X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f4dd8514f51bf1c17b34c5ac01cbc4030f3b1577;hb=baee331692f533011f566ba30a7a711f3326320f;hp=e11c0ecea37b61346ff31a4e7e95ddd0c3a807e5;hpb=ebca5f7880f838a5564dd419274ad6025b456dab;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e11c0ec..f4dd851 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -32,10 +32,9 @@ import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; -import jalview.api.FeatureSettingsModelI; 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; @@ -54,52 +53,44 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; -import jalview.datamodel.DBRefSource; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; 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.gff.SequenceOntologyI; 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.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; -import jalview.ws.SequenceFetcher; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -113,6 +104,7 @@ import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.StringSelection; import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; @@ -125,12 +117,13 @@ 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; @@ -146,8 +139,6 @@ import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -158,7 +149,7 @@ 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; @@ -172,14 +163,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + ViewportRanges vpRanges; + 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 @@ -241,7 +234,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param height * height of frame. */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); @@ -258,7 +251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param sequenceSetId * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId) { this(al, hiddenColumns, width, height, sequenceSetId, null); @@ -277,7 +270,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewId * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); @@ -296,7 +289,7 @@ 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); @@ -343,11 +336,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) { - BLOSUM62Colour.setEnabled(false); + // BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); // PIDColour.setEnabled(false); @@ -367,19 +361,28 @@ 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)); + addServiceListeners(); + setGUINucleotide(); + } if (viewport.getWrapAlignment()) { @@ -393,8 +396,8 @@ 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, @@ -407,7 +410,7 @@ 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()]); @@ -488,7 +491,7 @@ 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); @@ -651,8 +654,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; @@ -673,27 +678,21 @@ 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); - } + vpRanges.pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.getWrapAlignment()) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); - } + vpRanges.pageDown(); break; } } @@ -836,24 +835,23 @@ 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(); + 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(MessageManager - .getString(nucleotide ? "label.protein" : "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")); } /** @@ -879,7 +877,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); @@ -905,8 +905,8 @@ 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()); @@ -916,9 +916,6 @@ 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); @@ -1006,7 +1003,7 @@ 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++) @@ -1028,7 +1025,8 @@ 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 @@ -1036,7 +1034,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; + DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + : DataSourceType.FILE; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); @@ -1080,9 +1079,7 @@ 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); @@ -1102,11 +1099,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { - 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 @@ -1120,14 +1116,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat = chooser.getSelectedFormat(); while (currentFileFormat == null) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("label.select_file_format_before_saving"), MessageManager .getString("label.file_format_not_specified"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) @@ -1138,24 +1134,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); - if (currentFileFormat.indexOf(" ") > -1) - { - currentFileFormat = currentFileFormat.substring(0, - currentFileFormat.indexOf(" ")); - } + Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); } } - public boolean saveAlignment(String file, String format) + public boolean saveAlignment(String file, FileFormatI format) { boolean success = true; - if (format.equalsIgnoreCase("Jalview")) + if (FileFormat.Jalview.equals(format)) { String shortName = title; @@ -1174,17 +1164,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) - { - warningMessage("Cannot save file " + fileName + " using format " - + format, "Alignment output format not supported"); - if (!Jalview.isHeadlessMode()) - { - saveAs_actionPerformed(null); - } - return false; - } - AlignmentExportData exportData = getAlignmentForExport(format, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1198,8 +1177,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, exportData.getAlignment(), // class cast exceptions will // occur in the distant future exportData.getOmitHidden(), exportData.getStartEndPostions(), - f.getCacheSuffixDefault(format), - viewport.getColumnSelection()); + f.getCacheSuffixDefault(format), viewport.getAlignment() + .getHiddenColumns()); if (output == null) { @@ -1209,15 +1188,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); + PrintWriter out = new PrintWriter(new 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 })); + new