X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=92316b3e1dc3474b63715a80ffbe8b7836da028a;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=ca4b88073df161ebf2b91432c43de04fd2f90fdc;hpb=743539d4df78bc53527887a436004790ff850ffb;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index ca4b880..92316b3 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,44 +1,138 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.beans.*; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; -import javax.swing.event.MenuEvent; - -import jalview.analysis.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.Conservation; +import jalview.analysis.CrossRef; +import jalview.analysis.NJTree; +import jalview.analysis.ParseProperties; +import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignViewControllerGuiI; +import jalview.api.AlignViewControllerI; +import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; +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.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.FeaturesFile; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.HTMLOutput; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.io.TCoffeeScoreFile; +import jalview.jbgui.GAlignFrame; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +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.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.util.MessageManager; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.seqfetcher.DbSourceProxy; + +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.GridLayout; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.JButton; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JProgressBar; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; /** * DOCUMENT ME! @@ -47,7 +141,7 @@ import jalview.ws.jws2.Jws2Discoverer; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator + IProgressIndicator, AlignViewControllerGuiI { /** DOCUMENT ME!! */ @@ -59,6 +153,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public AlignmentPanel alignPanel; AlignViewport viewport; + + public AlignViewControllerI avc; + Vector alignPanels = new Vector(); @@ -202,7 +299,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { - if (viewport.conservation == null) + avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); + if (viewport.getAlignmentConservationAnnotation() == null) { BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); @@ -228,11 +326,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); addServiceListeners(); - setGUINucleotide(viewport.alignment.isNucleotide()); + setGUINucleotide(viewport.getAlignment().isNucleotide()); } setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); + buildTreeMenu(); if (viewport.wrapAlignment) { wrapMenuItem_actionPerformed(null); @@ -244,7 +343,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } addKeyListener(); - + } /** @@ -267,6 +366,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -322,6 +422,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } break; + // case KeyEvent.VK_A: + // if (viewport.cursorMode) + // { + // alignPanel.seqPanel.insertNucAtCursor(false,"A"); + // //System.out.println("A"); + // } + // break; + /* + * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { + * System.out.println("closing bracket"); } break; + */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) @@ -378,8 +489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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; @@ -436,6 +546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void keyReleased(KeyEvent evt) { switch (evt.getKeyCode()) @@ -459,6 +570,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) { ap.alignFrame = this; + avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); alignPanels.addElement(ap); @@ -488,12 +600,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (newPanel) { - if (ap.av.padGaps) + if (ap.av.isPadGaps()) { - ap.av.alignment.padGaps(); + ap.av.getAlignment().padGaps(); } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); } } @@ -519,6 +632,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.addJalviewPropertyChangeListener("services", thisListener = new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { // // System.out.println("Discoverer property change."); @@ -527,6 +641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { System.err @@ -540,6 +655,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -552,6 +668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Finally, build the menu once to get current service state new Thread(new Runnable() { + @Override public void run() { BuildWebServiceMenu(); @@ -565,11 +682,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); + rnahelicesColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(nucleotide); // Remember AlignFrame always starts as protein - if (!nucleotide) - { - calculateMenu.remove(calculateMenu.getItemCount() - 2); - } + // if (!nucleotide) + // { + // showTr + // calculateMenu.remove(calculateMenu.getItemCount() - 2); + // } } /** @@ -591,7 +711,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void setMenusFromViewport(AlignViewport av) { - padGapsMenuitem.setSelected(av.padGaps); + padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.showColourText); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); @@ -606,25 +726,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); - showNonconservedMenuItem.setSelected(av.showUnconserved); - showGroupConsensus.setSelected(av.showGroupConsensus); - showGroupConservation.setSelected(av.showGroupConservation); - showConsensusHistogram.setSelected(av.showConsensusHistogram); - showSequenceLogo.setSelected(av.showSequenceLogo); + showNonconservedMenuItem.setSelected(av.getShowUnconserved()); + showGroupConsensus.setSelected(av.isShowGroupConsensus()); + showGroupConservation.setSelected(av.isShowGroupConservation()); + showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); + showSequenceLogo.setSelected(av.isShowSequenceLogo()); + normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); - applyToAllGroups.setState(av.colourAppliesToAllGroups); + applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); showDbRefsMenuitem.setSelected(av.isShowDbRefs()); - + autoCalculate.setSelected(av.autoCalculateConsensus); + sortByTree.setSelected(av.sortByTree); + listenToViewSelections.setSelected(av.followSelection); + rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); + rnahelicesColour + .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); setShowProductsEnabled(); - updateEditMenuBar(); } + // methods for implementing IProgressIndicator + // need to refactor to a reusable stub class Hashtable progressBars, progressBarHandlers; /* @@ -632,6 +760,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ + @Override public void setProgressBar(String message, long id) { if (progressBars == null) @@ -675,10 +804,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBars.put(lId, progressPanel); } // update GUI - setMenusForViewport(); + // setMenusForViewport(); validate(); } + @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { @@ -691,11 +821,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { - JButton cancel = new JButton("Cancel"); + JButton cancel = new JButton(MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); @@ -713,6 +844,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return true if any progress bars are still active */ + @Override public boolean operationInProgress() { if (progressBars != null && progressBars.size() > 0) @@ -722,6 +854,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return false; } + @Override + public void setStatus(String text) { + statusBar.setText(text); + }; /* * Added so Castor Mapping file can obtain Jalview Version */ @@ -735,20 +871,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); } + @Override public void fetchSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); } + @Override public void addFromFile_actionPerformed(ActionEvent e) { Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } + @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) { + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. if (currentFileFormat.equals("Jalview")) @@ -757,6 +898,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int i = 0; i < frames.length; i++) { if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null && ((AlignFrame) frames[i]).fileName.equals(fileName)) { try @@ -794,6 +936,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { nfs.frame.setBounds(fspos); @@ -807,16 +950,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addFromText_actionPerformed(ActionEvent e) { Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); } + @Override public void addFromURL_actionPerformed(ActionEvent e) { Desktop.instance.inputURLMenuItem_actionPerformed(viewport); } + @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null @@ -838,6 +984,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void saveAs_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -848,7 +995,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -858,8 +1005,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (currentFileFormat == null) { JOptionPane.showInternalMessageDialog(Desktop.desktop, - "You must select a file format before saving!", - "File format not specified", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.select_file_format_before_saving"), + MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE); value = chooser.showSaveDialog(this); return; } @@ -895,8 +1042,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, success = new Jalview2XML().SaveAlignment(this, file, shortName); - statusBar.setText("Successfully saved to file: " + fileName + " in " - + format + " format."); + statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format})); + } else @@ -912,14 +1059,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to save only the visible alignment?", - "Save / Omit Hidden Columns", + MessageManager.getString("label.alignment_contains_hidden_columns"), + MessageManager.getString("action.save_omit_hidden_columns"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); @@ -930,9 +1076,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } FormatAdapter f = new FormatAdapter(); String output = f.formatSequences(format, - (Alignment) viewport.alignment, // class cast exceptions will + viewport.getAlignment(), // class cast exceptions will // occur in the distant future - omitHidden, f.getCacheSuffixDefault(format), viewport.colSel); + omitHidden, f.getCacheSuffixDefault(format), + viewport.getColumnSelection()); if (output == null) { @@ -948,8 +1095,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, out.print(output); out.close(); this.setTitle(file); - statusBar.setText("Successfully saved to file: " + fileName - + " in " + format + " format."); + statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format})); } catch (Exception ex) { success = false; @@ -960,8 +1106,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, "Couldn't save file: " - + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}), + MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE); } return success; @@ -988,18 +1134,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void outputText_actionPerformed(ActionEvent e) { String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to output only the visible alignment?", - "Save / Omit Hidden Columns", + MessageManager.getString("label.alignment_contains_hidden_columns"), + MessageManager.getString("action.save_omit_hidden_columns"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); @@ -1015,9 +1161,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.alignment, omitHidden, viewport.colSel)); + viewport.getAlignment(), omitHidden, + viewport.getColumnSelection())); Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, 500); + MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); } catch (OutOfMemoryError oom) { new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); @@ -1032,6 +1179,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { new HTMLOutput(alignPanel, @@ -1050,6 +1198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void createPNG(File f) { alignPanel.makePNG(f); @@ -1061,11 +1210,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void createEPS(File f) { alignPanel.makeEPS(f); } + @Override public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -1078,6 +1229,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems @@ -1085,29 +1237,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, thread.start(); } + @Override public void exportFeatures_actionPerformed(ActionEvent e) { new AnnotationExporter().exportFeatures(alignPanel); } + @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations( - alignPanel, - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + new AnnotationExporter().exportAnnotations(alignPanel, + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), ((Alignment) viewport + .getAlignment()).alignmentProperties); } + @Override public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Load Jalview Annotations or Features File"); - chooser.setToolTipText("Load Jalview Annotations / Features file"); + chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations")); + chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations")); int value = chooser.showOpenDialog(null); @@ -1115,7 +1269,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice); + loadJalviewDataFile(choice, null, null, null); } } @@ -1126,6 +1280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) @@ -1206,12 +1361,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setText("Undo " + command.getDescription()); + undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()})); } else { undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); + undoMenuItem.setText(MessageManager.getString("action.undo")); } if (viewport.redoList.size() > 0) @@ -1219,12 +1374,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setText("Redo " + command.getDescription()); + redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()})); } else { redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + redoMenuItem.setText(MessageManager.getString("action.redo")); } } @@ -1235,9 +1390,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.historyList.push(command); viewport.redoList.clear(); updateEditMenuBar(); - viewport.hasHiddenColumns = (viewport.colSel != null - && viewport.colSel.getHiddenColumns() != null && viewport.colSel - .getHiddenColumns().size() > 0); + viewport.updateHiddenColumns(); + // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); } } @@ -1260,7 +1417,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport != null) { return new AlignmentI[] - { viewport.alignment }; + { viewport.getAlignment() }; } return null; } @@ -1271,6 +1428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) @@ -1284,11 +1442,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != null) { - originalSource.hasHiddenColumns = (viewport.colSel != null - && viewport.colSel.getHiddenColumns() != null && viewport.colSel - .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + if (originalSource != viewport) + { + Cache.log + .warn("Implementation worry: mismatch of viewport origin for undo"); + } + originalSource.updateHiddenColumns(); + // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != + // null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } } @@ -1298,6 +1464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { if (viewport.redoList.size() < 1) @@ -1314,11 +1481,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != null) { - originalSource.hasHiddenColumns = (viewport.colSel != null - && viewport.colSel.getHiddenColumns() != null && viewport.colSel - .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + + if (originalSource != viewport) + { + Cache.log + .warn("Implementation worry: mismatch of viewport origin for redo"); + } + originalSource.updateHiddenColumns(); + // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != + // null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } } @@ -1340,7 +1516,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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; @@ -1355,7 +1531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1378,69 +1554,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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(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); - } - } - + viewport.getAlignment().moveSelectedSequencesByOne(sg, + 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) @@ -1450,15 +1582,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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.add(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + invertGroup.add(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[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) @@ -1517,6 +1647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed(ActionEvent e) { System.gc(); @@ -1529,7 +1660,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { omitHidden = viewport.getViewAsString(true); } @@ -1556,7 +1687,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } Vector hiddenColumns = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { hiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport @@ -1575,8 +1706,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } Desktop.jalviewClipboard = new Object[] - { seqs, viewport.alignment.getDataset(), hiddenColumns }; - statusBar.setText("Copied " + seqs.length + " sequences to clipboard."); + { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; + statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()})); } /** @@ -1585,6 +1716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); @@ -1596,6 +1728,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); @@ -1664,6 +1797,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } int alwidth = 0; + ArrayList newGraphGroups = new ArrayList(); + int fgroup = -1; if (newAlignment) { @@ -1731,6 +1866,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { newDs.clear(); // tidy up } + if (alignment.getAlignmentAnnotation() != null) + { + for (AlignmentAnnotation alan : alignment + .getAlignmentAnnotation()) + { + if (alan.graphGroup > fgroup) + { + fgroup = alan.graphGroup; + } + } + } if (pastedal.getAlignmentAnnotation() != null) { // Add any annotation attached to alignment. @@ -1741,6 +1887,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (alann[i].sequenceRef == null && !alann[i].autoCalculated) { AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, new Integer( + ++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } @@ -1760,11 +1922,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (sequences[i].getAnnotation() != null) { + AlignmentAnnotation newann; for (int a = 0; a < sequences[i].getAnnotation().length; a++) { annotationAdded = true; - sequences[i].getAnnotation()[a].adjustForAlignment(); - sequences[i].getAnnotation()[a].padAnnotation(alwidth); + newann = sequences[i].getAnnotation()[a]; + newann.adjustForAlignment(); + newann.padAnnotation(alwidth); + if (newann.graphGroup > -1) + { + if (newann.graphGroup > -1) + { + if (newGraphGroups.size() <= newann.graphGroup + || newGraphGroups.get(newann.graphGroup) == null) + { + for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup, new Integer( + ++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup) + .intValue(); + } + } alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation // was // duplicated @@ -1804,6 +1986,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newann.padAnnotation(avwidth); alview[avnum].addAnnotation(newann); // annotation was // duplicated earlier + // TODO JAL-1145 graphGroups are not updated for sequence + // annotation added to several views. This may cause + // strangeness alview[avnum].setAnnotationIndex(newann, a); } } @@ -1813,6 +1998,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.firePropertyChange("alignment", null, alignment.getSequences()); + if (alignPanels != null) + { + for (AlignmentPanel ap : ((Vector) alignPanels)) + { + ap.validateAnnotationDimensions(false); + } + } + else + { + alignPanel.validateAnnotationDimensions(false); + } } else @@ -1869,13 +2065,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override + protected void expand_newalign(ActionEvent e) + { + try { + AlignmentI alignment = AlignmentUtils.expandContext(getViewport().getAlignment(), -1); + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Flanking alignment"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + Vector hc = (Vector) Desktop.jalviewClipboard[2]; + for (int i = 0; i < hc.size(); i++) + { + int[] region = (int[]) hc.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + .transferSettings( + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. + { + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + } + + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here + } + catch (OutOfMemoryError oom) + { + new OOMWarning("Viewing flanking region of alignment", oom); + } + } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override protected void cut_actionPerformed(ActionEvent e) { copy_actionPerformed(null); @@ -1888,6 +2137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void delete_actionPerformed(ActionEvent evt) { @@ -1906,7 +2156,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // 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); @@ -1923,11 +2173,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + viewport.getAlignment())); viewport.setSelectionGroup(null); viewport.sendSelection(); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -1948,14 +2198,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void deleteGroups_actionPerformed(ActionEvent e) { - viewport.alignment.deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - PaintRefresher.Refresh(this, viewport.getSequenceSetId()); - alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + if (avc.deleteGroups()) { + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } } /** @@ -1964,6 +2214,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); @@ -1973,7 +2224,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth() - 1); + sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); alignPanel.paintAlignment(true); @@ -1986,6 +2237,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) @@ -2000,6 +2252,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } /** @@ -2008,6 +2261,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2025,14 +2279,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.paintAlignment(true); - viewport.sendSelection(); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } + @Override public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /** @@ -2041,6 +2297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); @@ -2052,6 +2309,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); @@ -2077,11 +2335,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } TrimRegionCommand trimRegion; @@ -2089,32 +2347,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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.get(i); - if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } @@ -2129,34 +2383,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { - 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()); @@ -2175,30 +2430,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { - 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); @@ -2213,9 +2469,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { - viewport.padGaps = padGapsMenuitem.isSelected(); + viewport.setPadGaps(padGapsMenuitem.isSelected()); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } @@ -2236,15 +2493,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { new Finder(); } + @Override public void newView_actionPerformed(ActionEvent e) { + newView(true); + } + + /** + * + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(boolean copyAnnotation) + { + return newView(null, copyAnnotation); + } + + /** + * + * @param viewTitle + * title of newly created view + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle) + { + return newView(viewTitle, true); + } + + /** + * + * @param viewTitle + * title of newly created view + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) + { AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, true); + if (!copyAnnotation) + { + // just remove all the current annotation except for the automatic stuff + newap.av.getAlignment().deleteAllGroups(); + for (AlignmentAnnotation alan : newap.av.getAlignment() + .getAlignmentAnnotation()) + { + if (!alan.autoCalculated) + { + newap.av.getAlignment().deleteAnnotation(alan); + } + ; + } + } newap.av.gatherViewsHere = false; @@ -2257,8 +2565,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.redoList = viewport.redoList; int index = Desktop.getViewCount(viewport.getSequenceSetId()); - String newViewName = "View " + index; - + // make sure the new view has a unique name - this is essential for Jalview + // 2 archives + boolean addFirstIndex = false; + if (viewTitle == null || viewTitle.trim().length() == 0) + { + viewTitle = "View"; + addFirstIndex = true; + } + else + { + index = 1;// we count from 1 if given a specific name + } + String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); Vector comps = (Vector) PaintRefresher.components.get(viewport .getSequenceSetId()); Vector existingNames = new Vector(); @@ -2276,25 +2595,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, while (existingNames.contains(newViewName)) { - newViewName = "View " + (++index); + newViewName = viewTitle + " " + (++index); } newap.av.viewName = newViewName; addAlignmentPanel(newap, true); - + newap.alignmentChanged(); + if (alignPanels.size() == 2) { viewport.gatherViewsHere = true; } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; } + @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } + @Override public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); @@ -2306,6 +2629,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); @@ -2317,6 +2641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); @@ -2326,12 +2651,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } + @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.rightAlignIds = idRightAlign.isSelected(); alignPanel.paintAlignment(true); } + @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); @@ -2343,6 +2670,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) @@ -2358,6 +2686,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); @@ -2370,6 +2699,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { scaleAbove.setVisible(wrapMenuItem.isSelected()); @@ -2379,17 +2709,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); } + @Override public void showAllSeqs_actionPerformed(ActionEvent e) { viewport.showAllHiddenSeqs(); } + @Override public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); repaint(); } + @Override public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); @@ -2412,8 +2745,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel - .getSelected().size() > 0) + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -2436,12 +2770,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (toggleSeqs) { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) { hideSelSequences_actionPerformed(null); hide = true; } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) { showAllSeqs_actionPerformed(null); } @@ -2449,12 +2784,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (toggleCols) { - if (viewport.colSel.getSelected().size() > 0) + if (viewport.getColumnSelection().getSelected().size() > 0) { hideSelColumns_actionPerformed(null); if (!toggleSeqs) { - viewport.selectionGroup = sg; + viewport.setSelectionGroup(sg); } } else if (!hide) @@ -2471,6 +2806,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ + @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); @@ -2483,6 +2819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ + @Override public void hideAllSelection_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2499,6 +2836,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ + @Override public void showAllhidden_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); @@ -2506,12 +2844,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } + @Override public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } + @Override public void hiddenMarkers_actionPerformed(ActionEvent e) { viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); @@ -2524,6 +2864,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); @@ -2536,6 +2877,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); @@ -2548,6 +2890,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); @@ -2560,6 +2903,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); @@ -2572,6 +2916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); @@ -2584,6 +2929,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); @@ -2592,6 +2938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureSettings featureSettings; + @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) @@ -2614,6 +2961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); @@ -2630,6 +2978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight @@ -2653,72 +3002,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } + @Override public void alignmentProperties() { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); - 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("
Sequences: " + viewport.alignment.getHeight()); - contents.append("
Minimum Sequence Length: " + min); - contents.append("
Maximum Sequence Length: " + max); - contents.append("
Average Length: " + (int) avg); - - if (((Alignment) viewport.alignment).getProperties() != null) - { - Hashtable props = ((Alignment) viewport.alignment).getProperties(); - Enumeration en = props.keys(); - contents.append("

"); - while (en.hasMoreElements()) - { - String key = en.nextElement().toString(); - StringBuffer val = new StringBuffer(); - String vals = props.get(key).toString(); - int pos = 0, npos; - do - { - npos = vals.indexOf("\n", pos); - if (npos == -1) - { - val.append(vals.substring(pos)); - } - else - { - val.append(vals.substring(pos, npos)); - val.append("
"); - } - pos = npos + 1; - } while (npos != -1); - contents.append(""); - } - contents.append("
" + key + "" + val + "
"); - } - editPane.setText(contents.toString() + ""); + StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) + .formatAsHtml(); + editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()})); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.instance.addInternalFrame(frame, "Alignment Properties: " - + getTitle(), 500, 400); + Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400); } /** @@ -2727,6 +3029,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) @@ -2737,12 +3040,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JInternalFrame frame = new JInternalFrame(); OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), + Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}), frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -2753,6 +3057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(overview); } + @Override public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); @@ -2764,6 +3069,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); @@ -2775,11 +3081,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void clustalColour_actionPerformed(ActionEvent e) { - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), - viewport.alignment.getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), + viewport.getHiddenRepSequences())); } /** @@ -2788,6 +3094,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); @@ -2799,6 +3106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); @@ -2810,6 +3118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); @@ -2821,6 +3130,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); @@ -2832,6 +3142,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); @@ -2843,6 +3154,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); @@ -2854,6 +3166,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); @@ -2865,22 +3178,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } + @Override + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + + /* + * public void covariationColour_actionPerformed(ActionEvent e) { + * changeColour(new + * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation + * ()[0])); } + */ + @Override public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } + @Override + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } + /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); @@ -2894,6 +3228,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void changeColour(ColourSchemeI cs) { + // TODO: compare with applet and pull up to model method int threshold = 0; if (cs != null) @@ -2902,10 +3237,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - - viewport.setGlobalColourScheme(cs); } else { @@ -2915,13 +3247,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getConservationSelected()) { - Alignment al = (Alignment) viewport.alignment; + Alignment al = (Alignment) viewport.getAlignment(); Conservation c = new Conservation("All", ResidueProperties.propHash, 3, al.getSequences(), 0, al.getWidth() - 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); @@ -2933,19 +3265,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cs.setConservation(null); } - cs.setConsensus(viewport.hconsensus); + cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); if (viewport.getColourAppliesToAllGroups()) { - 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 (cs == null) { sg.cs = null; @@ -2954,9 +3283,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), - sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg, + viewport.getHiddenRepSequences()); } else if (cs instanceof UserColourScheme) { @@ -2966,7 +3294,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + sg.cs = cs.getClass().newInstance(); } catch (Exception ex) { } @@ -2979,7 +3307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), + sg.getSequences(viewport.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); } else @@ -2990,11 +3318,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport.hiddenRepSequences), - sg.getStartRes(), sg.getEndRes() + 1); + ResidueProperties.propHash, 3, sg.getSequences(viewport + .getHiddenRepSequences()), sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); sg.cs.setConservation(c); } else @@ -3018,10 +3346,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); @@ -3035,13 +3364,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void modifyConservation_actionPerformed(ActionEvent e) { if (viewport.getConservationSelected() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } @@ -3052,6 +3382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -3070,6 +3401,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -3088,9 +3420,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void userDefinedColour_actionPerformed(ActionEvent e) { - if (e.getActionCommand().equals("User Defined...")) + if (e.getActionCommand().equals(MessageManager.getString("action.user_defined"))) { new UserDefinedColours(alignPanel, null); } @@ -3129,6 +3462,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() @@ -3138,8 +3472,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, - "Remove from default list?", - "Remove user defined colour", + MessageManager.getString("label.remove_from_default_list"), + MessageManager.getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { @@ -3151,6 +3485,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3162,6 +3497,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3180,6 +3516,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); @@ -3191,6 +3528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); @@ -3202,13 +3540,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3218,11 +3557,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3232,12 +3573,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3247,12 +3589,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3263,6 +3606,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); @@ -3274,20 +3618,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { JOptionPane.showInternalMessageDialog(this, - "You must select at least 2 sequences.", "Invalid Selection", + MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), JOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); + Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500); } } @@ -3297,6 +3642,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void PCAMenuItem_actionPerformed(ActionEvent e) { if (((viewport.getSelectionGroup() != null) @@ -3305,9 +3651,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || (viewport.getAlignment().getHeight() < 4)) { JOptionPane.showInternalMessageDialog(this, - "Principal component analysis must take\n" - + "at least 4 input sequences.", - "Sequence selection insufficient", + MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"), + MessageManager.getString("label.sequence_selection_insufficient"), JOptionPane.WARNING_MESSAGE); return; @@ -3316,6 +3661,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new PCAPanel(alignPanel); } + @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); @@ -3326,12 +3672,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + viewport.sortByTree = sortByTree.isSelected(); + } + + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + viewport.followSelection = listenToViewSelections.isSelected(); + } + /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "PID", "Average distance tree using PID"); @@ -3343,6 +3702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); @@ -3354,6 +3714,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); @@ -3365,6 +3726,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); @@ -3384,34 +3746,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { TreePanel tp; - if (viewport.getSelectionGroup() != null) + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 0) { if (viewport.getSelectionGroup().getSize() < 3) { JOptionPane .showMessageDialog( Desktop.desktop, - "You need to have more than two sequences selected to build a tree!", - "Not enough sequences", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"), + MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE); return; } - int s = 0; SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ - while (s < sg.getSize()) + for (SequenceI _s : sg.getSequences()) { - if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg - .getEndRes()) + if (_s.getLength() < sg.getEndRes()) { JOptionPane .showMessageDialog( Desktop.desktop, - "The selected region to create a tree may\nonly contain residues or gaps.\n" - + "Try using the Pad function in the edit menu,\n" - + "or one of the multiple sequence alignment web services.", - "Sequences in selection are not aligned", + MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager.getString("label.sequences_selection_not_aligned"), JOptionPane.WARNING_MESSAGE); return; @@ -3424,21 +3783,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // are the visible sequences aligned? - if (!viewport.alignment.isAligned(false)) + if (!viewport.getAlignment().isAligned(false)) { JOptionPane .showMessageDialog( Desktop.desktop, - "The sequences must be aligned before creating a tree.\n" - + "Try using the Pad function in the edit menu,\n" - + "or one of the multiple sequence alignment web services.", - "Sequences not aligned", + MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"), + MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE); return; } - if (viewport.alignment.getHeight() < 2) + if (viewport.getAlignment().getHeight() < 2) { return; } @@ -3473,6 +3830,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3481,8 +3839,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); - addHistoryItem(new OrderCommand(order.getName(), oldOrder, - viewport.alignment)); + addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport + .getAlignment())); alignPanel.paintAlignment(true); } @@ -3505,13 +3863,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } }); @@ -3529,23 +3888,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * rebuilding in subsequence calls. * */ + @Override public void buildSortByAnnotationScoresMenu() { - if (viewport.alignment.getAlignmentAnnotation() == null) + if (viewport.getAlignment().getAlignmentAnnotation() == null) { return; } - if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) + if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple Hashtable scoreSorts = new Hashtable(); AlignmentAnnotation aann[]; - Enumeration sq = viewport.alignment.getSequences().elements(); - while (sq.hasMoreElements()) + for (SequenceI sqa : viewport.getAlignment().getSequences()) { - aann = ((SequenceI) sq.nextElement()).getAnnotation(); + aann = sqa.getAnnotation(); for (int i = 0; aann != null && i < aann.length; i++) { if (aann[i].hasScore() && aann[i].sequenceRef != null) @@ -3563,7 +3922,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); - _annotationScoreVectorHash = viewport.alignment + _annotationScoreVectorHash = viewport.getAlignment() .getAlignmentAnnotation().hashCode(); } } @@ -3580,8 +3939,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param title * SortBy menu item title. */ + @Override public void buildTreeMenu() { + calculateTree.removeAll(); + // build the calculate menu + + for (final String type:new String[] {"NJ", "AV"}) + { + String treecalcnm = MessageManager.getString("label.tree_calc_"+type.toLowerCase()); + for (final Object pwtype: ResidueProperties.scoreMatrices.keySet()) + { + JMenuItem tm = new JMenuItem(); + ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); + if (sm.isProtein()==!viewport.getAlignment().isNucleotide()) + { + String smn = MessageManager.getStringOrReturn( + "label.score_model_", sm.getName()); + final String title = MessageManager.formatMessage( + "label.treecalc_title", treecalcnm, smn); + tm.setText(title);// + tm.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + NewTreePanel(type, (String) pwtype, title); + } + }); + calculateTree.add(tm); + } + + } + } sortByTreeMenu.removeAll(); Vector comps = (Vector) PaintRefresher.components.get(viewport @@ -3608,21 +3997,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (i = 0; i < treePanels.size(); i++) { - TreePanel tp = (TreePanel) treePanels.elementAt(i); + final TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - SequenceI[] oldOrder = viewport.getAlignment() - .getSequencesArray(); - AlignmentSorter.sortByTree(viewport.getAlignment(), tree); - - addHistoryItem(new OrderCommand("Tree Sort", oldOrder, - viewport.alignment)); + tp.sortByTree_actionPerformed(null); + addHistoryItem(tp.sortAlignmentIn(alignPanel)); - alignPanel.paintAlignment(true); } }); @@ -3630,6 +4015,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; + } + /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. @@ -3691,9 +4089,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // limit sequences - JBPNote in future - could spawn multiple prediction // jobs - // TODO: viewport.alignment.isAligned is a global state - the local + // TODO: viewport.getAlignment().isAligned is a global state - the local // selection may well be aligned - we preserve 2.0.8 behaviour for moment. - if (!viewport.alignment.isAligned(false)) + if (!viewport.getAlignment().isAligned(false)) { seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); @@ -3710,14 +4108,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Select a newick-like tree file"); - chooser.setToolTipText("Load a tree file"); + chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file")); + chooser.setToolTipText(MessageManager.getString("label.load_tree_file")); int value = chooser.showOpenDialog(null); @@ -3733,18 +4132,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - "Problem reading tree file", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { JOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), "Possible problem with tree file", + fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"), JOptionPane.WARNING_MESSAGE); } } } + @Override + protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } + public TreePanel ShowNewickTree(NewickFile nf, String title) { return ShowNewickTree(nf, title, 600, 500, 4, 5); @@ -3833,141 +4238,157 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } final AlignFrame me = this; buildingMenu = true; - new Thread(new Runnable() { - public void run() { - try + new Thread(new Runnable() { - System.err - .println("Building ws menu again " + Thread.currentThread()); - // TODO: add support for context dependent disabling of services based on - // alignment and current selection - // TODO: add additional serviceHandle parameter to specify abstract - // handler - // class independently of AbstractName - // TODO: add in rediscovery GUI function to restart discoverer - // TODO: group services by location as well as function and/or introduce - // object broker mechanism. - final Vector wsmenu = new Vector(); - final IProgressIndicator af = me; - if (Cache.getDefault("SHOW_JWS1_SERVICES", true) - && Discoverer.services != null - && (Discoverer.services.size() > 0)) + @Override + public void run() { - // TODO: refactor to allow list of AbstractName/Handler bindings to be - // stored or retrieved from elsewhere - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch"); - // TODO: move GUI generation code onto service implementation - so a - // client instance attaches itself to the GUI with method call like - // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, - // alignframe) - if (msaws != null) + final List legacyItems=new ArrayList(); + try { - // Add any Multiple Sequence Alignment Services + System.err.println("Building ws menu again " + + Thread.currentThread()); + // TODO: add support for context dependent disabling of services based + // on + // alignment and current selection + // TODO: add additional serviceHandle parameter to specify abstract + // handler + // class independently of AbstractName + // TODO: add in rediscovery GUI function to restart discoverer + // TODO: group services by location as well as function and/or + // introduce + // object broker mechanism. + final Vector wsmenu = new Vector(); + final IProgressIndicator af = me; final JMenu msawsmenu = new JMenu("Alignment"); - for (int i = 0, j = msaws.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(msawsmenu, me); - - } - wsmenu.add(msawsmenu); - } - if (secstrpr != null) - { - // Add any secondary structure prediction services final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); - for (int i = 0, j = secstrpr.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(secstrmenu, me); - } - wsmenu.add(secstrmenu); - } - if (seqsrch != null) - { - // Add any sequence search services final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - for (int i = 0, j = seqsrch.size(); i < j; i++) + final JMenu analymenu = new JMenu("Analysis"); + final JMenu dismenu = new JMenu("Protein Disorder"); + // JAL-940 - only show secondary structure prediction services from + // the legacy server + if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) + // && + Discoverer.services != null && (Discoverer.services.size() > 0)) { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch - .elementAt(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(seqsrchmenu, me); + // TODO: refactor to allow list of AbstractName/Handler bindings to + // be + // stored or retrieved from elsewhere + // No MSAWS used any more: + // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services + .get("SecStrPred"); + if (secstrpr != null) + { + // Add any secondary structure prediction services + for (int i = 0, j = secstrpr.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + int p=secstrmenu.getItemCount(); + impl.attachWSMenuEntry(secstrmenu, me); + int q=secstrmenu.getItemCount(); + for (int litm=p;litm 0) + { + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add(wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); + } + // TODO: move into separate menu builder class. + boolean new_sspred=false; + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) + { + if (jws2servs.hasServices()) + { + jws2servs.attachWSMenuEntry(webService, me); + for (Jws2Instance sv:jws2servs.getServices()) { + if (sv.description.toLowerCase().contains("jpred")) + { + for (JMenuItem jmi:legacyItems) + { + jmi.setVisible(false); + } + } + } + + } + if (jws2servs.isRunning()) + { + JMenuItem tm = new JMenuItem( + "Still discovering JABA Services"); + tm.setEnabled(false); + webService.add(tm); + } + } + } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + for (JMenu item : wsmenu) + { + if (item.getItemCount() == 0) + { + item.setEnabled(false); + } + else + { + item.setEnabled(true); + } + } + } catch (Exception e) + { + Cache.log + .debug("Exception during web service menu building process.", + e); + } + ; } - } - } - } - - javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { - try { - - resetWebServiceMenu(); - // finally, add the whole shebang onto the webservices menu - if (wsmenu.size() > 0) - { - for (int i = 0, j = wsmenu.size(); i < j; i++) + }); + } catch (Exception e) { - webService.add((JMenu) wsmenu.get(i)); } + ; + + buildingMenu = false; } - else - { - me.webService.add(me.webServiceNoServices); - } - } catch (Exception e) - { - } - ; - } - }); - } catch (Exception e) - { - } - ; - - buildingMenu = false; - }}).start(); - - } + }).start(); - /** - * empty the web service menu and add any ad-hoc functions not dynamically - * discovered. - * - */ - private void resetWebServiceMenu() - { - webService.removeAll(); - build_fetchdbmenu(webService); - build_urlServiceMenu(webService); } /** @@ -3977,10 +4398,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ private void build_urlServiceMenu(JMenu webService) { - if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + // TODO: remove this code when 2.7 is released + // DEBUG - alignmentView + /* + * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final + * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { + * + * @Override public void actionPerformed(ActionEvent e) { + * jalview.datamodel.AlignmentView + * .testSelectionViews(af.viewport.getAlignment(), + * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } + * + * }); webService.add(testAlView); + */ + // TODO: refactor to RestClient discoverer and merge menu entries for + // rest-style services with other types of analysis/calculation service + // SHmmr test client - still being implemented. + // DEBUG - alignmentView + + for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient + .getRestClients()) { - jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry( - webService, this); + client.attachWSMenuEntry( + JvSwingUtils.findOrCreateMenu(webService, client.getAction()), + this); } } @@ -4051,6 +4492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, xtype.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay @@ -4084,13 +4526,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Runnable foo = new Runnable() { + @Override public void run() { final long sttime = System.currentTimeMillis(); ths.setProgressBar("Searching for sequences from " + fsrc, sttime); try { - Alignment ds = ths.getViewport().alignment.getDataset(); // update + Alignment ds = ths.getViewport().getAlignment().getDataset(); // update // our local // dataset // reference @@ -4167,6 +4610,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void showProducts_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4189,17 +4633,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", - "Translation Failed", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), + MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), + Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } + @Override public void showTranslation_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4212,26 +4657,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true), viewport - .getGapCharacter(), viewport.alignment - .getAlignmentAnnotation(), viewport.alignment + .getGapCharacter(), viewport.getAlignment() + .getAlignmentAnnotation(), viewport.getAlignment() .getWidth(), viewport.getAlignment().getDataset()); } catch (Exception ex) { al = null; - jalview.bin.Cache.log.debug("Exception during translation.", ex); + jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex); + JOptionPane + .showMessageDialog( + Desktop.desktop, + MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"), + MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE); + return; } if (al == null) { JOptionPane .showMessageDialog( Desktop.desktop, - "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", - "Translation Failed", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), + MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), + Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } @@ -4250,10 +4701,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean featuresFile = false; try { - featuresFile = new FeaturesFile(file, type) - .parse(viewport.alignment.getDataset(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, - false); + featuresFile = new FeaturesFile(file, type).parse(viewport + .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureColours, false, + jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { ex.printStackTrace(); @@ -4278,22 +4729,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return featuresFile; } + @Override public void dragEnter(DropTargetDragEvent evt) { } + @Override public void dragExit(DropTargetEvent evt) { } + @Override public void dragOver(DropTargetDragEvent evt) { } + @Override public void dropActionChanged(DropTargetDragEvent evt) { } + @Override public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); @@ -4348,10 +4804,124 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - + // check to see if any of these files have names matching sequences in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher(viewport + .getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList(); + ArrayList filesnotmatched = new ArrayList(); for (int i = 0; i < files.size(); i++) { - loadJalviewDataFile(files.get(i).toString()); + String file = files.get(i).toString(); + String pdbfn = ""; + String protocol = FormatAdapter.checkProtocol(file); + if (protocol == jalview.io.FormatAdapter.FILE) + { + File fl = new File(file); + pdbfn = fl.getName(); + } + else if (protocol == jalview.io.FormatAdapter.URL) + { + URL url = new URL(file); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + String type = null; + try + { + type = new IdentifyFile().Identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null) + { + if (type.equalsIgnoreCase("PDB")) + { + filesmatched.add(new Object[] + { file, protocol, mtch }); + continue; + } + } + } + // File wasn't named like one of the sequences or wasn't a PDB file. + filesnotmatched.add(file); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) + || JOptionPane + .showConfirmDialog( + this, + MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name", + new String[]{Integer.valueOf(filesmatched.size()).toString()}), + MessageManager.getString("label.automatically_associate_pdb_files_by_name"), + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) + + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq((String) fm[0], + (String) fm[1], toassoc, false); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + alignPanel.paintAlignment(true); + } + } + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 + && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + .showConfirmDialog( + this, + MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}), + MessageManager.getString("label.ignore_unmatched_dropped_files"), + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + { + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + } } catch (Exception ex) { @@ -4369,47 +4939,116 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * either a filename or a URL string. */ - public void loadJalviewDataFile(String file) + public void loadJalviewDataFile(String file, String protocol, + String format, SequenceI assocSeq) { try { - String protocol = jalview.io.FormatAdapter.FILE; - String f = file.toLowerCase(); - if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0 - || f.indexOf("file:") == 0) + if (protocol == null) { - protocol = jalview.io.FormatAdapter.URL; + protocol = jalview.io.FormatAdapter.checkProtocol(file); } - - boolean isAnnotation = new AnnotationFile().readAnnotationFile( - viewport.alignment, file, protocol); + // if the file isn't identified, or not positively identified as some + // other filetype (PFAM is default unidentified alignment file type) then + // try to parse as annotation. + boolean isAnnotation = (format == null || format + .equalsIgnoreCase("PFAM")) ? new AnnotationFile() + .readAnnotationFile(viewport.getAlignment(), file, protocol) + : false; if (!isAnnotation) { - // try to see if its a JNet 'concise' style annotation file *before* we - // try to parse it as a features file - String format = new IdentifyFile().Identify(file, protocol); - if (format.equalsIgnoreCase("JnetFile")) + // first see if its a T-COFFEE score file + TCoffeeScoreFile tcf = null; + try { - jalview.io.JPredFile predictions = new jalview.io.JPredFile(file, - protocol); - new JnetAnnotationMaker().add_annotation(predictions, - viewport.getAlignment(), 0, false); - isAnnotation = true; + tcf = new TCoffeeScoreFile(file, protocol); + if (tcf.isValid()) + { + if (tcf.annotateAlignment(viewport.getAlignment(), true)) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + isAnnotation = true; + statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + } + else + { + // some problem - if no warning its probable that the ID matching + // process didn't work + JOptionPane + .showMessageDialog( + Desktop.desktop, + tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment") + : tcf.getWarningMessage(), + MessageManager.getString("label.problem_reading_tcoffee_score_file"), + JOptionPane.WARNING_MESSAGE); + } + } + else + { + tcf = null; + } + } catch (Exception x) + { + Cache.log + .debug("Exception when processing data source as T-COFFEE score file", + x); + tcf = null; } - else + if (tcf == null) { + // try to see if its a JNet 'concise' style annotation file *before* + // we // try to parse it as a features file - boolean isGroupsFile = parseFeaturesFile(file, protocol); - // if it wasn't a features file then we just treat it as a general - // alignment file to load into the current view. - if (!isGroupsFile) + if (format == null) + { + format = new IdentifyFile().Identify(file, protocol); + } + if (format.equalsIgnoreCase("JnetFile")) { - new FileLoader().LoadFile(viewport, file, protocol, format); + jalview.io.JPredFile predictions = new jalview.io.JPredFile( + file, protocol); + new JnetAnnotationMaker().add_annotation(predictions, + viewport.getAlignment(), 0, false); + isAnnotation = true; } else { - alignPanel.paintAlignment(true); + /* + * if (format.equalsIgnoreCase("PDB")) { + * + * String pdbfn = ""; // try to match up filename with sequence id + * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = + * new File(file); pdbfn = fl.getName(); } else if (protocol == + * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = + * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == + * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport + * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { + * // attempt to find a match in the alignment SequenceI mtch = + * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while + * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > + * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch + * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and + * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() + * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) + * { System.err.println("Associated file : " + file + " with " + + * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // + * TODO: maybe need to load as normal otherwise return; } } + */ + // try to parse it as a features file + boolean isGroupsFile = parseFeaturesFile(file, protocol); + // if it wasn't a features file then we just treat it as a general + // alignment file to load into the current view. + if (!isGroupsFile) + { + new FileLoader().LoadFile(viewport, file, protocol, format); + } + else + { + alignPanel.paintAlignment(true); + } } } } @@ -4424,25 +5063,44 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { ex.printStackTrace(); + } catch (OutOfMemoryError oom) + { + try + { + System.gc(); + } catch (Exception x) + { + } + ; + new OOMWarning( + "loading data " + + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." + : "using " + protocol + " from " + file) + : ".") + + (format != null ? "(parsing as '" + format + + "' file)" : ""), oom, Desktop.desktop); } } + @Override public void tabSelectionChanged(int index) { if (index > -1) { alignPanel = (AlignmentPanel) alignPanels.elementAt(index); viewport = alignPanel.av; + avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); } } + @Override public void tabbedPane_mousePressed(MouseEvent e) { if (SwingUtilities.isRightMouseButton(e)) { String reply = JOptionPane.showInternalInputDialog(this, - "Enter View Name", "Edit View Name", + MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"), JOptionPane.QUESTION_MESSAGE); if (reply != null) @@ -4461,10 +5119,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ + @Override protected void extractScores_actionPerformed(ActionEvent e) { ParseProperties pp = new jalview.analysis.ParseProperties( - viewport.alignment); + viewport.getAlignment()); // TODO: verify regex and introduce GUI dialog for version 2.5 // if (pp.getScoresFromDescription("col", "score column ", // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", @@ -4483,6 +5142,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showDbRefs_actionPerformed(ActionEvent e) { viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); @@ -4494,6 +5154,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void showNpFeats_actionPerformed(ActionEvent e) { viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); @@ -4534,20 +5195,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // TODO We probably want to store a sequence database checklist in // preferences and have checkboxes.. rather than individual sources selected // here - JMenu rfetch = new JMenu("Fetch DB References"); - rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences"); + final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references")); + rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); webService.add(rfetch); - JMenuItem fetchr = new JMenuItem("Standard Databases"); - fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources"); + final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(MessageManager.getString("option.trim_retrieved_seqs")); + trimrs.setToolTipText(MessageManager.getString("label.trim_retrieved_sequences")); + trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) { + trimrs.setSelected(trimrs.isSelected()); + Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", Boolean.valueOf(trimrs.isSelected()).toString()); + }; + }); + rfetch.add(trimrs); + JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases")); + fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot")); fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { new jalview.ws.DBRefFetcher(alignPanel.av @@ -4560,62 +5234,192 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); rfetch.add(fetchr); - JMenu dfetch = new JMenu(); - rfetch.add(dfetch); - jalview.ws.SequenceFetcher sf = SequenceFetcher - .getSequenceFetcherSingleton(this); - String[] otherdb = sf.getOrderedSupportedSources(); - // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); - // jalview.util.QuickSort.sort(otherdb, otherdb); - int comp = 0, mcomp = 15; - String mname = null; - if (otherdb != null && otherdb.length > 0) - { - for (int i = 0; i < otherdb.length; i++) + final AlignFrame me = this; + new Thread(new Runnable() + { + @Override + public void run() { - String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); - if (mname == null) - { - mname = "from '" + dbname + "'"; - } - fetchr = new JMenuItem(otherdb[i]); - final String[] dassource = new String[] - { otherdb[i] }; - fetchr.addActionListener(new ActionListener() + final jalview.ws.SequenceFetcher sf = SequenceFetcher + .getSequenceFetcherSingleton(me); + javax.swing.SwingUtilities.invokeLater(new Runnable() { - - public void actionPerformed(ActionEvent e) + @Override + public void run() { - new Thread(new Runnable() + String[] dbclasses = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + List otherdb; + JMenu dfetch = new JMenu(); + JMenu ifetch = new JMenu(); + JMenuItem fetchr = null; + int comp = 0, icomp = 0, mcomp = 15; + String mname = null; + int dbi = 0; + for (String dbclass : dbclasses) { + otherdb = sf.getSourceProxy(dbclass); + // add a single entry for this class, or submenu allowing 'fetch + // all' or pick one + if (otherdb == null || otherdb.size() < 1) + { + continue; + } + // List dbs=otherdb; + // otherdb=new ArrayList(); + // for (DbSourceProxy db:dbs) + // { + // if (!db.isA(DBRefSource.ALIGNMENTDB) + // } + if (mname == null) + { + mname = "From " + dbclass; + } + if (otherdb.size() == 1) + { + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(src.getDbSource()); + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource) + .fetchDBRefs(false); + } + }).start(); + } - public void run() + }); + fetchr.setToolTipText("" + + JvSwingUtils.wrapTooltip("Retrieve from " + + src.getDbName()) + ""); + dfetch.add(fetchr); + comp++; + } + else { - new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, - dassource).fetchDBRefs(false); + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + // fetch all entry + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()})); + fetchr.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource) + .fetchDBRefs(false); + } + }).start(); + } + }); + + fetchr.setToolTipText("" + + JvSwingUtils.wrapTooltip("Retrieve from all " + + otherdb.size() + " sources in " + + src.getDbSource() + "
First is :" + + src.getDbName()) + ""); + dfetch.add(fetchr); + comp++; + // and then build the rest of the individual menus + ifetch = new JMenu("Sources from " + src.getDbSource()); + icomp = 0; + String imname = null; + int i = 0; + for (DbSourceProxy sproxy : otherdb) + { + String dbname = sproxy.getDbName(); + String sname = dbname.length() > 5 ? dbname.substring(0, + 5) + "..." : dbname; + String msname = dbname.length() > 10 ? dbname.substring( + 0, 10) + "..." : dbname; + if (imname == null) + { + imname = "from '" + sname + "'"; + } + fetchr = new JMenuItem(msname); + final DbSourceProxy[] dassrc = + { sproxy }; + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassrc) + .fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("" + + JvSwingUtils.wrapTooltip("Retrieve from " + + dbname) + ""); + ifetch.add(fetchr); + ++i; + if (++icomp >= mcomp || i == (otherdb.size())) + { + ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname)); + dfetch.add(ifetch); + ifetch = new JMenu(); + imname = null; + icomp = 0; + comp++; + } + } + } + ++dbi; + if (comp >= mcomp || dbi >= (dbclasses.length)) + { + dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass)); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; } - }).start(); + } } - }); - fetchr.setToolTipText("Retrieve from " + dbname); - dfetch.add(fetchr); - if (comp++ == mcomp || i == (otherdb.length - 1)) - { - dfetch.setText(mname + " to '" + dbname + "'"); - rfetch.add(dfetch); - dfetch = new JMenu(); - mname = null; - comp = 0; - } } - } + }).start(); + } /** * Left justify the whole alignment. */ + @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -4626,6 +5430,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Right justify the whole alignment. */ + @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -4646,6 +5451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ + @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); @@ -4659,6 +5465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showGroupConsensus_actionPerformed(ActionEvent e) { viewport.setShowGroupConsensus(showGroupConsensus.getState()); @@ -4673,6 +5480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showGroupConservation_actionPerformed(ActionEvent e) { viewport.setShowGroupConservation(showGroupConservation.getState()); @@ -4686,6 +5494,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showConsensusHistogram_actionPerformed(ActionEvent e) { viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); @@ -4699,12 +5508,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { viewport.setShowSequenceLogo(showSequenceLogo.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + @Override + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); @@ -4717,37 +5537,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { - if (viewport.getSelectionGroup() != null) - { - SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( - viewport.getSequenceSelection(), - viewport.getAlignmentView(true).getSequenceStrings( - viewport.getGapCharacter()), - viewport.alignment.getGroups()); - viewport.alignment.deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - // set view properties for each group - for (int g = 0; g < gps.length; g++) - { - gps[g].setShowNonconserved(viewport.getShowUnconserved()); - gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); - viewport.alignment.addGroup(gps[g]); - Color col = new Color((int) (Math.random() * 255), - (int) (Math.random() * 255), (int) (Math.random() * 255)); - col = col.brighter(); - for (Enumeration sq = gps[g].getSequences(null).elements(); sq - .hasMoreElements(); viewport.setSequenceColour( - (SequenceI) sq.nextElement(), col)) - ; - } + if (avc.makeGroupsFromSelection()) { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } } + + @Override + protected void createGroup_actionPerformed(ActionEvent e) + { + if (avc.createGroup()) + { + alignPanel.alignmentChanged(); + } + } + + @Override + protected void unGroup_actionPerformed(ActionEvent e) + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); + } + } + + /** + * make the given alignmentPanel the currently selected tab + * + * @param alignmentPanel + */ + public void setDisplayedView(AlignmentPanel alignmentPanel) + { + if (!viewport.getSequenceSetId().equals( + alignmentPanel.av.getSequenceSetId())) + { + throw new Error( + "Implementation error: cannot show a view from another alignment in an AlignFrame."); + } + if (tabbedPane != null + & alignPanels.indexOf(alignmentPanel) != tabbedPane + .getSelectedIndex()) + { + tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); + } + } } class PrintThread extends Thread @@ -4761,6 +5598,7 @@ class PrintThread extends Thread static PageFormat pf; + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob();