X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=eb98d989e7151bac77c67431ceefc7f91b67d496;hb=c24ec44edbedba55005373c43bf712c047b56faa;hp=d8fec3aeb886adee209cd16d2f3e9c95ccf47efa;hpb=b364e1e6d199002069dab615d1007799b5bb71e1;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index d8fec3a..eb98d98 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -49,6 +49,7 @@ import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; import java.io.IOException; +import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; @@ -59,7 +60,6 @@ import java.util.Hashtable; import java.util.List; import java.util.Locale; import java.util.Vector; -import java.util.concurrent.Callable; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; @@ -112,6 +112,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; @@ -140,6 +141,7 @@ import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; +import jalview.io.exceptions.ImageOutputException; import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; import jalview.project.Jalview2XML; @@ -151,6 +153,7 @@ import jalview.util.HttpUtils; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.imagemaker.BitmapImageSizing; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; @@ -350,6 +353,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { + setFrameIcon(null); + // setBackground(Color.white); // BH 2019 if (!Jalview.isHeadlessMode()) @@ -619,12 +624,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // if (viewport.cursorMode) // { // alignPanel.seqPanel.insertNucAtCursor(false,"A"); - // //System.out.println("A"); + // //jalview.bin.Console.outPrintln("A"); // } // break; /* * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { - * System.out.println("closing bracket"); } break; + * jalview.bin.Console.outPrintln("closing bracket"); } break; */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: @@ -825,7 +830,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void propertyChange(PropertyChangeEvent evt) { - // // System.out.println("Discoverer property change."); + // // jalview.bin.Console.outPrintln("Discoverer property + // change."); // if (evt.getPropertyName().equals("services")) { SwingUtilities.invokeLater(new Runnable() @@ -834,7 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - System.err.println( + jalview.bin.Console.errPrintln( "Rebuild WS Menu for service change"); BuildWebServiceMenu(); } @@ -849,7 +855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { - // System.out.println("deregistering discoverer listener"); + // jalview.bin.Console.outPrintln("deregistering discoverer listener"); Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); @@ -978,14 +984,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void setProgressBar(String message, long id) { - progressBar.setProgressBar(message, id); + if (!Platform.isHeadless() && progressBar != null) + progressBar.setProgressBar(message, id); } @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - progressBar.registerHandler(id, handler); + if (progressBar != null) + progressBar.registerHandler(id, handler); } /** @@ -995,7 +1003,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public boolean operationInProgress() { - return progressBar.operationInProgress(); + return progressBar == null ? false : progressBar.operationInProgress(); } /** @@ -1244,8 +1252,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void saveAlignment(String file, FileFormatI format) { + saveAlignment(file, format, false); + } + + public void saveAlignment(String file, FileFormatI format, boolean stdout) + { lastSaveSuccessful = true; - lastFilenameSaved = file; + if (!stdout) + { + lastFilenameSaved = file; + } lastFormatSaved = format; if (FileFormat.Jalview.equals(format)) @@ -1256,6 +1272,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, shortName = shortName .substring(shortName.lastIndexOf(File.separatorChar) + 1); } + // TODO deal with stdout=true lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); @@ -1273,11 +1290,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - Callable cancelAction = () -> { + Runnable cancelAction = () -> { lastSaveSuccessful = false; - return null; }; - Callable outputAction = () -> { + Runnable outputAction = () -> { // todo defer this to inside formatSequences (or later) AlignmentExportData exportData = viewport.getAlignExportData(options); String output = new FormatAdapter(alignPanel, options) @@ -1292,7 +1308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // create backupfiles object and get new temp filename destination - boolean doBackup = BackupFiles.getEnabled(); + boolean doBackup = BackupFiles.getEnabled() && !stdout; BackupFiles backupfiles = null; if (doBackup) { @@ -1304,7 +1320,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; Console.trace("ALIGNFRAME setting PrintWriter"); - PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + PrintWriter out = stdout + ? new PrintWriter(new OutputStreamWriter(System.out)) + : new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { @@ -1313,13 +1331,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } out.print(output); - Console.trace("ALIGNFRAME about to close file"); - out.close(); - Console.trace("ALIGNFRAME closed file"); - AlignFrame.this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format.getName() })); + out.flush(); + if (!stdout) + { + Console.trace("ALIGNFRAME about to close file"); + out.close(); + Console.trace("ALIGNFRAME closed file"); + } + AlignFrame.this.setTitle(stdout ? "STDOUT" : file); + if (stdout) + { + statusBar.setText(MessageManager.formatMessage( + "label.successfully_printed_to_stdout_in_format", + new Object[] + { format.getName() })); + } + else + { + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new Object[] + { fileName, format.getName() })); + } lastSaveSuccessful = true; } catch (IOException e) { @@ -1355,7 +1388,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame.this.getViewport().setSavedUpToDate(true); } } - return null; }; /* @@ -1373,7 +1405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - outputAction.call(); + outputAction.run(); } catch (Exception e) { // TODO Auto-generated catch block @@ -1395,7 +1427,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FileFormatI fileFormat = FileFormats.getInstance() .forName(fileFormatName); AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - Callable outputAction = () -> { + Runnable outputAction = () -> { // todo defer this to inside formatSequences (or later) AlignmentExportData exportData = viewport.getAlignExportData(options); CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -1417,7 +1449,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, oom); cap.dispose(); } - return null; }; /* @@ -1434,7 +1465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - outputAction.call(); + outputAction.run(); } catch (Exception e) { e.printStackTrace(); @@ -1452,19 +1483,75 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void htmlMenuItem_actionPerformed(ActionEvent e) { HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); - htmlSVG.exportHTML(null); + try + { + htmlSVG.exportHTML(null); + } catch (ImageOutputException x) + { + // report problem to console and raise dialog + } } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); - bjs.exportHTML(null); + try + { + bjs.exportHTML(null); + } catch (ImageOutputException x) + { + // report problem to console and raise dialog + } } public void createImageMap(File file, String image) { - alignPanel.makePNGImageMap(file, image); + try + { + alignPanel.makePNGImageMap(file, image); + } catch (ImageOutputException x) + { + // report problem to console and raise dialog + } + } + + @Override + public void createPNG_actionPerformed(ActionEvent e) + { + try + { + createPNG(null); + } catch (ImageOutputException ioex) + { + // raise dialog, and report via console + } + } + + @Override + public void createEPS_actionPerformed(ActionEvent e) + { + try + { + createEPS(null); + } catch (ImageOutputException ioex) + { + // raise dialog, and report via console + } + + } + + @Override + public void createSVG_actionPerformed(ActionEvent e) + { + try + { + createSVG(null); + } catch (ImageOutputException ioex) + { + // raise dialog, and report via console + } + } /** @@ -1473,10 +1560,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override - public void createPNG(File f) + public void createPNG(File f) throws ImageOutputException { - alignPanel.makeAlignmentImage(TYPE.PNG, f); + createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing()); + } + + public void createPNG(File f, String renderer, BitmapImageSizing userBis) + throws ImageOutputException + { + alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); } /** @@ -1485,10 +1577,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override - public void createEPS(File f) + public void createEPS(File f) throws ImageOutputException + { + createEPS(f, null); + } + + public void createEPS(File f, String renderer) throws ImageOutputException { - alignPanel.makeAlignmentImage(TYPE.EPS, f); + alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer); } /** @@ -1497,10 +1593,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override - public void createSVG(File f) + public void createSVG(File f) throws ImageOutputException + { + createSVG(f, null); + } + + public void createSVG(File f, String renderer) throws ImageOutputException { - alignPanel.makeAlignmentImage(TYPE.SVG, f); + alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer); } @Override @@ -1550,7 +1650,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String choice = chooser.getSelectedFile().getPath(); Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); - return null; }); chooser.showOpenDialog(this); @@ -2282,10 +2381,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .intValue(); } } - alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation - // was - // duplicated - // earlier + // annotation was duplicated earlier + alignment.addAnnotation(sequences[i].getAnnotation()[a]); + // take care of contact matrix too + ContactMatrixI cm = sequences[i] + .getContactMatrixFor(sequences[i].getAnnotation()[a]); + if (cm != null) + { + alignment.addContactListFor(sequences[i].getAnnotation()[a], + cm); + } + alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a); } @@ -2393,7 +2499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { ex.printStackTrace(); - System.out.println("Exception whilst pasting: " + ex); + jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); // could be anything being pasted in here } @@ -2441,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { ex.printStackTrace(); - System.out.println("Exception whilst pasting: " + ex); + jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); // could be anything being pasted in here } catch (OutOfMemoryError oom) { @@ -2472,7 +2578,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Callable okAction = () -> { + Runnable okAction = () -> { SequenceI[] cut = sg.getSequences() .toArray(new SequenceI[sg.getSize()]); @@ -2496,7 +2602,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { } } - return null; }; /* @@ -2522,7 +2627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - okAction.call(); + okAction.run(); } catch (Exception e) { e.printStackTrace(); @@ -2632,6 +2737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.invertColumnSelection(); alignPanel.paintAlignment(true, false); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2912,6 +3018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setGatherViewsHere(true); } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; } @@ -3427,28 +3534,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Opens an Overview panel for the alignment, unless one is open already * * @param e - * DOCUMENT ME! */ @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { + boolean showHiddenRegions = Cache + .