X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ab705c2e152fdb71e8997fbd395678c862f8fd97;hb=fa48c836ad6e85a9e8146177cc865f4a061dc1a4;hp=06298ba09555a541e8083dc939f813b1bacf8034;hpb=80b889f0cca49103e1b20ed806755a0719789906;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 06298ba..ab705c2 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; @@ -112,6 +111,7 @@ 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 +140,7 @@ 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 +152,7 @@ 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; @@ -981,7 +983,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void setProgressBar(String message, long id) { - if (!Platform.isHeadless()) + if (!Platform.isHeadless() && progressBar != null) progressBar.setProgressBar(message, id); } @@ -989,7 +991,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - progressBar.registerHandler(id, handler); + if (progressBar != null) + progressBar.registerHandler(id, handler); } /** @@ -999,7 +1002,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public boolean operationInProgress() { - return progressBar.operationInProgress(); + return progressBar == null ? false : progressBar.operationInProgress(); } /** @@ -1277,11 +1280,10 @@ 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) @@ -1359,7 +1361,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame.this.getViewport().setSavedUpToDate(true); } } - return null; }; /* @@ -1377,7 +1378,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - outputAction.call(); + outputAction.run(); } catch (Exception e) { // TODO Auto-generated catch block @@ -1399,7 +1400,7 @@ 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(); @@ -1421,7 +1422,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, oom); cap.dispose(); } - return null; }; /* @@ -1438,7 +1438,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - outputAction.call(); + outputAction.run(); } catch (Exception e) { e.printStackTrace(); @@ -1456,31 +1456,76 @@ 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); + try { bjs.exportHTML(null); + } catch (ImageOutputException x) { + // report problem to console and raise dialog + } } public void createImageMap(File file, String 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 + } + + } /** * Creates a PNG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. * * @param f */ - @Override - public void createPNG(File f) + public void createPNG(File f) throws ImageOutputException + { + createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing()); + } + + public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException { - alignPanel.makeAlignmentImage(TYPE.PNG, f); + alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); } /** @@ -1489,10 +1534,14 @@ 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); } /** @@ -1501,10 +1550,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - @Override - public void createSVG(File f) + public void createSVG(File f) throws ImageOutputException { - alignPanel.makeAlignmentImage(TYPE.SVG, f); + createSVG(f, null); + } + + public void createSVG(File f, String renderer) throws ImageOutputException + { + alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer); } @Override @@ -1554,7 +1607,6 @@ 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); @@ -2286,10 +2338,15 @@ 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); } @@ -2476,7 +2533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Callable okAction = () -> { + Runnable okAction = () -> { SequenceI[] cut = sg.getSequences() .toArray(new SequenceI[sg.getSize()]); @@ -2500,7 +2557,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { } } - return null; }; /* @@ -2526,7 +2582,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - okAction.call(); + okAction.run(); } catch (Exception e) { e.printStackTrace(); @@ -4118,7 +4174,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.possible_problem_with_tree_file"), JvOptionPane.WARNING_MESSAGE); } - return null; }); chooser.showOpenDialog(this); } @@ -4185,7 +4240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } public void showContactMapTree(AlignmentAnnotation aa, - PAEContactMatrix cm) + ContactMatrixI cm) { int x = 4, y = 5; int w = 400, h = 500; @@ -4194,8 +4249,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { NewickFile fin = new NewickFile( new FileParse(cm.getNewick(), DataSourceType.PASTE)); - String title = "PAE Matrix Tree for " - + cm.getReferenceSeq().getDisplayId(false); + String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree" + + aa.sequenceRef != null + ? (" for " + aa.sequenceRef.getDisplayId(false)) + : ""; showColumnWiseTree(fin, aa, title, w, h, x, y); } catch (Throwable xx) @@ -5698,7 +5755,7 @@ 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() @@ -5964,7 +6021,6 @@ 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);