X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d8493980e2aaa56afe25f448eebf62811c5b1be3;hb=31b84e9690b026255a488724ef7b847da94e48af;hp=63620e5cceedbfc0fc45dc970116d26e90983178;hpb=678a8ac35bb269d80cda081bec11e7b403c9811a;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 63620e5..71ba94a 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -26,7 +26,7 @@ import jalview.analysis.CrossRef; import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; -import jalview.api.AlignExportSettingI; +import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; @@ -34,7 +34,7 @@ import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; -import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.commands.CommandI; @@ -45,6 +45,7 @@ import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; import jalview.commands.SlideSequencesCommand; import jalview.commands.TrimRegionCommand; +import jalview.datamodel.AlignExportSettingsAdapter; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -53,46 +54,43 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; -import jalview.datamodel.HiddenSequences; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; +import jalview.io.FileParse; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; +import jalview.io.JPredFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; +import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; +import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; -import jalview.schemes.Blosum62ColourScheme; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ClustalxColourScheme; import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.NucleotideColourScheme; -import jalview.schemes.PIDColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.RNAHelicesColourChooser; -import jalview.schemes.ResidueProperties; -import jalview.schemes.StrandColourScheme; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -101,6 +99,7 @@ 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.Rectangle; import java.awt.Toolkit; @@ -121,12 +120,13 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; -import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; @@ -137,13 +137,14 @@ import java.util.List; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComponent; import javax.swing.JEditorPane; import javax.swing.JInternalFrame; +import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; +import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -154,7 +155,7 @@ import javax.swing.SwingUtilities; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI + IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { public static final int DEFAULT_WIDTH = 700; @@ -170,18 +171,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public AlignViewControllerI avc; - List alignPanels = new ArrayList(); + List alignPanels = new ArrayList<>(); /** * Last format used to load or save alignments in this window */ - String currentFileFormat = null; + FileFormatI currentFileFormat = null; /** * Current filename for this alignment */ String fileName = null; + File fileObject; + /** * Creates a new AlignFrame object with specific width and height. * @@ -237,8 +240,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param height * height of frame. */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, - int width, int height) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height) { this(al, hiddenColumns, width, height, null); } @@ -254,8 +257,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param sequenceSetId * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, - int width, int height, String sequenceSetId) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height, String sequenceSetId) { this(al, hiddenColumns, width, height, sequenceSetId, null); } @@ -273,8 +276,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewId * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, - int width, int height, String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height, String sequenceSetId, String viewId) { setSize(width, height); @@ -292,7 +295,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection hiddenColumns, int width, int height) + HiddenColumns hiddenColumns, int width, int height) { setSize(width, height); @@ -334,6 +337,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { +// setBackground(Color.white); // BH 2019 + if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); @@ -343,7 +348,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) { - BLOSUM62Colour.setEnabled(false); + // BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); // PIDColour.setEnabled(false); @@ -363,19 +368,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortPairwiseMenuItem_actionPerformed(null); } - if (Desktop.desktop != null) - { - this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - addServiceListeners(); - setGUINucleotide(viewport.getAlignment().isNucleotide()); - } - this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); - buildTreeMenu(); + calculateTree.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + openTreePcaDialog(); + } + }); + buildColourMenu(); + + if (Desktop.desktop != null) + { + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + /** + * BH 2018 ignore service listeners + * + * @j2sNative + * + */ + { + addServiceListeners(); + } + setGUINucleotide(); + } if (viewport.getWrapAlignment()) { @@ -389,8 +411,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addKeyListener(); - final List selviews = new ArrayList(); - final List origview = new ArrayList(); + final List selviews = new ArrayList<>(); + final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, @@ -403,7 +425,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, origview.clear(); origview.add(alignPanel); // make an array of all alignment panels except for this one - List aps = new ArrayList( + List aps = new ArrayList<>( Arrays.asList(Desktop.getAlignmentPanels(null))); aps.remove(AlignFrame.this.alignPanel); return aps.toArray(new AlignmentPanel[aps.size()]); @@ -484,7 +506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ - public void setFileName(String file, String format) + public void setFileName(String file, FileFormatI format) { fileName = file; setFileFormat(format); @@ -492,6 +514,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** + * JavaScript will have this, maybe others. More dependable than a file name + * and maintains a reference to the actual bytes loaded. + * + * @param file + */ + public void setFileObject(File file) + { + this.fileObject = file; + } + + /** * Add a KeyListener with handlers for various KeyPressed and KeyReleased * events */ @@ -503,9 +536,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void keyPressed(KeyEvent evt) { if (viewport.cursorMode - && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt - .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt - .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && ((evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 + && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) { alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); @@ -545,7 +579,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); + slideSequences(false, + alignPanel.getSeqPanel().getKeyboardNo1()); } else { @@ -568,9 +603,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.getSeqPanel().insertGapAtCursor( - evt.isControlDown() || evt.isShiftDown() - || evt.isAltDown()); + alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); } break; @@ -593,9 +627,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().deleteGapAtCursor( - evt.isControlDown() || evt.isShiftDown() - || evt.isAltDown()); + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); } break; @@ -642,13 +675,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText(MessageManager.formatMessage( - "label.keyboard_editing_mode", - new String[] { (viewport.cursorMode ? "on" : "off") })); + setStatus(MessageManager + .formatMessage("label.keyboard_editing_mode", new String[] + { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + ViewportRanges ranges = viewport.getRanges(); + alignPanel.getSeqPanel().seqCanvas.cursorX = ranges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = ranges + .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; @@ -669,27 +705,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, toggleHiddenRegions(toggleSeqs, toggleCols); break; } + case KeyEvent.VK_B: + { + boolean toggleSel = evt.isControlDown() || evt.isMetaDown(); + boolean modifyExisting = true; // always modify, don't clear + // evt.isShiftDown(); + boolean invertHighlighted = evt.isAltDown(); + avc.markHighlightedColumns(invertHighlighted, modifyExisting, + toggleSel); + break; + } case KeyEvent.VK_PAGE_UP: - if (viewport.getWrapAlignment()) - { - alignPanel.scrollUp(true); - } - else - { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); - } + viewport.getRanges().pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.getWrapAlignment()) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); - } + viewport.getRanges().pageDown(); break; } } @@ -702,16 +732,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } break; } @@ -731,9 +761,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int aSize = alignPanels.size(); - tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); + tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); - if (aSize == 1 && ap.av.viewName == null) + if (aSize == 1 && ap.av.getViewName() == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } @@ -746,7 +776,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); - tabbedPane.addTab(ap.av.viewName, ap); + tabbedPane.addTab(ap.av.getViewName(), ap); ap.setVisible(false); } @@ -769,7 +799,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, gatherViews.setEnabled(true); tabbedPane.setVisible(true); AlignmentPanel first = alignPanels.get(0); - tabbedPane.addTab(first.av.viewName, first); + tabbedPane.addTab(first.av.getViewName(), first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } @@ -797,8 +827,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - System.err - .println("Rebuild WS Menu for service change"); + System.err.println( + "Rebuild WS Menu for service change"); BuildWebServiceMenu(); } @@ -832,25 +862,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Configure menu items that vary according to whether the alignment is * nucleotide or protein - * - * @param nucleotide */ - public void setGUINucleotide(boolean nucleotide) + public void setGUINucleotide() { + AlignmentI al = getViewport().getAlignment(); + boolean nucleotide = al.isNucleotide(); + + loadVcf.setVisible(nucleotide); showTranslation.setVisible(nucleotide); showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); - modifyConservation.setEnabled(!nucleotide); + modifyConservation + .setEnabled(!nucleotide && conservationMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); - rnahelicesColour.setEnabled(nucleotide); - purinePyrimidineColour.setEnabled(nucleotide); - showComplementMenuItem.setText(nucleotide ? MessageManager - .getString("label.protein") : MessageManager - .getString("label.nucleotide")); - setColourSelected(jalview.bin.Cache.getDefault( - nucleotide ? Preferences.DEFAULT_COLOUR_NUC - : Preferences.DEFAULT_COLOUR_PROT, "None")); + + showComplementMenuItem + .setText(nucleotide ? MessageManager.getString("label.protein") + : MessageManager.getString("label.nucleotide")); } /** @@ -871,12 +900,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ - void setMenusFromViewport(AlignViewport av) + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); + modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); @@ -902,8 +933,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); - setColourSelected(ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + ColourMenuHelper.setColourSelected(colourMenu, + av.getGlobalColourScheme()); showSeqFeatures.setSelected(av.isShowSequenceFeatures()); hiddenMarkers.setState(av.getShowHiddenMarkers()); @@ -913,9 +944,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); showProducts.setEnabled(canShowProducts()); setGroovyEnabled(Desktop.getGroovyConsole() != null); @@ -966,7 +994,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void setStatus(String text) { - statusBar.setText(text); + // BH note: If text width and height are 0, then the layout manager + // will dispense of it and change the frame height. + // In JavaScript, we use \u00A0 -- unicode "non-breaking space" + // which is the unicode encoding of   + + statusBar.setText(text == null || text.isEmpty() ? " " : text); } /* @@ -983,9 +1016,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { - new jalview.gui.SequenceFetcher(this); + new SequenceFetcher(this); } @Override @@ -1003,7 +1036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // originating file's format // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. - if (currentFileFormat.equals("Jalview")) + if (FileFormat.Jalview.equals(currentFileFormat)) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) @@ -1025,7 +1058,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL + : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else @@ -1033,9 +1068,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; - AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, - protocol, currentFileFormat); + + AlignFrame newframe = null; + + if (fileObject == null) + { + + DataSourceType protocol = (fileName.startsWith("http:") + ? DataSourceType.URL + : DataSourceType.FILE); + newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); + } + else + { + newframe = loader.LoadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); + } newframe.setBounds(bounds); if (featureSettings != null && featureSettings.isShowing()) @@ -1064,8 +1113,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport - .getAlignPanel()); + Desktop.instance + .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); } @Override @@ -1077,12 +1126,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void save_actionPerformed(ActionEvent e) { - if (fileName == null - || (currentFileFormat == null || !jalview.io.FormatAdapter - .isValidIOFormat(currentFileFormat, true)) + if (fileName == null || (currentFileFormat == null) || fileName.startsWith("http")) { - saveAs_actionPerformed(null); + saveAs_actionPerformed(); } else { @@ -1091,244 +1138,240 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Saves the alignment to a file with a name chosen by the user, if necessary + * warning if a file would be overwritten */ @Override - public void saveAs_actionPerformed(ActionEvent e) + public void saveAs_actionPerformed() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, - currentFileFormat, false); + String format = currentFileFormat == null ? null + : currentFileFormat.getName(); + JalviewFileChooser chooser = JalviewFileChooser + .forWrite(Cache.getProperty("LAST_DIRECTORY"), format); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_alignment_to_file")); + chooser.setDialogTitle( + MessageManager.getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); - if (value == JalviewFileChooser.APPROVE_OPTION) + if (value != JalviewFileChooser.APPROVE_OPTION) + { + return; + } + currentFileFormat = chooser.getSelectedFormat(); + // todo is this (2005) test now obsolete - value is never null? + while (currentFileFormat == null) { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("label.select_file_format_before_saving"), + MessageManager.getString("label.file_format_not_specified"), + JvOptionPane.WARNING_MESSAGE); currentFileFormat = chooser.getSelectedFormat(); - while (currentFileFormat == null) + value = chooser.showSaveDialog(this); + if (value != JalviewFileChooser.APPROVE_OPTION) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.select_file_format_before_saving"), - MessageManager - .getString("label.file_format_not_specified"), - JOptionPane.WARNING_MESSAGE); - currentFileFormat = chooser.getSelectedFormat(); - value = chooser.showSaveDialog(this); - if (value != JalviewFileChooser.APPROVE_OPTION) - { - return; - } + return; } + } - fileName = chooser.getSelectedFile().getPath(); - - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); + fileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); - if (currentFileFormat.indexOf(" ") > -1) - { - currentFileFormat = currentFileFormat.substring(0, - currentFileFormat.indexOf(" ")); - } - saveAlignment(fileName, currentFileFormat); - } + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); + Cache.setProperty("LAST_DIRECTORY", fileName); + saveAlignment(fileName, currentFileFormat); } - public boolean saveAlignment(String file, String format) + boolean lastSaveSuccessful = false; + + FileFormatI lastFormatSaved; + + String lastFilenameSaved; + + /** + * Raise a dialog or status message for the last call to saveAlignment. + * + * @return true if last call to saveAlignment(file, format) was successful. + */ + public boolean isSaveAlignmentSuccessful() { - boolean success = true; - if (format.equalsIgnoreCase("Jalview")) + if (!lastSaveSuccessful) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } + else { - String shortName = title; - if (shortName.indexOf(java.io.File.separatorChar) > -1) - { - shortName = shortName.substring(shortName - .lastIndexOf(java.io.File.separatorChar) + 1); - } + setStatus(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { lastFilenameSaved, lastFormatSaved })); - success = new Jalview2XML().saveAlignment(this, file, shortName); + } + return lastSaveSuccessful; + } - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] { - fileName, format })); + /** + * Saves the alignment to the specified file path, in the specified format, + * which may be an alignment format, or Jalview project format. If the + * alignment has hidden regions, or the format is one capable of including + * non-sequence data (features, annotations, groups), then the user may be + * prompted to specify what to include in the output. + * + * @param file + * @param format + */ + public void saveAlignment(String file, FileFormatI format) + { + lastSaveSuccessful = false; + lastFilenameSaved = file; + lastFormatSaved = format; - } - else + if (FileFormat.Jalview.equals(format)) { - if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) + String shortName = title; + if (shortName.indexOf(File.separatorChar) > -1) { - warningMessage("Cannot save file " + fileName + " using format " - + format, "Alignment output format not supported"); - if (!Jalview.isHeadlessMode()) - { - saveAs_actionPerformed(null); - } - return false; + shortName = shortName.substring( + shortName.lastIndexOf(File.separatorChar) + 1); } + lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file, + shortName); + + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { fileName, format })); + + return; + } - AlignmentExportData exportData = getAlignmentForExport(format, - viewport, null); - if (exportData.getSettings().isCancelled()) - { - return false; - } - FormatAdapter f = new FormatAdapter(alignPanel, - exportData.getSettings()); - String output = f.formatSequences( - format, - exportData.getAlignment(), // class cast exceptions will - // occur in the distant future - exportData.getOmitHidden(), exportData.getStartEndPostions(), - f.getCacheSuffixDefault(format), - viewport.getColumnSelection()); - - if (output == null) + AlignExportSettingsI options = new AlignExportSettingsAdapter(false); + Runnable cancelAction = new Runnable() + { + @Override + public void run() { - success = false; + lastSaveSuccessful = false; } - else + }; + Runnable outputAction = new Runnable() + { + @Override + public void run() { - try + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport + .getAlignExportData(options); + String output = new FormatAdapter(alignPanel, options) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns()); + if (output == null) { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); - - out.print(output); - out.close(); - this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", - new Object[] { fileName, format })); - } catch (Exception ex) + lastSaveSuccessful = false; + } + else { - success = false; - ex.printStackTrace(); + try + { + PrintWriter out = new PrintWriter(new FileWriter(file)); + out.print(output); + out.close(); + AlignFrame.this.setTitle(file); + setStatus(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new Object[] + { fileName, format.getName() })); + } catch (Exception ex) + { + lastSaveSuccessful = false; + ex.printStackTrace(); + } } } - } - - if (!success) - { - JOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", - new Object[] { fileName }), MessageManager - .getString("label.error_saving_file"), - JOptionPane.WARNING_MESSAGE); - } - - return success; - } + }; - private void warningMessage(String warning, String title) - { - if (new jalview.util.Platform().isHeadless()) + /* + * show dialog with export options if applicable; else just do it + */ + if (AlignExportOptions.isNeeded(viewport, format)) { - System.err.println("Warning: " + title + "\nWarning: " + warning); - + AlignExportOptions choices = new AlignExportOptions( + alignPanel.getAlignViewport(), format, options); + choices.setResponseAction(0, outputAction); + choices.setResponseAction(1, cancelAction); + choices.showDialog(); } else { - JOptionPane.showInternalMessageDialog(this, warning, title, - JOptionPane.WARNING_MESSAGE); + outputAction.run(); } - return; } /** - * DOCUMENT ME! + * Outputs the alignment to textbox in the requested format, if necessary + * first prompting the user for whether to include hidden regions or + * non-sequence data * - * @param e - * DOCUMENT ME! + * @param fileFormatName */ @Override - protected void outputText_actionPerformed(ActionEvent e) - { - - AlignmentExportData exportData = getAlignmentForExport( - e.getActionCommand(), viewport, null); - if (exportData.getSettings().isCancelled()) - { - return; - } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(null); - try - { - cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(e.getActionCommand(), - exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getColumnSelection())); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", - new Object[] { e.getActionCommand() }), 600, 500); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); - cap.dispose(); - } - - } - - public static AlignmentExportData getAlignmentForExport( - String exportFormat, AlignViewportI viewport, - AlignExportSettingI exportSettings) + protected void outputText_actionPerformed(String fileFormatName) { - AlignmentI alignmentToExport = null; - AlignExportSettingI settings = exportSettings; - String[] omitHidden = null; - - HiddenSequences hiddenSeqs = viewport.getAlignment() - .getHiddenSequences(); - - alignmentToExport = viewport.getAlignment(); - - boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; - if (settings == null) - { - settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFormat); - } - // settings.isExportAnnotations(); - - if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) + FileFormatI fileFormat = FileFormats.getInstance() + .forName(fileFormatName); + AlignExportSettingsI options = new AlignExportSettingsAdapter(false); + Runnable outputAction = new Runnable() { - omitHidden = viewport.getViewAsString(false, - settings.isExportHiddenSequences()); - } + @Override + public void run() + { + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport + .getAlignExportData(options); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + try + { + FileFormatI format = fileFormat; + cap.setText(new FormatAdapter(alignPanel, options) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new Object[] + { fileFormat.getName() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + fileFormat.getName(), + oom); + cap.dispose(); + } + } + }; - int[] alignmentStartEnd = new int[2]; - if (hasHiddenSeqs && settings.isExportHiddenSequences()) + /* + * show dialog with export options if applicable; else just do it + */ + if (AlignExportOptions.isNeeded(viewport, fileFormat)) { - alignmentToExport = hiddenSeqs.getFullAlignment(); + AlignExportOptions choices = new AlignExportOptions( + alignPanel.getAlignViewport(), fileFormat, options); + choices.setResponseAction(0, outputAction); + choices.showDialog(); } else { - alignmentToExport = viewport.getAlignment(); + outputAction.run(); } - alignmentStartEnd = alignmentToExport - .getVisibleStartAndEndIndex(viewport.getColumnSelection() - .getHiddenColumns()); - AlignmentExportData ed = new AlignmentExportData(alignmentToExport, - omitHidden, alignmentStartEnd, settings); - return ed; } /** @@ -1340,14 +1383,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HtmlSvgOutput(null, alignPanel); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); + htmlSVG.exportHTML(null); } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { - BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this); - bjs.exportJalviewAlignmentAsBioJsHtmlFile(); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); + bjs.exportHTML(null); } public void createImageMap(File file, String image) @@ -1356,33 +1400,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Creates a PNG image of the alignment and writes it to the given file. If + * the file is null, the user is prompted to choose a file. * - * @param e - * DOCUMENT ME! + * @param f */ @Override public void createPNG(File f) { - alignPanel.makePNG(f); + alignPanel.makeAlignmentImage(TYPE.PNG, f); } /** - * DOCUMENT ME! + * Creates an EPS image of the alignment and writes it to the given file. If + * the file is null, the user is prompted to choose a file. * - * @param e - * DOCUMENT ME! + * @param f */ @Override public void createEPS(File f) { - alignPanel.makeEPS(f); + alignPanel.makeAlignmentImage(TYPE.EPS, f); } + /** + * Creates an SVG image of the alignment and writes it to the given file. If + * the file is null, the user is prompted to choose a file. + * + * @param f + */ @Override public void createSVG(File f) { - alignPanel.makeSVG(f); + alignPanel.makeAlignmentImage(TYPE.SVG, f); } @Override @@ -1409,36 +1459,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportFeatures_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportFeatures(alignPanel); + new AnnotationExporter(alignPanel).exportFeatures(); } @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel); + new AnnotationExporter(alignPanel).exportAnnotations(); } @Override public void associatedData_actionPerformed(ActionEvent e) { - // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser( + final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.load_jalview_annotations")); - chooser.setToolTipText(MessageManager - .getString("label.load_jalview_annotations")); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setDialogTitle( + MessageManager.getString("label.load_jalview_annotations")); + chooser.setToolTipText( + MessageManager.getString("label.load_jalview_annotations")); + chooser.setResponseHandler(0, new Runnable() { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice, null, null, null); - } + @Override + public void run() + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); + } + }); + chooser.showOpenDialog(this); } /** @@ -1527,9 +1578,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { undoMenuItem.setEnabled(true); CommandI command = viewport.getHistoryList().peek(); - undoMenuItem.setText(MessageManager.formatMessage( - "label.undo_command", - new Object[] { command.getDescription() })); + undoMenuItem.setText(MessageManager + .formatMessage("label.undo_command", new Object[] + { command.getDescription() })); } else { @@ -1542,9 +1593,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, redoMenuItem.setEnabled(true); CommandI command = viewport.getRedoList().peek(); - redoMenuItem.setText(MessageManager.formatMessage( - "label.redo_command", - new Object[] { command.getDescription() })); + redoMenuItem.setText(MessageManager + .formatMessage("label.redo_command", new Object[] + { command.getDescription() })); } else { @@ -1616,8 +1667,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (originalSource != viewport) { - Cache.log - .warn("Implementation worry: mismatch of viewport origin for undo"); + Cache.log.warn( + "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != @@ -1625,8 +1676,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, originalSource - .getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.getAlignment().getSequences()); } } @@ -1656,8 +1707,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != viewport) { - Cache.log - .warn("Implementation worry: mismatch of viewport origin for redo"); + Cache.log.warn( + "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != @@ -1665,8 +1716,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, originalSource - .getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.getAlignment().getSequences()); } } @@ -1681,8 +1732,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); for (Component comp : comps) { @@ -1728,23 +1779,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } synchronized void slideSequences(boolean right, int size) { - List sg = new ArrayList(); + List sg = new ArrayList<>(); if (viewport.cursorMode) { - sg.add(viewport.getAlignment().getSequenceAt( - alignPanel.getSeqPanel().seqCanvas.cursorY)); + sg.add(viewport.getAlignment() + .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport .getAlignment().getHeight()) { - sg = viewport.getSelectionGroup().getSequences( - viewport.getHiddenRepSequences()); + sg = viewport.getSelectionGroup() + .getSequences(viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1752,7 +1803,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - List invertGroup = new ArrayList(); + List invertGroup = new ArrayList<>(); for (SequenceI seq : viewport.getAlignment().getSequences()) { @@ -1773,13 +1824,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SlideSequencesCommand ssc; if (right) { - ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, - size, viewport.getGapCharacter()); + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, + viewport.getGapCharacter()); } else { - ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, - size, viewport.getGapCharacter()); + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, + viewport.getGapCharacter()); } int groupAdjustment = 0; @@ -1824,9 +1875,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { - appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) historyList - .peek()); + appendHistoryItem = ssc.appendSlideCommand( + (SlideSequencesCommand) historyList.peek()); } if (!appendHistoryItem) @@ -1846,7 +1896,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -1861,8 +1910,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, omitHidden = viewport.getViewAsString(true); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden, null); + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -1874,35 +1923,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); - Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(ss, Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, + Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); return; } - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport - .getSelectionGroup().getEndRes(); - for (int[] region : viewport.getColumnSelection().getHiddenColumns()) - { - if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) - { - hiddenColumns.add(new int[] { region[0] - hiddenOffset, - region[1] - hiddenOffset }); - } - } + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); + + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; - statusBar.setText(MessageManager.formatMessage( - "label.copied_sequences_to_clipboard", new Object[] { Integer - .valueOf(seqs.length).toString() })); + setStatus(MessageManager.formatMessage( + "label.copied_sequences_to_clipboard", new Object[] + { Integer.valueOf(seqs.length).toString() })); } /** @@ -1948,7 +1994,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - String str, format; + String str; + FileFormatI format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); @@ -1957,7 +2004,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - format = new IdentifyFile().identify(str, "Paste"); + format = new IdentifyFile().identify(str, DataSourceType.PASTE); } catch (OutOfMemoryError er) { @@ -1987,12 +2034,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // parse the clipboard as an alignment. - alignment = new FormatAdapter().readFile(str, "Paste", format); + alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE, + format); sequences = alignment.getSequencesArray(); } int alwidth = 0; - ArrayList newGraphGroups = new ArrayList(); + ArrayList newGraphGroups = new ArrayList<>(); int fgroup = -1; if (newAlignment) @@ -2050,8 +2098,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // copy and derive new dataset sequence sequences[i] = sequences[i].deriveSequence(); - alignment.getDataset().addSequence( - sequences[i].getDatasetSequence()); + alignment.getDataset() + .addSequence(sequences[i].getDatasetSequence()); // TODO: avoid creation of duplicate dataset sequences with a // 'contains' method using SequenceI.equals()/SequenceI.contains() } @@ -2081,18 +2129,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, annotationAdded = true; if (alann[i].sequenceRef == null && !alann[i].autoCalculated) { - AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + 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++) + for (int q = newGraphGroups + .size(); q <= newann.graphGroup; q++) { newGraphGroups.add(q, null); } - newGraphGroups.set(newann.graphGroup, new Integer( - ++fgroup)); + newGraphGroups.set(newann.graphGroup, + new Integer(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2111,7 +2161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // addHistoryItem(new EditCommand( MessageManager.getString("label.add_sequences"), - Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); + Action.PASTE, sequences, 0, alignment.getWidth(), + alignment)); } // Add any annotations attached to sequences for (int i = 0; i < sequences.length; i++) @@ -2132,12 +2183,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (newGraphGroups.size() <= newann.graphGroup || newGraphGroups.get(newann.graphGroup) == null) { - for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + for (int q = newGraphGroups + .size(); q <= newann.graphGroup; q++) { newGraphGroups.add(q, null); } - newGraphGroups.set(newann.graphGroup, new Integer( - ++fgroup)); + newGraphGroups.set(newann.graphGroup, + new Integer(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2147,8 +2199,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // was // duplicated // earlier - alignment - .setAnnotationIndex(sequences[i].getAnnotation()[a], a); + alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], + a); } } } @@ -2156,7 +2208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2218,19 +2270,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int[] region : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings( - alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer()); + .transferSettings(alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2269,8 +2317,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - AlignmentI alignment = AlignmentUtils.expandContext(getViewport() - .getAlignment(), -1); + AlignmentI alignment = AlignmentUtils + .expandContext(getViewport().getAlignment(), -1); AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); @@ -2278,19 +2326,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int region[] : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings( - alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer()); + .transferSettings(alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2352,17 +2396,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ if (sg.getSize() == viewport.getAlignment().getHeight()) { - boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport - .getAlignment().getWidth()) ? true : false; + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + + 1) == viewport.getAlignment().getWidth()) ? true : false; if (isEntireAlignWidth) { - int confirm = JOptionPane.showConfirmDialog(this, + int confirm = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) { return; } @@ -2382,8 +2426,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.sendSelection(); viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); if (viewport.getAlignment().getHeight() < 1) { try @@ -2408,7 +2452,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -2434,7 +2478,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } @@ -2455,12 +2499,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2491,7 +2534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2500,7 +2543,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); viewport.sendSelection(); } @@ -2547,8 +2590,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); } else { @@ -2560,7 +2603,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + viewport.getRanges().setStartRes(0); } else { @@ -2568,10 +2611,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - statusBar.setText(MessageManager.formatMessage( - "label.removed_columns", - new String[] { Integer.valueOf(trimRegion.getSize()) - .toString() })); + setStatus(MessageManager + .formatMessage("label.removed_columns", new String[] + { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2584,8 +2626,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } @@ -2603,8 +2645,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2619,23 +2661,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", - new Object[] { Integer.valueOf(removeGapCols.getSize()) - .toString() })); + setStatus(MessageManager + .formatMessage("label.removed_empty_columns", new Object[] + { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + ViewportRanges ranges = viewport.getRanges(); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + ranges.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2653,8 +2695,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2666,15 +2708,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(viewport.getRanges().getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2688,8 +2730,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } /** @@ -2727,8 +2769,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Create a new AlignmentPanel (with its own, new Viewport) */ - AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, - true); + AlignmentPanel newap = new jalview.project.Jalview2XML() + .copyAlignPanel(alignPanel); if (!copyAnnotation) { /* @@ -2740,10 +2782,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.setGatherViewsHere(false); - if (viewport.viewName == null) + if (viewport.getViewName() == null) { - viewport.viewName = MessageManager - .getString("label.view_name_original"); + viewport.setViewName(MessageManager + .getString("label.view_name_original")); } /* @@ -2759,7 +2801,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ newap.av.replaceMappings(viewport.getAlignment()); - newap.av.viewName = getNewViewName(viewTitle); + /* + * start up cDNA consensus (if applicable) now mappings are in place + */ + if (newap.av.initComplementConsensus()) + { + newap.refresh(true); // adjust layout of annotations + } + + newap.av.setViewName(getNewViewName(viewTitle)); addAlignmentPanel(newap, true); newap.alignmentChanged(); @@ -2795,8 +2845,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); List existingNames = getExistingViewNames(comps); @@ -2816,15 +2866,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ protected List getExistingViewNames(List comps) { - List existingNames = new ArrayList(); + List existingNames = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof AlignmentPanel) { AlignmentPanel ap = (AlignmentPanel) comp; - if (!existingNames.contains(ap.av.viewName)) + if (!existingNames.contains(ap.av.getViewName())) { - existingNames.add(ap.av.viewName); + existingNames.add(ap.av.getViewName()); } } } @@ -2874,21 +2924,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getIdPanel().getIdCanvas() .setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.setRightAlignIds(idRightAlign.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -2907,8 +2957,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition( - alignPanel.getSeqPanel().seqCanvas.searchResults, false); + alignPanel.scrollToPosition(viewport.getSearchResults(), false); } } @@ -2922,7 +2971,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -2951,7 +3000,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - repaint(); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -2959,7 +3008,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - // alignPanel.paintAlignment(true); } /** @@ -2978,9 +3026,8 @@ 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.hasSelectedColumns() - || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg - .getEndRes())) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 + && sg.getStartRes() <= sg.getEndRes())) { // now invert the sequence set, if required - empty selection implies // that no hiding is required. @@ -3057,7 +3104,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3073,7 +3120,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3081,7 +3128,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3102,7 +3149,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.paintAlignment(true); + // TODO: do we actually need to update overview for scale above change ? + alignPanel.paintAlignment(true, false); } /** @@ -3115,7 +3163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3128,7 +3176,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3141,7 +3189,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3154,7 +3202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3167,7 +3215,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } public FeatureSettings featureSettings; @@ -3205,11 +3253,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); - alignPanel.paintAlignment(true); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } + alignPanel.paintAlignment(true, true); } /** @@ -3236,18 +3280,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void alignmentProperties() { - JEditorPane editPane = new JEditorPane("text/html", ""); - editPane.setEditable(false); + JComponent pane; StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) + .formatAsHtml(); - editPane.setText(MessageManager.formatMessage("label.html_content", - new Object[] { contents.toString() })); + String content = MessageManager.formatMessage("label.html_content", + new Object[] + { contents.toString() }); + contents = null; + + if (Jalview.isJS()) + { + JLabel textLabel = new JLabel(); + textLabel.setText(content); + textLabel.setBackground(Color.WHITE); + + pane = new JPanel(new BorderLayout()); + ((JPanel) pane).setOpaque(true); + pane.setBackground(Color.WHITE); + ((JPanel) pane).add(textLabel, BorderLayout.NORTH); + } + else + { + JEditorPane editPane = new JEditorPane("text/html", ""); + editPane.setEditable(false); + editPane.setText(content); + pane = editPane; + } + JInternalFrame frame = new JInternalFrame(); - frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new Object[] { getTitle() }), - 500, 400); + frame.getContentPane().add(new JScrollPane(pane)); + + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.alignment_properties", new Object[] + { getTitle() }), 500, 400); } /** @@ -3265,445 +3332,181 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JInternalFrame frame = new JInternalFrame(); - OverviewPanel overview = new OverviewPanel(alignPanel); + final OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.overview_params", new Object[] { this.getTitle() }), - frame.getWidth(), frame.getHeight()); + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.overview_params", new Object[] + { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), + true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + overview.dispose(); + alignPanel.setOverviewPanel(null); + }; + }); + if (getKeyListeners().length > 0) { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - alignPanel.setOverviewPanel(null); - }; - }); + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } @Override - public void textColour_actionPerformed(ActionEvent e) + public void textColour_actionPerformed() { new TextColourChooser().chooseColour(alignPanel, null); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + /* + * public void covariationColour_actionPerformed() { + * changeColour(new + * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation + * ()[0])); } */ @Override - protected void noColourmenuItem_actionPerformed(ActionEvent e) + public void annotationColour_actionPerformed() { - changeColour(null); + new AnnotationColourChooser(viewport, alignPanel); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ @Override - public void clustalColour_actionPerformed(ActionEvent e) + public void annotationColumn_actionPerformed(ActionEvent e) { - changeColour(new ClustalxColourScheme(viewport.getAlignment(), - viewport.getHiddenRepSequences())); + new AnnotationColumnChooser(viewport, alignPanel); } /** - * DOCUMENT ME! + * Action on the user checking or unchecking the option to apply the selected + * colour scheme to all groups. If unchecked, groups may have their own + * independent colour schemes. * - * @param e - * DOCUMENT ME! + * @param selected */ @Override - public void zappoColour_actionPerformed(ActionEvent e) + public void applyToAllGroups_actionPerformed(boolean selected) { - changeColour(new ZappoColourScheme()); + viewport.setColourAppliesToAllGroups(selected); } /** - * DOCUMENT ME! + * Action on user selecting a colour from the colour menu * - * @param e - * DOCUMENT ME! + * @param name + * the name (not the menu item label!) of the colour scheme */ @Override - public void taylorColour_actionPerformed(ActionEvent e) + public void changeColour_actionPerformed(String name) { - changeColour(new TaylorColourScheme()); + /* + * 'User Defined' opens a panel to configure or load a + * user-defined colour scheme + */ + if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) + { + new UserDefinedColours(alignPanel); + return; + } + + /* + * otherwise set the chosen colour scheme (or null for 'None') + */ + ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, + viewport.getAlignment(), viewport.getHiddenRepSequences()); + changeColour(cs); } /** - * DOCUMENT ME! + * Actions on setting or changing the alignment colour scheme * - * @param e - * DOCUMENT ME! + * @param cs */ @Override - public void hydrophobicityColour_actionPerformed(ActionEvent e) + public void changeColour(ColourSchemeI cs) { - changeColour(new HydrophobicColourScheme()); - } + // TODO: pull up to controller method + ColourMenuHelper.setColourSelected(colourMenu, cs); - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void helixColour_actionPerformed(ActionEvent e) - { - changeColour(new HelixColourScheme()); - } + viewport.setGlobalColourScheme(cs); - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void strandColour_actionPerformed(ActionEvent e) - { - changeColour(new StrandColourScheme()); + alignPanel.paintAlignment(true, true); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the PID threshold slider panel */ @Override - public void turnColour_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { - changeColour(new TurnColourScheme()); + SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), + alignPanel.getViewName()); + SliderPanel.showPIDSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the Conservation slider panel */ @Override - public void buriedColour_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { - changeColour(new BuriedColourScheme()); + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showConservationSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ @Override - public void nucleotideColour_actionPerformed(ActionEvent e) - { - changeColour(new NucleotideColourScheme()); - } - - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent e) + public void conservationMenuItem_actionPerformed(boolean selected) { - changeColour(new PurinePyrimidineColourScheme()); - } - - /* - * public void covariationColour_actionPerformed(ActionEvent e) { - * changeColour(new - * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation - * ()[0])); } - */ - @Override - public void annotationColour_actionPerformed(ActionEvent e) - { - new AnnotationColourChooser(viewport, alignPanel); - } - - @Override - public void annotationColumn_actionPerformed(ActionEvent e) - { - new AnnotationColumnChooser(viewport, alignPanel); - } + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); - @Override - public void rnahelicesColour_actionPerformed(ActionEvent e) - { - new RNAHelicesColourChooser(viewport, alignPanel); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void applyToAllGroups_actionPerformed(ActionEvent e) - { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); - } - - /** - * DOCUMENT ME! - * - * @param cs - * DOCUMENT ME! - */ - @Override - public void changeColour(ColourSchemeI cs) - { - // TODO: pull up to controller method - - if (cs != null) + changeColour(viewport.getGlobalColourScheme()); + if (selected) { - // Make sure viewport is up to date w.r.t. any sliders - if (viewport.getAbovePIDThreshold()) - { - int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); - viewport.setThreshold(threshold); - } - - if (viewport.getConservationSelected()) - { - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - } - if (cs instanceof TCoffeeColourScheme) - { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); - } + modifyConservation_actionPerformed(); } - - viewport.setGlobalColourScheme(cs); - - alignPanel.paintAlignment(true); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void modifyPID_actionPerformed(ActionEvent e) - { - if (viewport.getAbovePIDThreshold() - && viewport.getGlobalColourScheme() != null) + else { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showPIDSlider(); + SliderPanel.hideConservationSlider(); } } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) Above PID Threshold */ @Override - protected void modifyConservation_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed(boolean selected) { - if (viewport.getConservationSelected() - && viewport.getGlobalColourScheme() != null) + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + if (!selected) { - SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showConservationSlider(); + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); - - changeColour(viewport.getGlobalColourScheme()); - - modifyConservation_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) - { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void userDefinedColour_actionPerformed(ActionEvent e) - { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) + if (selected) { - new UserDefinedColours(alignPanel, null); + modifyPID_actionPerformed(); } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); - - changeColour(udc); + SliderPanel.hidePIDSlider(); } } - public void updateUserColourMenu() - { - - Component[] menuItems = colourMenu.getMenuComponents(); - int iSize = menuItems.length; - for (int i = 0; i < iSize; i++) - { - if (menuItems[i].getName() != null - && menuItems[i].getName().equals("USER_DEFINED")) - { - colourMenu.remove(menuItems[i]); - iSize--; - } - } - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); - - while (userColours.hasMoreElements()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColours.nextElement().toString()); - radioItem.setName("USER_DEFINED"); - radioItem.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Mac - { - offerRemoval(radioItem); - } - } - - @Override - public void mouseReleased(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Windows - { - offerRemoval(radioItem); - } - } - - /** - * @param radioItem - */ - void offerRemoval(final JRadioButtonMenuItem radioItem) - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JOptionPane.showInternalConfirmDialog( - jalview.gui.Desktop.desktop, MessageManager - .getString("label.remove_from_default_list"), - MessageManager - .getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - jalview.gui.UserDefinedColours - .removeColourFromDefaults(radioItem.getText()); - colourMenu.remove(radioItem); - } - else - { - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } - } - }); - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - - colourMenu.insert(radioItem, 15); - colours.add(radioItem); - } - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void PIDColour_actionPerformed(ActionEvent e) - { - changeColour(new PIDColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - changeColour(new Blosum62ColourScheme()); - } - /** * DOCUMENT ME! * @@ -3714,11 +3517,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0), null); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3732,9 +3535,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); + addHistoryItem( + new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } /** @@ -3750,7 +3553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3767,7 +3570,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3794,10 +3597,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JOptionPane.showInternalMessageDialog(this, MessageManager - .getString("label.you_must_select_least_two_sequences"), + JvOptionPane.showInternalMessageDialog(this, + MessageManager.getString( + "label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } else { @@ -3809,43 +3613,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void PCAMenuItem_actionPerformed(ActionEvent e) - { - if (((viewport.getSelectionGroup() != null) - && (viewport.getSelectionGroup().getSize() < 4) && (viewport - .getSelectionGroup().getSize() > 0)) - || (viewport.getAlignment().getHeight() < 4)) - { - 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; - } - - new PCAPanel(alignPanel); - } - @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); if (viewport.autoCalculateConsensus) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } @@ -3862,83 +3637,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("AV", "PID", "Average distance tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! + * Constructs a tree panel and adds it to the desktop * * @param type - * DOCUMENT ME! - * @param pwType - * DOCUMENT ME! - * @param title - * DOCUMENT ME! + * tree type (NJ or AV) + * @param modelName + * name of score model used to compute the tree + * @param options + * parameters for the distance or similarity calculation */ - void newTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String modelName, + SimilarityParamsI options) { + String frameTitle = ""; TreePanel tp; + boolean onSelection = false; if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 0) { - if (viewport.getSelectionGroup().getSize() < 3) - { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.you_need_more_two_sequences_selected_build_tree"), - MessageManager - .getString("label.not_enough_sequences"), - JOptionPane.WARNING_MESSAGE); - return; - } - SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ @@ -3946,57 +3663,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), - MessageManager - .getString("label.sequences_selection_not_aligned"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString( + "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager.getString( + "label.sequences_selection_not_aligned"), + JvOptionPane.WARNING_MESSAGE); return; } } - - title = title + " on region"; - tp = new TreePanel(alignPanel, type, pwType); + onSelection = true; } else { - // are the visible sequences aligned? - if (!viewport.getAlignment().isAligned(false)) - { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.sequences_must_be_aligned_before_creating_tree"), - MessageManager - .getString("label.sequences_not_aligned"), - JOptionPane.WARNING_MESSAGE); - - return; - } - if (viewport.getAlignment().getHeight() < 2) { return; } - - tp = new TreePanel(alignPanel, type, pwType); } - title += " from "; + tp = new TreePanel(alignPanel, type, modelName, options); + frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : ""); + + frameTitle += " from "; - if (viewport.viewName != null) + if (viewport.getViewName() != null) { - title += viewport.viewName + " of "; + frameTitle += viewport.getViewName() + " of "; } - title += this.title; + frameTitle += this.title; - Desktop.addInternalFrame(tp, title, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, 600, 500); } /** @@ -4010,8 +3709,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem(MessageManager.formatMessage( - "action.by_title_param", new Object[] { title })); + final JMenuItem item = new JMenuItem(MessageManager + .formatMessage("action.by_title_param", new Object[] + { title })); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @@ -4024,10 +3724,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); - addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport - .getAlignment())); + addHistoryItem(new OrderCommand(order.getName(), oldOrder, + viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -4056,7 +3756,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -4081,7 +3781,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) + if (viewport.getAlignment().getAlignmentAnnotation() + .hashCode() != _annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple @@ -4118,53 +3819,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * call. Listeners are added to remove the menu item when the treePanel is * closed, and adjust the tree leaf to sequence mapping when the alignment is * modified. - * - * @param treePanel - * Displayed tree window. - * @param title - * SortBy menu item title. */ @Override - public void buildTreeMenu() + public void buildTreeSortMenu() { - 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 String pwtype : ResidueProperties.scoreMatrices.keySet()) - { - JMenuItem tm = new JMenuItem(); - ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); - if (sm.isDNA() == viewport.getAlignment().isNucleotide() - || 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, pwtype, title); - } - }); - calculateTree.add(tm); - } - - } - } sortByTreeMenu.removeAll(); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); - List treePanels = new ArrayList(); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); + List treePanels = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof TreePanel) @@ -4208,7 +3871,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); return true; } @@ -4239,11 +3902,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() == 1) { - int option = JOptionPane.showConfirmDialog(this, + int option = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.oneseq_msainput_selection"), MessageManager.getString("label.invalid_selection"), - JOptionPane.OK_CANCEL_OPTION); - if (option == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION); + if (option == JvOptionPane.OK_OPTION) { msa = viewport.getAlignmentView(false); } @@ -4302,67 +3965,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.select_newick_like_tree_file")); - chooser.setToolTipText(MessageManager.getString("label.load_tree_file")); - - int value = chooser.showOpenDialog(null); + chooser.setDialogTitle( + MessageManager.getString("label.select_newick_like_tree_file")); + chooser.setToolTipText( + MessageManager.getString("label.load_tree_file")); - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0,new Runnable() { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - jalview.io.NewickFile fin = null; - try - { - fin = new jalview.io.NewickFile(choice, "File"); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); - } catch (Exception ex) - { - JOptionPane - .showMessageDialog( - Desktop.desktop, - ex.getMessage(), - MessageManager - .getString("label.problem_reading_tree_file"), - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - if (fin != null && fin.hasWarningMessage()) + @Override + public void run() { - JOptionPane.showMessageDialog(Desktop.desktop, fin - .getWarningMessage(), MessageManager - .getString("label.possible_problem_with_tree_file"), - JOptionPane.WARNING_MESSAGE); + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; + try + { + fin = new NewickFile(new FileParse(chooser.getSelectedFile(), + DataSourceType.FILE)); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); + } catch (Exception ex) + { + JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + MessageManager + .getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + if (fin != null && fin.hasWarningMessage()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager.getString( + "label.possible_problem_with_tree_file"), + JvOptionPane.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); + }); + chooser.showOpenDialog(this); } - public TreePanel ShowNewickTree(NewickFile nf, String title, - AlignmentView input) + public TreePanel showNewickTree(NewickFile nf, String treeTitle) { - return ShowNewickTree(nf, title, input, 600, 500, 4, 5); + return showNewickTree(nf, treeTitle, 600, 500, 4, 5); } - public TreePanel ShowNewickTree(NewickFile nf, String title, int w, + public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, int h, int x, int y) { - return ShowNewickTree(nf, title, null, w, h, x, y); + return showNewickTree(nf, treeTitle, null, w, h, x, y); } /** - * Add a treeviewer for the tree extracted from a newick file object to the + * Add a treeviewer for the tree extracted from a Newick file object to the * current alignment view * * @param nf @@ -4381,7 +4035,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * position * @return TreePanel handle */ - public TreePanel ShowNewickTree(NewickFile nf, String title, + public TreePanel showNewickTree(NewickFile nf, String treeTitle, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; @@ -4392,7 +4046,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { - tp = new TreePanel(alignPanel, "FromFile", title, nf, input); + tp = new TreePanel(alignPanel, nf, treeTitle, input); tp.setSize(w, h); @@ -4401,7 +4055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, title, w, h); + Desktop.addInternalFrame(tp, treeTitle, w, h); } } catch (Exception ex) { @@ -4436,7 +4090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - final List legacyItems = new ArrayList(); + final List legacyItems = new ArrayList<>(); try { // System.err.println("Building ws menu again " @@ -4451,7 +4105,7 @@ 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; /* @@ -4574,9 +4228,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { - Cache.log - .debug("Exception during web service menu building process.", - e); + Cache.log.debug( + "Exception during web service menu building process.", + e); } } }); @@ -4661,7 +4315,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void actionPerformed(ActionEvent e) { - showProductsFor(af.viewport.getSequenceSelection(), dna, source); + showProductsFor(af.viewport.getSequenceSelection(), dna, + source); } }); showProducts.add(xtype); @@ -4670,9 +4325,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.setEnabled(showp); } catch (Exception e) { - Cache.log - .warn("canShowProducts threw an exception - please report to help@jalview.org", - e); + Cache.log.warn( + "canShowProducts threw an exception - please report to help@jalview.org", + e); return false; } return showp; @@ -4689,10 +4344,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param source * the database to show cross-references for */ - protected void showProductsFor(final SequenceI[] sel, - final boolean _odna, final String source) + protected void showProductsFor(final SequenceI[] sel, final boolean _odna, + final String source) { - new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this)) + new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) .start(); } @@ -4713,31 +4368,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { jalview.bin.Cache.log.error( "Exception during translation. Please report this !", ex); - final String msg = MessageManager - .getString("label.error_when_translating_sequences_submit_bug_report"); + final String msg = MessageManager.getString( + "label.error_when_translating_sequences_submit_bug_report"); final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) { - final String msg = MessageManager - .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); + final String msg = MessageManager.getString( + "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); af.setFileFormat(this.currentFileFormat); - final String newTitle = MessageManager.formatMessage( - "label.translation_of_params", - new Object[] { this.getTitle() }); + final String newTitle = MessageManager + .formatMessage("label.translation_of_params", new Object[] + { this.getTitle() }); af.setTitle(newTitle); if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { @@ -4755,26 +4410,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set the file format * - * @param fileFormat + * @param format */ - public void setFileFormat(String fileFormat) + public void setFileFormat(FileFormatI format) { - this.currentFileFormat = fileFormat; + this.currentFileFormat = format; } /** * Try to load a features file onto the alignment. * * @param file - * contents or path to retrieve file - * @param type + * contents or path to retrieve file or a File object + * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(Object file, DataSourceType sourceType) { - return avc.parseFeaturesFile(file, type, - jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + // BH 2018 + return avc.parseFeaturesFile(file, sourceType, + Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } @@ -4819,7 +4475,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = new ArrayList(), protocols = new ArrayList(); + + final AlignFrame thisaf = this; + final List files = new ArrayList<>(); + List protocols = new ArrayList<>(); try { @@ -4830,175 +4489,199 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (files != null) { - try + new Thread(new Runnable() { - // check to see if any of these files have names matching sequences in - // the alignment - SequenceIdMatcher idm = new SequenceIdMatcher(viewport - .getAlignment().getSequencesArray()); - /** - * Object[] { String,SequenceI} - */ - ArrayList filesmatched = new ArrayList(); - ArrayList filesnotmatched = new ArrayList(); - for (int i = 0; i < files.size(); i++) + @Override + public void run() { - String file = files.get(i).toString(); - String pdbfn = ""; - String protocol = FormatAdapter.checkProtocol(file); - if (protocol == jalview.io.FormatAdapter.FILE) - { - File fl = new File(file); - pdbfn = fl.getName(); - } - else if (protocol == jalview.io.FormatAdapter.URL) - { - URL url = new URL(file); - pdbfn = url.getFile(); - } - if (pdbfn.length() > 0) + try { - // attempt to find a match in the alignment - SequenceI[] mtch = idm.findAllIdMatches(pdbfn); - int l = 0, c = pdbfn.indexOf("."); - while (mtch == null && c != -1) + // check to see if any of these files have names matching sequences + // in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher( + viewport.getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); + for (int i = 0; i < files.size(); i++) { - do + // BH 2018 + Object file = files.get(i); + String fileName = file.toString(); + String pdbfn = ""; + DataSourceType protocol = (file instanceof File + ? DataSourceType.FILE + : FormatAdapter.checkProtocol(fileName)); + if (protocol == DataSourceType.FILE) { - l = c; - } while ((c = pdbfn.indexOf(".", l)) > l); - if (l > -1) + File fl = (file instanceof File ? (File) file + : new File(fileName)); + pdbfn = fl.getName(); + } + else if (protocol == DataSourceType.URL) { - pdbfn = pdbfn.substring(0, l); + URL url = new URL(fileName); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + FileFormatI type; + try + { + type = new IdentifyFile().identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null && type.isStructureFile()) + { + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; + } + } + // File wasn't named like one of the sequences or wasn't a PDB + // file. + filesnotmatched.add(file); } - mtch = idm.findAllIdMatches(pdbfn); } - if (mtch != null) + int assocfiles = 0; + if (filesmatched.size() > 0) { - String type = null; - try + boolean autoAssociate = Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + if (!autoAssociate) { - type = new IdentifyFile().identify(file, protocol); - } catch (Exception ex) + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(thisaf, msg, + ttl, JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) { - type = null; + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(fm[0].toString(), + (DataSourceType) fm[1], toassoc, false, + Desktop.instance); + if (pe != null) + { + System.err.println("Associated file : " + + (fm[0].toString()) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } } - if (type != null) + else { - if (type.equalsIgnoreCase("PDB")) + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; + filesnotmatched.add(o[0]); } } } - // File wasn't named like one of the sequences or wasn't a PDB file. - filesnotmatched.add(file); - } - } - int assocfiles = 0; - if (filesmatched.size() > 0) - { - if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JOptionPane - .showConfirmDialog( - this, - MessageManager - .formatMessage( - "label.automatically_associate_pdb_files_with_sequences_same_name", - new Object[] { Integer - .valueOf( - filesmatched - .size()) - .toString() }), - MessageManager - .getString("label.automatically_associate_pdb_files_by_name"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) - - { - for (Object[] fm : filesmatched) + if (filesnotmatched.size() > 0) { - // 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]) + if (assocfiles > 0 && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(thisaf, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf( + filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { - 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++; - } + return; } - alignPanel.paintAlignment(true); + for (Object fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + } - } - } - if (filesnotmatched.size() > 0) - { - if (assocfiles > 0 - && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane - .showConfirmDialog( - this, - "" - + MessageManager - .formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] { Integer - .valueOf( - filesnotmatched - .size()) - .toString() }) - + "", - MessageManager - .getString("label.ignore_unmatched_dropped_files"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) - { - return; - } - for (String fn : filesnotmatched) + } catch (Exception ex) { - loadJalviewDataFile(fn, null, null, null); + ex.printStackTrace(); } - } - } catch (Exception ex) - { - ex.printStackTrace(); - } + }).start(); } } /** - * Attempt to load a "dropped" file or URL string: First by testing whether - * it's an Annotation file, then a JNet file, and finally a features file. If - * all are false then the user may have dropped an alignment file onto this - * AlignFrame. + * Attempt to load a "dropped" file or URL string, by testing in turn for + *
    + *
  • an Annotation file
    • + *
  • a JNet file
    • + *
  • a features file
    • + *
  • else try to interpret as an alignment file
    • + *
* * @param file * either a filename or a URL string. */ - public void loadJalviewDataFile(String file, String protocol, - String format, SequenceI assocSeq) + public void loadJalviewDataFile(Object file, DataSourceType sourceType, + FileFormatI format, SequenceI assocSeq) { + // BH 2018 was String file try { - if (protocol == null) + if (sourceType == null) { - protocol = FormatAdapter.checkProtocol(file); + sourceType = FormatAdapter.checkProtocol(file); } // if the file isn't identified, or not positively identified as some // other filetype (PFAM is default unidentified alignment file type) then // try to parse as annotation. - boolean isAnnotation = (format == null || format - .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, protocol) : false; + boolean isAnnotation = (format == null + || FileFormat.Pfam.equals(format)) + ? new AnnotationFile().annotateAlignmentView(viewport, + file, sourceType) + : false; if (!isAnnotation) { @@ -5006,32 +4689,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, TCoffeeScoreFile tcf = null; try { - tcf = new TCoffeeScoreFile(file, protocol); + tcf = new TCoffeeScoreFile(file, sourceType); if (tcf.isValid()) { if (tcf.annotateAlignment(viewport.getAlignment(), true)) { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); - changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + buildColourMenu(); + changeColour( + new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; - statusBar - .setText(MessageManager - .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + setStatus(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); + JvOptionPane.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"), + JvOptionPane.WARNING_MESSAGE); } } else @@ -5040,9 +4721,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception x) { - Cache.log - .debug("Exception when processing data source as T-COFFEE score file", - x); + Cache.log.debug( + "Exception when processing data source as T-COFFEE score file", + x); tcf = null; } if (tcf == null) @@ -5052,32 +4733,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse it as a features file if (format == null) { - format = new IdentifyFile().identify(file, protocol); + format = new IdentifyFile().identify(file, sourceType); + } + if (FileFormat.ScoreMatrix == format) + { + ScoreMatrixFile sm = new ScoreMatrixFile( + new FileParse(file, sourceType)); + sm.parse(); + // todo: i18n this message + setStatus(MessageManager.formatMessage( + "label.successfully_loaded_matrix", + sm.getMatrixName())); } - if (format.equalsIgnoreCase("JnetFile")) + else if (FileFormat.Jnet.equals(format)) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - file, protocol); + JPredFile predictions = new JPredFile(file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - ColumnSelection cs = new ColumnSelection(); - cs.hideInsertionsFor(repseq); - viewport.setColumnSelection(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } - else if (IdentifyFile.FeaturesFile.equals(format)) + // else if (IdentifyFile.FeaturesFile.equals(format)) + else if (FileFormat.Features.equals(format)) { - if (parseFeaturesFile(file, protocol)) + if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } else { - new FileLoader().LoadFile(viewport, file, protocol, format); + new FileLoader().LoadFile(viewport, file, sourceType, format); } } } @@ -5087,7 +4774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } catch (Exception ex) { @@ -5102,11 +4789,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } new OOMWarning( "loading data " - + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." - : "using " + protocol + " from " + file) + + (sourceType != null + ? (sourceType == DataSourceType.PASTE + ? "from clipboard." + : "using " + sourceType + " from " + + file) : ".") - + (format != null ? "(parsing as '" + format - + "' file)" : ""), oom, Desktop.desktop); + + (format != null + ? "(parsing as '" + format + "' file)" + : ""), + oom, Desktop.desktop); } } @@ -5126,6 +4818,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* + * 'focus' any colour slider that is open to the selected viewport + */ + if (viewport.getConservationSelected()) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hideConservationSlider(); + } + if (viewport.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hidePIDSlider(); + } + + /* * If there is a frame linked to this one in a SplitPane, switch it to the * same view tab index. No infinite recursion of calls should happen, since * tabSelectionChanged() should not get invoked on setting the selected @@ -5135,7 +4849,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignViewportI peer = viewport.getCodingComplement(); if (peer != null) { - AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame; + AlignFrame linkedAlignFrame = ((AlignViewport) peer) + .getAlignPanel().alignFrame; if (linkedAlignFrame.tabbedPane.getTabCount() > index) { linkedAlignFrame.tabbedPane.setSelectedIndex(index); @@ -5152,12 +4867,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (e.isPopupTrigger()) { String msg = MessageManager.getString("label.enter_view_name"); - String reply = JOptionPane.showInternalInputDialog(this, msg, msg, - JOptionPane.QUESTION_MESSAGE); + String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex()); + String reply = JvOptionPane.showInputDialog(msg, ttl); if (reply != null) { - viewport.viewName = reply; + viewport.setViewName(reply); // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } @@ -5250,30 +4965,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // here 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")); + rfetch.setToolTipText(MessageManager.getString( + "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); webService.add(rfetch); 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.setToolTipText( + MessageManager.getString("label.trim_retrieved_sequences")); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, 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.setToolTipText( + MessageManager.getString("label.fetch_embl_uniprot")); fetchr.addActionListener(new ActionListener() { @@ -5287,8 +5003,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { boolean isNucleotide = alignPanel.alignFrame.getViewport() .getAlignment().isNucleotide(); - DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, null, + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, null, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { @@ -5306,22 +5023,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); rfetch.add(fetchr); - final AlignFrame me = this; new Thread(new Runnable() { @Override public void run() { final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher - .getSequenceFetcherSingleton(me); + .getSequenceFetcherSingleton(); 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); + String[] dbclasses = sf.getNonAlignmentSources(); List otherdb; JMenu dfetch = new JMenu(); JMenu ifetch = new JMenu(); @@ -5338,12 +5052,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { continue; } - // List dbs=otherdb; - // otherdb=new ArrayList(); - // for (DbSourceProxy db:dbs) - // { - // if (!db.isA(DBRefSource.ALIGNMENTDB) - // } if (mname == null) { mname = "From " + dbclass; @@ -5391,8 +5099,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( - "label.fetch_retrieve_from", - new Object[] { src.getDbName() }))); + "label.fetch_retrieve_from", new Object[] + { src.getDbName() }))); dfetch.add(fetchr); comp++; } @@ -5402,9 +5110,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .toArray(new DbSourceProxy[0]); // fetch all entry DbSourceProxy src = otherdb.get(0); - fetchr = new JMenuItem(MessageManager.formatMessage( - "label.fetch_all_param", - new Object[] { src.getDbSource() })); + fetchr = new JMenuItem(MessageManager + .formatMessage("label.fetch_all_param", new Object[] + { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override @@ -5442,30 +5150,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( "label.fetch_retrieve_from_all_sources", - new Object[] { - Integer.valueOf(otherdb.size()) - .toString(), src.getDbSource(), - src.getDbName() }))); + new Object[] + { Integer.valueOf(otherdb.size()) + .toString(), + src.getDbSource(), src.getDbName() }))); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus ifetch = new JMenu(MessageManager.formatMessage( - "label.source_from_db_source", - new Object[] { src.getDbSource() })); + "label.source_from_db_source", new Object[] + { src.getDbSource() })); icomp = 0; String imname = null; int i = 0; for (DbSourceProxy sproxy : otherdb) { String dbname = sproxy.getDbName(); - String sname = dbname.length() > 5 ? dbname.substring(0, - 5) + "..." : dbname; - String msname = dbname.length() > 10 ? dbname.substring( - 0, 10) + "..." : dbname; + 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 Object[] { sname }); + imname = MessageManager + .formatMessage("label.from_msname", new Object[] + { sname }); } fetchr = new JMenuItem(msname); final DbSourceProxy[] dassrc = { sproxy }; @@ -5504,8 +5215,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText("" - + MessageManager.formatMessage( + fetchr.setToolTipText( + "" + MessageManager.formatMessage( "label.fetch_retrieve_from", new Object[] { dbname })); ifetch.add(fetchr); @@ -5580,7 +5291,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -5669,7 +5380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5681,7 +5392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().setSeqrep(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5690,6 +5401,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (avc.createGroup()) { + if (applyAutoAnnotationSettings.isSelected()) + { + alignPanel.updateAnnotation(true, false); + } alignPanel.alignmentChanged(); } } @@ -5710,17 +5425,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void setDisplayedView(AlignmentPanel alignmentPanel) { - if (!viewport.getSequenceSetId().equals( - alignmentPanel.av.getSequenceSetId())) + if (!viewport.getSequenceSetId() + .equals(alignmentPanel.av.getSequenceSetId())) { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_show_view_alignment_frame")); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_show_view_alignment_frame")); } - if (tabbedPane != null - && tabbedPane.getTabCount() > 0 - && alignPanels.indexOf(alignmentPanel) != tabbedPane - .getSelectedIndex()) + if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels + .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } @@ -5774,7 +5486,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -5783,7 +5495,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + // alignPanels is never null + // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + return alignPanels; } /** @@ -5799,7 +5513,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } - List cdnaSeqs = new ArrayList(); + List cdnaSeqs = new ArrayList<>(); for (SequenceI aaSeq : alignment.getSequences()) { for (AlignedCodonFrame acf : mappings) @@ -5823,15 +5537,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // show a warning dialog no mapped cDNA return; } - AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs - .size()])); - AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + AlignmentI cdna = new Alignment( + cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()])); + GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); cdna.alignAs(alignment); String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + this.title; - Desktop.addInternalFrame(alignFrame, newtitle, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); } /** @@ -5864,8 +5578,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al = dna.reverseCdna(complement); viewport.addAlignment(al, ""); addHistoryItem(new EditCommand( - MessageManager.getString("label.add_sequences"), - Action.PASTE, al.getSequencesArray(), 0, al.getWidth(), + MessageManager.getString("label.add_sequences"), Action.PASTE, + al.getSequencesArray(), 0, al.getWidth(), viewport.getAlignment())); } catch (Exception ex) { @@ -5892,12 +5606,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JOptionPane - .showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.couldnt_run_groovy_script"), - MessageManager - .getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.couldnt_run_groovy_script"), + MessageManager.getString("label.groovy_support_failed"), + JvOptionPane.ERROR_MESSAGE); } } else @@ -5930,6 +5642,80 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } return false; } + + @Override + protected void selectHighlightedColumns_actionPerformed( + ActionEvent actionEvent) + { + // include key modifier check in case user selects from menu + avc.markHighlightedColumns( + (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, + (actionEvent.getModifiers() & (ActionEvent.META_MASK + | ActionEvent.CTRL_MASK)) != 0); + } + + /** + * Rebuilds the Colour menu, including any user-defined colours which have + * been loaded either on startup or during the session + */ + public void buildColourMenu() + { + colourMenu.removeAll(); + + colourMenu.add(applyToAllGroups); + colourMenu.add(textColour); + colourMenu.addSeparator(); + + ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(), + false); + + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + + ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); + ColourMenuHelper.setColourSelected(colourMenu, colourScheme); + } + + /** + * Open a dialog (if not already open) that allows the user to select and + * calculate PCA or Tree analysis + */ + protected void openTreePcaDialog() + { + if (alignPanel.getCalculationDialog() == null) + { + new CalculationChooser(AlignFrame.this); + } + } + + @Override + protected void loadVcf_actionPerformed() + { + JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); + chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); + final AlignFrame us = this; + chooser.setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, us); + }; + }); + chooser.showOpenDialog(null); + + } + } class PrintThread extends Thread