/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; import java.beans.*; import java.io.*; import java.util.Hashtable; import java.util.Vector; import java.awt.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable, AlignmentViewPanel { public AlignViewport av; OverviewPanel overviewPanel; SeqPanel seqPanel; IdPanel idPanel; IdwidthAdjuster idwidthAdjuster; /** DOCUMENT ME!! */ public AlignFrame alignFrame; ScalePanel scalePanel; AnnotationPanel annotationPanel; AnnotationLabels alabels; // this value is set false when selection area being dragged boolean fastPaint = true; int hextent = 0; int vextent = 0; /** * Creates a new AlignmentPanel object. * * @param af * DOCUMENT ME! * @param av * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { alignFrame = af; this.av = av; seqPanel = new SeqPanel(av, this); idPanel = new IdPanel(av, this); scalePanel = new ScalePanel(av, this); idPanelHolder.add(idPanel, BorderLayout.CENTER); idwidthAdjuster = new IdwidthAdjuster(this); idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); annotationPanel = new AnnotationPanel(this); alabels = new AnnotationLabels(this); annotationScroller.setViewportView(annotationPanel); annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); scalePanelHolder.add(scalePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); setScrollValues(0, 0); setAnnotationVisible(av.getShowAnnotation()); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); final AlignmentPanel ap = this; av.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) { PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); alignmentChanged(); } } }); fontChanged(); adjustAnnotationHeight(); } public void alignmentChanged() { av.alignmentChanged(this); alignFrame.updateEditMenuBar(); paintAlignment(true); } /** * DOCUMENT ME! */ public void fontChanged() { // set idCanvas bufferedImage to null // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight + fm.getDescent())); idPanel.idCanvas.gg = null; seqPanel.seqCanvas.img = null; annotationPanel.adjustPanelHeight(); Dimension d = calculateIdWidth(); d.setSize(d.width + 4, d.height); idPanel.idCanvas.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); if (overviewPanel != null) { overviewPanel.setBoxPosition(); } repaint(); } /** * Calculate the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. * * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ public Dimension calculateIdWidth() { Container c = new Container(); FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth / 3)); 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); } i++; } // Also check annotation label widths i = 0; if (al.getAlignmentAnnotation() != null) { fm = c.getFontMetrics(alabels.getFont()); while (i < al.getAlignmentAnnotation().length) { String label = al.getAlignmentAnnotation()[i].label; if (fm.stringWidth(label) > idWidth) { idWidth = fm.stringWidth(label); } i++; } } return new Dimension(Math.min(maxwidth, idWidth), 12); } /** * Highlight the given results on the alignment. * */ public void highlightSearchResults(SearchResults results) { scrollToPosition(results); seqPanel.seqCanvas.highlightSearchResults(results); } /** * scroll the view to show the position of the highlighted region in results * (if any) and redraw the overview * * @param results */ public boolean scrollToPosition(SearchResults results) { return scrollToPosition(results, true); } /** * scroll the view to show the position of the highlighted region in results * (if any) * * @param results * @param redrawOverview * - when set, the overview will be recalculated (takes longer) * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, boolean redrawOverview) { int startv, endv, starts, ends, width; // TODO: properly locate search results in view when large numbers of hidden // columns exist before highlighted region // do we need to scroll the panel? // TODO: tons of nullpointereexceptions raised here. if (results != null && results.getSize() > 0 && av != null && av.alignment != null) { int seqIndex = av.alignment.findIndex(results); if (seqIndex == -1) { return false; } SequenceI seq = av.alignment.getSequenceAt(seqIndex); int[] r=results.getResults(seq, 0, av.alignment.getWidth()); if (r == null) { return false; } int start = r[0]; int end = r[1]; // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // // DEBUG if (start < 0) { return false; } if (end == seq.getEnd()) { return false; } if (av.hasHiddenColumns) { start = av.getColumnSelection().findColumnPosition(start); end = av.getColumnSelection().findColumnPosition(end); if (start==end) { if (!av.colSel.isVisible(r[0])) { // don't scroll - position isn't visible return false; } } } if (!av.wrapAlignment) { if ((startv = av.getStartRes()) >= start) { setScrollValues(start - 1, seqIndex); } else if ((endv = av.getEndRes()) <= end) { setScrollValues(startv + 1 + end - endv, seqIndex); } else if ((starts = av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) { setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } } else { scrollToWrappedVisible(start); } } if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); } paintAlignment(redrawOverview); return true; } void scrollToWrappedVisible(int res) { int cwidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); av.startRes = vscroll.getValue() * cwidth; } } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public OverviewPanel getOverviewPanel() { return overviewPanel; } /** * DOCUMENT ME! * * @param op * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { overviewPanel = op; } /** * * @param b Hide or show annotation panel * */ public void setAnnotationVisible(boolean b) { if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); annotationScroller.setVisible(b); } repaint(); } /** * automatically adjust annotation panel height for new annotation * whilst ensuring the alignment is still visible. */ public void adjustAnnotationHeight() { // TODO: display vertical annotation scrollbar if necessary // this is called after loading new annotation onto alignment if (alignFrame.getHeight() == 0) { System.out.println("NEEDS FIXING"); } validateAnnotationDimensions(true); addNotify(); paintAlignment(true); } /** * calculate the annotation dimensions and refresh slider values accordingly. * need to do repaints/notifys afterwards. */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { int height = annotationPanel.adjustPanelHeight(); if (hscroll.isVisible()) { height += hscroll.getPreferredSize().height; } if (height > alignFrame.getHeight() / 2) { height = alignFrame.getHeight() / 2; } if (!adjustPanelHeight) { // maintain same window layout whilst updating sliders height=annotationScroller.getSize().height; } hscroll.addNotify(); annotationScroller.setPreferredSize(new Dimension(annotationScroller .getWidth(), height)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); annotationScroller.addNotify(); } /** * DOCUMENT ME! * * @param wrap * DOCUMENT ME! */ public void setWrapAlignment(boolean wrap) { av.startSeq = 0; scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); if (wrap) { annotationScroller.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.showAnnotation) { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } idSpaceFillerPanel1.setVisible(!wrap); repaint(); } // return value is true if the scroll is valid public boolean scrollUp(boolean up) { if (up) { if (vscroll.getValue() < 1) { return false; } fastPaint = false; vscroll.setValue(vscroll.getValue() - 1); } else { if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) { return false; } fastPaint = false; vscroll.setValue(vscroll.getValue() + 1); } fastPaint = true; return true; } /** * DOCUMENT ME! * * @param right * DOCUMENT ME! * * @return DOCUMENT ME! */ public boolean scrollRight(boolean right) { if (!right) { if (hscroll.getValue() < 1) { return false; } fastPaint = false; hscroll.setValue(hscroll.getValue() - 1); } else { if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) { return false; } fastPaint = false; hscroll.setValue(hscroll.getValue() + 1); } fastPaint = true; return true; } /** * Adjust row/column scrollers to show a visible position in the alignment. * * @param x visible column to scroll to * DOCUMENT ME! * @param y visible row to scroll to * */ public void setScrollValues(int x, int y) { // System.err.println("Scroll to "+x+","+y); if (av == null || av.alignment == null) { return; } int width = av.alignment.getWidth(); int height = av.alignment.getHeight(); if (av.hasHiddenColumns) { width = av.getColumnSelection().findColumnPosition(width); } av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1); hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; if (hextent > width) { hextent = width; } if (vextent > height) { vextent = height; } if ((hextent + x) > width) { x = width - hextent; } if ((vextent + y) > height) { y = height - vextent; } if (y < 0) { y = 0; } if (x < 0) { x = 0; } hscroll.setValues(x, hextent, 0, width); vscroll.setValues(y, vextent, 0, height); } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { int oldX = av.getStartRes(); int oldY = av.getStartSeq(); if (evt.getSource() == hscroll) { int x = hscroll.getValue(); av.setStartRes(x); av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) { int offy = vscroll.getValue(); if (av.getWrapAlignment()) { if (offy > -1) { int rowSize = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); av.setStartRes(offy * rowSize); av.setEndRes((offy + 1) * rowSize); } else { // 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() { public void run() { setScrollValues(av.getStartRes(), av.getStartSeq()); } }); } } else { av.setStartSeq(offy); av.setEndSeq(offy + (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); } } if (overviewPanel != null) { overviewPanel.setBoxPosition(); } int scrollX = av.startRes - oldX; int scrollY = av.startSeq - oldY; if (av.getWrapAlignment() || !fastPaint) { repaint(); } else { // Make sure we're not trying to draw a panel // larger than the visible window if (scrollX > av.endRes - av.startRes) { scrollX = av.endRes - av.startRes; } else if (scrollX < av.startRes - av.endRes) { scrollX = av.startRes - av.endRes; } if (scrollX != 0 || scrollY != 0) { idPanel.idCanvas.fastPaint(scrollY); seqPanel.seqCanvas.fastPaint(scrollX, scrollY); scalePanel.repaint(); if (av.getShowAnnotation()) { annotationPanel.fastPaint(scrollX); } } } } public void paintAlignment(boolean updateOverview) { repaint(); if (updateOverview) { av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { overviewPanel.updateOverviewImage(); } } } /** * DOCUMENT ME! * * @param g * DOCUMENT ME! */ public void paintComponent(Graphics g) { invalidate(); Dimension d = idPanel.idCanvas.getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); validate(); if (av.getWrapAlignment()) { int maxwidth = av.alignment.getWidth(); if (av.hasHiddenColumns) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } int canvasWidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); if (canvasWidth > 0) { int max = maxwidth / seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas .getWidth()) + 1; vscroll.setMaximum(max); vscroll.setUnitIncrement(1); vscroll.setVisibleAmount(1); } } else { setScrollValues(av.getStartRes(), av.getStartSeq()); } } /** * DOCUMENT ME! * * @param pg * DOCUMENT ME! * @param pf * DOCUMENT ME! * @param pi * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException * DOCUMENT ME! */ public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); int pwidth = (int) pf.getImageableWidth(); int pheight = (int) pf.getImageableHeight(); if (av.getWrapAlignment()) { return printWrappedAlignment(pg, pwidth, pheight, pi); } else { return printUnwrapped(pg, pwidth, pheight, pi); } } /** * 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! */ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { int idWidth = getVisibleIdWidth(); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); pg.setColor(Color.white); pg.fillRect(0, 0, pwidth, pheight); pg.setFont(av.getFont()); // ////////////////////////////////// // / How many sequences and residues can we fit on a printable page? int totalRes = (pwidth - idWidth) / av.getCharWidth(); int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1; int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; // /////////////////////////// // / Only print these sequences and residues on this page int startRes; // /////////////////////////// // / Only print these sequences and residues on this page int endRes; // /////////////////////////// // / Only print these sequences and residues on this page int startSeq; // /////////////////////////// // / Only print these sequences and residues on this page int endSeq; startRes = (pi % pagesWide) * totalRes; endRes = (startRes + totalRes) - 1; if (endRes > (av.getAlignment().getWidth() - 1)) { endRes = av.getAlignment().getWidth() - 1; } startSeq = (pi / pagesWide) * totalSeq; endSeq = startSeq + totalSeq; if (endSeq > av.getAlignment().getHeight()) { endSeq = av.getAlignment().getHeight(); } int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight; if (av.showAnnotation) { pagesHigh += annotationPanel.adjustPanelHeight() + 3; } pagesHigh /= pheight; if (pi >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } // draw Scale pg.translate(idWidth, 0); scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); pg.translate(-idWidth, scaleHeight); // ////////////// // Draw the ids Color currentColor = null; Color currentTextColor = null; pg.setFont(idPanel.idCanvas.idfont); SequenceI seq; for (int i = startSeq; i < endSeq; i++) { seq = av.getAlignment().getSequenceAt(i); if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(seq)) { currentColor = Color.gray; currentTextColor = Color.black; } else { currentColor = av.getSequenceColour(seq); currentTextColor = Color.black; } pg.setColor(currentColor); pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av.getCharHeight()); pg.setColor(currentTextColor); int xPos = 0; if (av.rightAlignIds) { fm = pg.getFontMetrics(); xPos = idWidth - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) - 4; } pg.drawString( seq.getDisplayId(av.getShowJVSuffix()), xPos, (((i - startSeq) * av.charHeight) + av.getCharHeight()) - (av.getCharHeight() / 5)); } pg.setFont(av.getFont()); // draw main sequence panel pg.translate(idWidth, 0); seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); if (av.showAnnotation && (endSeq == av.alignment.getHeight())) { pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); alabels.drawComponent((Graphics2D) pg, idWidth); pg.translate(idWidth + 3, 0); annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1); } return Printable.PAGE_EXISTS; } /** * 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! */ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { int annotationHeight = 0; AnnotationLabels labels = null; if (av.showAnnotation) { annotationHeight = annotationPanel.adjustPanelHeight(); labels = new AnnotationLabels(av); } int hgap = av.charHeight; if (av.scaleAboveWrapped) { hgap += av.charHeight; } int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; int idWidth = getVisibleIdWidth(); int maxwidth = av.alignment.getWidth(); if (av.hasHiddenColumns) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - 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); int ypos = hgap; do { for (int i = 0; i < av.alignment.getHeight(); i++) { pg.setFont(idPanel.idCanvas.idfont); SequenceI s = av.alignment.getSequenceAt(i); String string = s.getDisplayId(av.getShowJVSuffix()); int xPos = 0; if (av.rightAlignIds) { FontMetrics fm = pg.getFontMetrics(); xPos = idWidth - fm.stringWidth(string) - 4; } pg.drawString(string, xPos, ((i * av.charHeight) + ypos + av.charHeight) - (av.charHeight / 5)); } if (labels != null) { pg.translate(-3, ypos + (av.getAlignment().getHeight() * av.charHeight)); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); pg.translate(+3, -ypos - (av.getAlignment().getHeight() * av.charHeight)); } ypos += cHeight; } while (ypos < totalHeight); pg.translate(idWidth, 0); seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) { return Printable.PAGE_EXISTS; } else { return Printable.NO_SUCH_PAGE; } } int getVisibleIdWidth() { return idPanel.getWidth() > 0 ? idPanel.getWidth() : calculateIdWidth().width + 4; } void makeAlignmentImage(int type, File file) { int maxwidth = av.alignment.getWidth(); if (av.hasHiddenColumns) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } int height = ((av.alignment.getHeight() + 1) * av.charHeight) + scalePanel.getHeight(); int width = getVisibleIdWidth() + (maxwidth * av.charWidth); if (av.getWrapAlignment()) { height = getWrappedHeight(); if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { // TODO: JAL-244 width = alignFrame.getWidth() - vscroll.getPreferredSize().width - alignFrame.getInsets().left - alignFrame.getInsets().right; } else { width = seqPanel.getWidth() + getVisibleIdWidth(); } } else if (av.getShowAnnotation()) { height += annotationPanel.adjustPanelHeight() + 3; } try { jalview.util.ImageMaker im; if (type == jalview.util.ImageMaker.PNG) { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, "Create PNG image from alignment", width, height, file, null); } else { im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, "Create EPS file from alignment", width, height, file, alignFrame.getTitle()); } if (av.getWrapAlignment()) { if (im.getGraphics() != null) { printWrappedAlignment(im.getGraphics(), width, height, 0); im.writeImage(); } } else { if (im.getGraphics() != null) { printUnwrapped(im.getGraphics(), width, height, 0); im.writeImage(); } } } 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(); } } /** * DOCUMENT ME! */ public void makeEPS(File epsFile) { makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); } /** * DOCUMENT ME! */ public void makePNG(File pngFile) { makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile); } public void makePNGImageMap(File imgMapFile, String imageName) { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); // Gen image map // //////////////////////////////// if (imgMapFile != null) { try { int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment .getWidth(), g, gSize, f, fSize, sy; StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); out.println("" + ""); for (s = 0; s < sSize; s++) { sy = s * av.charHeight + scaleHeight; SequenceI seq = av.alignment.getSequenceAt(s); SequenceFeature[] features = seq.getDatasetSequence() .getSequenceFeatures(); SequenceGroup[] groups = av.alignment.findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); Object obj = null; if (av.alignment.isNucleotide()) { obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + ""); } else { obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + ""); } if (obj == null) { continue; } String triplet = obj.toString(); int alIndex = seq.findPosition(res); gSize = groups.length; for (g = 0; g < gSize; g++) { if (text.length() < 1) { text.append(" res) { text.append("
