X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc81eef681a89e8823a45e44bd6ce4b530adbd0a;hb=c2b931a5a0ea81bdc93db1f0cf632b07717c5066;hp=f2ff1d4e238b543dae69ac55be81cad81d455e79;hpb=2e02b14ba33c2cf4618f65c831a506f81e621589;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f2ff1d4..cc81eef 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,10 +20,63 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Deque; +import java.util.List; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComponent; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; import jalview.analysis.Dna; +import jalview.analysis.GeneticCodeI; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignExportSettingsI; @@ -32,6 +85,7 @@ 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.SimilarityParamsI; @@ -62,8 +116,16 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.hmmer.HMMAlign; +import jalview.hmmer.HMMBuild; +import jalview.hmmer.HMMERParamStore; +import jalview.hmmer.HMMERPreset; +import jalview.hmmer.HMMSearch; +import jalview.hmmer.HmmerCommand; +import jalview.hmmer.JackHMMER; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; +import jalview.io.BackupFiles; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -83,71 +145,35 @@ import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; +import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; -import jalview.util.dialogrunner.RunResponse; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.ServiceChangeListener; +import jalview.ws.WSDiscovererI; +import jalview.ws.api.ServiceWithParameters; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; -import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.jws2.PreferredServiceRegistry; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.ParamDatastoreI; +import jalview.ws.params.WsParamSetI; import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.slivkaws.SlivkaWSDiscoverer; +import java.io.IOException; +import java.util.HashSet; +import java.util.Set; -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Component; -import java.awt.Rectangle; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.FocusAdapter; -import java.awt.event.FocusEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -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; -import java.util.Deque; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Vector; - -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JComponent; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLabel; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JPanel; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; +import javax.swing.JFileChooser; +import javax.swing.JOptionPane; /** * DOCUMENT ME! @@ -155,10 +181,11 @@ import javax.swing.SwingUtilities; * @author $author$ * @version $Revision$ */ -public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener +@SuppressWarnings("serial") +public class AlignFrame extends GAlignFrame + implements DropTargetListener, IProgressIndicator, + AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener { - public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -184,6 +211,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ String fileName = null; + /** + * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping + */ File fileObject; /** @@ -338,6 +368,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { + // setBackground(Color.white); // BH 2019 + if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); @@ -386,12 +418,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - /** - * BH 2018 ignore service listeners - * - * @j2sNative - * - */ + if (!Platform.isJS()) { addServiceListeners(); } @@ -622,7 +649,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) { - cut_actionPerformed(null); + cut_actionPerformed(); } else { @@ -789,6 +816,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ap.av.updateConservation(ap); ap.av.updateConsensus(ap); ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); } } @@ -807,55 +835,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return viewport; } + @Override + public void servicesChanged(WSDiscovererI discoverer, + Collection services) + { + buildWebServicesMenu(); + } + /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { - final java.beans.PropertyChangeListener thisListener; - Desktop.instance.addJalviewPropertyChangeListener("services", - thisListener = new java.beans.PropertyChangeListener() - { - @Override - public void propertyChange(PropertyChangeEvent evt) - { - // // System.out.println("Discoverer property change."); - // if (evt.getPropertyName().equals("services")) - { - SwingUtilities.invokeLater(new Runnable() - { - - @Override - public void run() - { - System.err.println( - "Rebuild WS Menu for service change"); - BuildWebServiceMenu(); - } - - }); - } - } - }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - // System.out.println("deregistering discoverer listener"); - Desktop.instance.removeJalviewPropertyChangeListener("services", - thisListener); - closeMenuItem_actionPerformed(true); - }; - }); - // Finally, build the menu once to get current service state - new Thread(new Runnable() + WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance(); + discoverer.addServiceChangeListener(this); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { + WSDiscovererI discoverer = Jws2Discoverer.getDiscoverer(); + discoverer.addServiceChangeListener(this); + } + // legacy event listener for compatibility with jws1 + PropertyChangeListener legacyListener = (changeEvent) -> { + buildWebServicesMenu(); + }; + Desktop.instance.addJalviewPropertyChangeListener("services",legacyListener); + + addInternalFrameListener(new InternalFrameAdapter() { @Override - public void run() - { - BuildWebServiceMenu(); + public void internalFrameClosed(InternalFrameEvent e) { + System.out.println("deregistering discoverer listener"); + SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this); + Jws2Discoverer.getDiscoverer().removeServiceChangeListener(AlignFrame.this); + Desktop.instance.removeJalviewPropertyChangeListener("services", legacyListener); + closeMenuItem_actionPerformed(true); } - }).start(); + }); + buildWebServicesMenu(); } /** @@ -931,6 +947,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + showInformationHistogram.setSelected(av.isShowInformationHistogram()); + showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo()); + normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo()); ColourMenuHelper.setColourSelected(colourMenu, av.getGlobalColourScheme()); @@ -972,6 +991,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { progressBar.setProgressBar(message, id); } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(final long id, @@ -990,10 +1015,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return progressBar.operationInProgress(); } + /** + * Sets the text of the status bar. Note that setting a null or empty value + * will cause the status bar to be hidden, with possibly undesirable flicker + * of the screen layout. + */ @Override public void setStatus(String text) { - statusBar.setText(text); + statusBar.setText(text == null || text.isEmpty() ? " " : text); } /* @@ -1022,6 +1052,257 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void hmmBuild_actionPerformed(boolean withDefaults) + { + if (!alignmentIsSufficient(1)) + { + return; + } + + /* + * get default parameters, and optionally show a dialog + * to allow them to be modified + */ + ParamDatastoreI store = HMMERParamStore.forBuild(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMBuild(this, args)).start(); + } + + @Override + public void hmmAlign_actionPerformed(boolean withDefaults) + { + if (!(checkForHMM() && alignmentIsSufficient(2))) + { + return; + } + + /* + * get default parameters, and optionally show a dialog + * to allow them to be modified + */ + ParamDatastoreI store = HMMERParamStore.forAlign(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMAlign(this, args)).start(); + } + + @Override + public void hmmSearch_actionPerformed(boolean withDefaults) + { + if (!checkForHMM()) + { + return; + } + + /* + * get default parameters, and (if requested) show + * dialog to allow modification + */ + ParamDatastoreI store = HMMERParamStore.forSearch(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); + } + + @Override + public void jackhmmer_actionPerformed(boolean withDefaults) + { + + /* + * get default parameters, and (if requested) show + * dialog to allow modification + */ + + ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new JackHMMER(this, args)).start(); + alignPanel.repaint(); + + } + + /** + * Checks if the alignment has at least one hidden Markov model, if not shows + * a dialog advising to run hmmbuild or load an HMM profile + * + * @return + */ + private boolean checkForHMM() + { + if (viewport.getAlignment().getHmmSequences().isEmpty()) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.no_hmm")); + return false; + } + return true; + } + + @Override + protected void filterByEValue_actionPerformed() + { + viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff")); + } + + @Override + protected void filterByScore_actionPerformed() + { + viewport.filterByScore(inputDouble("Enter Bit Score Threshold")); + } + + private double inputDouble(String message) + { + String str = null; + Double d = null; + while (d == null || d <= 0) + { + str = JOptionPane.showInputDialog(this.alignPanel, message); + try + { + d = Double.valueOf(str); + } catch (NumberFormatException e) + { + } + } + return d; + } + + /** + * Checks if the alignment contains the required number of sequences. + * + * @param required + * @return + */ + public boolean alignmentIsSufficient(int required) + { + if (getViewport().getSequenceSelection().length < required) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("label.not_enough_sequences")); + return false; + } + return true; + } + + /** + * Opens a file browser and adds the selected file, if in Fasta, Stockholm or + * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a + * comma-separated list) + */ + @Override + public void addDatabase_actionPerformed() throws IOException + { + if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null) + { + Cache.setProperty(Preferences.HMMSEARCH_DBS, ""); + } + + String path = openFileChooser(false); + if (path != null && 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 currentDbPaths = Cache + .getProperty(Preferences.HMMSEARCH_DBS); + currentDbPaths += Preferences.COMMA + path; + Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths); + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.invalid_format")); + } + } + } + + /** + * Opens a file chooser, optionally restricted to selecting folders + * (directories) only. Answers the path to the selected file or folder, or + * null if none is chosen. + * + * @param + * @return + */ + protected String openFileChooser(boolean forFolder) + { + // TODO duplicates GPreferences method - relocate to JalviewFileChooser? + 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 public void reload_actionPerformed(ActionEvent e) { if (fileName != null) @@ -1223,7 +1504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void saveAlignment(String file, FileFormatI format) { - lastSaveSuccessful = false; + lastSaveSuccessful = true; lastFilenameSaved = file; lastFormatSaved = format; @@ -1232,21 +1513,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String shortName = title; if (shortName.indexOf(File.separatorChar) > -1) { - shortName = shortName.substring( - shortName.lastIndexOf(File.separatorChar) + 1); + shortName = shortName + .substring(shortName.lastIndexOf(File.separatorChar) + 1); } - lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file, + lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); - + statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format })); - + return; } AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION) + Runnable cancelAction = new Runnable() { @Override public void run() @@ -1254,7 +1535,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, lastSaveSuccessful = false; } }; - RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION) + Runnable outputAction = new Runnable() { @Override public void run() @@ -1273,21 +1554,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { + // create backupfiles object and get new temp filename destination + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null; try { - PrintWriter out = new PrintWriter(new FileWriter(file)); + String tempFilePath = doBackup ? backupfiles.getTempFilePath() + : file; + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + out.print(output); out.close(); AlignFrame.this.setTitle(file); - setStatus(MessageManager.formatMessage( + statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format.getName() })); + lastSaveSuccessful = true; } catch (Exception ex) { lastSaveSuccessful = false; ex.printStackTrace(); } + + if (doBackup) + { + backupfiles.setWriteSuccess(lastSaveSuccessful); + // do the backup file roll and rename the temp file to actual file + lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); + } } } }; @@ -1299,8 +1594,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignExportOptions choices = new AlignExportOptions( alignPanel.getAlignViewport(), format, options); - choices.setResponseAction(outputAction); - choices.setResponseAction(cancelAction); + choices.setResponseAction(0, outputAction); + choices.setResponseAction(1, cancelAction); choices.showDialog(); } else @@ -1322,7 +1617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FileFormatI fileFormat = FileFormats.getInstance() .forName(fileFormatName); AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION) + Runnable outputAction = new Runnable() { @Override public void run() @@ -1359,7 +1654,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignExportOptions choices = new AlignExportOptions( alignPanel.getAlignViewport(), fileFormat, options); - choices.setResponseAction(outputAction); + choices.setResponseAction(0, outputAction); choices.showDialog(); } else @@ -1464,17 +1759,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.load_jalview_annotations")); - chooser.setToolTipText( - MessageManager.getString("label.load_jalview_annotations")); - chooser.addResponse(new RunResponse(JalviewFileChooser.APPROVE_OPTION) + String tooltip = MessageManager + .getString("label.load_jalview_annotations"); + chooser.setDialogTitle(tooltip); + chooser.setToolTipText(tooltip); + chooser.setResponseHandler(0, new Runnable() { - @Override public void run() { @@ -1482,7 +1777,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); } - }); chooser.showOpenDialog(this); @@ -1524,9 +1818,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, closeView(alignPanel); } } - if (closeAllTabs) { + if (featureSettings != null && featureSettings.isOpen()) + { + featureSettings.close(); + featureSettings = null; + } /* * this will raise an INTERNAL_FRAME_CLOSED event and this method will * be called recursively, with the frame now in 'closed' state @@ -1890,7 +2188,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void copy_actionPerformed(ActionEvent e) + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -1952,9 +2250,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ @Override protected void pasteNew_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(true); } @@ -1964,9 +2265,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ @Override protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(false); } @@ -1976,8 +2280,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param newAlignment * true to paste to a new alignment, otherwise add to this. + * @throws InterruptedException + * @throws IOException */ - void paste(boolean newAlignment) + void paste(boolean newAlignment) throws IOException, InterruptedException { boolean externalPaste = true; try @@ -2065,7 +2371,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, && Desktop.jalviewClipboard[1] != alignment.getDataset(); // importDs==true instructs us to copy over new dataset sequences from // an existing alignment - Vector newDs = (importDs) ? new Vector() : null; // used to create + Vector newDs = (importDs) ? new Vector<>() : null; // used to + // create // minimum dataset set for (int i = 0; i < sequences.length; i++) @@ -2138,7 +2445,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2185,7 +2492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2204,7 +2511,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.getRanges().setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight() - 1); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2305,7 +2612,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } - } @Override @@ -2359,26 +2665,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action Cut (delete and copy) the selected region */ @Override - protected void cut_actionPerformed(ActionEvent e) + protected void cut_actionPerformed() { - copy_actionPerformed(null); - delete_actionPerformed(null); + copy_actionPerformed(); + delete_actionPerformed(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Performs menu option to Delete the currently selected region */ @Override - protected void delete_actionPerformed(ActionEvent evt) + protected void delete_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2387,51 +2687,60 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - /* - * If the cut affects all sequences, warn, remove highlighted columns - */ - if (sg.getSize() == viewport.getAlignment().getHeight()) + Runnable okAction = new Runnable() { - boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) - + 1) == viewport.getAlignment().getWidth()) ? true : false; - if (isEntireAlignWidth) + @Override + public void run() { - int confirm = JvOptionPane.showConfirmDialog(this, - MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ - MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JvOptionPane.OK_CANCEL_OPTION); + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); + + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), + sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); + + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); - if (confirm == JvOptionPane.CANCEL_OPTION - || confirm == JvOptionPane.CLOSED_OPTION) + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + if (viewport.getAlignment().getHeight() < 1) { - return; + try + { + AlignFrame.this.setClosed(true); + } catch (Exception ex) + { + } } } - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - SequenceI[] cut = sg.getSequences() - .toArray(new SequenceI[sg.getSize()]); - - addHistoryItem(new EditCommand( - MessageManager.getString("label.cut_sequences"), Action.CUT, - cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.getAlignment())); - - viewport.setSelectionGroup(null); - viewport.sendSelection(); - viewport.getAlignment().deleteGroup(sg); + }; - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - if (viewport.getAlignment().getHeight() < 1) + /* + * If the cut affects all sequences, prompt for confirmation + */ + boolean wholeHeight = sg.getSize() == viewport.getAlignment() + .getHeight(); + boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) + + 1) == viewport.getAlignment().getWidth()) ? true : false; + if (wholeHeight && wholeWidth) + { + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); + dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION + Object[] options = new Object[] { + MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + dialog.showDialog(MessageManager.getString("warn.delete_all"), + MessageManager.getString("label.delete_all"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + } + else { - try - { - this.setClosed(true); - } catch (Exception ex) - { - } + okAction.run(); } } @@ -2461,15 +2770,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - SequenceGroup sg = new SequenceGroup(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); - } + SequenceGroup sg = new SequenceGroup( + viewport.getAlignment().getSequences()); sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); + viewport.isSelectionGroupChanged(true); viewport.sendSelection(); // JAL-2034 - should delegate to // alignPanel to decide if overview needs @@ -2791,6 +3097,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.setRedoList(viewport.getRedoList()); /* + * copy any visualisation settings that are not saved in the project + */ + newap.av.setColourAppliesToAllGroups( + viewport.getColourAppliesToAllGroups()); + + /* * Views share the same mappings; need to deregister any new mappings * created by copyAlignPanel, and register the new reference to the shared * mappings @@ -2953,7 +3265,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition(viewport.getSearchResults(), false); + alignPanel.scrollToPosition(viewport.getSearchResults()); } } @@ -3012,7 +3324,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param toggleSeqs * @param toggleCols */ - private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { boolean hide = false; @@ -3100,6 +3412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3124,6 +3437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3145,7 +3459,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - // TODO: do we actually need to update overview for scale above change ? + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3159,6 +3473,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3172,6 +3487,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3225,9 +3541,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void featureSettings_actionPerformed(ActionEvent e) { + showFeatureSettingsUI(); + } + + @Override + public FeatureSettingsControllerI showFeatureSettingsUI() + { if (featureSettings != null) { - featureSettings.close(); + featureSettings.closeOldSettings(); featureSettings = null; } if (!showSeqFeatures.isSelected()) @@ -3237,6 +3559,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); + return featureSettings; } /** @@ -3285,18 +3608,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { contents.toString() }); contents = null; - if (Jalview.isJS()) + if (Platform.isJS()) { JLabel textLabel = new JLabel(); textLabel.setText(content); textLabel.setBackground(Color.WHITE); - + pane = new JPanel(new BorderLayout()); ((JPanel) pane).setOpaque(true); pane.setBackground(Color.WHITE); ((JPanel) pane).add(textLabel, BorderLayout.NORTH); } else + /** + * Java only + * + * @j2sIgnore + */ { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); @@ -3345,7 +3673,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { overview.dispose(); alignPanel.setOverviewPanel(null); - }; + } }); if (getKeyListeners().length > 0) { @@ -3415,7 +3743,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, - viewport.getAlignment(), viewport.getHiddenRepSequences()); + viewport, viewport.getAlignment(), + viewport.getHiddenRepSequences()); changeColour(cs); } @@ -3569,6 +3898,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true, false); } + @Override + public void sortEValueMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByEValue(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); + + } + + @Override + public void sortBitScoreMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByBitScore(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.getAlignment())); + alignPanel.paintAlignment(true, false); + + } + /** * DOCUMENT ME! * @@ -3778,35 +4129,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.getAlignment().getAlignmentAnnotation() - .hashCode() != _annotationScoreVectorHash) + .hashCode() == _annotationScoreVectorHash) { - sortByAnnotScore.removeAll(); - // almost certainly a quicker way to do this - but we keep it simple - Hashtable scoreSorts = new Hashtable(); - AlignmentAnnotation aann[]; - for (SequenceI sqa : viewport.getAlignment().getSequences()) + return; + } + + sortByAnnotScore.removeAll(); + Set scoreSorts = new HashSet<>(); + for (SequenceI sqa : viewport.getAlignment().getSequences()) + { + AlignmentAnnotation[] anns = sqa.getAnnotation(); + for (int i = 0; anns != null && i < anns.length; i++) { - aann = sqa.getAnnotation(); - for (int i = 0; aann != null && i < aann.length; i++) + AlignmentAnnotation aa = anns[i]; + if (aa != null && aa.hasScore() && aa.sequenceRef != null) { - if (aann[i].hasScore() && aann[i].sequenceRef != null) - { - scoreSorts.put(aann[i].label, aann[i].label); - } + scoreSorts.add(aa.label); } } - Enumeration labels = scoreSorts.keys(); - while (labels.hasMoreElements()) - { - addSortByAnnotScoreMenuItem(sortByAnnotScore, - (String) labels.nextElement()); - } - sortByAnnotScore.setVisible(scoreSorts.size() > 0); - scoreSorts.clear(); - - _annotationScoreVectorHash = viewport.getAlignment() - .getAlignmentAnnotation().hashCode(); } + for (String label : scoreSorts) + { + addSortByAnnotScoreMenuItem(sortByAnnotScore, label); + } + sortByAnnotScore.setVisible(!scoreSorts.isEmpty()); + + _annotationScoreVectorHash = viewport.getAlignment() + .getAlignmentAnnotation().hashCode(); } /** @@ -3966,8 +4315,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.addResponse(new jalview.util.dialogrunner.RunResponse( - JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { @Override public void run() @@ -3997,7 +4345,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JvOptionPane.WARNING_MESSAGE); } } - }).showOpenDialog(this); + }); + chooser.showOpenDialog(this); } public TreePanel showNewickTree(NewickFile nf, String treeTitle) @@ -4061,182 +4410,79 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - private boolean buildingMenu = false; - /** - * Generates menu items and listener event actions for web service clients - * + * Schedule the web services menu rebuild to the event dispatch thread. */ - public void BuildWebServiceMenu() + public void buildWebServicesMenu() { - while (buildingMenu) - { - try + SwingUtilities.invokeLater(() -> { + Cache.log.info("Rebuiling WS menu"); + webService.removeAll(); + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - System.err.println("Waiting for building menu to finish."); - Thread.sleep(10); - } catch (Exception e) + SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance(); + JMenu submenu = new JMenu("Slivka"); + buildWebServicesMenu(discoverer, submenu); + webService.add(submenu); + } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { + WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer(); + JMenu submenu = new JMenu("JABAWS"); + buildLegacyWebServicesMenu(submenu); + buildWebServicesMenu(jws2servs, submenu); + webService.add(submenu); } - } - final AlignFrame me = this; - buildingMenu = true; - new Thread(new Runnable() + }); + } + + private void buildLegacyWebServicesMenu(JMenu menu) + { + JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); + if (Discoverer.services != null && Discoverer.services.size() > 0) { - @Override - public void run() + var secstrpred = Discoverer.services.get("SecStrPred"); + if (secstrpred != null) { - final List legacyItems = new ArrayList<>(); - try - { - // System.err.println("Building ws menu again " - // + Thread.currentThread()); - // TODO: add support for context dependent disabling of services based - // on - // alignment and current selection - // TODO: add additional serviceHandle parameter to specify abstract - // handler - // class independently of AbstractName - // TODO: add in rediscovery GUI function to restart discoverer - // TODO: group services by location as well as function and/or - // introduce - // object broker mechanism. - final Vector wsmenu = new Vector<>(); - final IProgressIndicator af = me; - - /* - * 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"); - // JAL-940 - only show secondary structure prediction services from - // the legacy server - if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) - // && - Discoverer.services != null && (Discoverer.services.size() > 0)) - { - // TODO: refactor to allow list of AbstractName/Handler bindings to - // be - // stored or retrieved from elsewhere - // No MSAWS used any more: - // Vector msaws = null; // (Vector) - // Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services - .get("SecStrPred"); - if (secstrpr != null) - { - // Add any secondary structure prediction services - for (int i = 0, j = secstrpr.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - int p = secstrmenu.getItemCount(); - impl.attachWSMenuEntry(secstrmenu, me); - int q = secstrmenu.getItemCount(); - for (int litm = p; litm < q; litm++) - { - legacyItems.add(secstrmenu.getItem(litm)); - } - } - } - } - - // Add all submenus in the order they should appear on the web - // services menu - wsmenu.add(msawsmenu); - wsmenu.add(secstrmenu); - wsmenu.add(dismenu); - wsmenu.add(analymenu); - // No search services yet - // wsmenu.add(seqsrchmenu); - - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - try - { - webService.removeAll(); - // first, add discovered services onto the webservices menu - if (wsmenu.size() > 0) - { - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add(wsmenu.get(i)); - } - } - else - { - webService.add(me.webServiceNoServices); - } - // TODO: move into separate menu builder class. - boolean new_sspred = false; - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) - { - Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) - { - jws2servs.attachWSMenuEntry(webService, me); - for (Jws2Instance sv : jws2servs.getServices()) - { - if (sv.description.toLowerCase().contains("jpred")) - { - for (JMenuItem jmi : legacyItems) - { - jmi.setVisible(false); - } - } - } - - } - if (jws2servs.isRunning()) - { - JMenuItem tm = new JMenuItem( - "Still discovering JABA Services"); - tm.setEnabled(false); - webService.add(tm); - } - } - } - build_urlServiceMenu(me.webService); - build_fetchdbmenu(webService); - for (JMenu item : wsmenu) - { - if (item.getItemCount() == 0) - { - item.setEnabled(false); - } - else - { - item.setEnabled(true); - } - } - } catch (Exception e) - { - Cache.log.debug( - "Exception during web service menu building process.", - e); - } - } - }); - } catch (Exception e) + for (ext.vamsas.ServiceHandle sh : secstrpred) { + var menuProvider = Discoverer.getServiceClient(sh); + menuProvider.attachWSMenuEntry(secstrmenu, this); } - buildingMenu = false; } - }).start(); + } + menu.add(secstrmenu); + } + /** + * Constructs the web services menu for the given discoverer under the + * specified menu. This method must be called on the EDT + * + * @param discoverer + * the discoverer used to build the menu + * @param menu + * parent component which the elements will be attached to + */ + private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu) + { + if (discoverer.hasServices()) + { + PreferredServiceRegistry.getRegistry().populateWSMenuEntry( + discoverer.getServices(), sv -> buildWebServicesMenu(), menu, + this, null); + } + if (discoverer.isRunning()) + { + JMenuItem item = new JMenuItem("Service discovery in progress."); + item.setEnabled(false); + menu.add(item); + } + else if (!discoverer.hasServices()) + { + JMenuItem item = new JMenuItem("No services available."); + item.setEnabled(false); + menu.add(item); + } } /** @@ -4244,7 +4490,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param webService */ - private void build_urlServiceMenu(JMenu webService) + protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released // DEBUG - alignmentView @@ -4352,14 +4598,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * frame's DNA sequences to their aligned protein (amino acid) equivalents. */ @Override - public void showTranslation_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(GeneticCodeI codeTable) { AlignmentI al = null; try { Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - al = dna.translateCdna(); + al = dna.translateCdna(codeTable); } catch (Exception ex) { jalview.bin.Cache.log.error( @@ -4388,7 +4634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, af.setFileFormat(this.currentFileFormat); final String newTitle = MessageManager .formatMessage("label.translation_of_params", new Object[] - { this.getTitle() }); + { this.getTitle(), codeTable.getId() }); af.setTitle(newTitle); if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { @@ -4513,8 +4759,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : FormatAdapter.checkProtocol(fileName)); if (protocol == DataSourceType.FILE) { - File fl = (file instanceof File ? (File) file - : new File(fileName)); + File fl; + if (file instanceof File) + { + fl = (File) file; + Platform.cacheFileData(fl); + } + else + { + fl = new File(fileName); + } pdbfn = fl.getName(); } else if (protocol == DataSourceType.URL) @@ -4659,6 +4913,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * either a filename or a URL string. + * @throws InterruptedException + * @throws IOException */ public void loadJalviewDataFile(Object file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) @@ -4755,7 +5011,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true, true); + SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); + if (splitFrame != null) + { + splitFrame.repaint(); + } + else + { + alignPanel.paintAlignment(true, true); + } } } else @@ -4766,7 +5030,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (isAnnotation) { - alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); @@ -4811,6 +5074,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); + if (featureSettings != null && featureSettings.isOpen() + && featureSettings.fr.getViewport() != viewport) + { + if (viewport.isShowSequenceFeatures()) + { + // refresh the featureSettings to reflect UI change + showFeatureSettingsUI(); + } + else + { + // close feature settings for this view. + featureSettings.close(); + } + } + } /* @@ -4979,7 +5257,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, trimrs.setSelected(trimrs.isSelected()); Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); - }; + } }); rfetch.add(trimrs); JMenuItem fetchr = new JMenuItem( @@ -5008,6 +5286,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + + for (FeatureSettingsModelI srcSettings : dbRefFetcher + .getFeatureSettingsModels()) + { + + alignPanel.av.mergeFeaturesStyle(srcSettings); + } AlignFrame.this.setMenusForViewport(); } }); @@ -5084,6 +5369,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + FeatureSettingsModelI srcSettings = dassource[0] + .getFeatureColourScheme(); + alignPanel.av.mergeFeaturesStyle( + srcSettings); AlignFrame.this.setMenusForViewport(); } }); @@ -5376,7 +5665,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true, true); + alignPanel.paintAlignment(true, + viewport.needToUpdateStructureViews()); } } @@ -5662,15 +5952,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(), - false); + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, + viewport.getAlignment(), false); + colourMenu.add(annotationColour); + bg.add(annotationColour); 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); @@ -5688,6 +5979,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + /** + * Sets the status of the HMMER menu + */ + public void updateHMMERStatus() + { + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + } + @Override protected void loadVcf_actionPerformed() { @@ -5697,24 +5996,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); final AlignFrame us = this; - chooser.addResponse(new RunResponse(JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { @Override public void run() { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, us); + } + }); + chooser.showOpenDialog(null); - { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); - new VCFLoader(choice).loadVCF(seqs, us); - } + } - }; - }).showOpenDialog(null); + private Rectangle lastFeatureSettingsBounds = null; + @Override + public void setFeatureSettingsGeometry(Rectangle bounds) + { + lastFeatureSettingsBounds = bounds; } + @Override + public Rectangle getFeatureSettingsGeometry() + { + return lastFeatureSettingsBounds; + } } class PrintThread extends Thread