X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2365fd2dbd810127285fc4f7ddf1a424bd1fbcba;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=35125faf9150e3966beff4e9de98e65004c12cd8;hpb=4a59f639cf5769d9ec66142ebecfa4961c5d3b04;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 35125fa..2365fd2 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,7 +59,6 @@ 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; @@ -151,10 +150,12 @@ 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; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -980,14 +981,16 @@ 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); } /** @@ -997,7 +1000,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public boolean operationInProgress() { - return progressBar.operationInProgress(); + return progressBar == null ? false : progressBar.operationInProgress(); } /** @@ -1275,11 +1278,10 @@ 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) @@ -1357,7 +1359,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame.this.getViewport().setSavedUpToDate(true); } } - return null; }; /* @@ -1375,7 +1376,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - outputAction.call(); + outputAction.run(); } catch (Exception e) { // TODO Auto-generated catch block @@ -1397,7 +1398,7 @@ 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(); @@ -1419,7 +1420,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, oom); cap.dispose(); } - return null; }; /* @@ -1436,7 +1436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - outputAction.call(); + outputAction.run(); } catch (Exception e) { e.printStackTrace(); @@ -1478,7 +1478,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void createPNG(File f) { - alignPanel.makeAlignmentImage(TYPE.PNG, f); + createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing()); + } + + public void createPNG(File f, String renderer, BitmapImageSizing userBis) + { + alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); } /** @@ -1490,7 +1495,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void createEPS(File f) { - alignPanel.makeAlignmentImage(TYPE.EPS, f); + createEPS(f, null); + } + + public void createEPS(File f, String renderer) + { + alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer); } /** @@ -1502,7 +1512,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void createSVG(File f) { - alignPanel.makeAlignmentImage(TYPE.SVG, f); + createSVG(f, null); + } + + public void createSVG(File f, String renderer) + { + alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer); } @Override @@ -1552,7 +1567,6 @@ 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); @@ -2474,7 +2488,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Callable okAction = () -> { + Runnable okAction = () -> { SequenceI[] cut = sg.getSequences() .toArray(new SequenceI[sg.getSize()]); @@ -2498,7 +2512,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { } } - return null; }; /* @@ -2524,7 +2537,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - okAction.call(); + okAction.run(); } catch (Exception e) { e.printStackTrace(); @@ -2634,6 +2647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.invertColumnSelection(); alignPanel.paintAlignment(true, false); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2914,6 +2928,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setGatherViewsHere(true); } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; } @@ -3429,29 +3444,34 @@ 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() { @@ -3460,7 +3480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, javax.swing.event.InternalFrameEvent evt) { overview.dispose(); - alignPanel.setOverviewPanel(null); + thePanel.setOverviewPanel(null); } }); if (getKeyListeners().length > 0) @@ -3469,6 +3489,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.setOverviewPanel(overview); + alignPanel.setOverviewTitle(this); + + return overview; } @Override @@ -4106,7 +4129,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.possible_problem_with_tree_file"), JvOptionPane.WARNING_MESSAGE); } - return null; }); chooser.showOpenDialog(this); } @@ -4172,6 +4194,56 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } + public void showContactMapTree(AlignmentAnnotation aa, + PAEContactMatrix cm) + { + int x = 4, y = 5; + int w = 400, h = 500; + + try + { + NewickFile fin = new NewickFile( + new FileParse(cm.getNewick(), DataSourceType.PASTE)); + String title = "PAE Matrix Tree for " + + cm.getReferenceSeq().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, title); + + tp.setSize(w, h); + + if (x > 0 && y > 0) + { + tp.setLocation(x, y); + } + + Desktop.addInternalFrame(tp, title, w, h); + return tp; + } catch (Throwable xx) + { + Console.error("Unexpected exception showing tree for contact matrix", + xx); + } + return null; + } + private boolean buildingMenu = false; /** @@ -4960,7 +5032,19 @@ 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); @@ -5624,7 +5708,7 @@ 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() @@ -5890,7 +5974,6 @@ 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); @@ -5909,6 +5992,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return lastFeatureSettingsBounds; } + } class PrintThread extends Thread