X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=16602c8374afc4265cfc513db794218b70dd4dd0;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=648b64250fa2a9703eefe75b063fe00d1ba1165f;hpb=5d5387084823fabaff0069493688221c43dd93e7;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java old mode 100755 new mode 100644 index 648b642..16602c8 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,39 +1,103 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 java.io.*; -import java.net.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; +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; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.AppletFormatAdapter; +import jalview.io.FeaturesFile; +import jalview.io.TCoffeeScoreFile; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.RNAInteractionColourScheme; +import jalview.schemes.ResidueProperties; +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; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.IOException; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +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; @@ -47,7 +111,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded) { - if (applet != null) { jalviewServletURL = applet.getParameter("APPLICATION_URL"); @@ -60,16 +123,44 @@ 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); annotationPanelMenuItem.setState(viewport.showAnnotation); - displayNonconservedMenuItem.setState(viewport.getShowunconserved()); - + displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); + followMouseOverFlag.setState(viewport.getFollowHighlight()); + showGroupConsensus.setState(viewport.isShowGroupConsensus()); + showGroupConservation.setState(viewport.isShowGroupConservation()); + showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); + showSequenceLogo.setState(viewport.isShowSequenceLogo()); + normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); + applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); + seqLimits.setState(viewport.showJVSuffix); if (applet != null) @@ -85,6 +176,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { sortPairwiseMenuItem_actionPerformed(); } + else if (param.equalsIgnoreCase("Length")) + { + sortLengthMenuItem_actionPerformed(); + } } param = applet.getParameter("wrap"); @@ -102,26 +197,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, centreColumnLabelFlag.setState(true); centreColumnLabelFlag_stateChanged(); } - try + + } + if (viewport.getAlignment().isNucleotide()) + { + viewport.updateStrucConsensus(alignPanel); + if (viewport.getAlignment().hasRNAStructure()) { - 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) + RNAHelixColour.setEnabled(true); + } + else { + RNAHelixColour.setEnabled(false); } - } - + else + { + RNAHelixColour.setEnabled(false); + purinePyrimidineColour.setEnabled(false); + } // Some JVMS send keyevents to Top frame or lowest panel, // Havent worked out why yet. So add to both this frame and seqCanvas for // now @@ -130,8 +224,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.idPanel.idCanvas.addKeyListener(this); alignPanel.scalePanel.addKeyListener(this); alignPanel.annotationPanel.addKeyListener(this); + alignPanel.annotationPanelHolder.addKeyListener(this); + alignPanel.annotationSpaceFillerHolder.addKeyListener(this); + alignPanel.alabels.addKeyListener(this); createAlignFrameWindow(embedded, title); - alignPanel.validate(); + + validate(); + alignPanel.adjustAnnotationHeight(); alignPanel.paintAlignment(true); } @@ -146,22 +245,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } /** - * DOCUMENT ME! + * Load a features file onto the alignment * - * @param String - * DOCUMENT ME! + * @param file + * file URL, content, or other resolvable path + * @param type + * is protocol for accessing data referred to by file */ - public void parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, String type) + { + return parseFeaturesFile(file, type, true); + } + + /** + * Load a features file onto the alignment + * + * @param file + * file URL, content, or other resolvable path + * @param type + * is protocol for accessing data referred to by file + * @param autoenabledisplay + * when true, display features flag will be automatically enabled if + * features are loaded + * @return true if data parsed as a features file + */ + public boolean parseFeaturesFile(String file, String type, + boolean autoenabledisplay) { + // TODO: test if importing a features file onto an alignment which already + // has features with links overwrites the original links. + Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try { - featuresFile = new jalview.io.FeaturesFile(file, type).parse( - viewport.alignment, alignPanel.seqPanel.seqCanvas + featuresFile = new jalview.io.FeaturesFile(file, type) + .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas .getFeatureRenderer().featureColours, featureLinks, - true); + true, viewport.applet.getDefaultParameter( + "relaxedidmatch", false)); } catch (Exception ex) { ex.printStackTrace(); @@ -173,13 +296,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; } - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); + if (autoenabledisplay) + { + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + } + if (viewport.featureSettings != null) + { + viewport.featureSettings.refreshTable(); + } alignPanel.paintAlignment(true); + statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment")); } - + return featuresFile; } + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -193,6 +325,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { case 27: // escape key deselectAllSequenceMenuItem_actionPerformed(); + + alignPanel.alabels.cancelDrag(); break; case KeyEvent.VK_X: if (evt.isControlDown() || evt.isMetaDown()) @@ -316,8 +450,7 @@ 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; @@ -336,37 +469,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { boolean toggleSeqs = !evt.isControlDown(); boolean toggleCols = !evt.isShiftDown(); - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); - - if (toggleSeqs) - { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) - { - hide = true; - viewport.hideAllSelectedSeqs(); - } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) - { - viewport.showAllHiddenSeqs(); - } - } - - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - viewport.hideSelectedColumns(); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - viewport.showAllHiddenColumns(); - } - } + toggleHiddenRegions(toggleSeqs, toggleCols); break; } @@ -440,15 +543,29 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (evt.isAltDown()) { - viewport.invertColumnSelection(); + invertColSel_actionPerformed(); } else { - this.invertSequenceMenuItem_actionPerformed(); + invertSequenceMenuItem_actionPerformed(); } } 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()) { @@ -467,14 +584,86 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.paintAlignment(true); } + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection and indicate it should be hidden. + invertColSel_actionPerformed(); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) + { + viewport.showAllHiddenSeqs(); + } + } + + if (toggleCols) + { + if (viewport.getColumnSelection().getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if (!toggleSeqs) + { + viewport.setSelectionGroup(sg); + } + } + else if (!hide) + { + viewport.showAllHiddenColumns(); + } + } + } + + @Override public void keyReleased(KeyEvent evt) { } + @Override public void keyTyped(KeyEvent evt) { } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == displayNonconservedMenuItem) @@ -541,23 +730,52 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (evt.getSource() == autoCalculate) { - viewport.autocalculateConsensus = autoCalculate.getState(); + viewport.autoCalculateConsensus = autoCalculate.getState(); + } + else if (evt.getSource() == sortByTree) + { + viewport.sortByTree = sortByTree.getState(); } else if (evt.getSource() == this.centreColumnLabelFlag) { centreColumnLabelFlag_stateChanged(); - } else if (evt.getSource() == this.followMouseOverFlag) + } + else if (evt.getSource() == this.followMouseOverFlag) { mouseOverFlag_stateChanged(); } - + else if (evt.getSource() == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (evt.getSource() == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (evt.getSource() == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (evt.getSource() == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } alignPanel.paintAlignment(true); } private void mouseOverFlag_stateChanged() { viewport.followHighlight = followMouseOverFlag.getState(); - // TODO: could kick the scrollTo mechanism to reset view for current searchresults. + // TODO: could kick the scrollTo mechanism to reset view for current + // searchresults. } private void centreColumnLabelFlag_stateChanged() @@ -566,6 +784,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.alignPanel.annotationPanel.repaint(); } + @Override public void actionPerformed(ActionEvent evt) { Object source = evt.getSource(); @@ -646,6 +865,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { delete_actionPerformed(); } + else if (source == grpsFromSelection) + { + makeGrpsFromSelection_actionPerformed(); + } else if (source == deleteGroups) { deleteGroups_actionPerformed(); @@ -703,6 +926,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == showSeqs) { viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); } else if (source == hideColumns) { @@ -713,6 +937,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getSelectionGroup() != null) { viewport.hideAllSelectedSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == hideAllButSelection) + { + toggleHiddenRegions(false, false); + alignPanel.paintAlignment(true); + } + else if (source == hideAllSelection) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showAllHidden) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (source == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (source == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (source == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (source == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (source == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); } else if (source == featureSettings) { @@ -720,44 +988,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (source == alProperties) { - StringBuffer contents = new StringBuffer(); - - float avg = 0; - int min = Integer.MAX_VALUE, max = 0; - for (int i = 0; i < viewport.alignment.getHeight(); i++) - { - int size = viewport.alignment.getSequenceAt(i).getEnd() - - viewport.alignment.getSequenceAt(i).getStart(); - avg += size; - if (size > max) - max = size; - if (size < min) - min = size; - } - avg = avg / (float) viewport.alignment.getHeight(); - - contents.append("\nSequences: " + viewport.alignment.getHeight()); - contents.append("\nMinimum Sequence Length: " + min); - contents.append("\nMaximum Sequence Length: " + max); - contents.append("\nAverage Length: " + (int) avg); - - if (((Alignment) viewport.alignment).alignmentProperties != null) - { - Hashtable props = ((Alignment) viewport.alignment).alignmentProperties; - Enumeration en = props.keys(); - while (en.hasMoreElements()) - { - String key = en.nextElement().toString(); - contents.append("\n" + key + "\t" + props.get(key)); - } - } - + StringBuffer contents = new jalview.io.AlignmentProperties( + viewport.getAlignment()).formatAsString(); CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); 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) { @@ -770,8 +1008,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == clustalColour) { abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme(viewport.alignment - .getSequences(), viewport.alignment.getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), null)); } else if (source == zappoColour) { @@ -805,6 +1042,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new NucleotideColourScheme()); } + else if (source == purinePyrimidineColour) + { + changeColour(new PurinePyrimidineColourScheme()); + } + else if (source == RNAInteractionColour) + { + changeColour(new RNAInteractionColourScheme()); + } + else if (source == RNAHelixColour) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } else if (source == modifyPID) { modifyPID_actionPerformed(); @@ -825,6 +1074,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new Blosum62ColourScheme()); } + else if (source == tcoffeeColour) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } else if (source == annotationColour) { new AnnotationColourChooser(viewport, alignPanel); @@ -837,6 +1090,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { sortIDMenuItem_actionPerformed(); } + else if (source == sortLengthMenuItem) + { + sortLengthMenuItem_actionPerformed(); + } else if (source == sortGroupMenuItem) { sortGroupMenuItem_actionPerformed(); @@ -885,7 +1142,7 @@ 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) @@ -893,67 +1150,101 @@ 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); - cap.setText(new AppletFormatAdapter().formatSequences(e - .getActionCommand(), viewport.getAlignment(), + 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)); } public void loadAnnotations() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your features / annotations 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.