X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=97557290774ede7f79ddd6f9513b550bf4c0e275;hb=81c9c8d460d5e2261111f7bdced2a75f1af64f9a;hp=dba6717b23f9ba589f6bb0c919fa91514246157c;hpb=29cd3c8168e0b16d14d58b9dedfe738ebb6070ac;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index dba6717..9755729 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -65,6 +65,10 @@ import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.hmmer.HMMAlignThread; import jalview.hmmer.HMMBuildThread; +import jalview.hmmer.HMMERParamStore; +import jalview.hmmer.HMMERPreset; +import jalview.hmmer.HMMSearchThread; +import jalview.hmmer.HmmerCommand; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; @@ -75,7 +79,6 @@ import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FileParse; import jalview.io.FormatAdapter; -import jalview.io.HMMFile; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.JPredFile; @@ -91,6 +94,7 @@ import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; +import jalview.util.StringUtils; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; @@ -98,6 +102,9 @@ import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.ParamDatastoreI; +import jalview.ws.params.WsParamSetI; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; @@ -138,14 +145,18 @@ import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.Map; +import java.util.Scanner; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; import javax.swing.JEditorPane; +import javax.swing.JFileChooser; +import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; +import javax.swing.JOptionPane; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -165,10 +176,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public static final int DEFAULT_HEIGHT = 500; - boolean autoAlignNewSequences; - - boolean recurring; - /* * The currently displayed panel (selected tabbed view if more than one) */ @@ -179,6 +186,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ViewportRanges vpRanges; public AlignViewControllerI avc; + /* + * The selected HMM for this align frame + */ + SequenceI selectedHMMSequence; List alignPanels = new ArrayList<>(); @@ -248,8 +259,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param height * height of frame. */ - public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, - int width, int height) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height) { this(al, hiddenColumns, width, height, null); } @@ -265,8 +276,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param sequenceSetId * (may be null) */ - public AlignFrame(AlignmentI al, HiddenColumns 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); } @@ -284,8 +295,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewId * (may be null) */ - public AlignFrame(AlignmentI al, HiddenColumns 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); @@ -390,7 +401,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); buildColourMenu(); - buildHMMERMenu(); if (Desktop.desktop != null) { @@ -497,19 +507,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } - private void buildHMMERMenu() - { - hmmerMenu.removeAll(); - - hmmerMenu.add(autoAlignSeqs); - hmmerMenu.addSeparator(); - - hmmerMenu.add(hmmAlign); - hmmerMenu.add(hmmBuild); - hmmerMenu.add(hmmSearch); - - } - /** * Change the filename and format for the alignment, and enable the 'reload' * button functionality. @@ -538,9 +535,10 @@ 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()); @@ -580,7 +578,8 @@ 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 { @@ -603,9 +602,8 @@ 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; @@ -628,9 +626,8 @@ 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; @@ -677,9 +674,9 @@ 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") })); + statusBar.setText(MessageManager + .formatMessage("label.keyboard_editing_mode", new String[] + { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges @@ -717,24 +714,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - if (viewport.getWrapAlignment()) - { - vpRanges.scrollUp(true); - } - else - { - vpRanges.pageUp(); - } + vpRanges.pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.getWrapAlignment()) - { - vpRanges.scrollUp(false); - } - else - { - vpRanges.pageDown(); - } + vpRanges.pageDown(); break; } } @@ -747,16 +730,16 @@ 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; } @@ -843,8 +826,8 @@ 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(); } @@ -888,13 +871,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); - modifyConservation.setEnabled(!nucleotide - && conservationMenuItem.isSelected()); + modifyConservation + .setEnabled(!nucleotide && conservationMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); - showComplementMenuItem.setText(nucleotide ? MessageManager - .getString("label.protein") : MessageManager - .getString("label.nucleotide")); + showComplementMenuItem + .setText(nucleotide ? MessageManager.getString("label.protein") + : MessageManager.getString("label.nucleotide")); } /** @@ -1041,35 +1024,201 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void hmmBuild_actionPerformed(ActionEvent e) - throws IOException, InterruptedException + public void hmmBuildSettings_actionPerformed() { - new Thread(new HMMBuildThread(this)).start(); + if (!