X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=f4cfc3fdf8629c6fdc427c89e6da26d7122c181b;hb=c1a4229bd662c4299301ee8827b36096d015c075;hp=3325525df9b48d777000fca36dbe23b17c374ea0;hpb=cd3065a2c67664b22dc06fb5f2fd4870ca79f717;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 3325525..f4cfc3f 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,29 +1,34 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; import jalview.analysis.AlignmentSorter; -import jalview.analysis.Conservation; +import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; +import jalview.api.FeatureRenderer; import jalview.api.SequenceStructureBinding; import jalview.bin.JalviewLite; import jalview.commands.CommandI; import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; import jalview.commands.OrderCommand; import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; @@ -51,13 +56,14 @@ import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.RNAHelicesColourChooser; -import jalview.schemes.ResidueProperties; +import jalview.schemes.RNAInteractionColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; 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; @@ -84,16 +90,18 @@ import java.awt.event.WindowEvent; import java.io.IOException; import java.net.URL; import java.net.URLEncoder; -import java.util.Enumeration; +import java.util.Arrays; import java.util.Hashtable; import java.util.List; +import java.util.Map; 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; @@ -119,10 +127,32 @@ 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(viewport, alignPanel); + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); viewport.updateConservation(alignPanel); viewport.updateConsensus(alignPanel); @@ -134,6 +164,7 @@ 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); @@ -171,23 +202,6 @@ 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()) @@ -273,7 +287,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { featuresFile = new jalview.io.FeaturesFile(file, type) .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, featureLinks, + .getFeatureRenderer().getFeatureColours(), featureLinks, true, viewport.applet.getDefaultParameter( "relaxedidmatch", false)); } catch (Exception ex) @@ -289,15 +303,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (autoenabledisplay) { - viewport.showSequenceFeatures = true; + viewport.setShowSequenceFeatures(true); sequenceFeatures.setState(true); } + if (alignPanel.seqPanel.seqCanvas.fr != null) + { + // update the min/max ranges where necessary + alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + } if (viewport.featureSettings != null) { viewport.featureSettings.refreshTable(); } alignPanel.paintAlignment(true); - statusBar.setText("Successfully added features to alignment."); + statusBar.setText(MessageManager + .getString("label.successfully_added_features_alignment")); } return featuresFile; } @@ -310,7 +330,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) + { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -371,16 +393,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: @@ -441,8 +471,9 @@ 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; @@ -557,7 +588,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } break; - + case KeyEvent.VK_U: if (evt.isControlDown()) { @@ -705,7 +736,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (evt.getSource() == sequenceFeatures) { - viewport.showSequenceFeatures(sequenceFeatures.getState()); + viewport.setShowSequenceFeatures(sequenceFeatures.getState()); alignPanel.seqPanel.seqCanvas.repaint(); } else if (evt.getSource() == conservationMenuItem) @@ -986,8 +1017,9 @@ 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) { @@ -1038,6 +1070,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new PurinePyrimidineColourScheme()); } + else if (source == RNAInteractionColour) + { + changeColour(new RNAInteractionColourScheme()); + } else if (source == RNAHelixColour) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -1130,7 +1166,8 @@ 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, "Cut & Paste Input", 500, 500); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.input_cut_paste"), 500, 500); } protected void outputText_actionPerformed(ActionEvent e) @@ -1138,8 +1175,9 @@ 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, - "Alignment output - " + 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)); @@ -1148,48 +1186,41 @@ 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); } public String outputAnnotations(boolean displayTextbox) { - String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.getAlignment() - .getAlignmentAnnotation() : null, viewport - .getAlignment().getGroups(), ((Alignment) viewport - .getAlignment()).alignmentProperties); + String annotation = new AnnotationFile() + .printAnnotationsForView(viewport); if (displayTextbox) { 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); } return annotation; } - private Hashtable getDisplayedFeatureCols() + private Map getDisplayedFeatureCols() { if (alignPanel.getFeatureRenderer() != null - && viewport.featuresDisplayed != null) + && viewport.getFeaturesDisplayed()!= null) { - FeatureRenderer fr = alignPanel.getFeatureRenderer(); - Hashtable fcols = new Hashtable(); - Enumeration en = viewport.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - Object col = en.nextElement(); - fcols.put(col, fr.featureColours.get(col)); - } - return fcols; + return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); + } return null; } @@ -1225,13 +1256,16 @@ 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 { if (features == null) + { features = ""; + } } return features; @@ -1363,12 +1397,14 @@ 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) @@ -1376,18 +1412,21 @@ 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")); } } /** * TODO: JAL-1104 */ + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1543,7 +1582,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + { invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); + } } SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); @@ -1551,30 +1592,44 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup .size()]); for (int i = 0; i < invertGroup.size(); i++) + { seqs2[i] = invertGroup.elementAt(i); + } SlideSequencesCommand ssc; if (right) + { ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) @@ -1595,7 +1650,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } @@ -1628,11 +1685,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); copiedHiddenColumns.addElement(new int[] { region[0] - hiddenOffset, region[1] - hiddenOffset }); @@ -1733,14 +1787,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (newAlignment) { - String newtitle = new String("Copied sequences"); - if (getTitle().startsWith("Copied sequences")) + String newtitle = MessageManager.getString("label.copied_sequences"); + if (getTitle().startsWith(MessageManager.getString("label.copied_sequences"))) { newtitle = getTitle(); } else { - newtitle = newtitle.concat("- from " + getTitle()); + newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()})); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), viewport.applet, newtitle, false); @@ -1775,7 +1829,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // !newAlignment - addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), Action.PASTE, seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment())); @@ -1825,8 +1880,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /* * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, - sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.getAlignment())); viewport.setSelectionGroup(null); @@ -1903,7 +1959,8 @@ 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); @@ -1914,6 +1971,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { avc.createGroup(); } + protected void unGroup_actionPerformed() { if (avc.unGroup()) @@ -1921,6 +1979,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.alignmentChanged(); } } + protected void deleteGroups_actionPerformed() { if (avc.deleteGroups()) @@ -2024,8 +2083,9 @@ 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()) @@ -2065,8 +2125,9 @@ 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 @@ -2205,7 +2266,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - return fr.getGroups(); + List gps = fr.getFeatureGroups(); + int p=0; + String[] _gps = new String[gps.size()]; + for (Object gp:gps) + { + _gps[p++] = gp.toString(); + } + return _gps; } return null; } @@ -2223,7 +2291,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - return fr.getGroups(visible); + List gps = fr.getGroups(visible); + int p=0; + String[] _gps = new String[gps.size()]; + for (Object gp:gps) + { + _gps[p++] = gp.toString(); + } + return _gps; } return null; } @@ -2240,11 +2315,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { FeatureRenderer fr = null; this.sequenceFeatures.setState(true); - viewport.showSequenceFeatures(true); + viewport.setShowSequenceFeatures(true); if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - fr.setGroupState(groups, state); + + fr.setGroupVisibility(Arrays.asList(groups), state); alignPanel.seqPanel.seqCanvas.repaint(); if (alignPanel.overviewPanel != null) { @@ -2293,8 +2369,9 @@ 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, "Overview " + 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(); @@ -2323,42 +2400,20 @@ 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); @@ -2471,7 +2526,8 @@ 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); } } @@ -2569,16 +2625,18 @@ 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); } @@ -2598,8 +2656,9 @@ 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, - viewport.getAlignment())); + addHistoryItem(new OrderCommand(MessageManager.formatMessage( + "label.order_by_params", new String[] + { title }), oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2695,28 +2754,32 @@ 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,", + g.drawString(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( - "Development managed by The Barton Group, University of Dundee, Scotland, UK.", - x, y += fh); + g.drawString(MessageManager.getString("label.jalview_authors_2"), + x + 50, y += fh + 8); g.drawString( - "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", - x, y += fh); - g.drawString("If you use 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( - "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", - x, y += fh); - g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033", + MessageManager.getString("label.jalview_cite_1_title"), x, + y += fh); + g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), x, y += fh); } } @@ -2724,7 +2787,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite .getBuildDate())); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.jalview"), 580, 220); } @@ -2745,33 +2809,43 @@ 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").concat("...")); - MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + MenuItem outputAnnotations = new MenuItem( + MessageManager.getString("label.export_annotations").concat("...")); - 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(); @@ -2827,6 +2901,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem purinePyrimidineColour = new MenuItem(); + MenuItem RNAInteractionColour = new MenuItem(); + MenuItem RNAHelixColour = new MenuItem(); MenuItem userDefinedColour = new MenuItem(); @@ -2847,7 +2923,8 @@ 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(); @@ -2978,193 +3055,251 @@ 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").concat("...")); 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"); + averageDistanceTreeMenuItem.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"); + RNAInteractionColour.setLabel(MessageManager + .getString("label.rna_interaction")); + RNAInteractionColour.addActionListener(this); + 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"); + avDistanceTreeBlosumMenuItem.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); - createGroup.setLabel("Create Group"); - unGroup.setLabel("Remove Group"); - 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); @@ -3181,9 +3316,9 @@ 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); @@ -3260,6 +3395,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(purinePyrimidineColour); + // colourMenu.add(RNAInteractionColour); colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); @@ -3322,6 +3458,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } + public void setStatus(String string) + { + statusBar.setText(string); + }; + MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); @@ -3374,7 +3515,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, fileMenu.remove(closeMenuItem); fileMenu.remove(3); // Remove Seperator embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", - Font.PLAIN, 10, false); // use our own fonts. + Font.PLAIN, 11, false); // use our own fonts. // and actually add the components to the applet area viewport.applet.setLayout(new BorderLayout()); viewport.applet.add(embeddedMenu, BorderLayout.NORTH); @@ -3556,6 +3697,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } pdbentry.getProperty().put("protocol", protocol); toaddpdb.addPDBId(pdbentry); + alignPanel.getStructureSelectionManager() + .registerPDBEntry(pdbentry); } } return true;