X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d992233ce52d93580dd71bbe150e21d8cddca11b;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=b0d30a28da9df4794050df0601c0588a08364701;hpb=1b85d0acd9a09b646ac2dd6f1ea6db5db6f3731d;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index b0d30a2..d992233 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,44 +1,136 @@ /* - * 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 2.8.1) + * 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. - * + * * 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 . + * 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 +139,7 @@ import jalview.ws.jws2.Jws2Discoverer; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator + IProgressIndicator, AlignViewControllerGuiI { /** DOCUMENT ME!! */ @@ -59,6 +151,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public AlignmentPanel alignPanel; AlignViewport viewport; + + public AlignViewControllerI avc; + Vector alignPanels = new Vector(); @@ -202,7 +297,8 @@ 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 +324,12 @@ 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 +341,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } addKeyListener(); - + } /** @@ -267,6 +364,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -322,6 +420,17 @@ 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 +487,7 @@ 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 +544,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void keyReleased(KeyEvent evt) { switch (evt.getKeyCode()) @@ -459,6 +568,7 @@ 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 +598,13 @@ 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 +630,7 @@ 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 +639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { System.err @@ -540,6 +653,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -550,9 +664,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }; }); // Finally, build the menu once to get current service state - javax.swing.SwingUtilities.invokeLater(new Runnable() { - public void run() { BuildWebServiceMenu();} - }); + new Thread(new Runnable() + { + @Override + public void run() + { + BuildWebServiceMenu(); + } + }).start(); } public void setGUINucleotide(boolean nucleotide) @@ -561,11 +680,14 @@ 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); + // } } /** @@ -587,7 +709,7 @@ 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()); @@ -602,25 +724,33 @@ 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; /* @@ -628,6 +758,7 @@ 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) @@ -671,10 +802,11 @@ 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) { @@ -687,16 +819,19 @@ 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); - us.setProgressBar("Cancelled " - + ((JLabel) progressPanel.getComponent(0)).getText(), id); + us.setProgressBar( + "Cancelled " + + ((JLabel) progressPanel.getComponent(0)) + .getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -707,6 +842,7 @@ 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) @@ -716,6 +852,10 @@ 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 */ @@ -729,20 +869,25 @@ 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")) @@ -751,6 +896,7 @@ 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 @@ -788,6 +934,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { nfs.frame.setBounds(fspos); @@ -801,16 +948,19 @@ 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 @@ -832,17 +982,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void saveAs_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -852,8 +1003,8 @@ 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; } @@ -889,8 +1040,8 @@ 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 @@ -906,14 +1057,13 @@ 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); @@ -924,9 +1074,10 @@ 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) { @@ -942,8 +1093,7 @@ 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; @@ -954,8 +1104,8 @@ 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; @@ -982,18 +1132,18 @@ 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); @@ -1006,14 +1156,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - try { + try + { cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.alignment, omitHidden, viewport.colSel)); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); + viewport.getAlignment(), omitHidden, + viewport.getColumnSelection())); + Desktop.addInternalFrame(cap, + MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); } catch (OutOfMemoryError oom) { - new OOMWarning("Outputting alignment as "+e.getActionCommand(),oom); + new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); cap.dispose(); } @@ -1025,11 +1177,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas - .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer()); + new HTMLOutput(alignPanel, + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) @@ -1043,6 +1196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void createPNG(File f) { alignPanel.makePNG(f); @@ -1054,11 +1208,13 @@ 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(); @@ -1071,6 +1227,7 @@ 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 @@ -1078,28 +1235,31 @@ 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); + 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")); + 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); @@ -1107,7 +1267,7 @@ 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); } } @@ -1118,6 +1278,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) @@ -1198,12 +1359,12 @@ 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) @@ -1211,12 +1372,12 @@ 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")); } } @@ -1227,9 +1388,11 @@ 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); } } @@ -1252,7 +1415,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport != null) { return new AlignmentI[] - { viewport.alignment }; + { viewport.getAlignment() }; } return null; } @@ -1263,6 +1426,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) @@ -1276,11 +1440,19 @@ 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()); } } @@ -1290,6 +1462,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { if (viewport.redoList.size() < 1) @@ -1306,11 +1479,20 @@ 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()); } } @@ -1332,7 +1514,7 @@ 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; @@ -1347,7 +1529,7 @@ 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; @@ -1370,69 +1552,25 @@ 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) @@ -1442,15 +1580,13 @@ 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++) @@ -1509,6 +1645,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed(ActionEvent e) { System.gc(); @@ -1521,7 +1658,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { omitHidden = viewport.getViewAsString(true); } @@ -1536,11 +1673,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.gui.Desktop.