Object[] { fileName, format.getName() })); } catch (Exception ex) { success = false; @@ -1228,11 +1206,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, MessageManager + JvOptionPane.showInternalMessageDialog(this, MessageManager .formatMessage("label.couldnt_save_file", new Object[] { fileName }), MessageManager .getString("label.error_saving_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return success; @@ -1247,8 +1225,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - JOptionPane.showInternalMessageDialog(this, warning, title, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, warning, title, + JvOptionPane.WARNING_MESSAGE); } return; } @@ -1262,9 +1240,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - - AlignmentExportData exportData = getAlignmentForExport( - e.getActionCommand(), viewport, null); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); + AlignmentExportData exportData = getAlignmentForExport(fileFormat, + viewport, null); if (exportData.getSettings().isCancelled()) { return; @@ -1273,12 +1252,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cap.setForInput(null); try { + FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(e.getActionCommand(), - exportData.getAlignment(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getColumnSelection())); + exportData + .getStartEndPostions(), viewport + .getAlignment().getHiddenColumns())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); @@ -1291,7 +1271,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } public static AlignmentExportData getAlignmentForExport( - String exportFormat, AlignViewportI viewport, + FileFormatI format, AlignViewportI viewport, AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; @@ -1307,7 +1287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (settings == null) { settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFormat); + viewport.hasHiddenColumns(), format); } // settings.isExportAnnotations(); @@ -1326,9 +1306,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { alignmentToExport = viewport.getAlignment(); } - alignmentStartEnd = alignmentToExport - .getVisibleStartAndEndIndex(viewport.getColumnSelection() - .getHiddenColumns()); + alignmentStartEnd = viewport.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; @@ -1343,14 +1322,15 @@ 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) @@ -1736,7 +1716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, synchronized void slideSequences(boolean right, int size) { - List sg = new ArrayList(); + List sg = new ArrayList<>(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( @@ -1755,7 +1735,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - List invertGroup = new ArrayList(); + List invertGroup = new ArrayList<>(); for (SequenceI seq : viewport.getAlignment().getSequences()) { @@ -1864,8 +1844,8 @@ 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); @@ -1888,10 +1868,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ArrayList hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport - .getSelectionGroup().getEndRes(); - for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + hiddenColumns = new ArrayList<>(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); + ArrayList hiddenRegions = viewport.getAlignment() + .getHiddenColumns().getHiddenColumnsCopy(); + for (int[] region : hiddenRegions) { if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { @@ -1951,7 +1933,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - String str, format; + String str; + FileFormatI format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); @@ -1960,7 +1943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - format = new IdentifyFile().identify(str, "Paste"); + format = new IdentifyFile().identify(str, DataSourceType.PASTE); } catch (OutOfMemoryError er) { @@ -1990,12 +1973,13 @@ 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) @@ -2159,7 +2143,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + vpRanges.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2359,13 +2343,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .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; } @@ -2563,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + vpRanges.setStartRes(0); } else { @@ -2630,13 +2614,13 @@ 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(vpRanges.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); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2669,12 +2653,12 @@ 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(vpRanges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2762,6 +2746,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ newap.av.replaceMappings(viewport.getAlignment()); + /* + * start up cDNA consensus (if applicable) now mappings are in place + */ + if (newap.av.initComplementConsensus()) + { + newap.refresh(true); // adjust layout of annotations + } + newap.av.viewName = getNewViewName(viewTitle); addAlignmentPanel(newap, true); @@ -2819,7 +2811,7 @@ 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) @@ -2840,7 +2832,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void expandViews_actionPerformed(ActionEvent e) { - Desktop.instance.explodeViews(this); + Desktop.explodeViews(this); } /** @@ -2910,8 +2902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition( - alignPanel.getSeqPanel().seqCanvas.searchResults, false); + alignPanel.scrollToPosition(viewport.getSearchResults(), false); } } @@ -2954,7 +2945,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - repaint(); + alignPanel.paintAlignment(true); viewport.sendSelection(); } @@ -2962,7 +2953,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - // alignPanel.paintAlignment(true); } /** @@ -2981,9 +2971,7 @@ 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.getColumnSelection() != null - && viewport.getColumnSelection().getSelected() != null && viewport - .getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -3011,8 +2999,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hideSelSequences_actionPerformed(null); hide = true; } - else if (!(toggleCols && viewport.getColumnSelection().getSelected() - .size() > 0)) + else if (!(toggleCols && viewport.hasSelectedColumns())) { showAllSeqs_actionPerformed(null); } @@ -3020,7 +3007,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { hideSelColumns_actionPerformed(null); if (!toggleSeqs) @@ -3212,34 +3199,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); alignPanel.paintAlignment(true); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - } - - /** - * Set or clear 'Show Sequence Features' - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) - { - viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight - .isSelected()); - if (viewport.isShowSequenceFeaturesHeight()) - { - // ensure we're actually displaying features - viewport.setShowSequenceFeatures(true); - showSeqFeatures.setSelected(true); - } - alignPanel.paintAlignment(true); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } } /** @@ -3295,11 +3254,11 @@ 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()); + true, frame.getWidth(), frame.getHeight(), true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() @@ -3308,6 +3267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { + overview.dispose(); alignPanel.setOverviewPanel(null); }; }); @@ -3316,160 +3276,151 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @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; + } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void hydrophobicityColour_actionPerformed(ActionEvent e) - { - changeColour(new HydrophobicColourScheme()); + /* + * 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 helixColour_actionPerformed(ActionEvent e) + public void changeColour(ColourSchemeI cs) { - changeColour(new HelixColourScheme()); - } + // TODO: pull up to controller method + ColourMenuHelper.setColourSelected(colourMenu, cs); - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void strandColour_actionPerformed(ActionEvent e) - { - changeColour(new StrandColourScheme()); + viewport.setGlobalColourScheme(cs); + + alignPanel.paintAlignment(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) + public void conservationMenuItem_actionPerformed(boolean selected) { - changeColour(new NucleotideColourScheme()); - } + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent e) - { - changeColour(new PurinePyrimidineColourScheme()); + changeColour(viewport.getGlobalColourScheme()); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } - /* - * public void covariationColour_actionPerformed(ActionEvent e) { - * changeColour(new - * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation - * ()[0])); } + /** + * Action on selecting or deselecting (Colour) Above PID Threshold */ @Override - public void annotationColour_actionPerformed(ActionEvent e) - { - new AnnotationColourChooser(viewport, alignPanel); - } - - @Override - public void annotationColumn_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed(boolean selected) { - new AnnotationColumnChooser(viewport, alignPanel); - } + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } - @Override - public void rnahelicesColour_actionPerformed(ActionEvent e) - { - new RNAHelicesColourChooser(viewport, alignPanel); + changeColour(viewport.getGlobalColourScheme()); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } /** @@ -3479,46 +3430,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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) + public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { - // TODO: pull up to controller method - - if (cs != null) - { - // 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); - } - } - - viewport.setGlobalColourScheme(cs); - + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0)); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3529,15 +3447,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void modifyPID_actionPerformed(ActionEvent e) + public void sortIDMenuItem_actionPerformed(ActionEvent e) { - if (viewport.getAbovePIDThreshold() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showPIDSlider(); - } + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } /** @@ -3547,15 +3463,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void modifyConservation_actionPerformed(ActionEvent e) + public void sortLengthMenuItem_actionPerformed(ActionEvent e) { - if (viewport.getConservationSelected() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showConservationSlider(); - } + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true); } /** @@ -3565,16 +3479,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) + public void sortGroupMenuItem_actionPerformed(ActionEvent e) { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); - - changeColour(viewport.getGlobalColourScheme()); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); - modifyConservation_actionPerformed(null); + alignPanel.paintAlignment(true); } /** @@ -3584,16 +3496,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); - - changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(null); + new RedundancyPanel(alignPanel, this); } /** @@ -3603,260 +3508,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void userDefinedColour_actionPerformed(ActionEvent e) + public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) + if ((viewport.getSelectionGroup() == null) + || (viewport.getSelectionGroup().getSize() < 2)) { - new UserDefinedColours(alignPanel, null); + JvOptionPane.showInternalMessageDialog(this, MessageManager + .getString("label.you_must_select_least_two_sequences"), + MessageManager.getString("label.invalid_selection"), + JvOptionPane.WARNING_MESSAGE); } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); - - changeColour(udc); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(new PairwiseAlignPanel(viewport)); + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); } } - public void updateUserColourMenu() + @Override + public void autoCalculate_actionPerformed(ActionEvent e) { - - 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()) - { - 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! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0), null); - addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void sortIDMenuItem_actionPerformed(ActionEvent e) - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void sortLengthMenuItem_actionPerformed(ActionEvent e) - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByLength(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Length Sort", oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void sortGroupMenuItem_actionPerformed(ActionEvent e) - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByGroup(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.getAlignment())); - - alignPanel.paintAlignment(true); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) - { - new RedundancyPanel(alignPanel, this); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) - { - if ((viewport.getSelectionGroup() == null) - || (viewport.getSelectionGroup().getSize() < 2)) - { - JOptionPane.showInternalMessageDialog(this, MessageManager - .getString("label.you_must_select_least_two_sequences"), - MessageManager.getString("label.invalid_selection"), - JOptionPane.WARNING_MESSAGE); - } - else - { - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, - MessageManager.getString("action.pairwise_alignment"), 600, - 500); - } - } - - /** - * 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.autoCalculateConsensus = autoCalculate.isSelected(); + if (viewport.autoCalculateConsensus) { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); @@ -3876,83 +3552,24 @@ 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 */ @@ -3960,57 +3577,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JOptionPane + JvOptionPane .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.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) { - title += viewport.viewName + " of "; + frameTitle += viewport.viewName + " of "; } - title += this.title; + frameTitle += this.title; - Desktop.addInternalFrame(tp, title, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, 600, 500); } /** @@ -4132,53 +3733,15 @@ 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 treePanels = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof TreePanel) @@ -4253,11 +3816,11 @@ 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); } @@ -4324,59 +3887,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - jalview.io.NewickFile fin = null; + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; try { - fin = new jalview.io.NewickFile(choice, "File"); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + fin = new NewickFile(filePath, DataSourceType.FILE); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); } catch (Exception ex) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, ex.getMessage(), MessageManager .getString("label.problem_reading_tree_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { - JOptionPane.showMessageDialog(Desktop.desktop, fin + JvOptionPane.showMessageDialog(Desktop.desktop, fin .getWarningMessage(), MessageManager .getString("label.possible_problem_with_tree_file"), - JOptionPane.WARNING_MESSAGE); + 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); - } - - 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 @@ -4395,7 +3946,7 @@ 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; @@ -4406,7 +3957,7 @@ 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); @@ -4415,7 +3966,7 @@ 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) { @@ -4450,7 +4001,7 @@ 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 " @@ -4465,24 +4016,20 @@ 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; + + /* + * do not i18n these strings - they are hard-coded in class + * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and + * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() + */ final JMenu msawsmenu = new JMenu("Alignment"); final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); - // final JMenu msawsmenu = new - // JMenu(MessageManager.getString("label.alignment")); - // final JMenu secstrmenu = new - // JMenu(MessageManager.getString("label.secondary_structure_prediction")); - // final JMenu seqsrchmenu = new - // JMenu(MessageManager.getString("label.sequence_database_search")); - // final JMenu analymenu = new - // JMenu(MessageManager.getString("label.analysis")); - // final JMenu dismenu = new - // JMenu(MessageManager.getString("label.protein_disorder")); // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) @@ -4653,14 +4200,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); AlignmentI dataset = viewport.getAlignment().getDataset(); + + showProducts.removeAll(); + final boolean dna = viewport.getAlignment().isNucleotide(); + + if (seqs == null || seqs.length == 0) + { + // nothing to see here. + return false; + } + boolean showp = false; try { - showProducts.removeAll(); - final boolean dna = viewport.getAlignment().isNucleotide(); - List ptypes = (seqs == null || seqs.length == 0) ? null - : new CrossRef(seqs, dataset) - .findXrefSourcesForSequences(dna); + List ptypes = new CrossRef(seqs, dataset) + .findXrefSourcesForSequences(dna); for (final String source : ptypes) { @@ -4703,231 +4257,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showProductsFor(final SequenceI[] sel, final boolean _odna, final String source) { - Runnable foo = new Runnable() - { - - @Override - public void run() - { - final long sttime = System.currentTimeMillis(); - AlignFrame.this.setProgressBar(MessageManager.formatMessage( - "status.searching_for_sequences_from", - new Object[] { source }), sttime); - try - { - AlignmentI