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false); + openOverviewPanel(showHiddenRegions); + } + + public OverviewPanel openOverviewPanel(boolean showHidden) + { if (alignPanel.overviewPanel != null) { - return; + return alignPanel.overviewPanel; } - JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + final OverviewPanel overview = new OverviewPanel(alignPanel, frame, + showHidden); 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, "", true, frame.getWidth(), + frame.getHeight(), true, true); + frame.setFrameIcon(null); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); + final AlignmentPanel thePanel = this.alignPanel; frame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { @@ -3457,7 +3570,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, javax.swing.event.InternalFrameEvent evt) { overview.dispose(); - alignPanel.setOverviewPanel(null); + thePanel.setOverviewPanel(null); } }); if (getKeyListeners().length > 0) @@ -3466,6 +3579,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.setOverviewPanel(overview); + alignPanel.setOverviewTitle(this); + + return overview; } @Override @@ -4103,7 +4219,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.possible_problem_with_tree_file"), JvOptionPane.WARNING_MESSAGE); } - return null; }); chooser.showOpenDialog(this); } @@ -4169,6 +4284,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } + public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm) + { + int x = 4, y = 5; + int w = 400, h = 500; + + try + { + NewickFile fin = new NewickFile( + new FileParse(cm.getNewick(), DataSourceType.PASTE)); + String title = aa.label + " " + cm.getTreeMethod() + " tree" + + (aa.sequenceRef != null + ? (" for " + aa.sequenceRef.getDisplayId(false)) + : ""); + + showColumnWiseTree(fin, aa, title, w, h, x, y); + } catch (Throwable xx) + { + Console.error("Unexpected exception showing tree for contact matrix", + xx); + } + } + + public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, + String treeTitle, int w, int h, int x, int y) + { + try + { + nf.parse(); + if (nf.getTree() == null) + { + return null; + } + TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle); + + tp.setSize(w, h); + + if (x > 0 && y > 0) + { + tp.setLocation(x, y); + } + + Desktop.addInternalFrame(tp, treeTitle, w, h); + return tp; + } catch (Throwable xx) + { + Console.error("Unexpected exception showing tree for contact matrix", + xx); + } + return null; + } + private boolean buildingMenu = false; /** @@ -4181,7 +4347,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - System.err.println("Waiting for building menu to finish."); + jalview.bin.Console + .errPrintln("Waiting for building menu to finish."); Thread.sleep(10); } catch (Exception e) { @@ -4197,7 +4364,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final List legacyItems = new ArrayList<>(); try { - // System.err.println("Building ws menu again " + // jalview.bin.Console.errPrintln("Building ws menu again " // + Thread.currentThread()); // TODO: add support for context dependent disabling of services based // on @@ -4735,7 +4902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance); if (pe != null) { - System.err.println("Associated file : " + jalview.bin.Console.errPrintln("Associated file : " + (fm[0].toString()) + " with " + toassoc.getDisplayId(true)); assocfiles++; @@ -4957,7 +5124,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (index > -1) { + /* + * update current Overview window title (if there is one) + * to add view name "Original" if necessary + */ + alignPanel.setOverviewTitle(this); + + /* + * switch panels and set Overview title (if there is one + * because it was opened automatically) + */ alignPanel = alignPanels.get(index); + alignPanel.setOverviewTitle(this); + viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); @@ -5621,7 +5800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * update non-sequence-related annotations */ @Override - protected void setAnnotationsVisibility(boolean visible, + public void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) { AlignmentAnnotation[] anns = alignPanel.getAlignment() @@ -5756,7 +5935,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment())); } catch (Exception ex) { - System.err.println(ex.getMessage()); + jalview.bin.Console.errPrintln(ex.getMessage()); return; } } @@ -5778,7 +5957,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, console.runScript(); } catch (Exception ex) { - System.err.println((ex.toString())); + jalview.bin.Console.errPrintln((ex.toString())); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_run_groovy_script"), MessageManager.getString("label.groovy_support_failed"), @@ -5787,7 +5966,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - System.err.println("Can't run Groovy script as console not found"); + jalview.bin.Console + .errPrintln("Can't run Groovy script as console not found"); } } @@ -5827,6 +6007,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, | ActionEvent.CTRL_MASK)) != 0); } + @Override + protected void copyHighlightedColumns_actionPerformed( + ActionEvent actionEvent) + { + avc.copyHighlightedRegionsToClipboard(); + } + /** * Rebuilds the Colour menu, including any user-defined colours which have * been loaded either on startup or during the session @@ -5880,7 +6067,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Cache.setProperty("LAST_DIRECTORY", choice); SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); new VCFLoader(choice).loadVCF(seqs, us); - return null; }); chooser.showOpenDialog(null); @@ -5899,6 +6085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return lastFeatureSettingsBounds; } + } class PrintThread extends Thread