X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=216db0e2ba9d5e42084ea191ed0ff15cdc1d8a41;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=b61d44b7a319ae3915b0a831a796965a9e354c0a;hpb=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index b61d44b..216db0e --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,32 +1,41 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import 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.AlignmentViewPanel; +import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; import jalview.commands.OrderCommand; import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; @@ -55,6 +64,7 @@ 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; @@ -66,18 +76,21 @@ 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.ws.WSMenuEntryProviderI; +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.Color; import java.awt.Component; import java.awt.GridLayout; import java.awt.Rectangle; @@ -103,11 +116,14 @@ import java.beans.PropertyChangeEvent; import java.io.File; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; 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; @@ -128,7 +144,7 @@ import javax.swing.SwingUtilities; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator + IProgressIndicator, AlignViewControllerGuiI { /** DOCUMENT ME!! */ @@ -141,6 +157,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + public AlignViewControllerI avc; + Vector alignPanels = new Vector(); /** @@ -248,21 +266,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); - viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); - - alignPanel = new AlignmentPanel(this, viewport); if (al.getDataset() == null) { al.setDataset(null); } + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); + + alignPanel = new AlignmentPanel(this, viewport); + + addAlignmentPanel(alignPanel, true); init(); } /** - * Make a new AlignFrame from exisiting alignmentPanels + * Make a new AlignFrame from existing alignmentPanels * * @param ap * AlignmentPanel @@ -283,7 +303,9 @@ 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); @@ -309,11 +331,13 @@ 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); @@ -348,6 +372,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -355,7 +380,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) + { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -367,32 +394,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(false); + } if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(0, 1); + } break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(true); + } if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(0, -1); + } break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: @@ -402,21 +445,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || evt.isShiftDown() || evt.isAltDown()); } 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_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: @@ -474,8 +513,9 @@ 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; @@ -487,14 +527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F1: try { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, - "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); - - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setCurrentID("home"); - hb.setDisplayed(true); + Help.showHelpWindow(); } catch (Exception ex) { ex.printStackTrace(); @@ -532,20 +565,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void keyReleased(KeyEvent evt) { switch (evt.getKeyCode()) { case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; } } @@ -555,6 +593,8 @@ 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); @@ -584,9 +624,9 @@ 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); @@ -616,6 +656,7 @@ 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."); @@ -624,6 +665,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { System.err @@ -637,6 +679,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -649,6 +692,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Finally, build the menu once to get current service state new Thread(new Runnable() { + @Override public void run() { BuildWebServiceMenu(); @@ -662,11 +706,14 @@ 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); + // } } /** @@ -688,7 +735,7 @@ 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()); @@ -701,30 +748,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, scaleLeft.setVisible(av.wrapAlignment); scaleRight.setVisible(av.wrapAlignment); annotationPanelMenuItem.setState(av.showAnnotation); + /* + * Show/hide annotations only enabled if annotation panel is shown + */ + showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); 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; /* @@ -732,6 +791,7 @@ 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) @@ -779,30 +839,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, validate(); } + @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { - throw new Error( - "call setProgressBar before registering the progress bar's handler."); + throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); 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(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -813,6 +872,7 @@ 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) @@ -822,6 +882,12 @@ 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 */ @@ -835,20 +901,25 @@ 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")) @@ -857,6 +928,7 @@ 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 @@ -894,6 +966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { nfs.frame.setBounds(fspos); @@ -907,16 +980,19 @@ 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 @@ -938,6 +1014,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void saveAs_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -947,8 +1024,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -957,9 +1034,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat = chooser.getSelectedFormat(); if (currentFileFormat == null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "You must select a file format before saving!", - "File format not specified", JOptionPane.WARNING_MESSAGE); + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.select_file_format_before_saving"), + MessageManager + .getString("label.file_format_not_specified"), + JOptionPane.WARNING_MESSAGE); value = chooser.showSaveDialog(this); return; } @@ -995,8 +1077,9 @@ 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 @@ -1012,14 +1095,15 @@ 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); @@ -1030,9 +1114,10 @@ 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) { @@ -1048,8 +1133,10 @@ 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; @@ -1060,8 +1147,11 @@ 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; @@ -1088,18 +1178,20 @@ 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); @@ -1115,9 +1207,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -1132,6 +1226,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { new HTMLOutput(alignPanel, @@ -1150,6 +1245,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void createPNG(File f) { alignPanel.makePNG(f); @@ -1161,11 +1257,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void createEPS(File f) { alignPanel.makeEPS(f); } + public void createSVG(File f) + { + alignPanel.makeSVG(f); + } + @Override public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -1178,6 +1280,7 @@ 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 @@ -1185,29 +1288,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, thread.start(); } + @Override public void exportFeatures_actionPerformed(ActionEvent e) { new AnnotationExporter().exportFeatures(alignPanel); } + @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations( - alignPanel, - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + new AnnotationExporter().exportAnnotations(alignPanel, + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), ((Alignment) viewport + .getAlignment()).alignmentProperties); } + @Override public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Load Jalview Annotations or Features File"); - chooser.setToolTipText("Load Jalview Annotations / Features file"); + chooser.setDialogTitle(MessageManager + .getString("label.load_jalview_annotations")); + chooser.setToolTipText(MessageManager + .getString("label.load_jalview_annotations")); int value = chooser.showOpenDialog(null); @@ -1226,6 +1333,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) @@ -1305,26 +1413,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setText("Undo " + command.getDescription()); + CommandI command = viewport.historyList.peek(); + 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) { redoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setText("Redo " + command.getDescription()); + CommandI command = viewport.redoList.peek(); + redoMenuItem.setText(MessageManager.formatMessage( + "label.redo_command", new String[] + { command.getDescription() })); } else { redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + redoMenuItem.setText(MessageManager.getString("action.redo")); } } @@ -1335,9 +1447,11 @@ 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); } } @@ -1360,7 +1474,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport != null) { return new AlignmentI[] - { viewport.alignment }; + { viewport.getAlignment() }; } return null; } @@ -1371,11 +1485,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) + { return; - CommandI command = (CommandI) viewport.historyList.pop(); + } + CommandI command = viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); @@ -1384,11 +1501,19 @@ 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()); } } @@ -1398,6 +1523,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { if (viewport.redoList.size() < 1) @@ -1405,7 +1531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - CommandI command = (CommandI) viewport.redoList.pop(); + CommandI command = viewport.redoList.pop(); viewport.historyList.push(command); command.doCommand(getViewAlignments()); @@ -1414,11 +1540,20 @@ 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()); } } @@ -1440,7 +1575,7 @@ 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; @@ -1455,7 +1590,7 @@ 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; @@ -1478,69 +1613,25 @@ 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) @@ -1550,42 +1641,56 @@ 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++) + { seqs2[i] = (SequenceI) invertGroup.elementAt(i); + } SlideSequencesCommand ssc; if (right) + { ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) @@ -1606,7 +1711,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } @@ -1617,6 +1724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed(ActionEvent e) { System.gc(); @@ -1629,7 +1737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { omitHidden = viewport.getViewAsString(true); } @@ -1656,7 +1764,7 @@ 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 @@ -1675,8 +1783,10 @@ 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() })); } /** @@ -1685,6 +1795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); @@ -1696,6 +1807,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); @@ -1764,6 +1876,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } int alwidth = 0; + ArrayList newGraphGroups = new ArrayList(); + int fgroup = -1; if (newAlignment) { @@ -1831,6 +1945,17 @@ 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. @@ -1841,6 +1966,22 @@ 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); } @@ -1852,7 +1993,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // ///// // ADD HISTORY ITEM // - addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences @@ -1860,11 +2003,31 @@ 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 @@ -1887,7 +2050,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) + { continue; + } for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) @@ -1904,6 +2069,9 @@ 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); } } @@ -1913,6 +2081,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.firePropertyChange("alignment", null, alignment.getSequences()); + if (alignPanels != null) + { + for (AlignmentPanel ap : ((Vector) alignPanels)) + { + ap.validateAnnotationDimensions(false); + } + } + else + { + alignPanel.validateAnnotationDimensions(false); + } } else @@ -1970,12 +2149,67 @@ 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); @@ -1988,6 +2222,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void delete_actionPerformed(ActionEvent evt) { @@ -1997,17 +2232,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector seqs = new Vector(); + List seqs = new ArrayList(sg.getSize()); SequenceI seq; for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); - seqs.addElement(seq); + seqs.add(seq); } - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) + // If the cut affects all sequences, warn, remove highlighted columns + if (sg.getSize() == viewport.getAlignment().getHeight()) { + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); + + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } @@ -2015,19 +2260,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] cut = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { - cut[i] = (SequenceI) seqs.elementAt(i); + cut[i] = seqs.get(i); } /* * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, - sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); viewport.setSelectionGroup(null); viewport.sendSelection(); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2048,14 +2294,15 @@ 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); + } } /** @@ -2064,6 +2311,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); @@ -2073,7 +2321,7 @@ 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); @@ -2086,6 +2334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) @@ -2109,6 +2358,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2130,6 +2380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.sendSelection(); } + @Override public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); @@ -2143,6 +2394,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); @@ -2154,6 +2406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); @@ -2179,11 +2432,11 @@ 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; @@ -2191,32 +2444,30 @@ 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); } } @@ -2231,34 +2482,37 @@ 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()); @@ -2277,30 +2531,31 @@ 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); @@ -2315,9 +2570,10 @@ 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()); } @@ -2338,11 +2594,13 @@ 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); @@ -2385,13 +2643,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!copyAnnotation) { // just remove all the current annotation except for the automatic stuff - newap.av.alignment.deleteAllGroups(); - for (AlignmentAnnotation alan : newap.av.alignment + newap.av.getAlignment().deleteAllGroups(); + for (AlignmentAnnotation alan : newap.av.getAlignment() .getAlignmentAnnotation()) { if (!alan.autoCalculated) { - newap.av.alignment.deleteAnnotation(alan); + newap.av.getAlignment().deleteAnnotation(alan); } ; } @@ -2413,7 +2671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { - viewTitle = "View"; + viewTitle = MessageManager.getString("action.view"); addFirstIndex = true; } else @@ -2444,6 +2702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.viewName = newViewName; addAlignmentPanel(newap, true); + newap.alignmentChanged(); if (alignPanels.size() == 2) { @@ -2453,11 +2712,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return newap; } + @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } + @Override public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); @@ -2469,6 +2730,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); @@ -2480,6 +2742,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); @@ -2489,12 +2752,14 @@ 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(); @@ -2506,6 +2771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) @@ -2521,6 +2787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); @@ -2533,6 +2800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { scaleAbove.setVisible(wrapMenuItem.isSelected()); @@ -2542,17 +2810,20 @@ 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(); @@ -2575,8 +2846,9 @@ 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())) { @@ -2599,12 +2871,13 @@ 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); } @@ -2612,12 +2885,12 @@ 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) @@ -2634,6 +2907,7 @@ 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); @@ -2646,6 +2920,7 @@ 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(); @@ -2662,6 +2937,7 @@ 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(); @@ -2669,12 +2945,14 @@ 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()); @@ -2687,6 +2965,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); @@ -2699,6 +2978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); @@ -2711,6 +2991,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); @@ -2723,6 +3004,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); @@ -2735,6 +3017,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); @@ -2747,6 +3030,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); @@ -2755,6 +3039,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureSettings featureSettings; + @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) @@ -2777,6 +3062,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); @@ -2793,6 +3079,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight @@ -2811,29 +3098,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Action on toggle of the 'Show annotations' menu item. This shows or hides + * the annotations panel as a whole. + * + * The options to show/hide all annotations should be enabled when the panel + * is shown, and disabled when the panel is hidden. * * @param e - * DOCUMENT ME! */ + @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); + final boolean setVisible = annotationPanelMenuItem.isSelected(); + viewport.setShowAnnotation(setVisible); + alignPanel.setAnnotationVisible(setVisible); + this.showAllSeqAnnotations.setEnabled(setVisible); + this.hideAllSeqAnnotations.setEnabled(setVisible); + this.showAllAlAnnotations.setEnabled(setVisible); + this.hideAllAlAnnotations.setEnabled(setVisible); } + @Override public void alignmentProperties() { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); - StringBuffer contents = new AlignmentProperties(viewport.alignment) + StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); - editPane.setText("" + contents.toString() + ""); + 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); } /** @@ -2842,6 +3142,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) @@ -2852,12 +3153,14 @@ 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() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -2868,6 +3171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(overview); } + @Override public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); @@ -2879,6 +3183,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); @@ -2890,11 +3195,11 @@ 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())); } /** @@ -2903,6 +3208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); @@ -2914,6 +3220,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); @@ -2925,6 +3232,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); @@ -2936,6 +3244,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); @@ -2947,6 +3256,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); @@ -2958,6 +3268,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); @@ -2969,6 +3280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); @@ -2980,26 +3292,31 @@ 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.alignment.getAlignmentAnnotation()[0])); - } - */ + * 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); @@ -3011,6 +3328,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); @@ -3024,6 +3342,7 @@ 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) @@ -3032,10 +3351,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - - viewport.setGlobalColourScheme(cs); } else { @@ -3045,13 +3361,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getConservationSelected()) { - Alignment al = (Alignment) viewport.alignment; + Alignment al = (Alignment) viewport.getAlignment(); Conservation c = new Conservation("All", ResidueProperties.propHash, 3, al.getSequences(), 0, al.getWidth() - 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); @@ -3063,19 +3379,16 @@ 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; @@ -3084,9 +3397,8 @@ 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) { @@ -3096,7 +3408,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + sg.cs = cs.getClass().newInstance(); } catch (Exception ex) { } @@ -3109,7 +3421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), + sg.getSequences(viewport.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); } else @@ -3120,11 +3432,11 @@ 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 @@ -3148,10 +3460,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); @@ -3165,13 +3478,14 @@ 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(); } } @@ -3182,6 +3496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -3200,6 +3515,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -3218,9 +3534,11 @@ 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); } @@ -3259,6 +3577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() @@ -3268,8 +3587,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, - "Remove from default list?", - "Remove user defined colour", + MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { @@ -3281,6 +3602,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3292,6 +3614,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3310,6 +3633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); @@ -3321,6 +3645,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); @@ -3332,13 +3657,14 @@ 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); } @@ -3348,11 +3674,13 @@ 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); } @@ -3362,12 +3690,13 @@ 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); } @@ -3377,12 +3706,13 @@ 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); } @@ -3393,6 +3723,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); @@ -3404,20 +3735,24 @@ 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", + JOptionPane.showInternalMessageDialog(this, 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); } } @@ -3427,6 +3762,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override public void PCAMenuItem_actionPerformed(ActionEvent e) { if (((viewport.getSelectionGroup() != null) @@ -3434,11 +3770,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { - JOptionPane.showInternalMessageDialog(this, - "Principal component analysis must take\n" - + "at least 4 input sequences.", - "Sequence selection insufficient", - JOptionPane.WARNING_MESSAGE); + JOptionPane + .showInternalMessageDialog( + this, + MessageManager + .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), + MessageManager + .getString("label.sequence_selection_insufficient"), + JOptionPane.WARNING_MESSAGE); return; } @@ -3446,6 +3785,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new PCAPanel(alignPanel); } + @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); @@ -3455,6 +3795,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getAlignment().getSequences()); } } + + @Override public void sortByTreeOption_actionPerformed(ActionEvent e) { viewport.sortByTree = sortByTree.isSelected(); @@ -3465,12 +3807,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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"); @@ -3482,6 +3826,7 @@ 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"); @@ -3493,6 +3838,7 @@ 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"); @@ -3504,6 +3850,7 @@ 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"); @@ -3523,34 +3870,36 @@ 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; @@ -3563,21 +3912,21 @@ 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; } @@ -3608,10 +3957,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem("by " + title); + final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title})); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3620,8 +3970,8 @@ 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); } @@ -3644,13 +3994,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } }); @@ -3668,23 +4019,23 @@ 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) @@ -3702,7 +4053,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); - _annotationScoreVectorHash = viewport.alignment + _annotationScoreVectorHash = viewport.getAlignment() .getAlignmentAnnotation().hashCode(); } } @@ -3719,8 +4070,41 @@ 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + NewTreePanel(type, (String) pwtype, title); + } + }); + calculateTree.add(tm); + } + + } + } sortByTreeMenu.removeAll(); Vector comps = (Vector) PaintRefresher.components.get(viewport @@ -3752,11 +4136,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { tp.sortByTree_actionPerformed(null); addHistoryItem(tp.sortAlignmentIn(alignPanel)); - + } }); @@ -3771,7 +4156,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (undoname != null) { addHistoryItem(new OrderCommand(undoname, oldOrder, - viewport.alignment)); + viewport.getAlignment())); } alignPanel.paintAlignment(true); return true; @@ -3801,16 +4186,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ msa = viewport.getAlignmentView(true); } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() == 1) + { + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); + if (option == JOptionPane.OK_OPTION) + { + msa = viewport.getAlignmentView(false); + } + } else { - /* - * Vector seqs = viewport.getAlignment().getSequences(); - * - * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * - * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) - * seqs.elementAt(i); } } - */ msa = viewport.getAlignmentView(false); } return msa; @@ -3838,9 +4227,9 @@ 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] }); @@ -3857,14 +4246,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param e * DOCUMENT ME! */ + @Override protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Select a newick-like tree file"); - chooser.setToolTipText("Load a tree file"); + chooser.setDialogTitle(MessageManager + .getString("label.select_newick_like_tree_file")); + chooser.setToolTipText(MessageManager.getString("label.load_tree_file")); int value = chooser.showOpenDialog(null); @@ -3879,19 +4270,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { - JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - "Problem reading tree file", JOptionPane.WARNING_MESSAGE); + JOptionPane + .showMessageDialog( + Desktop.desktop, + ex.getMessage(), + 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); @@ -3982,8 +4385,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, buildingMenu = true; new Thread(new Runnable() { + @Override public void run() { + final List legacyItems = new ArrayList(); try { System.err.println("Building ws menu again " @@ -3998,45 +4403,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // TODO: group services by location as well as function and/or // introduce // object broker mechanism. - final Vector wsmenu = new Vector(); + final Vector wsmenu = new Vector(); final IProgressIndicator af = me; final JMenu msawsmenu = new JMenu("Alignment"); final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); - final JMenu seqsrchmenu = new JMenu( - "Sequence Database Search"); - final JMenu analymenu = new JMenu( - "Analysis"); - // JAL-940 - only show secondary structure prediction services from the legacy server + final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); + final JMenu analymenu = new JMenu("Analysis"); + final JMenu dismenu = new JMenu("Protein Disorder"); + // final JMenu msawsmenu = new + // JMenu(MessageManager.getString("label.alignment")); + // final JMenu secstrmenu = new + // JMenu(MessageManager.getString("label.secondary_structure_prediction")); + // final JMenu seqsrchmenu = new + // JMenu(MessageManager.getString("label.sequence_database_search")); + // final JMenu analymenu = new + // JMenu(MessageManager.getString("label.analysis")); + // final JMenu dismenu = new + // JMenu(MessageManager.getString("label.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)) + // && + Discoverer.services != null && (Discoverer.services.size() > 0)) { // TODO: refactor to allow list of AbstractName/Handler bindings to // be // stored or retrieved from elsewhere - Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS"); + // No MSAWS used any more: + // Vector msaws = null; // (Vector) + // Discoverer.services.get("MsaWS"); Vector secstrpr = (Vector) Discoverer.services .get("SecStrPred"); - Vector seqsrch = null; // (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) - { - // Add any Multiple Sequence Alignment Services - for (int i = 0, j = msaws.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(msawsmenu, me); - - } - } if (secstrpr != null) { // Add any secondary structure prediction services @@ -4046,44 +4444,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .get(i); jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); + int p = secstrmenu.getItemCount(); impl.attachWSMenuEntry(secstrmenu, me); - } - } - if (seqsrch != null) - { - // Add any sequence search services - for (int i = 0, j = seqsrch.