X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f72379453e551b21384870118062d0e9c827d830;hb=f820a6e0b7ec599b0e040109c3361cdb3e6d9aa0;hp=55fd185bdbcc7a6bbba7dc644290704419163bde;hpb=13e054c5117102197ee0b22073603a6a38962865;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 55fd185..f723794 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -23,21 +23,24 @@ 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.util.Platform; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; @@ -48,7 +51,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; -import java.awt.Insets; +import java.awt.Graphics2D; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; @@ -71,6 +74,7 @@ import javax.swing.SwingUtilities; * @author $author$ * @version $Revision: 1.161 $ */ +@SuppressWarnings("serial") public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { @@ -82,11 +86,8 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; - private boolean headless; - IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; private ScalePanel scalePanel; @@ -117,6 +118,8 @@ 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)); @@ -229,7 +232,7 @@ 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(); @@ -329,16 +332,16 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Highlight the given results on the alignment. + * Highlight the given results on the alignment * */ public void highlightSearchResults(SearchResultsI results) { - boolean scrolled = scrollToPosition(results, 0, true, false); + 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); } /** @@ -346,13 +349,11 @@ public class AlignmentPanel extends GAlignmentPanel implements * (if any) * * @param searchResults - * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResultsI searchResults, - boolean redrawOverview) + public boolean scrollToPosition(SearchResultsI searchResults) { - return scrollToPosition(searchResults, 0, redrawOverview, false); + return scrollToPosition(searchResults, 0, false); } /** @@ -365,14 +366,12 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param verticalOffset * if greater than zero, allows scrolling to a position below the * first displayed sequence - * @param redrawOverview - * - when set, the overview will be recalculated (takes longer) * @param centre * if true, try to centre the search results horizontally in the view * @return */ protected boolean scrollToPosition(SearchResultsI results, - int verticalOffset, boolean redrawOverview, boolean centre) + int verticalOffset, boolean centre) { int startv, endv, starts, ends; ViewportRanges ranges = av.getRanges(); @@ -478,7 +477,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview, false); + paintAlignment(false, false); return scrollNeeded; } @@ -537,7 +536,7 @@ 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()); } /** @@ -546,47 +545,27 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int annotationHeight = getAnnotationPanel().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. - if (adjustPanelHeight) - { - int rowHeight = av.getCharHeight(); - int alignmentHeight = rowHeight * av.getAlignment().getHeight(); - - /* - * Estimate available height in the AlignFrame for alignment + - * annotations. Deduct an estimate for title bar, menu bar, scale panel, - * hscroll, status bar (as these are not laid out we can't inspect their - * actual heights). Insets gives frame borders. - */ - int stuff = Platform.isAMac() ? 80 : 100; - Insets insets = alignFrame.getInsets(); - int availableHeight = alignFrame.getHeight() - stuff - insets.top - - insets.bottom; + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + annotationHeight = getAnnotationPanel() + .adjustForAlignFrame(adjustPanelHeight, annotationHeight); - /* - * If not enough vertical space, maximize annotation height while keeping - * at least two rows of alignment visible - */ - if (annotationHeight + alignmentHeight > availableHeight) - { - annotationHeight = Math.min(annotationHeight, - availableHeight - 2 * rowHeight); - } - } - else - { - // maintain same window layout whilst updating sliders - annotationHeight = annotationScroller.getSize().height; - } hscroll.addNotify(); - annotationScroller.setPreferredSize( new Dimension(annotationScroller.getWidth(), annotationHeight)); Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), annotationHeight)); annotationScroller.validate(); @@ -619,6 +598,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); + validateAnnotationDimensions(false); } int canvasWidth = getSeqPanel().seqCanvas.getWidth(); @@ -671,16 +651,9 @@ 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(); @@ -888,6 +861,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ ViewportRanges ranges = av.getRanges(); setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); + super.paintComponent(g); } /** @@ -946,30 +920,16 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! - * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! - * - * @return DOCUMENT ME! - * - * @throws PrinterException - * DOCUMENT ME! - */ - /** * Draws the alignment image, including sequence ids, sequences, and * annotation labels and annotations if shown, on either one or two Graphics - * context. + * contexts. * * @param pageWidth + * in pixels * @param pageHeight - * @param pi + * in pixels + * @param pageIndex + * (0, 1, ...) * @param idGraphics * the graphics context for sequence ids and annotation labels * @param alignmentGraphics @@ -978,7 +938,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return * @throws PrinterException */ - public int printUnwrapped(int pageWidth, int pageHeight, int pi, + public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex, Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { @@ -992,8 +952,8 @@ public class AlignmentPanel extends GAlignmentPanel implements : idWidth; FontMetrics fm = getFontMetrics(av.getFont()); - int charHeight = av.getCharHeight(); - int scaleHeight = charHeight + fm.getDescent(); + final int charHeight = av.getCharHeight(); + final int scaleHeight = charHeight + fm.getDescent(); idGraphics.setColor(Color.white); idGraphics.fillRect(0, 0, pageWidth, pageHeight); @@ -1002,29 +962,20 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * How many sequences and residues can we fit on a printable page? */ - int totalRes = (pageWidth - idWidth) / av.getCharWidth(); + final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; + final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - int alignmentWidth = av.getAlignment().getWidth(); + final int alignmentWidth = av.getAlignment().getVisibleWidth(); int pagesWide = (alignmentWidth / totalRes) + 1; - final int startRes = (pi % pagesWide) * totalRes; - int endRes = (startRes + totalRes) - 1; - - if (endRes > (alignmentWidth - 1)) - { - endRes = alignmentWidth - 1; - } - - final int startSeq = (pi / pagesWide) * totalSeq; - int endSeq = startSeq + totalSeq; + final int startRes = (pageIndex % pagesWide) * totalRes; + final int endRes = Math.min(startRes + totalRes - 1, + alignmentWidth - 1); - int alignmentHeight = av.getAlignment().getHeight(); - if (endSeq > alignmentHeight) - { - endSeq = alignmentHeight; - } + final int startSeq = (pageIndex / pagesWide) * totalSeq; + final int alignmentHeight = av.getAlignment().getHeight(); + final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight); int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; @@ -1035,7 +986,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pagesHigh /= pageHeight; - if (pi >= (pagesWide * pagesHigh)) + if (pageIndex >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } @@ -1054,47 +1005,12 @@ public class AlignmentPanel extends GAlignmentPanel implements * then reset to top left (0, 0) */ idGraphics.translate(0, scaleHeight); - idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont()); - Color currentColor = null; - Color currentTextColor = null; - - SequenceI seq; - for (int i = startSeq; i < endSeq; i++) - { - seq = av.getAlignment().getSequenceAt(i); - if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null).contains(seq)) - { - /* - * gray out ids of sequences in selection group (if any) - */ - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; - } - - idGraphics.setColor(currentColor); - idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth, - charHeight); + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + List selection = av.getSelectionGroup() == null ? null + : av.getSelectionGroup().getSequences(null); + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, + selection); - idGraphics.setColor(currentTextColor); - - int xPos = 0; - String displayId = seq.getDisplayId(av.getShowJVSuffix()); - if (av.isRightAlignIds()) - { - fm = idGraphics.getFontMetrics(); - xPos = idWidth - fm.stringWidth(displayId) - 4; - } - - idGraphics.drawString(displayId, xPos, - (((i - startSeq) * charHeight) + charHeight) - - (charHeight / 5)); - } idGraphics.setFont(av.getFont()); idGraphics.translate(0, -scaleHeight); @@ -1104,7 +1020,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, - endRes, startSeq, endSeq); + endRes, startSeq, endSeq - 1); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1134,31 +1050,27 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Prints one page of an alignment in wrapped mode. Returns + * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if + * no page could be drawn (page number out of range). * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! + * @param pageWidth + * @param pageHeight + * @param pageNumber + * (0, 1, ...) + * @param g * - * @return DOCUMENT ME! + * @return * * @throws PrinterException - * DOCUMENT ME! */ - public int printWrappedAlignment(int pwidth, int pheight, int pi, - Graphics pg) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, + Graphics g) throws PrinterException { int annotationHeight = 0; - AnnotationLabels labels = null; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); - labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); @@ -1172,72 +1084,42 @@ 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(pwidth - idWidth); + .getWrappedCanvasWidth(pageWidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); - - // ////////////// - // Draw the ids - pg.setColor(Color.black); - - pg.translate(0, -pi * pheight); - - pg.setClip(0, pi * pheight, pwidth, pheight); + g.setColor(Color.white); + g.fillRect(0, 0, pageWidth, pageHeight); + g.setFont(av.getFont()); + g.setColor(Color.black); - int ypos = hgap; - - do - { - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); - SequenceI s = av.getAlignment().getSequenceAt(i); - String string = s.getDisplayId(av.getShowJVSuffix()); - int xPos = 0; - if (av.isRightAlignIds()) - { - FontMetrics fm = pg.getFontMetrics(); - xPos = idWidth - fm.stringWidth(string) - 4; - } - pg.drawString(string, xPos, - ((i * av.getCharHeight()) + ypos + av.getCharHeight()) - - (av.getCharHeight() / 5)); - } - if (labels != null) - { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.getCharHeight())); + /* + * 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) + */ + g.translate(0, -pageNumber * pageHeight); - pg.setFont(av.getFont()); - labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.getCharHeight())); - } + g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); - ypos += cHeight; - } while (ypos < totalHeight); + /* + * draw sequence ids and annotation labels (if shown) + */ + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight); - pg.translate(idWidth, 0); + g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, totalHeight, 0); - if ((pi * pheight) < totalHeight) + if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; - } else { @@ -1268,13 +1150,13 @@ 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_USERIDWIDTH")) == null) + .getIntegerProperty(Preferences.FIGURE_FIXEDIDWIDTH)) == null) { int w = getIdPanel().getWidth(); return (w > 0 ? w : calculateIdWidth().width + 4); @@ -1282,94 +1164,55 @@ 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(); @@ -1378,7 +1221,7 @@ 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 @@ -1402,27 +1245,6 @@ 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 @@ -1556,8 +1378,7 @@ 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 @@ -1684,7 +1505,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public String getViewName() { - return av.viewName; + return av.getViewName(); } /** @@ -1815,7 +1636,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void scrollToCentre(SearchResultsI sr, int verticalOffset) { - scrollToPosition(sr, verticalOffset, true, true); + scrollToPosition(sr, verticalOffset, true); } /** @@ -1902,4 +1723,116 @@ 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; + } + }