(alignmentIsSufficient(1))) + { + return; + } + WsParamSetI set = new HMMERPreset(); + List args = new ArrayList<>(); + ParamDatastoreI store = new HMMERParamStore("hmmbuild"); + WsJobParameters params = new WsJobParameters(new JFrame(), store, set, + args); + if (params.showRunDialog()) + { + new Thread(new HMMBuildThread(this, params.getJobParams())).start(); + } alignPanel.repaint(); } @Override - public void hmmAlign_actionPerformed(ActionEvent e) - throws IOException, InterruptedException + public void hmmAlignSettings_actionPerformed() { - SequenceI seq = getViewport().getAlignment() - .getHMMConsensusSequences(false).get(0); - new Thread(new HMMAlignThread(this, true)).start(); + if (!(checkForHMM() && alignmentIsSufficient(2))) + { + return; + } + WsParamSetI set = new HMMERPreset(); + List args = new ArrayList<>(); + ParamDatastoreI store = new HMMERParamStore("hmmalign"); + WsJobParameters params = new WsJobParameters(new JFrame(), store, set, + args); + if (params.showRunDialog()) + { + new Thread(new HMMAlignThread(this, true, params.getJobParams())) + .start(); + } alignPanel.repaint(); } @Override - public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs) + public void hmmSearchSettings_actionPerformed() { - autoAlignNewSequences = autoAlignSeqs; + if (!checkForHMM()) + { + return; + } + WsParamSetI set = new HMMERPreset(); + List args = new ArrayList<>(); + ParamDatastoreI store = new HMMERParamStore("hmmsearch"); + WsJobParameters params = new WsJobParameters(new JFrame(), store, set, + args); + if (params.showRunDialog()) + { + new Thread(new HMMSearchThread(this, true, params.getJobParams())) + .start(); + } alignPanel.repaint(); } @Override - public void hmmSearch_actionPerformed(ActionEvent e) + public void hmmBuildRun_actionPerformed() { - alignPanel.repaint(); + if (!alignmentIsSufficient(1)) + { + return; + } + new Thread(new HMMBuildThread(this, null)) + .start(); + } + + @Override + public void hmmAlignRun_actionPerformed() + { + if (!(checkForHMM() && alignmentIsSufficient(2))) + { + return; + } + new Thread(new HMMAlignThread(this, true, null)) + .start(); + } + + @Override + public void hmmSearchRun_actionPerformed() + { + if (!checkForHMM()) + { + return; + } + new Thread(new HMMSearchThread(this, true, null)) + .start(); + } + + /** + * Checks if the frame has a selected hidden Markov model + * + * @return + */ + private boolean checkForHMM() + { + if (getSelectedHMM() == null) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.no_selected_hmm")); + return false; + } + return true; + } + + /** + * Checks if the alignment contains the required number of sequences. + * + * @param required + * @return + */ + public boolean alignmentIsSufficient(int required) + { + if (getViewport().getAlignment().getSequences().size() < required) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.not_enough_sequences")); + return false; + } + return true; + } + + @Override + public void addDatabase_actionPerformed() throws IOException + { + if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null) + { + Cache.setProperty(Preferences.HMMSEARCH_DBS, ""); + Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, ""); + } + + String path = openFileChooser(false); + if (new File(path).exists()) + { + IdentifyFile identifier = new IdentifyFile(); + FileFormatI format = identifier.identify(path, DataSourceType.FILE); + if (format == FileFormat.Fasta || format == FileFormat.Stockholm + || format == FileFormat.Pfam) + { + String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS); + String currentDbPaths = Cache + .getProperty(Preferences.HMMSEARCH_DB_PATHS); + currentDbPaths += " " + path; + + String fileName = StringUtils.getLastToken(path, File.separator); + Scanner scanner = new Scanner(fileName).useDelimiter("."); + String name = scanner.next(); + scanner.close(); + currentDbs += " " + path; // TODO remove path from file name + scanner.close(); + + Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths); + Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths); + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.invalid_format")); + } + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.not_enough_sequences")); + } + } + + /** + * Opens a file chooser + * + * @param forFolder + * @return + */ + protected String openFileChooser(boolean forFolder) + { + String choice = null; + JFileChooser chooser = new JFileChooser(); + if (forFolder) + { + chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); + } + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); + + int value = chooser.showOpenDialog(this); + + if (value == JFileChooser.APPROVE_OPTION) + { + choice = chooser.getSelectedFile().getPath(); + } + return choice; } @Override @@ -1103,7 +1252,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } @@ -1112,7 +1262,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL : DataSourceType.FILE; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); @@ -1144,8 +1295,8 @@ 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 @@ -1177,14 +1328,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { - String format = currentFileFormat == null ? null : currentFileFormat - .getName(); - JalviewFileChooser chooser = JalviewFileChooser.forWrite( - Cache.getProperty("LAST_DIRECTORY"), format); + 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); @@ -1194,14 +1345,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat = chooser.getSelectedFormat(); 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); + 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(); value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) @@ -1229,15 +1377,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (shortName.indexOf(java.io.File.separatorChar) > -1) { - shortName = shortName.substring(shortName - .lastIndexOf(java.io.File.separatorChar) + 1); + shortName = shortName.substring( + shortName.lastIndexOf(java.io.File.separatorChar) + 1); } success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] { - fileName, format })); + "label.successfully_saved_to_file_in_format", new Object[] + { fileName, format })); } else @@ -1250,13 +1398,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } FormatAdapter f = new FormatAdapter(alignPanel, exportData.getSettings()); - String output = f.formatSequences( - format, - exportData.getAlignment(), // class cast exceptions will + String output = f.formatSequences(format, exportData.getAlignment(), // class + // cast + // exceptions + // will // occur in the distant future exportData.getOmitHidden(), exportData.getStartEndPostions(), - f.getCacheSuffixDefault(format), viewport.getAlignment() - .getHiddenColumns()); + f.getCacheSuffixDefault(format), + viewport.getAlignment().getHiddenColumns()); if (output == null) { @@ -1272,8 +1421,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, out.close(); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", - new Object[] { fileName, format.getName() })); + "label.successfully_saved_to_file_in_format", new Object[] + { fileName, format.getName() })); } catch (Exception ex) { success = false; @@ -1285,9 +1434,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", - new Object[] { fileName }), MessageManager - .getString("label.error_saving_file"), + .formatMessage("label.couldnt_save_file", new Object[] + { fileName }), + MessageManager.getString("label.error_saving_file"), JvOptionPane.WARNING_MESSAGE); } @@ -1318,8 +1467,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - FileFormatI fileFormat = FileFormats.getInstance().forName( - e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); AlignmentExportData exportData = getAlignmentForExport(fileFormat, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1334,15 +1483,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), - exportData - .getStartEndPostions(), viewport - .getAlignment().getHiddenColumns())); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", - new Object[] { e.getActionCommand() }), 600, 500); + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + 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); + new OOMWarning("Outputting alignment as " + e.getActionCommand(), + oom); cap.dispose(); } @@ -1384,10 +1533,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { alignmentToExport = viewport.getAlignment(); } - alignmentStartEnd = alignmentToExport - .getVisibleStartAndEndIndex(viewport.getAlignment() - .getHiddenColumns() - .getHiddenRegions()); + alignmentStartEnd = viewport.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; @@ -1489,10 +1636,10 @@ 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.load_jalview_annotations")); - chooser.setToolTipText(MessageManager - .getString("label.load_jalview_annotations")); + chooser.setDialogTitle( + MessageManager.getString("label.load_jalview_annotations")); + chooser.setToolTipText( + MessageManager.getString("label.load_jalview_annotations")); int value = chooser.showOpenDialog(null); @@ -1591,9 +1738,9 @@ 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 { @@ -1606,9 +1753,9 @@ 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 { @@ -1680,8 +1827,8 @@ 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() != @@ -1689,8 +1836,8 @@ 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()); } } @@ -1720,8 +1867,8 @@ 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() != @@ -1729,8 +1876,8 @@ 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()); } } @@ -1745,8 +1892,8 @@ 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) { @@ -1800,15 +1947,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -1837,13 +1984,13 @@ 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; @@ -1888,9 +2035,8 @@ 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) @@ -1938,8 +2084,8 @@ 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); @@ -1950,15 +2096,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.hasHiddenColumns()) { hiddenColumns = new ArrayList<>(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport - .getSelectionGroup().getEndRes(); - for (int[] region : viewport.getAlignment().getHiddenColumns() - .getHiddenRegions()) + + 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) { - hiddenColumns.add(new int[] { region[0] - hiddenOffset, - region[1] - hiddenOffset }); + hiddenColumns + .add(new int[] + { region[0] - hiddenOffset, region[1] - hiddenOffset }); } } } @@ -1966,8 +2116,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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() })); + "label.copied_sequences_to_clipboard", new Object[] + { Integer.valueOf(seqs.length).toString() })); } /** @@ -2125,8 +2275,8 @@ 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() } @@ -2156,18 +2306,20 @@ 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(); @@ -2186,7 +2338,8 @@ 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++) @@ -2207,12 +2360,13 @@ 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(); @@ -2222,8 +2376,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // was // duplicated // earlier - alignment - .setAnnotationIndex(sequences[i].getAnnotation()[a], a); + alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], + a); } } } @@ -2303,9 +2457,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // >>>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. @@ -2343,8 +2496,8 @@ 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"); @@ -2362,9 +2515,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // >>>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. @@ -2426,8 +2578,8 @@ 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 = JvOptionPane.showConfirmDialog(this, @@ -2456,8 +2608,8 @@ 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 @@ -2621,8 +2773,8 @@ 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 { @@ -2642,10 +2794,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - statusBar.setText(MessageManager.formatMessage( - "label.removed_columns", - new String[] { Integer.valueOf(trimRegion.getSize()) - .toString() })); + statusBar.setText(MessageManager + .formatMessage("label.removed_columns", new String[] + { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2658,8 +2809,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } @@ -2677,8 +2828,8 @@ 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(); } @@ -2693,10 +2844,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", - new Object[] { Integer.valueOf(removeGapCols.getSize()) - .toString() })); + statusBar.setText(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 @@ -2708,8 +2858,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); vpRanges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2727,8 +2877,8 @@ 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(); } @@ -2747,8 +2897,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, vpRanges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2762,8 +2912,8 @@ 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()); } /** @@ -2877,8 +3027,8 @@ 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); @@ -3032,7 +3182,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - repaint(); + alignPanel.paintAlignment(true); viewport.sendSelection(); } @@ -3040,7 +3190,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - // alignPanel.paintAlignment(true); } /** @@ -3059,9 +3208,8 @@ 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. @@ -3287,10 +3435,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); alignPanel.paintAlignment(true); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } } /** @@ -3321,14 +3465,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, editPane.setEditable(false); StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); - editPane.setText(MessageManager.formatMessage("label.html_content", - new Object[] { contents.toString() })); + editPane.setText( + MessageManager.formatMessage("label.html_content", new Object[] + { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new Object[] { getTitle() }), - 500, 400); + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.alignment_properties", new Object[] + { getTitle() }), 500, 400); } /** @@ -3346,22 +3491,25 @@ 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() }), - true, frame.getWidth(), frame.getHeight(), true, true); + 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() - { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - alignPanel.setOverviewPanel(null); - }; - }); + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + overview.dispose(); + alignPanel.setOverviewPanel(null); + }; + }); alignPanel.setOverviewPanel(overview); } @@ -3416,7 +3564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 'User Defined' opens a panel to configure or load a * user-defined colour scheme */ - if (ResidueColourScheme.USER_DEFINED.equals(name)) + if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) { new UserDefinedColours(alignPanel); return; @@ -3452,8 +3600,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void modifyPID_actionPerformed() { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), + alignPanel.getViewName()); SliderPanel.showPIDSlider(); } @@ -3524,8 +3672,8 @@ 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)); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); @@ -3542,8 +3690,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.getAlignment())); + addHistoryItem( + new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3604,8 +3752,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JvOptionPane.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"), JvOptionPane.WARNING_MESSAGE); } @@ -3625,8 +3774,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.autoCalculateConsensus = autoCalculate.isSelected(); if (viewport.autoCalculateConsensus) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } @@ -3652,7 +3801,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param options * parameters for the distance or similarity calculation */ - void newTreePanel(String type, String modelName, SimilarityParamsI options) + void newTreePanel(String type, String modelName, + SimilarityParamsI options) { String frameTitle = ""; TreePanel tp; @@ -3668,14 +3818,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - 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); + 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; } @@ -3716,8 +3864,9 @@ 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() { @@ -3730,8 +3879,8 @@ 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); } @@ -3787,7 +3936,8 @@ 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 @@ -3830,8 +3980,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sortByTreeMenu.removeAll(); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); List treePanels = new ArrayList<>(); for (Component comp : comps) { @@ -3970,9 +4120,10 @@ 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")); + chooser.setDialogTitle( + MessageManager.getString("label.select_newick_like_tree_file")); + chooser.setToolTipText( + MessageManager.getString("label.load_tree_file")); int value = chooser.showOpenDialog(null); @@ -3987,20 +4138,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + 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.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager + .getString("label.possible_problem_with_tree_file"), JvOptionPane.WARNING_MESSAGE); } } @@ -4230,9 +4378,9 @@ 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); } } }); @@ -4317,7 +4465,8 @@ 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); @@ -4326,9 +4475,9 @@ 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; @@ -4345,8 +4494,8 @@ 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)) .start(); @@ -4369,8 +4518,8 @@ 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"); @@ -4380,8 +4529,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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"); JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, @@ -4391,9 +4540,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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)) { @@ -4491,8 +4640,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // check to see if any of these files have names matching sequences in // the alignment - SequenceIdMatcher idm = new SequenceIdMatcher(viewport - .getAlignment().getSequencesArray()); + SequenceIdMatcher idm = new SequenceIdMatcher( + viewport.getAlignment().getSequencesArray()); /** * Object[] { String,SequenceI} */ @@ -4554,20 +4703,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (filesmatched.size() > 0) { if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JvOptionPane - .showConfirmDialog( - this, - MessageManager - .formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] { Integer - .valueOf( - filesmatched - .size()) - .toString() }), - MessageManager - .getString("label.automatically_associate_structure_files_by_name"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) + || JvOptionPane.showConfirmDialog(this, + MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }), + MessageManager.getString( + "label.automatically_associate_structure_files_by_name"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) { for (Object[] fm : filesmatched) @@ -4583,9 +4727,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance); if (pe != null) { - System.err.println("Associated file : " - + ((String) fm[0]) + " with " - + toassoc.getDisplayId(true)); + System.err.println("Associated file : " + ((String) fm[0]) + + " with " + toassoc.getDisplayId(true)); assocfiles++; } } @@ -4595,24 +4738,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (filesnotmatched.size() > 0) { - if (assocfiles > 0 - && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane - .showConfirmDialog( - this, - "" - + 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)) + if (assocfiles > 0 && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(this, + "" + 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)) { return; } @@ -4645,7 +4782,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void loadJalviewDataFile(String file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) - throws IOException, InterruptedException { try { @@ -4656,9 +4792,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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 || FileFormat.Pfam - .equals(format)) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, sourceType) : false; + boolean isAnnotation = (format == null + || FileFormat.Pfam.equals(format)) + ? new AnnotationFile().annotateAlignmentView(viewport, + file, sourceType) + : false; if (!isAnnotation) { @@ -4672,25 +4810,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (tcf.annotateAlignment(viewport.getAlignment(), true)) { buildColourMenu(); - changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + changeColour( + new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; - statusBar - .setText(MessageManager - .