X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8e7c7455cacc5a4bd5800cc1ecb95f5f149d2a5d;hb=2f09be746416f434aeccbb2d0233df7931afa582;hp=77a76fde687ee862e7f913195f3b55595fe28b76;hpb=c561fedabd582a8ac2ca1fae6522dae595610ab2;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 77a76fd..8e7c745 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,26 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.io.HTMLOutput; -import jalview.jbgui.GAlignmentPanel; -import jalview.math.AlignmentDimension; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureSelectionManager; -import jalview.util.Comparison; -import jalview.util.MessageManager; -import jalview.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -65,15 +45,48 @@ import java.util.List; import javax.swing.BoundedRangeModel; import javax.swing.SwingUtilities; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.bin.Jalview; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.HTMLOutput; +import jalview.io.exceptions.ImageOutputException; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.imagemaker.BitmapImageSizing; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.161 $ */ +@SuppressWarnings("serial") public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { + /* + * spare space in pixels between sequence id and alignment panel + */ + private static final int ID_WIDTH_PADDING = 4; + public AlignViewport av; OverviewPanel overviewPanel; @@ -82,11 +95,8 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; - private boolean headless; - IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; private ScalePanel scalePanel; @@ -117,6 +127,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { + // setBackground(Color.white); // BH 2019 alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); @@ -223,19 +234,21 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); + // update the flag controlling whether the grid is too small to render the + // font + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); + scalePanelHolder.setPreferredSize( new Dimension(10, av.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize( new Dimension(10, av.getCharHeight() + fm.getDescent())); idwidthAdjuster.invalidate(); scalePanelHolder.invalidate(); - getIdPanel().getIdCanvas().gg = null; + // BH 2018 getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); - - d.setSize(d.width + 4, d.height); getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); @@ -243,21 +256,24 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Calculate the width of the alignment labels based on the displayed names + * Calculates the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. * + * The calculated width is set as a property of the viewport and the layout is + * updated. + * * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ public Dimension calculateIdWidth() { + int oldWidth = av.getIdWidth(); + // calculate sensible default width when no preference is available Dimension r = null; if (av.getIdWidth() < 0) { - int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3)); - r = calculateIdWidth(maxwidth); + r = calculateDefaultAlignmentIdWidth(); av.setIdWidth(r.width); } else @@ -266,19 +282,90 @@ public class AlignmentPanel extends GAlignmentPanel implements r.width = av.getIdWidth(); r.height = 0; } + + /* + * fudge: if desired width has changed, update layout + * (see also paintComponent - updates layout on a repaint) + */ + if (r.width != oldWidth) + { + idPanelHolder.setPreferredSize(r); + validate(); + } return r; } + public Dimension calculateDefaultAlignmentIdWidth() + { + return calculateIdWidth(-1, false, false); + } + + /** + * pre 2.11.3 Id width calculation - used when importing old projects only + * + * @return + */ + public int getLegacyIdWidth() + { + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3); + int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth); + Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false); + return w.width; + } + + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. Also includes annotations + * not actually visible. + * + * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation + * label decorators and only called during tests + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. + */ + protected Dimension calculateIdWidth(int maxwidth) + { + return calculateIdWidth(maxwidth, true, false); + } + /** * Calculate the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. * * @param maxwidth * -1 or maximum width allowed for IdWidth + * @param includeAnnotations + * - when true includes width of any additional marks in annotation + * id panel + * @param visibleOnly + * - when true, ignore label widths for hidden annotation rows * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ - public Dimension