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), ((Alignment) viewport + .getAlignment()).alignmentProperties); 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() + { + if (alignPanel.getFeatureRenderer() != null + && viewport.featuresDisplayed != 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 null; + } + public String outputFeatures(boolean displayTextbox, String format) { String features; if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat(viewport.alignment - .getSequencesArray(), viewport.featuresDisplayed); + features = new FeaturesFile().printJalviewFormat(viewport + .getAlignment().getSequencesArray(), + getDisplayedFeatureCols()); } else { - features = new FeaturesFile().printGFFFormat(viewport.alignment - .getSequencesArray(), viewport.featuresDisplayed); + features = new FeaturesFile().printGFFFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } if (displayTextbox) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + boolean frimport = false; + if (features == null || features.equals("No Features Visible")) + { + features = "# No features visible - paste some and import them here."; + frimport = true; + } + + CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this); + if (frimport) + { + cap.setAnnotationImport(); + } 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; } @@ -974,9 +1265,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.applet.getParameter("annotations") != null) { url.append("&annotations="); - url - .append(appendProtocol(viewport.applet - .getParameter("annotations"))); + url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } if (viewport.applet.getParameter("jnetfile") != null) @@ -1054,19 +1343,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void closeMenuItem_actionPerformed() { PaintRefresher.RemoveComponent(alignPanel); - PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + if (alignPanel.seqPanel != null + && alignPanel.seqPanel.seqCanvas != null) + { + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + } + if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null) + { + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + } if (PaintRefresher.components.size() == 0 && viewport.applet == null) { System.exit(0); } - + else + { + } + viewport = null; + alignPanel = null; this.dispose(); } /** - * DOCUMENT ME! + * TODO: JAL-1104 */ void updateEditMenuBar() { @@ -1075,12 +1375,12 @@ 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) @@ -1088,15 +1388,18 @@ 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 + */ public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1104,15 +1407,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.historyList.push(command); viewport.redoList.removeAllElements(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + viewport.updateHiddenColumns(); } } /** - * DOCUMENT ME! + * TODO: JAL-1104 DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed() { @@ -1126,18 +1429,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, command.undoCommand(null); AlignViewport originalSource = getOriginatingSource(command); - - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + // JBPNote Test + if (originalSource != viewport) + { + System.err + .println("Warning: Viewport object mismatch whilst undoing"); + } + originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = + // viewport.getColumnSelection().getHiddenColumns() + // != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } /** - * DOCUMENT ME! + * TODO: JAL-1104 DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed() { @@ -1151,11 +1461,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, command.doCommand(null); AlignViewport originalSource = getOriginatingSource(command); - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + // JBPNote Test + if (originalSource != viewport) + { + System.err + .println("Warning: Viewport object mismatch whilst re-doing"); + } + originalSource.updateHiddenColumns(); // sethasHiddenColumns(); = + // viewport.getColumnSelection().getHiddenColumns() + // != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } AlignViewport getOriginatingSource(CommandI command) @@ -1175,7 +1493,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (comps.elementAt(i) instanceof AlignmentPanel) { - if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) { originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; @@ -1190,7 +1508,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1206,65 +1524,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { return; } - - if (up) - { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); - } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - + viewport.getAlignment().moveSelectedSequencesByOne(sg, + up ? null : viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true); } synchronized void slideSequences(boolean right, int size) { - Vector sg = new Vector(); + List sg = new Vector(); if (viewport.cursorMode) { - sg.addElement(viewport.alignment - .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + sg.add(viewport.getAlignment().getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport.alignment - .getHeight()) + && viewport.getSelectionGroup().getSize() != viewport + .getAlignment().getHeight()) { sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1272,21 +1550,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return; } - Vector invertGroup = new Vector(); + Vector invertGroup = new Vector(); - for (int i = 0; i < viewport.alignment.getHeight(); i++) + for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { - if (!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); } - SequenceI[] seqs1 = new SequenceI[sg.size()]; - for (int i = 0; i < sg.size(); i++) - seqs1[i] = (SequenceI) sg.elementAt(i); + SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); - SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup + .size()]); for (int i = 0; i < invertGroup.size(); i++) - seqs2[i] = (SequenceI) invertGroup.elementAt(i); + seqs2[i] = invertGroup.elementAt(i); SlideSequencesCommand ssc; if (right) @@ -1352,14 +1629,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); + int index = viewport.getAlignment().findIndex(seq); orderedSeqs.put(index + "", seq); } int index = 0, startRes, endRes; char ch; - if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); @@ -1506,16 +1783,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { for (int i = 0; i < seqs.length; i++) { - viewport.alignment.addSequence(seqs[i]); + viewport.getAlignment().addSequence(seqs[i]); } // !newAlignment addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, - seqs, 0, viewport.alignment.getWidth(), viewport.alignment)); + seqs, 0, viewport.getAlignment().getWidth(), + viewport.getAlignment())); - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, viewport.alignment + viewport.setEndSeq(viewport.getAlignment().getHeight()); + viewport.getAlignment().getWidth(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } @@ -1544,7 +1822,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) + if (sg.getSize() == viewport.getAlignment().getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); @@ -1561,10 +1839,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, */ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + viewport.getAlignment())); viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -1573,28 +1851,108 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { this.setVisible(false); } + viewport.sendSelection(); } - protected void deleteGroups_actionPerformed() + /** + * group consensus toggled + * + */ + protected void showGroupConsensus_actionPerformed() { - viewport.alignment.deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - alignPanel.paintAlignment(true); } - public void selectAllSequenceMenuItem_actionPerformed() + /** + * group conservation toggled. + */ + protected void showGroupConservation_actionPerformed() { - SequenceGroup sg = new SequenceGroup(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); - } - sg.setEndRes(viewport.alignment.getWidth() - 1); + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed() + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showSequenceLogo_actionPerformed() + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void normSequenceLogo_actionPerformed() + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void applyAutoAnnotationSettings_actionPerformed() + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void makeGrpsFromSelection_actionPerformed() + { + 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() + { + if (avc.deleteGroups()) + { + alignPanel.alignmentChanged(); + } + } + + public void selectAllSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = new SequenceGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + } + sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void deselectAllSequenceMenuItem_actionPerformed() @@ -1611,6 +1969,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void invertSequenceMenuItem_actionPerformed() @@ -1622,6 +1981,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + public void invertColSel_actionPerformed() + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } void trimAlignment(boolean trimLeft) @@ -1644,11 +2012,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } TrimRegionCommand trimRegion; @@ -1656,32 +2024,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { trimRegion = new TrimRegionCommand("Remove Left", TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); } - statusBar.setText("Removed " + trimRegion.getSize() + " columns."); - + statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()})); addHistoryItem(trimRegion); - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) + for (SequenceGroup sg : viewport.getAlignment().getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } @@ -1692,32 +2055,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void removeGappedColumnMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } RemoveGapColCommand removeGapCols = new RemoveGapColCommand( - "Remove Gapped Columns", seqs, start, end, viewport.alignment); + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); 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 - SequenceI seq = viewport.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); @@ -1732,28 +2095,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void removeAllGapsMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.alignment)); + viewport.getAlignment())); viewport.setStartRes(seq.findIndex(startRes) - 1); @@ -1776,35 +2139,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public AlignFrame newView(String viewtitle) { AlignmentI newal; - if (viewport.hasHiddenRows) + if (viewport.hasHiddenRows()) { newal = new Alignment(viewport.getAlignment().getHiddenSequences() .getFullAlignment().getSequencesArray()); } else { - newal = new Alignment(viewport.alignment.getSequencesArray()); + newal = new Alignment(viewport.getAlignment().getSequencesArray()); } - if (viewport.alignment.getAlignmentAnnotation() != null) + if (viewport.getAlignment().getAlignmentAnnotation() != null) { - for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) + for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++) { - if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) + if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated) { - newal - .addAnnotation(viewport.alignment - .getAlignmentAnnotation()[i]); + newal.addAnnotation(viewport.getAlignment() + .getAlignmentAnnotation()[i]); } } } AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); - newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId()); PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); - PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av - .getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, newaf.alignPanel.av.getSequenceSetId()); @@ -1862,7 +2224,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * get sequence feature groups that are hidden or shown * * @param visible - * true is visible + * true is visible * @return list */ public String[] getFeatureGroupsOfState(boolean visible) @@ -1880,9 +2242,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * Change the display state for the given feature groups * * @param groups - * list of group strings + * list of group strings * @param state - * visible or invisible + * visible or invisible */ public void setFeatureGroupState(String[] groups, boolean state) { @@ -1941,16 +2303,21 @@ 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); frame.pack(); + final AlignmentPanel ap = alignPanel; frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { - alignPanel.setOverviewPanel(null); + if (ap != null) + { + ap.setOverviewPanel(null); + } }; }); @@ -1966,115 +2333,31 @@ 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.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, al - .getWidth() - 1); - - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - - 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.hconsensus); - } viewport.setGlobalColourScheme(cs); - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (cs == null) - { - sg.cs = null; - continue; - } - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme(sg - .getSequences(viewport.hiddenRepSequences), sg.getWidth()); - } - else - { - try - { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); - } catch (Exception ex) - { - ex.printStackTrace(); - sg.cs = cs; - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(viewport.hiddenRepSequences), 0, sg - .getWidth())); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(viewport.hiddenRepSequences), 0, - viewport.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - } - } - if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged( - alignPanel); + .getStructureSelectionManager(viewport.applet) + .sequenceColoursChanged(alignPanel); alignPanel.paintAlignment(true); } @@ -2082,10 +2365,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { - SliderPanel.setPIDSliderSource(alignPanel, viewport - .getGlobalColourScheme(), "Background"); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } @@ -2093,10 +2376,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } @@ -2124,6 +2407,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, modifyPID_actionPerformed(); } + public void sortPairwiseMenuItem_actionPerformed() { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -2131,7 +2415,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2140,7 +2424,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); + alignPanel.paintAlignment(true); + } + + public void sortLengthMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2149,7 +2442,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2166,7 +2459,7 @@ 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); } } @@ -2174,7 +2467,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void PCAMenuItem_actionPerformed() { // are the sequences aligned? - if (!viewport.alignment.isAligned()) + if (!viewport.getAlignment().isAligned(false)) { SequenceI current; int Width = viewport.getAlignment().getWidth(); @@ -2231,7 +2524,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, void NewTreePanel(String type, String pwType, String title) { // are the sequences aligned? - if (!viewport.alignment.isAligned()) + if (!viewport.getAlignment().isAligned(false)) { SequenceI current; int Width = viewport.getAlignment().getWidth(); @@ -2251,10 +2544,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if ((viewport.getSelectionGroup() != null && viewport .getSelectionGroup().getSize() > 1) - || (viewport.getSelectionGroup() == null && viewport.alignment - .getHeight() > 1)) + || (viewport.getAlignment().getHeight() > 1)) { - final TreePanel tp = new TreePanel(viewport, type, pwType); + final TreePanel tp = new TreePanel(alignPanel, type, pwType); addTreeMenuItem(tp, title); @@ -2265,46 +2557,55 @@ 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(viewport, 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); } + /** * sort the alignment using the given treePanel - * @param treePanel tree used to sort view - * @param title string used for undo event name + * + * @param treePanel + * tree used to sort view + * @param title + * string used for undo event name */ public void sortByTree(TreePanel treePanel, String title) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel - .getTree()); + AlignmentSorter + .sortByTree(viewport.getAlignment(), treePanel.getTree()); // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); - addHistoryItem(new OrderCommand("Order by "+title, oldOrder, - viewport.alignment)); + addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } + /** - * Do any automatic reordering of the alignment and add the necessary bits to the menu structure for the new tree + * Do any automatic reordering of the alignment and add the necessary bits to + * the menu structure for the new tree + * * @param treePanel * @param title */ - protected void addTreeMenuItem(final TreePanel treePanel, final String title) + protected void addTreeMenuItem(final TreePanel treePanel, + final String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { sortByTree(treePanel, title); // treePanel.getTitle()); @@ -2313,6 +2614,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, treePanel.addWindowListener(new WindowAdapter() { + @Override public void windowOpened(WindowEvent e) { if (viewport.sortByTree) @@ -2322,6 +2624,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, super.windowOpened(e); } + @Override public void windowClosing(WindowEvent e) { sortByTreeMenu.remove(item); @@ -2329,9 +2632,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, }); } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + if (viewport.applet.debug) + { + System.err.println("Sorting " + alorder.getOrder().size() + + " in alignment '" + getTitle() + "'"); + } + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; + } + protected void documentation_actionPerformed() { - showURL("http://www.jalview.org/help.html", "HELP"); + alignPanel.av.applet.openJalviewHelpUrl(); } protected void about_actionPerformed() @@ -2341,11 +2662,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { String version; - public AboutPanel(String version) + String builddate; + + public AboutPanel(String version, String builddate) { this.version = version; + this.builddate = builddate; } + @Override public void paint(Graphics g) { g.setColor(Color.white); @@ -2358,54 +2683,36 @@ 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(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g - .drawString( - "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,", - x, y += fh * 1.5); - g.drawString("David Martin & Geoff Barton.", x + 50, y += fh); - g - .drawString( - "Development managed by The Barton Group, University of Dundee, Scotland, UK.", - x, y += fh); - 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); g.drawString( - "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",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",x,y+=fh); - } - } - - String version = "test"; - java.net.URL url = getClass().getResource("/.build_properties"); - if (url != null) - { - try - { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); - String line; - while ((line = reader.readLine()) != null) - { - if (line.indexOf("VERSION") > -1) - { - version = line.substring(line.indexOf("=") + 1); - } - } - } catch (Exception ex) - { - ex.printStackTrace(); + MessageManager.getString("label.jalview_authors_1"), + x, y += fh * 1.5); + g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8); + g.drawString( + MessageManager.getString("label.jalview_dev_managers"), + x, y += fh); + g.drawString( + MessageManager.getString("label.jalview_distribution_lists"), + x, y += fh); + g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8); + g.drawString( + MessageManager.getString("label.jalview_cite_1_authors"), + x, y += fh); + g.drawString( + MessageManager.getString("label.jalview_cite_1_title"), + x, y += fh); + g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), + x, y += fh); } } Frame frame = new Frame(); - frame.add(new AboutPanel(version)); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); + frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite + .getBuildDate())); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220); } @@ -2417,28 +2724,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - try - { - if (url.indexOf(":")==-1) - { - // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL - if (url.indexOf("/")==0) - { - String codebase = viewport.applet.getCodeBase().toString(); - url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url; - } else { - url = viewport.applet.getCodeBase()+url; - } - System.out.println("Show url (prepended codebase): " + url); - } else { - System.out.println("Show url: " + url); - } - viewport.applet.getAppletContext().showDocument( - new java.net.URL(url), target); - } catch (Exception ex) - { - ex.printStackTrace(); - } + viewport.applet.showURL(url, target); } } @@ -2447,33 +2733,33 @@ 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(); @@ -2491,6 +2777,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem sortIDMenuItem = new MenuItem(); + MenuItem sortLengthMenuItem = new MenuItem(); + MenuItem sortGroupMenuItem = new MenuItem(); MenuItem removeRedundancyMenuItem = new MenuItem(); @@ -2525,12 +2813,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem buriedColour = new MenuItem(); + MenuItem purinePyrimidineColour = new MenuItem(); + + MenuItem RNAInteractionColour = new MenuItem(); + + MenuItem RNAHelixColour = new MenuItem(); + MenuItem userDefinedColour = new MenuItem(); MenuItem PIDColour = new MenuItem(); MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem tcoffeeColour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); @@ -2541,7 +2837,7 @@ 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(); @@ -2565,6 +2861,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem deleteGroups = new MenuItem(); + MenuItem grpsFromSelection = new MenuItem(); + + MenuItem createGroup = new MenuItem(); + + MenuItem unGroup = new MenuItem(); + MenuItem delete = new MenuItem(); MenuItem copy = new MenuItem(); @@ -2594,6 +2896,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem autoCalculate = new CheckboxMenuItem( "Autocalculate Consensus", true); + CheckboxMenuItem sortByTree = new CheckboxMenuItem( + "Sort Alignment With New Tree", true); + Menu sortByTreeMenu = new Menu(); Menu sort = new Menu(); @@ -2614,6 +2919,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); + Menu autoAnnMenu = new Menu(); + + CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem(); + + CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); + + CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); + + CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); + + CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); + + CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem(); + private void jbInit() throws Exception { @@ -2630,6 +2949,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -2648,175 +2968,214 @@ 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); - sortGroupMenuItem.setLabel("by Group"); + sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length")); + sortLengthMenuItem.addActionListener(this); + 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); - userDefinedColour.setLabel("User Defined..."); + purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine")); + purinePyrimidineColour.addActionListener(this); + RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction")); + RNAInteractionColour.addActionListener(this); + RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes")); + RNAHelixColour.addActionListener(this); + 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(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 non-conserved"); + 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); - copy.setLabel("Copy"); + 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("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); - inputText.setLabel("Input from textbox"); + sortByTree.addItemListener(this); + 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"); + 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(MessageManager.getString("label.autocalculated_annotation")); + invertColSel.addActionListener(this); showColumns.addActionListener(this); showSeqs.addActionListener(this); hideColumns.addActionListener(this); hideSequences.addActionListener(this); - formatMenu.setLabel("Format"); - selectMenu.setLabel("Select"); - newView.setLabel("New View"); + hideAllButSelection.addActionListener(this); + hideAllSelection.addActionListener(this); + showAllHidden.addActionListener(this); + showGroupConsensus.addItemListener(this); + showGroupConservation.addItemListener(this); + showConsensusHistogram.addItemListener(this); + showSequenceLogo.addItemListener(this); + normSequenceLogo.addItemListener(this); + + applyAutoAnnotationSettings.addItemListener(this); + 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); @@ -2863,6 +3222,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewMenu.addSeparator(); viewMenu.add(followMouseOverFlag); viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); viewMenu.add(featureSettings); @@ -2884,6 +3251,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + // colourMenu.add(RNAInteractionColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -2891,16 +3261,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(RNAHelixColour); calculateMenu.add(sort); calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.add(autoCalculate); + calculateMenu.add(sortByTree); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); sort.add(sortByTreeMenu); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); @@ -2912,8 +3285,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, helpMenu.add(about); menu1.add(showColumns); menu1.add(showSeqs); + menu1.add(showAllHidden); menu2.add(hideColumns); menu2.add(hideSequences); + menu2.add(hideAllSelection); + menu2.add(hideAllButSelection); formatMenu.add(font); formatMenu.add(seqLimits); formatMenu.add(wrapMenuItem); @@ -2932,9 +3308,18 @@ 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(); @@ -2955,6 +3340,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem hideSequences = new MenuItem(); + MenuItem hideAllButSelection = new MenuItem(); + + MenuItem hideAllSelection = new MenuItem(); + + MenuItem showAllHidden = new MenuItem(); + Menu formatMenu = new Menu(); Menu selectMenu = new Menu(); @@ -2967,8 +3358,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * platform independent manner to avoid OSX/Mac menu appendage daftness. * * @param reallyEmbedded - * true to attach the view to the applet area on the page - * rather than in a new window + * true to attach the view to the applet area on the page rather than + * in a new window */ public void createAlignFrameWindow(boolean reallyEmbedded, String title) { @@ -2981,15 +3372,34 @@ 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); viewport.applet.add(statusBar, BorderLayout.SOUTH); - alignPanel.setSize(viewport.applet.getSize().width, viewport.applet - .getSize().height - - embeddedMenu.HEIGHT - statusBar.HEIGHT); + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().height - embeddedMenu.HEIGHT + - statusBar.HEIGHT); viewport.applet.add(alignPanel, BorderLayout.CENTER); + final AlignFrame me = this; + viewport.applet.addFocusListener(new FocusListener() + { + + @Override + public void focusLost(FocusEvent e) + { + if (me.viewport.applet.currentAlignFrame == me) + { + me.viewport.applet.currentAlignFrame = null; + } + } + + @Override + public void focusGained(FocusEvent e) + { + me.viewport.applet.currentAlignFrame = me; + } + }); viewport.applet.validate(); } else @@ -3010,4 +3420,345 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, DEFAULT_HEIGHT); } } + + /** + * create a new binding between structures in an existing jmol viewer instance + * and an alignpanel with sequences that have existing PDBFile entries. Note, + * this does not open a new Jmol window, or modify the display of the + * structures in the original jmol window. Note This method doesn't work + * without an additional javascript library to exchange messages between the + * distinct applets. See http://issues.jalview.org/browse/JAL-621 + * + * @param viewer + * JmolViewer instance + * @param sequenceIds + * - sequence Ids to search for associations + */ + public SequenceStructureBinding addStructureViewInstance( + Object jmolviewer, String[] sequenceIds) + { + org.jmol.api.JmolViewer viewer = null; + try + { + viewer = (org.jmol.api.JmolViewer) jmolviewer; + } catch (ClassCastException ex) + { + System.err.println("Unsupported viewer object :" + + jmolviewer.getClass()); + } + if (viewer == null) + { + System.err.println("Can't use this object as a structure viewer:" + + jmolviewer.getClass()); + return null; + } + SequenceI[] seqs = null; + if (sequenceIds == null || sequenceIds.length == 0) + { + seqs = viewport.getAlignment().getSequencesArray(); + } + else + { + Vector sqi = new Vector(); + AlignmentI al = viewport.getAlignment(); + for (int sid = 0; sid < sequenceIds.length; sid++) + { + SequenceI sq = al.findName(sequenceIds[sid]); + if (sq != null) + { + sqi.addElement(sq); + } + } + if (sqi.size() > 0) + { + seqs = new SequenceI[sqi.size()]; + for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++) + { + seqs[sid] = (SequenceI) sqi.elementAt(sid); + } + } + else + { + return null; + } + } + ExtJmol jmv = null; + // TODO: search for a jmv that involves viewer + if (jmv == null) + { // create a new viewer/jalview binding. + jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] + { seqs }); + } + return jmv; + + } + + /** + * bind a pdb file to a sequence in the current view + * + * @param sequenceId + * - sequenceId within the dataset. + * @param pdbEntryString + * - the short name for the PDB file + * @param pdbFile + * - pdb file - either a URL or a valid PDB file. + * @return true if binding was as success TODO: consider making an exception + * structure for indicating when PDB parsing or sequenceId location + * fails. + */ + public boolean addPdbFile(String sequenceId, String pdbEntryString, + String pdbFile) + { + SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); + boolean needtoadd = false; + if (toaddpdb != null) + { + Vector pdbe = toaddpdb.getPDBId(); + PDBEntry pdbentry = null; + if (pdbe != null && pdbe.size() > 0) + { + for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) + { + pdbentry = (PDBEntry) pdbe.elementAt(pe); + if (!pdbentry.getId().equals(pdbEntryString) + && !pdbentry.getFile().equals(pdbFile)) + { + pdbentry = null; + } + else + { + continue; + } + } + } + if (pdbentry == null) + { + pdbentry = new PDBEntry(); + pdbentry.setId(pdbEntryString); + pdbentry.setFile(pdbFile); + needtoadd = true; // add this new entry to sequence. + } + // resolve data source + // TODO: this code should be a refactored to an io package + String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + if (protocol == null) + { + return false; + } + if (needtoadd) + { + // make a note of the access mode and add + if (pdbentry.getProperty() == null) + { + pdbentry.setProperty(new Hashtable()); + } + pdbentry.getProperty().put("protocol", protocol); + toaddpdb.addPDBId(pdbentry); + } + } + return true; + } + + private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains) + { + if (seqs != null) + { + Vector sequences = new Vector(); + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i] != null) + { + sequences.addElement(new Object[] + { seqs[i], (chains != null) ? chains[i] : null }); + } + } + seqs = new SequenceI[sequences.size()]; + chains = new String[sequences.size()]; + for (int i = 0, isize = sequences.size(); i < isize; i++) + { + Object[] oj = (Object[]) sequences.elementAt(i); + + seqs[i] = (SequenceI) oj[0]; + chains[i] = (String) oj[1]; + } + } + return new Object[] + { seqs, chains }; + + } + + public void newStructureView(JalviewLite applet, PDBEntry pdb, + SequenceI[] seqs, String[] chains, String protocol) + { + // Scrub any null sequences from the array + Object[] sqch = cleanSeqChainArrays(seqs, chains); + seqs = (SequenceI[]) sqch[0]; + chains = (String[]) sqch[1]; + if (seqs == null || seqs.length == 0) + { + System.err + .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); + } + if (protocol == null || protocol.trim().length() == 0 + || protocol.equals("null")) + { + protocol = (String) pdb.getProperty().get("protocol"); + if (protocol == null) + { + System.err.println("Couldn't work out protocol to open structure: " + + pdb.getId()); + return; + } + } + if (applet.useXtrnalSviewer) + { + // register the association(s) and quit, don't create any windows. + if (StructureSelectionManager.getStructureSelectionManager(applet) + .setMapping(seqs, chains, pdb.getFile(), protocol) == null) + { + System.err.println("Failed to map " + pdb.getFile() + " (" + + protocol + ") to any sequences"); + } + return; + } + if (applet.isAlignPdbStructures() && applet.jmolAvailable) + { + // can only do alignments with Jmol + // find the last jmol window assigned to this alignment + jalview.appletgui.AppletJmol ajm = null, tajm; + Vector jmols = applet + .getAppletWindow(jalview.appletgui.AppletJmol.class); + for (int i = 0, iSize = jmols.size(); i < iSize; i++) + { + tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + if (tajm.ap.alignFrame == this) + { + ajm = tajm; + break; + } + } + if (ajm != null) + { + System.err + .println("Incremental adding and aligning structure to existing Jmol view not yet implemented."); + // try and add the pdb structure + // ajm.addS + ajm = null; + } + } + // otherwise, create a new window + if (applet.jmolAvailable) + { + new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + protocol); + applet.lastFrameX += 40; + applet.lastFrameY += 40; + } + else + { + new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); + } + + } + + public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb, + SequenceI[][] seqs, String[][] chains, String[] protocols) + { + // TODO Auto-generated method stub + System.err.println("Aligned Structure View: Not yet implemented."); + } + + /** + * modify the current selection, providing the user has not made a selection + * already. + * + * @param sel + * - sequences from this alignment + * @param csel + * - columns to be selected on the alignment + */ + public void select(SequenceGroup sel, ColumnSelection csel) + { + alignPanel.seqPanel.selection(sel, csel, null); + } + + public void scrollTo(int row, int column) + { + alignPanel.seqPanel.scrollTo(row, column); + } + + public void scrollToRow(int row) + { + alignPanel.seqPanel.scrollToRow(row); + } + + public void scrollToColumn(int column) + { + alignPanel.seqPanel.scrollToColumn(column); + } + + /** + * @return the alignments unique ID. + */ + public String getSequenceSetId() + { + return viewport.getSequenceSetId(); + } + + /** + * Load the (T-Coffee) score file from the specified url + * + * @param source + * File/URL/T-COFFEE score file contents + * @throws IOException + * @return true if alignment was annotated with data from source + */ + public boolean loadScoreFile(String source) throws IOException + { + + TCoffeeScoreFile file = new TCoffeeScoreFile(source, + AppletFormatAdapter.checkProtocol(source)); + if (!file.isValid()) + { + // TODO: raise dialog for gui + System.err.println("Problems parsing T-Coffee scores: " + + file.getWarningMessage()); + System.err.println("Origin was:\n" + source); + return false; + } + + /* + * check that the score matrix matches the alignment dimensions + */ + AlignmentI aln; + if ((aln = viewport.getAlignment()) != null + && (aln.getHeight() != file.getHeight() || aln.getWidth() != file + .getWidth())) + { + // TODO: raise a dialog box here rather than bomb out. + System.err + .println("The scores matrix does not match the alignment dimensions"); + + } + + // TODO add parameter to indicate if matching should be done + if (file.annotateAlignment(alignPanel.getAlignment(), false)) + { + alignPanel.fontChanged(); + tcoffeeColour.setEnabled(true); + // switch to this color + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + return true; + } + else + { + System.err.println("Problems resolving T-Coffee scores:"); + if (file.getWarningMessage() != null) + { + System.err.println(file.getWarningMessage()); + } + } + return false; + } + }