X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=98639be8354fbbd504ef649b421ed70e026a4262;hb=744e4ade5413aa7e8006a8d4d29fdb718489bf08;hp=2aa21bb78a76a6d86060dd00974d00c1b7af2271;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 2aa21bb..98639be 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,29 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.bin.Jalview; -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.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.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -67,15 +44,48 @@ import java.util.List; 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; @@ -116,7 +126,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { -// setBackground(Color.white); // BH 2019 + // setBackground(Color.white); // BH 2019 alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); @@ -223,6 +233,10 @@ 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( @@ -234,8 +248,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); - - d.setSize(d.width + 4, d.height); getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); @@ -243,21 +255,22 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Calculate the width of the alignment labels based on the displayed names - * and any bounds on label width set in preferences. + * 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 + * also set as a property of the viewport. * * @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 @@ -266,9 +279,27 @@ 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() + { + 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); + return calculateIdWidth(-1, false, false); + } + /** * Calculate the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. @@ -278,7 +309,13 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ - public Dimension calculateIdWidth(int maxwidth) + protected Dimension calculateIdWidth(int maxwidth) + { + return calculateIdWidth(maxwidth, true, false); + } + + public Dimension calculateIdWidth(int maxwidth, + boolean includeAnnotations, boolean visibleOnly) { Container c = new Container(); @@ -288,44 +325,47 @@ 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 (Jalview.isHeadlessMode()) { - String label = al.getAlignmentAnnotation()[i].label; + AnnotationLabels aal = this.getAlabels(); + int stringWidth = aal.drawLabels(null, false, idWidth, false, fm); + idWidth = Math.max(idWidth, stringWidth); + } + else + { + fm = c.getFontMetrics(getAlabels().getFont()); - if (fm.stringWidth(label) > idWidth) + 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); } /** @@ -461,8 +501,7 @@ 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 @@ -542,21 +581,38 @@ 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. + + AnnotationPanel ap = getAnnotationPanel(); + int annotationHeight = ap.adjustPanelHeight(); + annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight, + annotationHeight); hscroll.addNotify(); - annotationScroller.setPreferredSize( - new Dimension(annotationScroller.getWidth(), annotationHeight)); - Dimension e = idPanel.getSize(); - alabels.setSize(new Dimension(e.width, annotationHeight)); + int idWidth = e.width; + boolean manuallyAdjusted = this.getIdPanel().getIdCanvas() + .manuallyAdjusted(); + 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(); } /** @@ -574,7 +630,8 @@ public class AlignmentPanel extends GAlignmentPanel implements ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); + // Allow idPanel width adjustment in wrap mode + idwidthAdjuster.setVisible(true); if (wrap) { @@ -608,7 +665,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - idSpaceFillerPanel1.setVisible(!wrap); + // idSpaceFillerPanel1.setVisible(!wrap); repaint(); } @@ -786,7 +843,7 @@ 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 @@ -825,12 +882,6 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - */ @Override public void paintComponent(Graphics g) { @@ -1006,8 +1057,8 @@ 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)) @@ -1029,6 +1080,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + updateLayout(); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, startRes, endRes + 1); } @@ -1051,9 +1103,11 @@ 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()) { @@ -1075,6 +1129,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int resWidth = getSeqPanel().seqCanvas .getWrappedCanvasWidth(pageWidth - idWidth); + av.getRanges().setViewportStartAndWidth(0, resWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -1086,8 +1141,8 @@ 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); @@ -1101,8 +1156,8 @@ public class AlignmentPanel extends GAlignmentPanel implements g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, - totalHeight, 0); + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, + pageWidth - idWidth, totalHeight, 0); if ((pageNumber * pageHeight) < totalHeight) { @@ -1134,21 +1189,30 @@ 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).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 = this.calculateIdWidth(-1, true, true).width; + return (w > 0 ? w : calculateIdWidth().width); + } + + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) + throws ImageOutputException + { + makeAlignmentImage(type, file, renderer, + BitmapImageSizing.nullBitmapImageSizing()); } /** @@ -1157,12 +1221,16 @@ public class AlignmentPanel extends GAlignmentPanel implements * * @param type * @param file + * @param textrenderer + * @param bitmapscale */ - void makeAlignmentImage(ImageMaker.TYPE type, File file) + 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() { @@ -1188,7 +1256,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int imageWidth = aDimension.getWidth(); int imageHeight = aDimension.getHeight() + borderBottomOffset; String of = MessageManager.getString("label.alignment"); - exporter.doExport(file, this, imageWidth, imageHeight, of); + exporter.doExport(file, this, imageWidth, imageHeight, of, renderer, + userBis); } /** @@ -1233,6 +1302,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } public void makePNGImageMap(File imgMapFile, String imageName) + throws ImageOutputException { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// @@ -1266,13 +1336,13 @@ 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) @@ -1289,7 +1359,8 @@ 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()) @@ -1355,18 +1427,24 @@ 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 @@ -1385,6 +1463,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int annotationHeight = 0; if (av.isShowAnnotation()) { + hgap += SeqCanvas.SEQS_ANNOTATION_GAP; annotationHeight = getAnnotationPanel().adjustPanelHeight(); } @@ -1439,9 +1518,9 @@ 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."); } } } @@ -1516,13 +1595,17 @@ 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() { @@ -1711,4 +1794,43 @@ 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; + } + } + }