X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=c43e0b6bd6f72dc49e74cbc00c5fac7bbfa16277;hb=801c367379086cc38bf4d3059a8e30ca9f4e78c0;hp=82e2113eccc5f31bb39636ae7dd3b6347985e1a1;hpb=6007f0f4e720ede8ca8ff70e866f2f2b870cde3e;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 82e2113..c43e0b6 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -23,19 +23,23 @@ package jalview.gui; import jalview.analysis.AnnotationSorter; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.SequenceRenderer; 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; @@ -52,6 +56,7 @@ import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; +import java.awt.image.BufferedImage; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; @@ -62,14 +67,20 @@ import java.io.FileWriter; import java.io.PrintWriter; import java.util.List; -import javax.swing.SwingUtilities; - /** - * DOCUMENT ME! + * The main panel of an AlignFrame, containing holders for the IdPanel, + * SeqPanel, AnnotationLabels (a JPanel), and AnnotationPanel. + * + * Additional holders contain an IdPanelWidthAdjuster space above the idPanel, + * AnnotationScroller (JScrollPane for AnnotationPanel), and vertical and + * horizontal scrollbars. + * + * * * @author $author$ * @version $Revision: 1.161 $ */ +@SuppressWarnings("serial") public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { @@ -81,11 +92,8 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; - private boolean headless; - IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; private ScalePanel scalePanel; @@ -116,6 +124,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { + setBackground(Color.white); // BH 2019 + setOpaque(true); alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); @@ -132,7 +142,11 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationScroller.setViewportView(getAnnotationPanel()); annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); - + if (!av.isShowAnnotation()) + { + annotationScroller.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); @@ -165,6 +179,9 @@ public class AlignmentPanel extends GAlignmentPanel implements ranges.setViewportWidth(widthInRes); ranges.setViewportHeight(heightInSeq); + ViewportRanges.sTest += "AP.resize chht=" + av.getCharHeight() + + "canvHt=" + getSeqPanel().seqCanvas.getHeight() + " " + + heightInSeq + "\n"; } } @@ -228,7 +245,7 @@ public class AlignmentPanel extends GAlignmentPanel implements 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(); @@ -335,9 +352,9 @@ 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); } /** @@ -532,7 +549,7 @@ public class AlignmentPanel extends GAlignmentPanel implements addNotify(); // TODO: many places call this method and also paintAlignment with various // different settings. this means multiple redraws are triggered... - paintAlignment(true, false); + paintAlignment(true, av.needToUpdateStructureViews()); } /** @@ -541,6 +558,15 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { + // 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. + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); annotationHeight = getAnnotationPanel() .adjustForAlignFrame(adjustPanelHeight, annotationHeight); @@ -552,6 +578,7 @@ public class AlignmentPanel extends GAlignmentPanel implements Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), annotationHeight)); annotationScroller.validate(); @@ -566,7 +593,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void updateLayout() { - fontChanged(); + fontChanged(); // fires repaint setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); ViewportRanges ranges = av.getRanges(); @@ -637,16 +664,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - int width = av.getAlignment().getWidth(); + int width = av.getAlignment().getVisibleWidth(); int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns()) - { - // reset the width to exclude hidden columns - width = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(width); - } - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -727,6 +747,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int y = vscroll.getValue(); int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); + // if we're scrolling to the position we're already at, stop // this prevents infinite recursion of events when the scroll/viewport // ranges values are the same @@ -734,6 +755,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } + + ViewportRanges.sTest += "AP.valChanged chht=" + av.getCharHeight() + + "canvHt=" + getSeqPanel().seqCanvas.getHeight() + " " + + height + "\n"; + ranges.setViewportStartAndHeight(y, height); } repaint(); @@ -783,7 +809,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // This is only called if file loaded is a jar file that // was wrapped when saved and user has wrap alignment true // as preference setting - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -823,7 +849,6 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (updateOverview) { - if (overviewPanel != null) { overviewPanel.updateOverviewImage(); @@ -840,6 +865,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void paintComponent(Graphics g) { + invalidate(); // needed so that the id width adjuster works correctly Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); @@ -854,6 +880,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ ViewportRanges ranges = av.getRanges(); setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); + super.paintComponent(g); } /** @@ -958,8 +985,8 @@ public class AlignmentPanel extends GAlignmentPanel implements final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - final int alignmentWidth = av.getAlignment().getWidth(); - final int pagesWide = (alignmentWidth / totalRes) + 1; + final int alignmentWidth = av.getAlignment().getVisibleWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; final int startRes = (pageIndex % pagesWide) * totalRes; final int endRes = Math.min(startRes + totalRes - 1, @@ -1059,6 +1086,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, Graphics g) throws PrinterException { + int annotationHeight = 0; if (av.isShowAnnotation()) { @@ -1076,18 +1104,15 @@ public class AlignmentPanel extends GAlignmentPanel implements int idWidth = getVisibleIdWidth(false); - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(maxwidth) - 1; - } + int maxwidth = av.getAlignment().getVisibleWidth(); int resWidth = getSeqPanel().seqCanvas .getWrappedCanvasWidth(pageWidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); + g = g.create(); + g.setColor(Color.white); g.fillRect(0, 0, pageWidth, pageHeight); g.setFont(av.getFont()); @@ -1101,7 +1126,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ g.translate(0, -pageNumber * pageHeight); - g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); + // BH 2020.03.19 avoiding g.setClip + g.clipRect(0, pageNumber * pageHeight, pageWidth, pageHeight); /* * draw sequence ids and annotation labels (if shown) @@ -1114,6 +1140,7 @@ public class AlignmentPanel extends GAlignmentPanel implements getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, totalHeight, 0); + g.dispose(); if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; @@ -1147,13 +1174,13 @@ public class AlignmentPanel extends GAlignmentPanel implements public int getVisibleIdWidth(boolean onscreen) { // see if rendering offscreen - check preferences and calc width accordingly - if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) + if (!onscreen && Cache.getDefault(Preferences.FIGURE_AUTOIDWIDTH, false)) { return calculateIdWidth(-1).width + 4; } Integer idwidth = null; if (onscreen || (idwidth = Cache - .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + .getIntegerProperty(Preferences.FIGURE_FIXEDIDWIDTH)) == null) { int w = getIdPanel().getWidth(); return (w > 0 ? w : calculateIdWidth().width + 4); @@ -1161,94 +1188,55 @@ public class AlignmentPanel extends GAlignmentPanel implements return idwidth.intValue() + 4; } - void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + /** + * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and + * writes it to the specified file + * + * @param type + * @param file + */ + void makeAlignmentImage(ImageMaker.TYPE type, File file) { - 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 + 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); } + /** + * Calculates and returns a suitable width and height (in pixels) for an + * exported image + * + * @return + */ public AlignmentDimension getAlignmentDimension() { - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + getScalePanel().getHeight(); @@ -1257,7 +1245,7 @@ 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 @@ -1281,27 +1269,6 @@ 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) { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS @@ -1435,8 +1402,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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 @@ -1781,4 +1747,155 @@ public class AlignmentPanel extends GAlignmentPanel implements { return calculationDialog; } + + @Override + public SequenceRenderer getSequenceRenderer() + { + return seqPanel.seqCanvas.getSequenceRenderer(); + } + + public boolean scrollTo(int ostart, int end, int seqIndex, + boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends;// , width; + + int start = -1; + if (av.hasHiddenColumns()) + { + AlignmentI al = av.getAlignment(); + start = al.getHiddenColumns().absoluteToVisibleColumn(ostart); + end = al.getHiddenColumns().absoluteToVisibleColumn(end); + if (start == end) + { + if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart)) + { + // don't scroll - position isn't visible + return false; + } + } + } + else + { + start = ostart; + } + + ViewportRanges ranges = av.getRanges(); + if (!av.getWrapAlignment()) + { + /* + * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv = + * av.getStartRes()) >= start) { spos=start-1; // seqIn // + * setScrollValues(start - 1, seqIndex); } else if ((endv = + * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end - + * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts = + * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), + * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) { + * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } + */ + + // below is scrolling logic up to Jalview 2.8.2 + // if ((av.getStartRes() > end) + // || (av.getEndRes() < start) + // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + // { + // if (start > av.getAlignment().getWidth() - hextent) + // { + // start = av.getAlignment().getWidth() - hextent; + // if (start < 0) + // { + // start = 0; + // } + // + // } + // if (seqIndex > av.getAlignment().getHeight() - vextent) + // { + // seqIndex = av.getAlignment().getHeight() - vextent; + // if (seqIndex < 0) + // { + // seqIndex = 0; + // } + // } + // setScrollValues(start, seqIndex); + // } + // logic copied from jalview.gui.AlignmentPanel: + if ((startv = ranges.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start - 1, seqIndex); + } + else if ((endv = ranges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = ranges.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(ranges.getStartRes(), seqIndex); + } + else if ((ends = ranges.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1); + } + /* + * Else results are already visible - no need to scroll + */ + } + else + { + ranges.scrollToWrappedVisible(start); + } + + paintAlignment(redrawOverview, false); + return true; + } + + @Override + public void overviewDone(BufferedImage miniMe) + { + overviewPanel.canvas.finalizeDraw(miniMe); + } + + + private boolean holdRepaint = false; + + public boolean getHoldRepaint() + { + return holdRepaint; + } + + public void setHoldRepaint(boolean b) + { + if (holdRepaint == b) + { + return; + } + holdRepaint = b; + if (!b) + { + repaint(); + } + } + + @Override + public void repaint() + { + if (holdRepaint) + { + // System.out.println("AP repaint holding"); + // Platform.stackTrace(); + return; + } + super.repaint(); + } + }