alignment = AlignFrame.this.getViewport() - .getAlignment(); - AlignmentI dataset = alignment.getDataset() == null ? alignment - : alignment.getDataset(); - boolean dna = alignment.isNucleotide(); - if (_odna != dna) - { - System.err - .println("Conflict: showProducts for alignment originally " - + "thought to be " - + (_odna ? "DNA" : "Protein") - + " now searching for " - + (dna ? "DNA" : "Protein") + " Context."); - } - AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences( - source, dna); - if (xrefs == null) - { - return; - } - /* - * get display scheme (if any) to apply to features - */ - FeatureSettingsModelI featureColourScheme = new SequenceFetcher() - .getFeatureColourScheme(source); - - AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset, - xrefs); - if (!dna) - { - xrefsAlignment = AlignmentUtils.makeCdsAlignment( - xrefsAlignment.getSequencesArray(), dataset, sel); - xrefsAlignment.alignAs(alignment); - } - - /* - * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset - * sequences). If we are DNA, drop introns and update mappings - */ - AlignmentI copyAlignment = null; - - if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) - { - boolean copyAlignmentIsAligned = false; - if (dna) - { - copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset, - xrefsAlignment.getSequencesArray()); - if (copyAlignment.getHeight() == 0) - { - System.err.println("Failed to make CDS alignment"); - } - - /* - * pending getting Embl transcripts to 'align', - * we are only doing this for Ensembl - */ - // TODO proper criteria for 'can align as cdna' - if (DBRefSource.ENSEMBL.equalsIgnoreCase(source) - || AlignmentUtils.looksLikeEnsembl(alignment)) - { - copyAlignment.alignAs(alignment); - copyAlignmentIsAligned = true; - } - } - else - { - copyAlignment = AlignmentUtils.makeCopyAlignment(sel, - xrefs.getSequencesArray(), dataset); - } - copyAlignment.setGapCharacter(AlignFrame.this.viewport - .getGapCharacter()); - - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - - /* - * register any new mappings for sequence mouseover etc - * (will not duplicate any previously registered mappings) - */ - ssm.registerMappings(dataset.getCodonFrames()); - - if (copyAlignment.getHeight() <= 0) - { - System.err.println("No Sequences generated for xRef type " - + source); - return; - } - /* - * align protein to dna - */ - if (dna && copyAlignmentIsAligned) - { - xrefsAlignment.alignAs(copyAlignment); - } - else - { - /* - * align cdna to protein - currently only if - * fetching and aligning Ensembl transcripts! - */ - // TODO: generalise for other sources of locus/transcript/cds data - if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source)) - { - copyAlignment.alignAs(xrefsAlignment); - } - } - } - /* - * build AlignFrame(s) according to available alignment data - */ - AlignFrame newFrame = new AlignFrame(xrefsAlignment, - DEFAULT_WIDTH, DEFAULT_HEIGHT); - if (Cache.getDefault("HIDE_INTRONS", true)) - { - newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false); - } - String newtitle = String.format("%s %s %s", MessageManager - .getString(dna ? "label.proteins" : "label.nucleotides"), - MessageManager.getString("label.for"), getTitle()); - newFrame.setTitle(newtitle); - - if (copyAlignment == null) - { - /* - * split frame display is turned off in preferences file - */ - Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - return; // via finally clause - } - AlignFrame copyThis = new AlignFrame(copyAlignment, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - copyThis.setTitle(AlignFrame.this.getTitle()); - - boolean showSequenceFeatures = viewport.isShowSequenceFeatures(); - newFrame.setShowSeqFeatures(showSequenceFeatures); - copyThis.setShowSeqFeatures(showSequenceFeatures); - FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer(); - - /* - * copy feature rendering settings to split frame - */ - newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(myFeatureStyling); - copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(myFeatureStyling); - - /* - * apply 'database source' feature configuration - * if any was found - */ - // TODO is this the feature colouring for the original - // alignment or the fetched xrefs? either could be Ensembl - newFrame.getViewport().applyFeaturesStyle(featureColourScheme); - copyThis.getViewport().applyFeaturesStyle(featureColourScheme); - - SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame, - dna ? newFrame : copyThis); - newFrame.setVisible(true); - copyThis.setVisible(true); - String linkedTitle = MessageManager - .getString("label.linked_view_title"); - Desktop.addInternalFrame(sf, linkedTitle, -1, -1); - sf.adjustDivider(); - } catch (OutOfMemoryError e) - { - new OOMWarning("whilst fetching crossreferences", e); - } catch (Throwable e) - { - Cache.log.error("Error when finding crossreferences", e); - } finally - { - AlignFrame.this.setProgressBar(MessageManager.formatMessage( - "status.finished_searching_for_sequences_from", - new Object[] { source }), sttime); - } - } - - /** - * Makes an alignment containing the given sequences, and adds them to the - * given dataset, which is also set as the dataset for the new alignment - * - * TODO: refactor to DatasetI method - * - * @param dataset - * @param seqs - * @return - */ - protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset, - AlignmentI seqs) - { - SequenceI[] sprods = new SequenceI[seqs.getHeight()]; - for (int s = 0; s < sprods.length; s++) - { - sprods[s] = (seqs.getSequenceAt(s)).deriveSequence(); - if (dataset.getSequences() == null - || !dataset.getSequences().contains( - sprods[s].getDatasetSequence())) - { - dataset.addSequence(sprods[s].getDatasetSequence()); - } - sprods[s].updatePDBIds(); - } - Alignment al = new Alignment(sprods); - al.setDataset(dataset); - return al; - } - - }; - Thread frunner = new Thread(foo); - frunner.start(); + new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this)) + .start(); } /** @@ -4952,8 +4283,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -4962,8 +4293,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .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 { @@ -4989,11 +4320,11 @@ 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; } /** @@ -5001,14 +4332,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * contents or path to retrieve file - * @param type + * @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(String file, DataSourceType sourceType) { - return avc.parseFeaturesFile(file, type, - jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + return avc.parseFeaturesFile(file, sourceType, + Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } @@ -5049,8 +4380,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void drop(DropTargetDropEvent evt) { + // JAL-1552 - acceptDrop required before getTransferable call for + // 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(); + List files = new ArrayList<>(); + List protocols = new ArrayList<>(); try { @@ -5070,19 +4405,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Object[] { String,SequenceI} */ - ArrayList filesmatched = new ArrayList(); - ArrayList filesnotmatched = new ArrayList(); + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); for (int i = 0; i < files.size(); i++) { String file = files.get(i).toString(); String pdbfn = ""; - String protocol = FormatAdapter.checkProtocol(file); - if (protocol == jalview.io.FormatAdapter.FILE) + DataSourceType protocol = FormatAdapter.checkProtocol(file); + if (protocol == DataSourceType.FILE) { File fl = new File(file); pdbfn = fl.getName(); } - else if (protocol == jalview.io.FormatAdapter.URL) + else if (protocol == DataSourceType.URL) { URL url = new URL(file); pdbfn = url.getFile(); @@ -5106,7 +4441,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (mtch != null) { - String type = null; + FileFormatI type = null; try { type = new IdentifyFile().identify(file, protocol); @@ -5114,13 +4449,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { type = null; } - if (type != null) + if (type != null && type.isStructureFile()) { - if (type.equalsIgnoreCase("PDB")) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; } } // File wasn't named like one of the sequences or wasn't a PDB file. @@ -5131,20 +4463,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (filesmatched.size() > 0) { if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JOptionPane + || JvOptionPane .showConfirmDialog( this, MessageManager .formatMessage( - "label.automatically_associate_pdb_files_with_sequences_same_name", + "label.automatically_associate_structure_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) + .getString("label.automatically_associate_structure_files_by_name"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) { for (Object[] fm : filesmatched) @@ -5156,7 +4488,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq((String) fm[0], - (String) fm[1], toassoc, false, + (DataSourceType) fm[1], toassoc, false, Desktop.instance); if (pe != null) { @@ -5174,7 +4506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane .showConfirmDialog( this, "" @@ -5189,7 +4521,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + "", MessageManager .getString("label.ignore_unmatched_dropped_files"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { return; } @@ -5207,29 +4539,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * 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(String file, DataSourceType sourceType, + FileFormatI format, SequenceI assocSeq) { 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) { @@ -5237,13 +4572,12 @@ 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); + buildColourMenu(); changeColour(new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; statusBar @@ -5254,7 +4588,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // some problem - if no warning its probable that the ID matching // process didn't work - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, tcf.getWarningMessage() == null ? MessageManager @@ -5262,7 +4596,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : tcf.getWarningMessage(), MessageManager .getString("label.problem_reading_tcoffee_score_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } else @@ -5283,32 +4617,43 @@ 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 + statusBar + .setText(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(); + HiddenColumns cs = new HiddenColumns(); cs.hideInsertionsFor(repseq); - viewport.setColumnSelection(cs); + viewport.getAlignment().setHiddenColumns(cs); 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); } } else { - new FileLoader().LoadFile(viewport, file, protocol, format); + new FileLoader().LoadFile(viewport, file, sourceType, format); } } } @@ -5333,8 +4678,8 @@ 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); @@ -5357,6 +4702,28 @@ 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 @@ -5383,8 +4750,8 @@ 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 reply = JvOptionPane.showInternalInputDialog(this, msg, msg, + JvOptionPane.QUESTION_MESSAGE); if (reply != null) { @@ -6030,7 +5397,7 @@ 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) @@ -6056,7 +5423,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs .size()])); - AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); cdna.alignAs(alignment); String newtitle = "cDNA " + MessageManager.getString("label.for") + " " @@ -6123,12 +5490,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JOptionPane + JvOptionPane .showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.couldnt_run_groovy_script"), MessageManager .getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } else @@ -6161,6 +5528,55 @@ 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); + } + } } class PrintThread extends Thread