calculateIdWidth(int maxwidth) + public Dimension calculateIdWidth(int maxwidth, + boolean includeAnnotations, boolean visibleOnly) + { + return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, + visibleOnly); + } + + /** + * legacy mode or post 2.11.3 ID width calculation + * + * @param legacy + * - uses annotation labels, not rendered label width (excludes + * additional decorators) + * @param maxwidth + * @param includeAnnotations + * @param visibleOnly + * @return + */ + private Dimension calculateIdWidthOrLegacy(boolean legacy, int maxwidth, + boolean includeAnnotations, boolean visibleOnly) { Container c = new Container(); @@ -288,44 +375,48 @@ public class AlignmentPanel extends GAlignmentPanel implements AlignmentI al = av.getAlignment(); int i = 0; int idWidth = 0; - String id; while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) { SequenceI s = al.getSequenceAt(i); - - id = s.getDisplayId(av.getShowJVSuffix()); - - if (fm.stringWidth(id) > idWidth) - { - idWidth = fm.stringWidth(id); - } - + String id = s.getDisplayId(av.getShowJVSuffix()); + int stringWidth = fm.stringWidth(id); + idWidth = Math.max(idWidth, stringWidth); i++; } // Also check annotation label widths - i = 0; - - if (al.getAlignmentAnnotation() != null) + if (includeAnnotations && al.getAlignmentAnnotation() != null) { fm = c.getFontMetrics(getAlabels().getFont()); - while (i < al.getAlignmentAnnotation().length) + if (!legacy || Jalview.isHeadlessMode()) { - String label = al.getAlignmentAnnotation()[i].label; - - if (fm.stringWidth(label) > idWidth) + AnnotationLabels aal = getAlabels(); + int stringWidth = aal.drawLabels(null, false, idWidth, false, false, + fm, !visibleOnly); + idWidth = Math.max(idWidth, stringWidth); + } + else + { + for (i = 0; i < al.getAlignmentAnnotation().length; i++) { - idWidth = fm.stringWidth(label); + AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; + if (visibleOnly && !aa.visible) + { + continue; + } + String label = aa.label; + int stringWidth = fm.stringWidth(label); + idWidth = Math.max(idWidth, stringWidth); } - - i++; } } - return new Dimension( - maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); + int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth); + w += ID_WIDTH_PADDING; + + return new Dimension(w, 12); } /** @@ -336,9 +427,9 @@ public class AlignmentPanel extends GAlignmentPanel implements { boolean scrolled = scrollToPosition(results, 0, false); - boolean noFastPaint = scrolled && av.getWrapAlignment(); + boolean fastPaint = !(scrolled && av.getWrapAlignment()); - getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint); + getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint); } /** @@ -461,8 +552,7 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Scroll down to make end of search results visible */ - setScrollValues(ranges.getStartRes(), starts + seqIndex - ends - + 1); + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1); } /* * Else results are already visible - no need to scroll @@ -527,7 +617,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // this is called after loading new annotation onto alignment if (alignFrame.getHeight() == 0) { - System.out.println("NEEDS FIXING"); + jalview.bin.Console.error( + "adjustAnnotationHeight called with zero height alignment window"); } validateAnnotationDimensions(true); addNotify(); @@ -542,21 +633,38 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int annotationHeight = getAnnotationPanel().adjustPanelHeight(); - annotationHeight = getAnnotationPanel() - .adjustForAlignFrame(adjustPanelHeight, annotationHeight); + // BH 2018.04.18 comment: addNotify() is not appropriate here. We + // are not changing ancestors, and keyboard action listeners do + // not need to be reset. addNotify() is a very expensive operation, + // requiring a full re-layout of all parents and children. + // Note in JComponent: + // This method is called by the toolkit internally and should + // not be called directly by programs. + // I note that addNotify() is called in several areas of Jalview. - hscroll.addNotify(); - annotationScroller.setPreferredSize( - new Dimension(annotationScroller.getWidth(), annotationHeight)); + AnnotationPanel ap = getAnnotationPanel(); + int annotationHeight = ap.adjustPanelHeight(); + annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight, + annotationHeight); + hscroll.addNotify(); Dimension e = idPanel.getSize(); - alabels.setSize(new Dimension(e.width, annotationHeight)); + int idWidth = e.width; + boolean manuallyAdjusted = this.getIdPanel().getIdCanvas() + .isManuallyAdjusted(); + annotationScroller.setPreferredSize(new Dimension( + manuallyAdjusted ? idWidth : annotationScroller.getWidth(), + annotationHeight)); + + alabels.setPreferredSize(new Dimension(idWidth, annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), annotationHeight)); + manuallyAdjusted ? idWidth + : annotationSpaceFillerHolder.getWidth(), + annotationHeight)); annotationScroller.validate(); annotationScroller.addNotify(); + ap.validate(); } /** @@ -572,9 +680,10 @@ public class AlignmentPanel extends GAlignmentPanel implements boolean wrap = av.getWrapAlignment(); ViewportRanges ranges = av.getRanges(); ranges.setStartSeq(0); - scalePanelHolder.setVisible(!wrap); + // scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); + // Allow idPanel width adjustment in wrap mode + idwidthAdjuster.setVisible(true); if (wrap) { @@ -608,7 +717,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - idSpaceFillerPanel1.setVisible(!wrap); + // idSpaceFillerPanel1.setVisible(!wrap); repaint(); } @@ -802,7 +911,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // could not be validated and it is not clear if it is now being // called. Log warning here in case it is called and unforeseen // problems occur - Cache.log.warn( + Console.warn( "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel @@ -841,20 +950,31 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - */ @Override public void paintComponent(Graphics g) { invalidate(); // needed so that the id width adjuster works correctly - Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); - idPanelHolder.setPreferredSize(d); - hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); + int idWidth = d.width; + + // check wrapped alignment as at least 1 residue width + if (av.getWrapAlignment()) + { + SeqCanvas sc = this.getSeqPanel().seqCanvas; + if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth()) + { + // need to make some adjustments + idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth()); + av.setIdWidth(idWidth); + av.getAlignPanel().getIdPanel().getIdCanvas() + .setManuallyAdjusted(true); + + validateAnnotationDimensions(false); + } + } + + idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height)); + hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12)); validate(); // needed so that the id width adjuster works correctly @@ -864,6 +984,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ ViewportRanges ranges = av.getRanges(); setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); + super.paintComponent(g); } /** @@ -944,8 +1065,16 @@ public class AlignmentPanel extends GAlignmentPanel implements Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { - final int idWidth = getVisibleIdWidth(false); - + final int idWidth, idWidthForGui; + // otherwise calculate it + idWidth = getVisibleIdWidth(false); + // if (getIdPanel()!=null && getIdPanel().getWidth()>0) + // { + // // use the current IdPanel's width, if its set and non-zero + // idWidthForGui = getIdPanel().getWidth(); + // } else { + // idWidthForGui=0; + // } /* * Get the horizontal offset to where we draw the sequences. * This is idWidth if using a single Graphics context, else zero. @@ -994,6 +1123,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; + alignmentGraphics.setColor(Color.white); + alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight + scaleHeight); + /* * draw the Scale at horizontal offset, then reset to top left (0, 0) */ @@ -1010,8 +1142,9 @@ public class AlignmentPanel extends GAlignmentPanel implements IdCanvas idCanvas = getIdPanel().getIdCanvas(); List selection = av.getSelectionGroup() == null ? null : av.getSelectionGroup().getSequences(null); + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, - selection); + selection, false, idWidth); idGraphics.setFont(av.getFont()); idGraphics.translate(0, -scaleHeight); @@ -1021,8 +1154,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, - endRes, startSeq, endSeq - 1); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, + startRes, endRes, startSeq, endSeq - 1); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1035,7 +1168,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int offset = getAlabels().getScrollOffset(); idGraphics.translate(0, -offset); idGraphics.translate(0, alignmentDrawnHeight); - getAlabels().drawComponent(idGraphics, idWidth); + getAlabels().drawComponentNotGUI(idGraphics, idWidth); idGraphics.translate(0, -alignmentDrawnHeight); /* @@ -1044,6 +1177,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + updateLayout(); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, startRes, endRes + 1); } @@ -1066,9 +1200,11 @@ public class AlignmentPanel extends GAlignmentPanel implements * * @throws PrinterException */ - public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, - Graphics g) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, + int pageNumber, Graphics g) throws PrinterException { + getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(), + getHeight()); int annotationHeight = 0; if (av.isShowAnnotation()) { @@ -1090,6 +1226,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int resWidth = getSeqPanel().seqCanvas .getWrappedCanvasWidth(pageWidth - idWidth); + av.getRanges().setViewportStartAndWidth(0, resWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -1101,8 +1238,8 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * method: print the whole wrapped alignment, but with a clip region that * is restricted to the requested page; this supports selective print of - * single pages or ranges, (at the cost of some repeated processing in - * the 'normal' case, when all pages are printed) + * single pages or ranges, (at the cost of repeated processing in the + * 'normal' case, when all pages are printed) */ g.translate(0, -pageNumber * pageHeight); @@ -1112,12 +1249,12 @@ public class AlignmentPanel extends GAlignmentPanel implements * draw sequence ids and annotation labels (if shown) */ IdCanvas idCanvas = getIdPanel().getIdCanvas(); - idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight); + idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight); g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, - totalHeight, 0); + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, + pageWidth - idWidth, totalHeight, 0); if ((pageNumber * pageHeight) < totalHeight) { @@ -1149,103 +1286,83 @@ public class AlignmentPanel extends GAlignmentPanel implements * be returned * @return */ - public int getVisibleIdWidth(boolean onscreen) + protected int getVisibleIdWidth(boolean onscreen) { // see if rendering offscreen - check preferences and calc width accordingly if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) { - return calculateIdWidth(-1).width + 4; + return calculateIdWidth(-1, true, true).width; } - Integer idwidth = null; - if (onscreen || (idwidth = Cache - .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + Integer idwidth = onscreen ? null + : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); + if (idwidth != null) { - int w = getIdPanel().getWidth(); - return (w > 0 ? w : calculateIdWidth().width + 4); + return idwidth.intValue() + ID_WIDTH_PADDING; } - return idwidth.intValue() + 4; + + int w = getIdPanel().getWidth(); + w = calculateIdWidth(-1, true, true).width; + return (w > 0 ? w : calculateIdWidth().width); } - void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) + throws ImageOutputException { - int boarderBottomOffset = 5; - long pSessionId = System.currentTimeMillis(); - headless = (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")); - if (alignFrame != null && !headless) - { - if (file != null) - { - alignFrame.setProgressBar(MessageManager - .formatMessage("status.saving_file", new Object[] - { type.getLabel() }), pSessionId); - } - } - try + makeAlignmentImage(type, file, renderer, + BitmapImageSizing.defaultBitmapImageSizing()); + } + + /** + * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and + * writes it to the specified file + * + * @param type + * @param file + * @param textrenderer + * @param bitmapscale + */ + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer, + BitmapImageSizing userBis) throws ImageOutputException + { + final int borderBottomOffset = 5; + + AlignmentDimension aDimension = getAlignmentDimension(); + + // todo use a lambda function in place of callback here? + ImageWriterI writer = new ImageWriterI() { - AlignmentDimension aDimension = getAlignmentDimension(); - try + @Override + public void exportImage(Graphics graphics) throws Exception { - jalview.util.ImageMaker im; - final String imageAction, imageTitle; - if (type == jalview.util.ImageMaker.TYPE.PNG) - { - imageAction = "Create PNG image from alignment"; - imageTitle = null; - } - else if (type == jalview.util.ImageMaker.TYPE.EPS) - { - imageAction = "Create EPS file from alignment"; - imageTitle = alignFrame.getTitle(); - } - else - { - imageAction = "Create SVG file from alignment"; - imageTitle = alignFrame.getTitle(); - } - - im = new jalview.util.ImageMaker(this, type, imageAction, - aDimension.getWidth(), - aDimension.getHeight() + boarderBottomOffset, file, - imageTitle, alignFrame, pSessionId, headless); - Graphics graphics = im.getGraphics(); if (av.getWrapAlignment()) { - if (graphics != null) - { - printWrappedAlignment(aDimension.getWidth(), - aDimension.getHeight() + boarderBottomOffset, 0, - graphics); - im.writeImage(); - } + printWrappedAlignment(aDimension.getWidth(), + aDimension.getHeight() + borderBottomOffset, 0, graphics); } else { - if (graphics != null) - { - printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, - graphics, graphics); - im.writeImage(); - } + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + graphics, graphics); } - - } catch (OutOfMemoryError err) - { - // Be noisy here. - System.out.println("########################\n" + "OUT OF MEMORY " - + file + "\n" + "########################"); - new OOMWarning("Creating Image for " + file, err); - // System.out.println("Create IMAGE: " + err); - } catch (Exception ex) - { - ex.printStackTrace(); } - } finally - { + }; - } + String fileTitle = alignFrame.getTitle(); + ImageExporter exporter = new ImageExporter(writer, alignFrame, type, + fileTitle); + int imageWidth = aDimension.getWidth(); + int imageHeight = aDimension.getHeight() + borderBottomOffset; + String of = MessageManager.getString("label.alignment"); + exporter.doExport(file, this, imageWidth, imageHeight, of, renderer, + userBis); } + /** + * Calculates and returns a suitable width and height (in pixels) for an + * exported image + * + * @return + */ public AlignmentDimension getAlignmentDimension() { int maxwidth = av.getAlignment().getVisibleWidth(); @@ -1257,7 +1374,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getWrapAlignment()) { height = getWrappedHeight(); - if (headless) + if (Jalview.isHeadlessMode()) { // need to obtain default alignment width and then add in any // additional allowance for id margin @@ -1281,28 +1398,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } - /** - * DOCUMENT ME! - */ - public void makeEPS(File epsFile) - { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); - } - - /** - * DOCUMENT ME! - */ - public void makePNG(File pngFile) - { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile); - } - - public void makeSVG(File svgFile) - { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); - } - public void makePNGImageMap(File imgMapFile, String imageName) + throws ImageOutputException { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// @@ -1336,13 +1433,13 @@ public class AlignmentPanel extends GAlignmentPanel implements String triplet = null; if (av.getAlignment().isNucleotide()) { - triplet = ResidueProperties.nucleotideName.get(seq - .getCharAt(column) + ""); + triplet = ResidueProperties.nucleotideName + .get(seq.getCharAt(column) + ""); } else { - triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) - + ""); + triplet = ResidueProperties.aa2Triplet + .get(seq.getCharAt(column) + ""); } if (triplet == null) @@ -1359,7 +1456,8 @@ public class AlignmentPanel extends GAlignmentPanel implements text.append(" features = seq.findFeatures(column, column); + List features = seq.findFeatures(column, + column); for (SequenceFeature sf : features) { if (sf.isContactFeature()) @@ -1425,18 +1524,24 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { - ex.printStackTrace(); + throw new ImageOutputException( + "couldn't write ImageMap due to unexpected error", ex); } } // /////////END OF IMAGE MAP } + /** + * Answers the height of the entire alignment in pixels, assuming it is in + * wrapped mode + * + * @return + */ int getWrappedHeight() { int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + if (Jalview.isHeadlessMode()) { seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() - vscroll.getPreferredSize().width @@ -1455,6 +1560,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int annotationHeight = 0; if (av.isShowAnnotation()) { + hgap += SeqCanvas.SEQS_ANNOTATION_GAP; annotationHeight = getAnnotationPanel().adjustPanelHeight(); } @@ -1509,9 +1615,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.warn("Closing alignment panel which is already closed."); + Console.warn("Closing alignment panel which is already closed."); } } } @@ -1586,13 +1692,17 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { } - if (b) { - alignFrame.setDisplayedView(this); + setAlignFrameView(); } } + public void setAlignFrameView() + { + alignFrame.setDisplayedView(this); + } + @Override public StructureSelectionManager getStructureSelectionManager() { @@ -1781,4 +1891,42 @@ public class AlignmentPanel extends GAlignmentPanel implements { return calculationDialog; } + + /** + * Constructs and sets the title for the Overview window (if there is one), + * including the align frame's title, and view name (if applicable). Returns + * the title, or null if this panel has no Overview window open. + * + * @param alignFrame + * @return + */ + public String setOverviewTitle(AlignFrame alignFrame) + { + if (this.overviewPanel == null) + { + return null; + } + String overviewTitle = MessageManager + .formatMessage("label.overview_params", new Object[] + { alignFrame.getTitle() }); + String viewName = getViewName(); + if (viewName != null) + { + overviewTitle += (" " + viewName); + } + overviewPanel.setTitle(overviewTitle); + return overviewTitle; + } + + /** + * If this alignment panel has an Overview panel open, closes it + */ + public void closeOverviewPanel() + { + if (overviewPanel != null) + { + overviewPanel.close(); + overviewPanel = null; + } + } }