X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=3c5c9561ad8f5892a767234a621ad53e08c53062;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=ab99e065edd79a2053a65ca1de46f243d9e88ccc;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index ab99e06..3c5c956 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. @@ -20,6 +20,8 @@ package jalview.appletgui; import jalview.analysis.AlignmentSorter; import jalview.analysis.Conservation; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewControllerI; import jalview.api.SequenceStructureBinding; import jalview.bin.JalviewLite; import jalview.commands.CommandI; @@ -58,6 +60,7 @@ import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; import java.awt.BorderLayout; import java.awt.Canvas; @@ -91,8 +94,9 @@ import java.util.StringTokenizer; import java.util.Vector; public class AlignFrame extends EmbmenuFrame implements ActionListener, - ItemListener, KeyListener + ItemListener, KeyListener, AlignViewControllerGuiI { + public AlignViewControllerI avc; public AlignmentPanel alignPanel; public AlignViewport viewport; @@ -118,10 +122,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { ex.printStackTrace(); } - + // need to get window geometry before we calculate alignment layout + if (applet != null) + { + String param; + try + { + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + DEFAULT_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + DEFAULT_HEIGHT = height; + } + } catch (Exception ex) + { + } + } viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); - + avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); viewport.updateConservation(alignPanel); viewport.updateConsensus(alignPanel); @@ -133,7 +158,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); showSequenceLogo.setState(viewport.isShowSequenceLogo()); normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); - + applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); + seqLimits.setState(viewport.showJVSuffix); if (applet != null) @@ -170,23 +196,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, centreColumnLabelFlag.setState(true); centreColumnLabelFlag_stateChanged(); } - try - { - param = applet.getParameter("windowWidth"); - if (param != null) - { - int width = Integer.parseInt(param); - DEFAULT_WIDTH = width; - } - param = applet.getParameter("windowHeight"); - if (param != null) - { - int height = Integer.parseInt(param); - DEFAULT_HEIGHT = height; - } - } catch (Exception ex) - { - } } if (viewport.getAlignment().isNucleotide()) @@ -296,7 +305,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.featureSettings.refreshTable(); } alignPanel.paintAlignment(true); - statusBar.setText("Successfully added features to alignment."); + statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment")); } return featuresFile; } @@ -440,8 +449,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " - + (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; @@ -543,6 +551,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } break; + case KeyEvent.VK_G: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) + { + this.unGroup_actionPerformed(); + } + else + { + this.createGroup_actionPerformed(); + } + } + break; + case KeyEvent.VK_U: if (evt.isControlDown()) { @@ -971,8 +993,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cap.setText(contents.toString()); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: " - + getTitle(), 400, 250); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), + 400, 250); } else if (source == overviewMenuItem) { @@ -1115,7 +1137,7 @@ 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, "Cut & Paste Input", 500, 500); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500); } protected void outputText_actionPerformed(ActionEvent e) @@ -1124,7 +1146,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, - "Alignment output - " + e.getActionCommand(), 600, 500); + MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500); cap.setText(new AppletFormatAdapter().formatSequences( e.getActionCommand(), viewport.getAlignment(), viewport.showJVSuffix)); @@ -1133,11 +1155,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void loadAnnotations() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your features / annotations / T-coffee score file 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, "Paste Annotations ", 400, 300); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300); } @@ -1154,7 +1176,7 @@ 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, "Annotations", 600, 500); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500); cap.setText(annotation); } @@ -1210,7 +1232,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500); cap.setText(features); } else @@ -1348,12 +1370,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setLabel("Undo " + command.getDescription()); + undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()})); } else { undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); + undoMenuItem.setLabel(MessageManager.getString("action.undo")); } if (viewport.redoList.size() > 0) @@ -1361,12 +1383,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setLabel("Redo " + command.getDescription()); + redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()})); } else { redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); + redoMenuItem.setLabel(MessageManager.getString("action.redo")); } } @@ -1888,41 +1910,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void makeGrpsFromSelection_actionPerformed() { - if (viewport.getSelectionGroup() != null) - { - SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( - viewport.getSequenceSelection(), - viewport.getAlignmentView(true).getSequenceStrings( - viewport.getGapCharacter()), viewport.getAlignment() - .getGroups()); - viewport.getAlignment().deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - // set view properties for each group - for (int g = 0; g < gps.length; g++) - { - // gps[g].setShowunconserved(viewport.getShowUnconserved()); - gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); - viewport.getAlignment().addGroup(gps[g]); - Color col = new Color((int) (Math.random() * 255), - (int) (Math.random() * 255), (int) (Math.random() * 255)); - col = col.brighter(); - for (SequenceI sq : gps[g].getSequences(null)) - viewport.setSequenceColour(sq, col); - } + if (avc.makeGroupsFromSelection()) { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } } + protected void createGroup_actionPerformed() + { + avc.createGroup(); + } + protected void unGroup_actionPerformed() + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); + } + } protected void deleteGroups_actionPerformed() { - viewport.getAlignment().deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - - alignPanel.paintAlignment(true); + if (avc.deleteGroups()) + { + alignPanel.alignmentChanged(); + } } public void selectAllSequenceMenuItem_actionPerformed() @@ -2020,8 +2031,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.getSelectionGroup()); } - statusBar.setText("Removed " + trimRegion.getSize() + " columns."); - + statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()})); addHistoryItem(trimRegion); for (SequenceGroup sg : viewport.getAlignment().getGroups()) @@ -2061,8 +2071,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, addHistoryItem(removeGapCols); - statusBar.setText("Removed " + removeGapCols.getSize() - + " empty columns."); + 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 @@ -2289,7 +2298,7 @@ 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, "Overview " + this.getTitle(), + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}), overview.getPreferredSize().width, overview.getPreferredSize().height + 50); @@ -2319,42 +2328,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); - - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - - viewport.setGlobalColourScheme(cs); - } - else - { - cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } + viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background")); + } if (viewport.getConservationSelected()) { - - Alignment al = (Alignment) viewport.getAlignment(); - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); - - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - - cs.setConservation(c); - - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs.setConservationApplied(true); + viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); - } else { - cs.setConservation(null); + cs.setConservationApplied(false); } - - cs.setConsensus(viewport.getSequenceConsensusHash()); - } viewport.setGlobalColourScheme(cs); @@ -2467,7 +2454,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500); } } @@ -2565,16 +2552,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, void loadTree_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your Newick tree file here."); + cap.setText(MessageManager.getString("label.paste_newick_tree_file")); cap.setTreeImport(); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "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, "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); } @@ -2594,7 +2581,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .sortByTree(viewport.getAlignment(), treePanel.getTree()); // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); - addHistoryItem(new OrderCommand("Order by " + title, oldOrder, + addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2691,28 +2678,28 @@ 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("JalviewLite - Release " + 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("Build date: " + 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( - "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,", + MessageManager.getString("label.jalview_authors_1"), x, y += fh * 1.5); - g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8); + g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8); g.drawString( - "Development managed by The Barton Group, University of Dundee, Scotland, UK.", + MessageManager.getString("label.jalview_dev_managers"), x, y += fh); g.drawString( - "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", + MessageManager.getString("label.jalview_distribution_lists"), x, y += fh); - g.drawString("If you use Jalview, please cite:", x, y += fh + 8); + g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8); g.drawString( - "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)", + MessageManager.getString("label.jalview_cite_1_authors"), x, y += fh); g.drawString( - "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench", + MessageManager.getString("label.jalview_cite_1_title"), x, y += fh); - g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033", + g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), x, y += fh); } } @@ -2720,7 +2707,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite .getBuildDate())); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220); } @@ -2741,33 +2728,33 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuBar alignFrameMenuBar = new MenuBar(); - Menu fileMenu = new Menu("File"); + Menu fileMenu = new Menu(MessageManager.getString("action.file")); - MenuItem loadApplication = new MenuItem("View in Full Application"); + MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application")); - MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree")); - MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); + MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations")); - MenuItem outputFeatures = new MenuItem("Export Features ..."); + MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features")); - MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations")); - MenuItem closeMenuItem = new MenuItem("Close"); + MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close")); - Menu editMenu = new Menu("Edit"); + Menu editMenu = new Menu(MessageManager.getString("action.edit")); - Menu viewMenu = new Menu("View"); + Menu viewMenu = new Menu(MessageManager.getString("action.view")); - Menu colourMenu = new Menu("Colour"); + Menu colourMenu = new Menu(MessageManager.getString("action.colour")); - Menu calculateMenu = new Menu("Calculate"); + Menu calculateMenu = new Menu(MessageManager.getString("action.calculate")); - MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all")); - MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all")); - MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection")); MenuItem remove2LeftMenuItem = new MenuItem(); @@ -2843,7 +2830,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); - MenuItem alProperties = new MenuItem("Alignment Properties..."); + MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props")); MenuItem overviewMenuItem = new MenuItem(); @@ -2869,6 +2856,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem grpsFromSelection = new MenuItem(); + MenuItem createGroup = new MenuItem(); + + MenuItem unGroup = new MenuItem(); + MenuItem delete = new MenuItem(); MenuItem copy = new MenuItem(); @@ -2970,191 +2961,193 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, selectAllSequenceMenuItem.addActionListener(this); deselectAllSequenceMenuItem.addActionListener(this); invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left")); remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right")); remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns")); removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps")); removeAllGapsMenuItem.addActionListener(this); - viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes")); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addItemListener(this); - viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setLabel(MessageManager.getString("action.text")); viewTextMenuItem.setState(true); viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id")); sortPairwiseMenuItem.addActionListener(this); - sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.setLabel(MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(this); - sortLengthMenuItem.setLabel("by Length"); + sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length")); sortLengthMenuItem.addActionListener(this); - sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy")); removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment")); pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(this); averageDistanceTreeMenuItem - .setLabel("Average Distance Using % Identity"); + .setLabel(MessageManager.getString("label.average_distance_identity")); averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % 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("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); + statusBar.setText(MessageManager.getString("label.status_bar")); + outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox")); + clustalColour.setLabel(MessageManager.getString("label.clustalx")); clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); + zappoColour.setLabel(MessageManager.getString("label.zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); + taylorColour.setLabel(MessageManager.getString("label.taylor")); taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity")); hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix Propensity"); + helixColour.setLabel(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(this); - strandColour.setLabel("Strand Propensity"); + strandColour.setLabel(MessageManager.getString("label.strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel("Turn Propensity"); + turnColour.setLabel(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); + buriedColour.setLabel(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(this); - purinePyrimidineColour.setLabel("Purine/Pyrimidine"); + purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine")); purinePyrimidineColour.addActionListener(this); - RNAHelixColour.setLabel("by RNA Helices"); + RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes")); RNAHelixColour.addActionListener(this); - userDefinedColour.setLabel("User Defined..."); + userDefinedColour.setLabel(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); + PIDColour.setLabel(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour.setLabel("T-Coffee 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("Average Distance Using BLOSUM62"); + .setLabel(MessageManager.getString("label.average_distance_bloslum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62")); njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations")); annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text")); colourTextMenuItem.addItemListener(this); - displayNonconservedMenuItem.setLabel("Show nonconserved"); + displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed")); displayNonconservedMenuItem.addItemListener(this); alProperties.addActionListener(this); - overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.setLabel(MessageManager.getString("label.overview_window")); overviewMenuItem.addActionListener(this); undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); + undoMenuItem.setLabel(MessageManager.getString("action.undo")); undoMenuItem.addActionListener(this); redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); + redoMenuItem.setLabel(MessageManager.getString("action.redo")); redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation")); conservationMenuItem.addItemListener(this); - noColourmenuItem.setLabel("None"); + noColourmenuItem.setLabel(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(this); - wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps")); renderGapsMenuItem.setState(true); renderGapsMenuItem.addItemListener(this); - findMenuItem.setLabel("Find..."); + findMenuItem.setLabel(MessageManager.getString("action.find")); findMenuItem.addActionListener(this); - abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); + deleteGroups.setLabel(MessageManager.getString("action.undefine_groups")); deleteGroups.addActionListener(this); - grpsFromSelection.setLabel("Make Groups for selection"); + grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection")); grpsFromSelection.addActionListener(this); - copy.setLabel("Copy"); + createGroup.setLabel(MessageManager.getString("action.create_group")); + unGroup.setLabel(MessageManager.getString("action.remove_group")); + copy.setLabel(MessageManager.getString("action.copy")); copy.addActionListener(this); - cut.setLabel("Cut"); + cut.setLabel(MessageManager.getString("action.cut")); cut.addActionListener(this); - delete.setLabel("Delete"); + delete.setLabel(MessageManager.getString("action.delete")); delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); + pasteMenu.setLabel(MessageManager.getString("action.paste")); + pasteNew.setLabel(MessageManager.getString("label.to_new_alignment")); pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); + pasteThis.setLabel(MessageManager.getString("label.to_this_alignment")); pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); + font.setLabel(MessageManager.getString("action.font")); font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); + scaleAbove.setLabel(MessageManager.getString("action.scale_above")); scaleAbove.setState(true); scaleAbove.setEnabled(false); scaleAbove.addItemListener(this); scaleLeft.setEnabled(false); scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); + scaleLeft.setLabel(MessageManager.getString("action.scale_left")); scaleLeft.addItemListener(this); scaleRight.setEnabled(false); scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); + scaleRight.setLabel(MessageManager.getString("action.scale_right")); scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold")); modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold")); modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); + 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("Input from textbox"); + inputText.setLabel(MessageManager.getString("label.input_from_textbox")); inputText.addActionListener(this); - centreColumnLabelFlag.setLabel("Centre column labels"); + centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels")); centreColumnLabelFlag.addItemListener(this); - followMouseOverFlag.setLabel("Automatic Scrolling"); + followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling")); followMouseOverFlag.addItemListener(this); - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); + helpMenu.setLabel(MessageManager.getString("action.help")); + documentation.setLabel(MessageManager.getString("label.documentation")); documentation.addActionListener(this); - about.setLabel("About..."); + about.setLabel(MessageManager.getString("label.about")); about.addActionListener(this); seqLimits.setState(true); - seqLimits.setLabel("Show Sequence Limits"); + seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits")); seqLimits.addItemListener(this); - featureSettings.setLabel("Feature Settings..."); + featureSettings.setLabel(MessageManager.getString("label.feature_settings")); featureSettings.addActionListener(this); - sequenceFeatures.setLabel("Sequence Features"); + sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features")); sequenceFeatures.addItemListener(this); sequenceFeatures.setState(false); - annotationColour.setLabel("by Annotation..."); + annotationColour.setLabel(MessageManager.getString("action.by_annotation")); annotationColour.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Sequence Selection"); - invertColSel.setLabel("Invert Column Selection"); - menu1.setLabel("Show"); - showColumns.setLabel("All Columns "); - showSeqs.setLabel("All Sequences"); - menu2.setLabel("Hide"); - hideColumns.setLabel("Selected Columns"); - hideSequences.setLabel("Selected Sequences"); - hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)"); - hideAllSelection.setLabel("Selected Region"); - showAllHidden.setLabel("All Sequences and Columns"); - showGroupConsensus.setLabel("Group Consensus"); - showGroupConservation.setLabel("Group Conservation"); - showConsensusHistogram.setLabel("Show Consensus Histogram"); - showSequenceLogo.setLabel("Show Consensus Logo"); - normSequenceLogo.setLabel("Normalise Consensus Logo"); - applyAutoAnnotationSettings.setLabel("Apply to all groups"); + 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")); applyAutoAnnotationSettings.setState(true); - autoAnnMenu.setLabel("Autocalculated Annotation"); + autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation")); invertColSel.addActionListener(this); showColumns.addActionListener(this); @@ -3171,9 +3164,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, normSequenceLogo.addItemListener(this); applyAutoAnnotationSettings.addItemListener(this); - formatMenu.setLabel("Format"); - selectMenu.setLabel("Select"); - newView.setLabel("New View"); + formatMenu.setLabel(MessageManager.getString("action.format")); + selectMenu.setLabel(MessageManager.getString("action.select")); + newView.setLabel(MessageManager.getString("action.new_view")); newView.addActionListener(this); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); @@ -3305,11 +3298,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, selectMenu.add(deselectAllSequenceMenuItem); selectMenu.add(invertSequenceMenuItem); selectMenu.add(invertColSel); + selectMenu.add(createGroup); + selectMenu.add(unGroup); selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); } + + public void setStatus(String string) { + statusBar.setText(string); + }; + MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();