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch - .elementAt(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(seqsrchmenu, me); + int q = secstrmenu.getItemCount(); + for (int litm = p; litm < q; litm++) + { + legacyItems.add(secstrmenu.getItem(litm)); + } } } } - // TODO: move into separate menu builder class. - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) - { - Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) - { - jws2servs.attachWSMenuEntry(msawsmenu, me); - } - } - } - // Add all submenus in the order they should appear on the web services menu + // Add all submenus in the order they should appear on the web + // services menu wsmenu.add(msawsmenu); wsmenu.add(secstrmenu); + wsmenu.add(dismenu); wsmenu.add(analymenu); // No search services yet // wsmenu.add(seqsrchmenu); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { try @@ -4094,17 +4477,62 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { for (int i = 0, j = wsmenu.size(); i < j; i++) { - webService.add((JMenu) wsmenu.get(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); } ; } @@ -4120,7 +4548,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } - /** * construct any groupURL type service menu entries. * @@ -4135,8 +4562,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { * * @Override public void actionPerformed(ActionEvent e) { - * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment, - * af.viewport.colSel, af.viewport.selectionGroup); } + * jalview.datamodel.AlignmentView + * .testSelectionViews(af.viewport.getAlignment(), + * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } * * }); webService.add(testAlView); */ @@ -4144,15 +4572,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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()) { - client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this); - } - if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + 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); } } @@ -4223,6 +4649,7 @@ 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 @@ -4256,13 +4683,14 @@ 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); + ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime); try { - Alignment ds = ths.getViewport().alignment.getDataset(); // update + Alignment ds = ths.getViewport().getAlignment().getDataset(); // update // our local // dataset // reference @@ -4277,7 +4705,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) + { ds.addSequence(sprods[s].getDatasetSequence()); + } sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); @@ -4313,7 +4743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.bin.Cache.log.error("Error when finding crossreferences", e); } - ths.setProgressBar("Finished searching for sequences from " + fsrc, + ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}), sttime); } @@ -4339,6 +4769,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void showProducts_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4361,17 +4792,21 @@ 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(), - DEFAULT_WIDTH, DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, MessageManager.formatMessage( + "label.translation_of_params", new String[] + { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } + @Override public void showTranslation_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4384,27 +4819,42 @@ 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(), - DEFAULT_WIDTH, DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, MessageManager.formatMessage( + "label.translation_of_params", new String[] + { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } @@ -4422,11 +4872,10 @@ 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, jalview.bin.Cache.getDefault( - "RELAXEDSEQIDMATCHING", 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(); @@ -4451,22 +4900,27 @@ 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(); @@ -4552,7 +5006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int l = 0, c = pdbfn.indexOf("."); while (mtch == null && c != -1) { - do + do { l = c; } while ((c = pdbfn.indexOf(".", l)) > l); @@ -4593,10 +5047,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || JOptionPane .showConfirmDialog( this, - "Do you want to automatically associate the " - + filesmatched.size() - + " PDB files with sequences in the alignment that have the same name ?", - "Automatically Associate PDB files by name", + 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) { @@ -4605,18 +5065,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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) + for (SequenceI toassoc : (SequenceI[]) fm[2]) { - System.err - .println("Associated file : " + ((String) fm[0]) - + " with " - + toassoc.getDisplayId(true)); - assocfiles++; - } + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq((String) fm[0], + (String) fm[1], toassoc, false, + Desktop.instance); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } } alignPanel.paintAlignment(true); } @@ -4629,10 +5090,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane .showConfirmDialog( this, - "Do you want to ignore the " - + filesnotmatched.size() - + " files whose names did not match any sequence IDs ?", - "Ignore unmatched dropped files ?", + ""+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; @@ -4673,59 +5140,106 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse as annotation. boolean isAnnotation = (format == null || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .readAnnotationFile(viewport.alignment, file, protocol) + .