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + statusBar.setText(MessageManager.getString( + "label.successfully_pasted_tcoffee_scores_to_alignment")); } else { // some problem - if no warning its probable that the ID matching // process didn't work - 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); + 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 @@ -4699,9 +4836,9 @@ 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) @@ -4715,25 +4852,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (FileFormat.ScoreMatrix == format) { - ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file, - sourceType)); + ScoreMatrixFile sm = new ScoreMatrixFile( + new FileParse(file, sourceType)); sm.parse(); // todo: i18n this message - statusBar - .setText(MessageManager.formatMessage( - "label.successfully_loaded_matrix", - sm.getMatrixName())); - } - else if (FileFormat.HMMER3.equals(format)) - { - HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); - HiddenMarkovModel hmm = hmmFile.getHMM(); - SequenceI hmmSeq = hmm.initHMMSequence(this, 0); - getViewport().initInformation(hmmSeq); - getViewport().updateInformation(alignPanel); - - isAnnotation = true; - + statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_matrix", + sm.getMatrixName())); } else if (FileFormat.Jnet.equals(format)) { @@ -4782,20 +4907,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } new OOMWarning( "loading data " - + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard." - : "using " + sourceType + " from " + file) + + (sourceType != null + ? (sourceType == DataSourceType.PASTE + ? "from clipboard." + : "using " + sourceType + " from " + + file) : ".") - + (format != null ? "(parsing as '" + format - + "' file)" : ""), oom, Desktop.desktop); - } - if (autoAlignNewSequences && !recurring) - { - recurring = true; - HiddenMarkovModel hmm = getViewport().getAlignment() - .getHMMConsensusSequences(false).get(0).getHMM(); - new Thread(new HMMAlignThread(this, false)).start(); + + (format != null + ? "(parsing as '" + format + "' file)" + : ""), + oom, Desktop.desktop); } - recurring = false; } /** @@ -4845,7 +4967,8 @@ 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); @@ -4960,14 +5083,14 @@ 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.setToolTipText( + MessageManager.getString("label.trim_retrieved_sequences")); trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); trimrs.addActionListener(new ActionListener() { @@ -4982,8 +5105,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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() { @@ -4997,8 +5120,9 @@ 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() { @@ -5101,8 +5225,8 @@ 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++; } @@ -5112,9 +5236,9 @@ 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 @@ -5152,30 +5276,33 @@ 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 }; @@ -5214,8 +5341,8 @@ 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); @@ -5444,17 +5571,14 @@ 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)); } @@ -5557,15 +5681,15 @@ 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()])); + 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); } /** @@ -5598,8 +5722,8 @@ 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) { @@ -5626,12 +5750,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JvOptionPane - .showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.couldnt_run_groovy_script"), - MessageManager - .getString("label.groovy_support_failed"), - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.couldnt_run_groovy_script"), + MessageManager.getString("label.groovy_support_failed"), + JvOptionPane.ERROR_MESSAGE); } } else @@ -5671,9 +5793,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // 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); + (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, + (actionEvent.getModifiers() & (ActionEvent.META_MASK + | ActionEvent.CTRL_MASK)) != 0); } /** @@ -5688,8 +5810,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, - viewport.getAlignment(), false); + ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(), + false); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -5713,6 +5835,69 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new CalculationChooser(AlignFrame.this); } } + + /** + * Sets the status of the HMMER menu + */ + public void updateHMMERStatus() + { + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + } + + /** + * Returns the selected hidden Markov model. + * + * @return + */ + public HiddenMarkovModel getSelectedHMM() + { + if (selectedHMMSequence == null) + { + return null; + } + return selectedHMMSequence.getHMM(); + } + + /** + * Returns the selected hidden Markov model. + * + * @return + */ + public SequenceI getSelectedHMMSequence() + { + return selectedHMMSequence; + } + + /** + * Sets the selected hidden Markov model + * + * @param selectedHMM + */ + public void setSelectedHMMSequence(SequenceI selectedHMM) + { + this.selectedHMMSequence = selectedHMM; + hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to " + + selectedHMM.getHMM().getName()); + hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with " + + selectedHMM.getHMM().getName()); + } + + @Override + public void hmmerMenu_actionPerformed(ActionEvent e) + { + SequenceGroup grp = getViewport().getSelectionGroup(); + if (grp != null) + { + hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from " + + grp.getName()); + } + else + { + hmmBuild.setText(MessageManager.getString("label.hmmbuild") + + " from Alignment"); + } + } + } class PrintThread extends Thread @@ -5751,5 +5936,4 @@ class PrintThread extends Thread } } } - }