" + groups[g].getName() + ""); } } if (features != null) { if (text.length() < 1) { text.append("= seq.findPosition(res))) { if (features[f].getType().equals("disulfide bond")) { if (features[f].getBegin() == seq.findPosition(res) || features[f].getEnd() == seq .findPosition(res)) { text.append("
disulfide bond " + features[f].getBegin() + ":" + features[f].getEnd()); } } else { text.append("
"); text.append(features[f].getType()); if (features[f].getDescription() != null && !features[f].getType().equals( features[f].getDescription())) { text.append(" " + features[f].getDescription()); } if (features[f].getValue("status") != null) { text.append(" (" + features[f].getValue("status") + ")"); } } } } } if (text.length() > 1) { text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); out.println(text.toString()); } } } out.println(""); out.close(); } catch (Exception ex) { ex.printStackTrace(); } } // /////////END OF IMAGE MAP } int getWrappedHeight() { int seqPanelWidth = seqPanel.seqCanvas.getWidth(); if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() - vscroll.getPreferredSize().width - alignFrame.getInsets().left - alignFrame.getInsets().right; } int chunkWidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanelWidth); int hgap = av.charHeight; if (av.scaleAboveWrapped) { hgap += av.charHeight; } int annotationHeight = 0; if (av.showAnnotation) { annotationHeight = annotationPanel.adjustPanelHeight(); } int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; int maxwidth = av.alignment.getWidth(); if (av.hasHiddenColumns) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; return height; } /** * close the panel - deregisters all listeners and nulls any references to * alignment data. */ public void closePanel() { PaintRefresher.RemoveComponent(seqPanel.seqCanvas); PaintRefresher.RemoveComponent(idPanel.idCanvas); PaintRefresher.RemoveComponent(this); if (av != null) { jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); ssm.removeStructureViewerListener(seqPanel, null); ssm.removeSelectionListener(seqPanel); av.alignment = null; av = null; } else { if (Cache.log.isDebugEnabled()) { Cache.log.warn("Closing alignment panel which is already closed."); } } } /** * hides or shows dynamic annotation rows based on groups and av state flags */ public void updateAnnotation() { updateAnnotation(false); } public void updateAnnotation(boolean applyGlobalSettings) { // TODO: this should be merged with other annotation update stuff - that // sits on AlignViewport boolean updateCalcs = false; boolean conv = av.isShowGroupConservation(); boolean cons = av.isShowGroupConsensus(); boolean showprf = av.isShowSequenceLogo(); boolean showConsHist = av.isShowConsensusHistogram(); boolean sortg = true; // remove old automatic annotation // add any new annotation Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); // intersect alignment annotation with alignment groups AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); Hashtable oldrfs = new Hashtable(); if (aan != null) { for (int an = 0; an < aan.length; an++) { if (aan[an].autoCalculated && aan[an].groupRef != null) { oldrfs.put(aan[an].groupRef, aan[an].groupRef); av.alignment.deleteAnnotation(aan[an]); aan[an] = null; } } } SequenceGroup sg; if (gr != null) { for (int g = 0; g < gr.size(); g++) { updateCalcs = false; sg = (SequenceGroup) gr.elementAt(g); if (applyGlobalSettings || !oldrfs.containsKey(sg)) { // set defaults for this group's conservation/consensus sg.setshowSequenceLogo(showprf); sg.setShowConsensusHistogram(showConsHist); } if (conv) { updateCalcs = true; av.alignment.addAnnotation(sg.getConservationRow(), 0); } if (cons) { updateCalcs = true; av.alignment.addAnnotation(sg.getConsensus(), 0); } // refresh the annotation rows if (updateCalcs) { sg.recalcConservation(); } } } oldrfs.clear(); adjustAnnotationHeight(); } @Override public AlignmentI getAlignment() { return av.alignment; } /** * get the name for this view * @return */ public String getViewName() { return av.viewName; } /** * Make/Unmake this alignment panel the current input focus * @param b */ public void setSelected(boolean b) { try { alignFrame.setSelected(b); } catch (Exception ex) {}; if (b) { alignFrame.setDisplayedView(this); } } @Override public StructureSelectionManager getStructureSelectionManager() { return av.getStructureSelectionManager(); } }