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 - if (format == null) + // first see if its a T-COFFEE score file + TCoffeeScoreFile tcf = null; + try { - format = new IdentifyFile().Identify(file, protocol); - } - if (format.equalsIgnoreCase("JnetFile")) + 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) { - /* - * 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 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); + } } } } @@ -4740,25 +5254,45 @@ 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) @@ -4777,10 +5311,11 @@ 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*)", @@ -4799,6 +5334,7 @@ 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()); @@ -4810,6 +5346,7 @@ 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()); @@ -4850,20 +5387,42 @@ 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 - final 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() + { + @Override + 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 @@ -4879,43 +5438,61 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignFrame me = this; new Thread(new Runnable() { + @Override public void run() { final jalview.ws.SequenceFetcher sf = SequenceFetcher .getSequenceFetcherSingleton(me); - final String[] otherdb = sf.getOrderedSupportedSources(); - // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); - // jalview.util.QuickSort.sort(otherdb, otherdb); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - + String[] dbclasses = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + List otherdb; JMenu dfetch = new JMenu(); - JMenuItem fetchr; - rfetch.add(dfetch); - int comp = 0, mcomp = 15; + JMenu ifetch = new JMenu(); + JMenuItem fetchr = null; + int comp = 0, icomp = 0, mcomp = 15; String mname = null; - if (otherdb != null && otherdb.length > 0) + int dbi = 0; + for (String dbclass : dbclasses) { - for (int i = 0; i < otherdb.length; i++) + 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) { - String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); - if (mname == null) - { - mname = "from '" + dbname + "'"; - } - fetchr = new JMenuItem(otherdb[i]); - final String[] dassource = new String[] - { otherdb[i] }; + 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 @@ -4927,17 +5504,108 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText("Retrieve from " + dbname); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{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(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()}))); dfetch.add(fetchr); - if (comp++ == mcomp || i == (otherdb.length - 1)) + comp++; + // and then build the rest of the individual menus + ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()})); + icomp = 0; + String imname = null; + int i = 0; + for (DbSourceProxy sproxy : otherdb) { - dfetch.setText(mname + " to '" + dbname + "'"); - rfetch.add(dfetch); - dfetch = new JMenu(); - mname = null; - comp = 0; + 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 = MessageManager.formatMessage("label.from_msname", new String[]{sname}); + } + fetchr = new JMenuItem(msname); + final DbSourceProxy[] dassrc = + { sproxy }; + fetchr.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassrc) + .fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("" + + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname})); + ifetch.add(fetchr); + ++i; + if (++icomp >= mcomp || i == (otherdb.size())) + { + ifetch.setText(MessageManager.formatMessage( + "label.source_to_target", imname, sname)); + dfetch.add(ifetch); + ifetch = new JMenu(); + imname = null; + icomp = 0; + comp++; + } } } + ++dbi; + if (comp >= mcomp || dbi >= (dbclasses.length)) + { + dfetch.setText(MessageManager.formatMessage( + "label.source_to_target", mname, dbclass)); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } } } }); @@ -4949,6 +5617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Left justify the whole alignment. */ + @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -4959,6 +5628,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Right justify the whole alignment. */ + @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -4979,6 +5649,7 @@ 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()); @@ -4992,6 +5663,7 @@ 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()); @@ -5006,6 +5678,7 @@ 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()); @@ -5019,6 +5692,7 @@ 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()); @@ -5032,12 +5706,23 @@ 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()); @@ -5050,38 +5735,35 @@ 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) + if (avc.makeGroupsFromSelection()) { - 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)) - ; - } 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 * @@ -5092,15 +5774,63 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!viewport.getSequenceSetId().equals( alignmentPanel.av.getSequenceSetId())) { - throw new Error( - "Implementation error: cannot show a view from another alignment in an AlignFrame."); + throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame")); } if (tabbedPane != null - & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) + & alignPanels.indexOf(alignmentPanel) != tabbedPane + .getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } } + + /** + * Action on selection of menu options to Show or Hide annotations. + * + * @param visible + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + @Override + protected void setAnnotationsVisibility(boolean visible, + boolean forSequences, boolean forAlignment) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + boolean apply = (aa.sequenceRef == null && forAlignment) + || (aa.sequenceRef != null && forSequences); + if (apply) + { + aa.visible = visible; + } + } + alignPanel.validateAnnotationDimensions(false); + alignPanel.alignmentChanged(); + } + + /** + * Store selected annotation sort order for the view and repaint. + */ + @Override + protected void sortAnnotations_actionPerformed() + { + this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + alignPanel.paintAlignment(true); + } + + /** + * + * @return alignment panels in this alignemnt frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + } } class PrintThread extends Thread @@ -5114,6 +5844,7 @@ class PrintThread extends Thread static PageFormat pf; + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob();