X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;fp=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=cc1703c2a89ca8e29118b78377396bf8c597519d;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=a8bd6fdd3b05a4d6a8749bc63964ce7a5c4e4dd8;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index a8bd6fd..cc1703c 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -100,6 +100,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener, AlignViewControllerGuiI { public AlignViewControllerI avc; + public AlignmentPanel alignPanel; public AlignViewport viewport; @@ -149,7 +150,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); - avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); viewport.updateConservation(alignPanel); viewport.updateConsensus(alignPanel); @@ -162,7 +164,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, showSequenceLogo.setState(viewport.isShowSequenceLogo()); normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); - + seqLimits.setState(viewport.showJVSuffix); if (applet != null) @@ -308,7 +310,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.featureSettings.refreshTable(); } alignPanel.paintAlignment(true); - statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment")); + statusBar.setText(MessageManager + .getString("label.successfully_added_features_alignment")); } return featuresFile; } @@ -452,7 +455,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")})); + statusBar.setText(MessageManager.formatMessage( + "label.keyboard_editing_mode", new String[] + { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; @@ -567,7 +572,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } break; - + case KeyEvent.VK_U: if (evt.isControlDown()) { @@ -996,8 +1001,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cap.setText(contents.toString()); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), - 400, 250); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.alignment_properties", new String[] + { getTitle() }), 400, 250); } else if (source == overviewMenuItem) { @@ -1144,7 +1150,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.input_cut_paste"), 500, 500); } protected void outputText_actionPerformed(ActionEvent e) @@ -1152,8 +1159,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.alignment_output_command", new String[] + { e.getActionCommand() }), 600, 500); cap.setText(new AppletFormatAdapter().formatSequences( e.getActionCommand(), viewport.getAlignment(), viewport.showJVSuffix)); @@ -1162,11 +1170,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void loadAnnotations() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here")); + cap.setText(MessageManager + .getString("label.paste_features_annotations_Tcoffee_here")); cap.setAnnotationImport(); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("action.paste_annotations"), 400, 300); } @@ -1183,7 +1193,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.annotations"), 600, 500); cap.setText(annotation); } @@ -1239,7 +1250,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.features"), 600, 500); cap.setText(features); } else @@ -1377,7 +1389,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()})); + undoMenuItem.setLabel(MessageManager.formatMessage( + "label.undo_command", new String[] + { command.getDescription() })); } else { @@ -1390,7 +1404,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()})); + redoMenuItem.setLabel(MessageManager.formatMessage( + "label.redo_command", new String[] + { command.getDescription() })); } else { @@ -1917,7 +1933,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void makeGrpsFromSelection_actionPerformed() { - if (avc.makeGroupsFromSelection()) { + if (avc.makeGroupsFromSelection()) + { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); @@ -1928,6 +1945,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { avc.createGroup(); } + protected void unGroup_actionPerformed() { if (avc.unGroup()) @@ -1935,6 +1953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.alignmentChanged(); } } + protected void deleteGroups_actionPerformed() { if (avc.deleteGroups()) @@ -2038,7 +2057,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.getSelectionGroup()); } - statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()})); + statusBar.setText(MessageManager.formatMessage( + "label.removed_columns", new String[] + { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); for (SequenceGroup sg : viewport.getAlignment().getGroups()) @@ -2078,7 +2099,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()})); + statusBar.setText(MessageManager.formatMessage( + "label.removed_empty_columns", new String[] + { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence @@ -2305,8 +2328,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, OverviewPanel overview = new OverviewPanel(alignPanel); frame.add(overview); // +50 must allow for applet frame window - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}), - overview.getPreferredSize().width, + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.overview_params", new String[] + { this.getTitle() }), overview.getPreferredSize().width, overview.getPreferredSize().height + 50); frame.pack(); @@ -2335,9 +2359,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (viewport.getAbovePIDThreshold()) { - viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background")); - } + viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, + cs, "Background")); + } if (viewport.getConservationSelected()) { @@ -2461,7 +2485,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, 500); } } @@ -2563,12 +2588,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cap.setTreeImport(); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.paste_newick_file"), 400, 300); } public void loadTree(jalview.io.NewickFile tree, String treeFile) { - TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree); + TreePanel tp = new TreePanel(alignPanel, treeFile, + MessageManager.getString("label.load_tree_from_file"), tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } @@ -2588,8 +2615,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .sortByTree(viewport.getAlignment(), treePanel.getTree()); // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); - addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder, - viewport.getAlignment())); + addHistoryItem(new OrderCommand(MessageManager.formatMessage( + "label.order_by_params", new String[] + { title }), oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2685,27 +2713,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // TODO: update this text for each release or centrally store it for // lite and application g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh); + g.drawString(MessageManager.formatMessage( + "label.jalviewLite_release", new String[] + { version }), x, y += fh); g.setFont(new Font("Helvetica", Font.BOLD, 12)); - g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh); + g.drawString(MessageManager.formatMessage( + "label.jaview_build_date", new String[] + { builddate }), x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString( - MessageManager.getString("label.jalview_authors_1"), + g.drawString(MessageManager.getString("label.jalview_authors_1"), x, y += fh * 1.5); - g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8); - g.drawString( - MessageManager.getString("label.jalview_dev_managers"), - x, y += fh); + g.drawString(MessageManager.getString("label.jalview_authors_2"), + x + 50, y += fh + 8); g.drawString( - MessageManager.getString("label.jalview_distribution_lists"), - x, y += fh); - g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8); + MessageManager.getString("label.jalview_dev_managers"), x, + y += fh); + g.drawString(MessageManager + .getString("label.jalview_distribution_lists"), x, y += fh); + g.drawString(MessageManager.getString("label.jalview_please_cite"), + x, y += fh + 8); g.drawString( MessageManager.getString("label.jalview_cite_1_authors"), x, y += fh); g.drawString( - MessageManager.getString("label.jalview_cite_1_title"), - x, y += fh); + MessageManager.getString("label.jalview_cite_1_title"), x, + y += fh); g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), x, y += fh); } @@ -2714,7 +2746,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite .getBuildDate())); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.jalview"), 580, 220); } @@ -2737,17 +2770,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Menu fileMenu = new Menu(MessageManager.getString("action.file")); - MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application")); + MenuItem loadApplication = new MenuItem( + MessageManager.getString("label.view_full_application")); - MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree")); + MenuItem loadTree = new MenuItem( + MessageManager.getString("label.load_associated_tree")); - MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations")); + MenuItem loadAnnotations = new MenuItem( + MessageManager.getString("label.load_features_annotations")); - MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features")); + MenuItem outputFeatures = new MenuItem( + MessageManager.getString("label.export_features")); - MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations")); + MenuItem outputAnnotations = new MenuItem( + MessageManager.getString("label.export_annotations")); - MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close")); + MenuItem closeMenuItem = new MenuItem( + MessageManager.getString("action.close")); Menu editMenu = new Menu(MessageManager.getString("action.edit")); @@ -2755,13 +2794,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Menu colourMenu = new Menu(MessageManager.getString("action.colour")); - Menu calculateMenu = new Menu(MessageManager.getString("action.calculate")); + Menu calculateMenu = new Menu( + MessageManager.getString("action.calculate")); - MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all")); + MenuItem selectAllSequenceMenuItem = new MenuItem( + MessageManager.getString("action.select_all")); - MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all")); + MenuItem deselectAllSequenceMenuItem = new MenuItem( + MessageManager.getString("action.deselect_all")); - MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection")); + MenuItem invertSequenceMenuItem = new MenuItem( + MessageManager.getString("action.invert_selection")); MenuItem remove2LeftMenuItem = new MenuItem(); @@ -2839,7 +2882,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); - MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props")); + MenuItem alProperties = new MenuItem( + MessageManager.getString("label.alignment_props")); MenuItem overviewMenuItem = new MenuItem(); @@ -2970,13 +3014,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, selectAllSequenceMenuItem.addActionListener(this); deselectAllSequenceMenuItem.addActionListener(this); invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left")); + remove2LeftMenuItem.setLabel(MessageManager + .getString("action.remove_left")); remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right")); + remove2RightMenuItem.setLabel(MessageManager + .getString("action.remove_right")); remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns")); + removeGappedColumnMenuItem.setLabel(MessageManager + .getString("action.remove_empty_columns")); removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps")); + removeAllGapsMenuItem.setLabel(MessageManager + .getString("action.remove_all_gaps")); removeAllGapsMenuItem.addActionListener(this); viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes")); viewBoxesMenuItem.setState(true); @@ -2984,29 +3032,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewTextMenuItem.setLabel(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id")); + sortPairwiseMenuItem.setLabel(MessageManager + .getString("action.by_pairwise_id")); sortPairwiseMenuItem.addActionListener(this); sortIDMenuItem.setLabel(MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(this); - sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length")); + sortLengthMenuItem.setLabel(MessageManager + .getString("action.by_length")); sortLengthMenuItem.addActionListener(this); sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy")); + removeRedundancyMenuItem.setLabel(MessageManager + .getString("action.remove_redundancy")); removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment")); + pairwiseAlignmentMenuItem.setLabel(MessageManager + .getString("action.pairwise_alignment")); pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis")); + PCAMenuItem.setLabel(MessageManager + .getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem - .setLabel(MessageManager.getString("label.average_distance_identity")); + averageDistanceTreeMenuItem.setLabel(MessageManager + .getString("label.average_distance_identity")); averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity")); + neighbourTreeMenuItem.setLabel(MessageManager + .getString("label.neighbour_joining_identity")); neighbourTreeMenuItem.addActionListener(this); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setText(MessageManager.getString("label.status_bar")); - outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox")); + outputTextboxMenu.setLabel(MessageManager + .getString("label.out_to_textbox")); clustalColour.setLabel(MessageManager.getString("label.clustalx")); clustalColour.addActionListener(this); @@ -3014,45 +3069,60 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, zappoColour.addActionListener(this); taylorColour.setLabel(MessageManager.getString("label.taylor")); taylorColour.addActionListener(this); - hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity")); + hydrophobicityColour.setLabel(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour.addActionListener(this); - helixColour.setLabel(MessageManager.getString("label.helix_propensity")); + helixColour + .setLabel(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(this); - strandColour.setLabel(MessageManager.getString("label.strand_propensity")); + strandColour.setLabel(MessageManager + .getString("label.strand_propensity")); strandColour.addActionListener(this); turnColour.setLabel(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(this); buriedColour.setLabel(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(this); - purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine")); + purinePyrimidineColour.setLabel(MessageManager + .getString("label.purine_pyrimidine")); purinePyrimidineColour.addActionListener(this); - RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction")); + RNAInteractionColour.setLabel(MessageManager + .getString("label.rna_interaction")); RNAInteractionColour.addActionListener(this); - RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes")); + RNAHelixColour.setLabel(MessageManager + .getString("action.by_rna_helixes")); RNAHelixColour.addActionListener(this); - userDefinedColour.setLabel(MessageManager.getString("action.user_defined")); + userDefinedColour.setLabel(MessageManager + .getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel(MessageManager.getString("label.percentage_identity")); + PIDColour.setLabel(MessageManager + .getString("label.percentage_identity")); PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score")); + BLOSUM62Colour.setLabel(MessageManager + .getString("label.blosum62_score")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour + .setLabel(MessageManager.getString("label.tcoffee_scores")); tcoffeeColour.setEnabled(false); // it will enabled only if a score file is // provided tcoffeeColour.addActionListener(this); - avDistanceTreeBlosumMenuItem - .setLabel(MessageManager.getString("label.average_distance_bloslum62")); + avDistanceTreeBlosumMenuItem.setLabel(MessageManager + .getString("label.average_distance_bloslum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62")); + njTreeBlosumMenuItem.setLabel(MessageManager + .getString("label.neighbour_blosum62")); njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations")); + annotationPanelMenuItem.setLabel(MessageManager + .getString("label.show_annotations")); annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text")); + colourTextMenuItem.setLabel(MessageManager + .getString("label.colour_text")); colourTextMenuItem.addItemListener(this); - displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed")); + displayNonconservedMenuItem.setLabel(MessageManager + .getString("label.show_non_conversed")); displayNonconservedMenuItem.addItemListener(this); alProperties.addActionListener(this); - overviewMenuItem.setLabel(MessageManager.getString("label.overview_window")); + overviewMenuItem.setLabel(MessageManager + .getString("label.overview_window")); overviewMenuItem.addActionListener(this); undoMenuItem.setEnabled(false); undoMenuItem.setLabel(MessageManager.getString("action.undo")); @@ -3060,24 +3130,29 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, redoMenuItem.setEnabled(false); redoMenuItem.setLabel(MessageManager.getString("action.redo")); redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation")); + conservationMenuItem.setLabel(MessageManager + .getString("action.by_conservation")); conservationMenuItem.addItemListener(this); noColourmenuItem.setLabel(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(this); wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps")); + renderGapsMenuItem.setLabel(MessageManager + .getString("action.show_gaps")); renderGapsMenuItem.setState(true); renderGapsMenuItem.addItemListener(this); findMenuItem.setLabel(MessageManager.getString("action.find")); findMenuItem.addActionListener(this); - abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold")); + abovePIDThreshold.setLabel(MessageManager + .getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(this); - deleteGroups.setLabel(MessageManager.getString("action.undefine_groups")); + deleteGroups.setLabel(MessageManager + .getString("action.undefine_groups")); deleteGroups.addActionListener(this); - grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection")); + grpsFromSelection.setLabel(MessageManager + .getString("action.make_groups_selection")); grpsFromSelection.addActionListener(this); createGroup.setLabel(MessageManager.getString("action.create_group")); unGroup.setLabel(MessageManager.getString("action.remove_group")); @@ -3092,7 +3167,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, pasteNew.addActionListener(this); pasteThis.setLabel(MessageManager.getString("label.to_this_alignment")); pasteThis.addActionListener(this); - applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups")); + applyToAllGroups.setLabel(MessageManager + .getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); font.setLabel(MessageManager.getString("action.font")); @@ -3109,20 +3185,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, scaleRight.setState(true); scaleRight.setLabel(MessageManager.getString("action.scale_right")); scaleRight.addItemListener(this); - modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold")); + modifyPID.setLabel(MessageManager + .getString("label.modify_identity_thereshold")); modifyPID.addActionListener(this); - modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold")); + modifyConservation.setLabel(MessageManager + .getString("label.modify_conservation_thereshold")); modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order")); + sortByTreeMenu.setLabel(MessageManager + .getString("action.by_tree_order")); sort.setLabel(MessageManager.getString("action.sort")); calculate.setLabel(MessageManager.getString("action.calculate_tree")); autoCalculate.addItemListener(this); sortByTree.addItemListener(this); - inputText.setLabel(MessageManager.getString("label.input_from_textbox")); + inputText + .setLabel(MessageManager.getString("label.input_from_textbox")); inputText.addActionListener(this); - centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels")); + centreColumnLabelFlag.setLabel(MessageManager + .getString("label.centre_column_labels")); centreColumnLabelFlag.addItemListener(this); - followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling")); + followMouseOverFlag.setLabel(MessageManager + .getString("label.automatic_scrolling")); followMouseOverFlag.addItemListener(this); helpMenu.setLabel(MessageManager.getString("action.help")); documentation.setLabel(MessageManager.getString("label.documentation")); @@ -3131,34 +3213,52 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, about.setLabel(MessageManager.getString("label.about")); about.addActionListener(this); seqLimits.setState(true); - seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits")); + seqLimits.setLabel(MessageManager + .getString("label.show_sequence_limits")); seqLimits.addItemListener(this); - featureSettings.setLabel(MessageManager.getString("label.feature_settings")); + featureSettings.setLabel(MessageManager + .getString("label.feature_settings")); featureSettings.addActionListener(this); - sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features")); + sequenceFeatures.setLabel(MessageManager + .getString("label.sequence_features")); sequenceFeatures.addItemListener(this); sequenceFeatures.setState(false); - annotationColour.setLabel(MessageManager.getString("action.by_annotation")); + annotationColour.setLabel(MessageManager + .getString("action.by_annotation")); annotationColour.addActionListener(this); - invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection")); - invertColSel.setLabel(MessageManager.getString("action.invert_column_selection")); + invertSequenceMenuItem.setLabel(MessageManager + .getString("action.invert_sequence_selection")); + invertColSel.setLabel(MessageManager + .getString("action.invert_column_selection")); menu1.setLabel(MessageManager.getString("action.show")); showColumns.setLabel(MessageManager.getString("label.all_columns")); showSeqs.setLabel(MessageManager.getString("label.all_sequences")); menu2.setLabel(MessageManager.getString("action.hide")); - hideColumns.setLabel(MessageManager.getString("label.selected_columns")); - hideSequences.setLabel(MessageManager.getString("label.selected_sequences")); - hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region")); - hideAllSelection.setLabel(MessageManager.getString("label.selected_region")); - showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns")); - showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus")); - showGroupConservation.setLabel(MessageManager.getString("label.group_conservation")); - showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram")); - showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo")); - normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo")); - applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups")); + hideColumns + .setLabel(MessageManager.getString("label.selected_columns")); + hideSequences.setLabel(MessageManager + .getString("label.selected_sequences")); + hideAllButSelection.setLabel(MessageManager + .getString("label.all_but_selected_region")); + hideAllSelection.setLabel(MessageManager + .getString("label.selected_region")); + showAllHidden.setLabel(MessageManager + .getString("label.all_sequences_columns")); + showGroupConsensus.setLabel(MessageManager + .getString("label.group_consensus")); + showGroupConservation.setLabel(MessageManager + .getString("label.group_conservation")); + showConsensusHistogram.setLabel(MessageManager + .getString("label.show_consensus_histogram")); + showSequenceLogo.setLabel(MessageManager + .getString("label.show_consensus_logo")); + normSequenceLogo.setLabel(MessageManager + .getString("label.norm_consensus_logo")); + applyAutoAnnotationSettings.setLabel(MessageManager + .getString("label.apply_all_groups")); applyAutoAnnotationSettings.setState(true); - autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation")); + autoAnnMenu.setLabel(MessageManager + .getString("label.autocalculated_annotation")); invertColSel.addActionListener(this); showColumns.addActionListener(this); @@ -3254,7 +3354,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(purinePyrimidineColour); - // colourMenu.add(RNAInteractionColour); + // colourMenu.add(RNAInteractionColour); colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); @@ -3317,8 +3417,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } - - public void setStatus(String string) { + public void setStatus(String string) + { statusBar.setText(string); };