X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=3c5c9561ad8f5892a767234a621ad53e08c53062;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=f55bb6cbb7a9203277cd2aa26d1029478b046104;hpb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index f55bb6c..3c5c956 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* - * 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 2.8.1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,11 +14,14 @@ * 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 . + * 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.SequenceStructureBinding; import jalview.bin.JalviewLite; import jalview.commands.CommandI; @@ -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()) @@ -542,6 +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()) { @@ -970,8 +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) { @@ -1114,7 +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) @@ -1123,7 +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)); @@ -1153,7 +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); } @@ -1209,7 +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 @@ -1887,41 +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() @@ -2286,7 +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); @@ -2316,42 +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); @@ -2464,7 +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); } } @@ -2566,12 +2556,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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); } @@ -2688,28 +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); } } @@ -2717,7 +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); } @@ -2738,33 +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(); @@ -2840,7 +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(); @@ -2866,6 +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(); @@ -3074,6 +3068,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, deleteGroups.addActionListener(this); 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")); copy.setLabel(MessageManager.getString("action.copy")); copy.addActionListener(this); cut.setLabel(MessageManager.getString("action.cut")); @@ -3138,7 +3134,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, menu1.setLabel(MessageManager.getString("action.show")); showColumns.setLabel(MessageManager.getString("label.all_columns")); showSeqs.setLabel(MessageManager.getString("label.all_sequences")); - menu2.setLabel(MessageManager.getString("aciton.hide")); + 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")); @@ -3302,11 +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();