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! - Toolkit.getDefaultToolkit().getSystemClipboard().setContents( - new StringSelection(""), null); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(""), null); - Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(ss, Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -1548,7 +1685,7 @@ 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 @@ -1567,8 +1704,8 @@ 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()})); } /** @@ -1577,6 +1714,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); @@ -1588,6 +1726,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); @@ -1656,6 +1795,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } int alwidth = 0; + ArrayList newGraphGroups = new ArrayList(); + int fgroup = -1; if (newAlignment) { @@ -1723,6 +1864,17 @@ 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. @@ -1733,6 +1885,22 @@ 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); } @@ -1752,11 +1920,31 @@ 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 @@ -1796,6 +1984,9 @@ 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); } } @@ -1803,8 +1994,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, alignment - .getSequences()); + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); + if (alignPanels != null) + { + for (AlignmentPanel ap : ((Vector) alignPanels)) + { + ap.validateAnnotationDimensions(false); + } + } + else + { + alignPanel.validateAnnotationDimensions(false); + } } else @@ -1861,13 +2063,66 @@ 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); @@ -1880,6 +2135,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void delete_actionPerformed(ActionEvent evt) { @@ -1898,7 +2154,7 @@ 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); @@ -1915,11 +2171,11 @@ 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()); @@ -1940,14 +2196,14 @@ 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); + } } /** @@ -1956,6 +2212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); @@ -1965,7 +2222,7 @@ 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); @@ -1978,6 +2235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) @@ -1992,6 +2250,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } /** @@ -2000,6 +2259,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2017,14 +2277,16 @@ 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(); } /** @@ -2033,6 +2295,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); @@ -2044,6 +2307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); @@ -2069,11 +2333,11 @@ 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; @@ -2081,32 +2345,28 @@ 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); } } @@ -2121,34 +2381,35 @@ 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()); @@ -2167,30 +2428,31 @@ 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); @@ -2205,9 +2467,10 @@ 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()); } @@ -2228,15 +2491,66 @@ 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; @@ -2249,8 +2563,19 @@ 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(); @@ -2268,25 +2593,29 @@ 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); @@ -2298,6 +2627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); @@ -2309,6 +2639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); @@ -2318,12 +2649,14 @@ 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(); @@ -2335,6 +2668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) @@ -2350,6 +2684,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); @@ -2362,6 +2697,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { scaleAbove.setVisible(wrapMenuItem.isSelected()); @@ -2371,17 +2707,20 @@ 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(); @@ -2404,8 +2743,9 @@ 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())) { @@ -2428,12 +2768,13 @@ 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); } @@ -2441,12 +2782,12 @@ 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) @@ -2463,6 +2804,7 @@ 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); @@ -2475,6 +2817,7 @@ 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(); @@ -2491,6 +2834,7 @@ 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(); @@ -2498,12 +2842,14 @@ 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()); @@ -2516,6 +2862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); @@ -2528,6 +2875,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); @@ -2540,6 +2888,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); @@ -2552,6 +2901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); @@ -2564,6 +2914,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); @@ -2576,6 +2927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); @@ -2584,6 +2936,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureSettings featureSettings; + @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) @@ -2606,6 +2959,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); @@ -2622,6 +2976,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight @@ -2645,73 +3000,25 @@ 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); } /** @@ -2720,6 +3027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) @@ -2730,23 +3038,24 @@ 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(), frame - .getWidth(), frame.getHeight()); + 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() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - alignPanel.setOverviewPanel(null); - }; - }); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + alignPanel.setOverviewPanel(null); + }; + }); alignPanel.setOverviewPanel(overview); } + @Override public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); @@ -2758,6 +3067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); @@ -2769,11 +3079,11 @@ 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())); } /** @@ -2782,6 +3092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); @@ -2793,6 +3104,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); @@ -2804,6 +3116,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); @@ -2815,6 +3128,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); @@ -2826,6 +3140,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); @@ -2837,6 +3152,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); @@ -2848,6 +3164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); @@ -2859,22 +3176,43 @@ 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()); @@ -2888,6 +3226,7 @@ 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) @@ -2896,10 +3235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - - viewport.setGlobalColourScheme(cs); } else { @@ -2909,13 +3245,13 @@ 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); + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); @@ -2927,19 +3263,16 @@ 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; @@ -2948,8 +3281,8 @@ 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) { @@ -2959,7 +3292,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + sg.cs = cs.getClass().newInstance(); } catch (Exception ex) { } @@ -2971,9 +3304,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(viewport.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); } else { @@ -2983,11 +3316,11 @@ 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 @@ -3011,13 +3344,14 @@ 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"); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } @@ -3028,13 +3362,14 @@ 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(); } } @@ -3045,6 +3380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -3063,6 +3399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -3081,9 +3418,10 @@ 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); } @@ -3122,18 +3460,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - radioItem - .removeActionListener(radioItem.getActionListeners()[0]); + radioItem.removeActionListener(radioItem.getActionListeners()[0]); 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) { @@ -3145,6 +3483,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3156,6 +3495,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3174,6 +3514,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); @@ -3185,6 +3526,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); @@ -3196,13 +3538,14 @@ 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); } @@ -3212,11 +3555,13 @@ 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); } @@ -3226,12 +3571,13 @@ 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); } @@ -3241,12 +3587,13 @@ 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); } @@ -3257,6 +3604,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); @@ -3268,20 +3616,21 @@ 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); } } @@ -3291,6 +3640,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void PCAMenuItem_actionPerformed(ActionEvent e) { if (((viewport.getSelectionGroup() != null) @@ -3299,9 +3649,8 @@ 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; @@ -3310,6 +3659,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new PCAPanel(alignPanel); } + @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); @@ -3320,12 +3670,25 @@ 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"); @@ -3337,6 +3700,7 @@ 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"); @@ -3348,6 +3712,7 @@ 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"); @@ -3359,6 +3724,7 @@ 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"); @@ -3378,34 +3744,31 @@ 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; @@ -3418,21 +3781,19 @@ 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; } @@ -3467,6 +3828,7 @@ 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(); @@ -3475,8 +3837,8 @@ 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); } @@ -3499,13 +3861,14 @@ 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()); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } }); @@ -3523,23 +3886,23 @@ 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) @@ -3551,13 +3914,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Enumeration labels = scoreSorts.keys(); while (labels.hasMoreElements()) { - addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels - .nextElement()); + addSortByAnnotScoreMenuItem(sortByAnnotScore, + (String) labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); - _annotationScoreVectorHash = viewport.alignment + _annotationScoreVectorHash = viewport.getAlignment() .getAlignmentAnnotation().hashCode(); } } @@ -3574,8 +3937,38 @@ 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 @@ -3602,21 +3995,17 @@ 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); } }); @@ -3624,6 +4013,19 @@ 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. @@ -3685,9 +4087,9 @@ 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] }); @@ -3704,14 +4106,15 @@ 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")); + 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); @@ -3727,18 +4130,24 @@ 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", + JOptionPane.showMessageDialog(Desktop.desktop, + 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); @@ -3825,127 +4234,159 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } ; } + final AlignFrame me = this; buildingMenu = true; - 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. - Vector wsmenu = new Vector(); - final IProgressIndicator af = this; - 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, this); - - } - 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, this); - } - 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, this); + // 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); + } + ; } - } - } - } - 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 - { - this.webService.add(this.webServiceNoServices); - } - } catch (Exception e) - { - } - ; - buildingMenu = false; - } + }).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); } /** @@ -3955,10 +4396,30 @@ 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); } } @@ -4029,6 +4490,7 @@ 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 @@ -4044,8 +4506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception e) { jalview.bin.Cache.log - .warn( - "canTranslate threw an exception - please report to help@jalview.org", + .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } @@ -4063,13 +4524,14 @@ 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 @@ -4135,18 +4597,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // old way try { - return (jalview.analysis.Dna.canTranslate(selection, viewport - .getViewAsVisibleContigs(true))); + return (jalview.analysis.Dna.canTranslate(selection, + viewport.getViewAsVisibleContigs(true))); } catch (Exception e) { jalview.bin.Cache.log - .warn( - "canTranslate threw an exception - please report to help@jalview.org", + .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } } + @Override public void showProducts_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4169,17 +4631,18 @@ 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) { // ///////////////////////////// @@ -4192,26 +4655,32 @@ 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); } } @@ -4230,9 +4699,10 @@ 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(); @@ -4257,22 +4727,27 @@ 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(); @@ -4327,10 +4802,124 @@ 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) { @@ -4348,47 +4937,116 @@ 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 + { + 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) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile(file, - protocol); - new JnetAnnotationMaker().add_annotation(predictions, viewport - .getAlignment(), 0, false); - isAnnotation = true; + 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); + } } } } @@ -4403,25 +5061,44 @@ 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) @@ -4440,10 +5117,11 @@ 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*)", @@ -4462,6 +5140,7 @@ 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()); @@ -4473,6 +5152,7 @@ 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()); @@ -4513,22 +5193,33 @@ 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 @@ -4541,62 +5232,192 @@ 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) + final jalview.ws.SequenceFetcher sf = SequenceFetcher + .getSequenceFetcherSingleton(me); + javax.swing.SwingUtilities.invokeLater(new Runnable() { - mname = "from '" + dbname + "'"; - } - fetchr = new JMenuItem(otherdb[i]); - final String[] dassource = new String[] - { otherdb[i] }; - fetchr.addActionListener(new ActionListener() - { - - 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(); + } + + }); + fetchr.setToolTipText("" + + JvSwingUtils.wrapTooltip("Retrieve from " + + src.getDbName()) + ""); + dfetch.add(fetchr); + comp++; + } + else + { + 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(); + } - public void run() + }); + 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)) { - new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, - dassource).fetchDBRefs(false); + 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(); @@ -4607,6 +5428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Right justify the whole alignment. */ + @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -4627,6 +5449,7 @@ 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()); @@ -4640,6 +5463,7 @@ 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()); @@ -4654,6 +5478,7 @@ 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()); @@ -4667,6 +5492,7 @@ 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()); @@ -4680,12 +5506,23 @@ 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()); @@ -4698,36 +5535,54 @@ 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 @@ -4741,6 +5596,7 @@ class PrintThread extends Thread static PageFormat pf; + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob();