overview_window")); overviewMenuItem.addActionListener(new ActionListener() @@ -679,7 +696,7 @@ public class GAlignFrame extends JInternalFrame overviewMenuItem_actionPerformed(e); } }); - + undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, @@ -693,7 +710,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); - + redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, @@ -707,7 +724,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); - + wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new ActionListener() { @@ -717,7 +734,7 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem_actionPerformed(e); } }); - + JMenuItem printMenuItem = new JMenuItem( MessageManager.getString("action.print")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, @@ -731,7 +748,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, printMenuItem, al); - + renderGapsMenuItem .setText(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); @@ -743,7 +760,7 @@ public class GAlignFrame extends JInternalFrame renderGapsMenuItem_actionPerformed(e); } }); - + JMenuItem findMenuItem = new JMenuItem( MessageManager.getString("action.find")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, @@ -762,6 +779,7 @@ public class GAlignFrame extends JInternalFrame showSeqFeatures.setText( MessageManager.getString("label.show_sequence_features")); + showSeqFeatures.addActionListener(new ActionListener() { @Override @@ -780,86 +798,86 @@ public class GAlignFrame extends JInternalFrame .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.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showNpFeats_actionPerformed(e); } - + }); 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.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showGroupConsensus_actionPerformed(e); } - + }); 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.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showSequenceLogo_actionPerformed(e); } - + }); 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")); @@ -873,7 +891,7 @@ public class GAlignFrame extends JInternalFrame applyAutoAnnotationSettings_actionPerformed(e); } }); - + ButtonGroup buttonGroup = new ButtonGroup(); final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( MessageManager.getString("label.show_first")); @@ -904,7 +922,7 @@ public class GAlignFrame extends JInternalFrame sortAnnotations_actionPerformed(); } }); - + JMenuItem deleteGroups = new JMenuItem( MessageManager.getString("action.undefine_groups")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, @@ -918,7 +936,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, deleteGroups, al); - + JMenuItem annotationColumn = new JMenuItem( MessageManager.getString("action.select_by_annotation")); annotationColumn.addActionListener(new ActionListener() @@ -929,7 +947,7 @@ public class GAlignFrame extends JInternalFrame annotationColumn_actionPerformed(e); } }); - + JMenuItem createGroup = new JMenuItem( MessageManager.getString("action.create_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, @@ -943,7 +961,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, createGroup, al); - + JMenuItem unGroup = new JMenuItem( MessageManager.getString("action.remove_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, @@ -959,7 +977,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, unGroup, al); - + copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); @@ -973,7 +991,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, copy, al); - + cut.setText(MessageManager.getString("action.cut")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); @@ -986,7 +1004,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, cut, al); - + JMenuItem delete = new JMenuItem( MessageManager.getString("action.delete")); delete.addActionListener(new ActionListener() @@ -997,7 +1015,7 @@ public class GAlignFrame extends JInternalFrame delete_actionPerformed(e); } }); - + pasteMenu.setText(MessageManager.getString("action.paste")); JMenuItem pasteNew = new JMenuItem( MessageManager.getString("label.to_new_alignment")); @@ -1010,11 +1028,18 @@ public class GAlignFrame extends JInternalFrame @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, @@ -1024,11 +1049,18 @@ public class GAlignFrame extends JInternalFrame @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() { @@ -1040,7 +1072,6 @@ public class GAlignFrame extends JInternalFrame }); createPNG.setActionCommand( MessageManager.getString("label.save_png_image")); - JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); font.addActionListener(new ActionListener() { @@ -1070,7 +1101,7 @@ public class GAlignFrame extends JInternalFrame createEPS(null); } }); - + JMenuItem createSVG = new JMenuItem("SVG"); createSVG.addActionListener(new ActionListener() { @@ -1080,7 +1111,7 @@ public class GAlignFrame extends JInternalFrame createSVG(null); } }); - + JMenuItem loadTreeMenuItem = new JMenuItem( MessageManager.getString("label.load_associated_tree")); loadTreeMenuItem.setActionCommand( @@ -1093,7 +1124,7 @@ public class GAlignFrame extends JInternalFrame loadTreeMenuItem_actionPerformed(e); } }); - + scaleAbove.setVisible(false); scaleAbove.setText(MessageManager.getString("action.scale_above")); scaleAbove.addActionListener(new ActionListener() @@ -1144,15 +1175,15 @@ public class GAlignFrame extends JInternalFrame .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")); @@ -1163,12 +1194,12 @@ public class GAlignFrame extends JInternalFrame { buildTreeSortMenu(); } - + @Override public void menuDeselected(MenuEvent e) { } - + @Override public void menuCanceled(MenuEvent e) { @@ -1179,17 +1210,17 @@ public class GAlignFrame extends JInternalFrame 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) { @@ -1269,7 +1300,7 @@ public class GAlignFrame extends JInternalFrame showReverse_actionPerformed(true); } }); - + JMenuItem extractScores = new JMenuItem( MessageManager.getString("label.extract_scores")); extractScores.addActionListener(new ActionListener() @@ -1282,10 +1313,10 @@ 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")); @@ -1297,7 +1328,7 @@ public class GAlignFrame extends JInternalFrame runGroovy_actionPerformed(); } }); - + JMenuItem openFeatureSettings = new JMenuItem( MessageManager.getString("action.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() @@ -1318,7 +1349,7 @@ public class GAlignFrame extends JInternalFrame fetchSequence_actionPerformed(e); } }); - + JMenuItem associatedData = new JMenuItem( MessageManager.getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() @@ -1326,7 +1357,14 @@ 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(); + } } }); loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file")); @@ -1380,7 +1418,7 @@ public class GAlignFrame extends JInternalFrame listenToViewSelections_actionPerformed(e); } }); - + JMenu addSequenceMenu = new JMenu( MessageManager.getString("label.add_sequences")); JMenuItem addFromFile = new JMenuItem( @@ -1526,7 +1564,7 @@ public class GAlignFrame extends JInternalFrame hiddenMarkers_actionPerformed(e); } }); - + JMenuItem invertColSel = new JMenuItem( MessageManager.getString("action.invert_column_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, @@ -1542,7 +1580,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, invertColSel, al); - + showComplementMenuItem.setVisible(false); showComplementMenuItem.addActionListener(new ActionListener() { @@ -1552,7 +1590,7 @@ public class GAlignFrame extends JInternalFrame showComplement_actionPerformed(showComplementMenuItem.getState()); } }); - + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { @Override @@ -1573,7 +1611,7 @@ public class GAlignFrame extends JInternalFrame tabbedPane_mousePressed(e); } } - + @Override public void mouseReleased(MouseEvent e) { @@ -1591,7 +1629,7 @@ public class GAlignFrame extends JInternalFrame tabbedPane_focusGained(e); } }); - + JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); @@ -1604,7 +1642,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, save, al); - + reload.setEnabled(false); reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() @@ -1615,7 +1653,7 @@ public class GAlignFrame extends JInternalFrame reload_actionPerformed(e); } }); - + JMenuItem newView = new JMenuItem( MessageManager.getString("action.new_view")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, @@ -1629,11 +1667,11 @@ 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")); @@ -1647,7 +1685,7 @@ 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); @@ -1660,7 +1698,7 @@ 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); @@ -1673,7 +1711,7 @@ public class GAlignFrame extends JInternalFrame } }; addMenuActionAndAccelerator(keyStroke, expandViews, al); - + JMenuItem pageSetup = new JMenuItem( MessageManager.getString("action.page_setup")); pageSetup.addActionListener(new ActionListener() @@ -1711,7 +1749,7 @@ 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")); @@ -1724,7 +1762,8 @@ 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); @@ -1744,7 +1783,7 @@ public class GAlignFrame extends JInternalFrame fileMenu.add(loadVcf); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); - + pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); editMenu.add(undoMenuItem); @@ -1766,7 +1805,7 @@ public class GAlignFrame extends JInternalFrame // editMenu.add(justifyRightMenuItem); // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); - + showMenu.add(showAllColumns); showMenu.add(showAllSeqs); showMenu.add(showAllhidden); @@ -1794,7 +1833,7 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(alignmentProperties); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); - + annotationsMenu.add(annotationPanelMenuItem); annotationsMenu.addSeparator(); annotationsMenu.add(showAllAlAnnotations); @@ -1838,7 +1877,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(extractScores); calculateMenu.addSeparator(); calculateMenu.add(runGroovy); - + webServiceNoServices = new JMenuItem( MessageManager.getString("label.no_services")); webService.add(webServiceNoServices); @@ -1853,7 +1892,7 @@ 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); @@ -1887,6 +1926,121 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + /** + * Constructs the entries on the HMMER menu + */ + protected void initHMMERMenu() + { + /* + * hmmbuild + */ + 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) + { + hmmBuild_actionPerformed(false); + } + }); + JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmbuild")); + hmmBuildRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmBuild_actionPerformed(true); + } + }); + 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) + { + hmmAlign_actionPerformed(true); + } + }); + JMenuItem hmmAlignSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmAlignSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmAlign_actionPerformed(false); + } + }); + 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) + { + hmmSearch_actionPerformed(false); + } + }); + JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmsearch")); + hmmSearchRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmSearch_actionPerformed(true); + } + }); + JMenuItem addDatabase = new JMenuItem( + MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + hmmSearch.add(hmmSearchRun); + hmmSearch.add(hmmSearchSettings); + // hmmSearch.add(addDatabase); + + /* + * top level menu + */ + hmmerMenu.setText(MessageManager.getString("action.hmmer")); + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + hmmerMenu.add(hmmBuild); + hmmerMenu.add(hmmAlign); + hmmerMenu.add(hmmSearch); + + } + protected void loadVcf_actionPerformed() { } @@ -2363,10 +2517,12 @@ public class GAlignFrame extends JInternalFrame } protected void pasteNew_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { } protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { } @@ -2374,6 +2530,23 @@ public class GAlignFrame extends JInternalFrame { } + protected void hmmBuild_actionPerformed(boolean withDefaults) + { + } + + protected void hmmSearch_actionPerformed(boolean withDefaults) + { + } + + protected void addDatabase_actionPerformed() + throws FileFormatException, IOException + { + } + + protected void hmmAlign_actionPerformed(boolean withDefaults) + { + } + public void createPNG(java.io.File f) { } @@ -2489,6 +2662,7 @@ public class GAlignFrame extends JInternalFrame } public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { }