/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import jalview.analysis.AnnotationSorter; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.HTMLOutput; import jalview.jbgui.GAlignmentPanel; import jalview.math.AlignmentDimension; import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Insets; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileWriter; import java.io.PrintWriter; import java.util.List; import javax.swing.SwingUtilities; /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; OverviewPanel overviewPanel; private SeqPanel seqPanel; private IdPanel idPanel; private boolean headless; IdwidthAdjuster idwidthAdjuster; /** DOCUMENT ME!! */ public AlignFrame alignFrame; private ScalePanel scalePanel; private AnnotationPanel annotationPanel; private AnnotationLabels alabels; private int hextent = 0; private int vextent = 0; /* * Flag set while scrolling to follow complementary cDNA/protein scroll. When * false, suppresses invoking the same method recursively. */ private boolean scrollComplementaryPanel = true; private PropertyChangeListener propertyChangeListener; private CalculationChooser calculationDialog; /** * Creates a new AlignmentPanel object. * * @param af * @param av */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); setIdPanel(new IdPanel(av, this)); setScalePanel(new ScalePanel(av, this)); idPanelHolder.add(getIdPanel(), BorderLayout.CENTER); idwidthAdjuster = new IdwidthAdjuster(this); idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); setAnnotationPanel(new AnnotationPanel(this)); setAlabels(new AnnotationLabels(this)); annotationScroller.setViewportView(getAnnotationPanel()); annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); setScrollValues(0, 0); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); addComponentListener(new ComponentAdapter() { @Override public void componentResized(ComponentEvent evt) { // reset the viewport ranges when the alignment panel is resized // in particular, this initialises the end residue value when Jalview // is initialised ViewportRanges ranges = av.getRanges(); if (av.getWrapAlignment()) { int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( getSeqPanel().seqCanvas.getWidth()); ranges.setViewportWidth(widthInRes); } else { int widthInRes = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); ranges.setViewportWidth(widthInRes); ranges.setViewportHeight(heightInSeq); } } }); final AlignmentPanel ap = this; propertyChangeListener = new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) { PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); alignmentChanged(); } } }; av.addPropertyChangeListener(propertyChangeListener); av.getRanges().addPropertyChangeListener(this); fontChanged(); adjustAnnotationHeight(); updateLayout(); } @Override public AlignViewportI getAlignViewport() { return av; } public void alignmentChanged() { av.alignmentChanged(this); if (getCalculationDialog() != null) { getCalculationDialog().validateCalcTypes(); } alignFrame.updateEditMenuBar(); // no idea if we need to update structure paintAlignment(true, 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.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize( new Dimension(10, av.getCharHeight() + fm.getDescent())); idwidthAdjuster.invalidate(); scalePanelHolder.invalidate(); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); d.setSize(d.width + 4, d.height); getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); 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() { // 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); av.setIdWidth(r.width); } else { r = new Dimension(); r.width = av.getIdWidth(); r.height = 0; } return r; } /** * Calculate the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. * * @param maxwidth * -1 or maximum width allowed for IdWidth * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ public Dimension calculateIdWidth(int maxwidth) { Container c = new Container(); FontMetrics fm = c.getFontMetrics( new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); 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); } i++; } // Also check annotation label widths i = 0; if (al.getAlignmentAnnotation() != null) { fm = c.getFontMetrics(getAlabels().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( maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** * Highlight the given results on the alignment. * */ public void highlightSearchResults(SearchResultsI results) { boolean scrolled = scrollToPosition(results, 0, true, false); boolean noFastPaint = scrolled && av.getWrapAlignment(); getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint); } /** * Scroll the view to show the position of the highlighted region in results * (if any) * * @param searchResults * @param redrawOverview * @return */ public boolean scrollToPosition(SearchResultsI searchResults, boolean redrawOverview) { return scrollToPosition(searchResults, 0, redrawOverview, false); } /** * Scrolls the view (if necessary) to show the position of the first * highlighted region in results (if any). Answers true if the view was * scrolled, or false if no matched region was found, or it is already * visible. * * @param results * @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 startv, endv, starts, ends; ViewportRanges ranges = av.getRanges(); if (results == null || results.isEmpty() || av == null || av.getAlignment() == null) { return false; } int seqIndex = av.getAlignment().findIndex(results); if (seqIndex == -1) { return false; } SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; } int start = r[0]; int end = r[1]; /* * To centre results, scroll to positions half the visible width * left/right of the start/end positions */ if (centre) { int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1; start = Math.max(start - offset, 0); end = end + offset - 1; } if (start < 0) { return false; } if (end == seq.getEnd()) { return false; } if (av.hasHiddenColumns()) { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); start = hidden.findColumnPosition(start); end = hidden.findColumnPosition(end); if (start == end) { if (!hidden.isVisible(r[0])) { // don't scroll - position isn't visible return false; } } } /* * allow for offset of target sequence (actually scroll to one above it) */ seqIndex = Math.max(0, seqIndex - verticalOffset); boolean scrollNeeded = true; if (!av.getWrapAlignment()) { if ((startv = ranges.getStartRes()) >= start) { /* * Scroll left to make start of search results visible */ setScrollValues(start, seqIndex); } else if ((endv = ranges.getEndRes()) <= end) { /* * Scroll right to make end of search results visible */ setScrollValues(startv + 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 */ scrollNeeded = false; } else { scrollNeeded = ranges.scrollToWrappedVisible(start); } paintAlignment(redrawOverview, false); return scrollNeeded; } /** * 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.getWrapAlignment()) { annotationSpaceFillerHolder.setVisible(b); annotationScroller.setVisible(b); } repaint(); } /** * automatically adjust annotation panel height for new annotation whilst * ensuring the alignment is still visible. */ @Override 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(); // TODO: many places call this method and also paintAlignment with various // different settings. this means multiple redraws are triggered... paintAlignment(true, false); } /** * calculate the annotation dimensions and refresh slider values accordingly. * need to do repaints/notifys afterwards. */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { int annotationHeight = getAnnotationPanel().adjustPanelHeight(); 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; /* * 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(); annotationScroller.addNotify(); } /** * update alignment layout for viewport settings * * @param wrap * DOCUMENT ME! */ public void updateLayout() { fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); ViewportRanges ranges = av.getRanges(); ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); if (wrap) { annotationScroller.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.isShowAnnotation()) { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } int canvasWidth = getSeqPanel().seqCanvas.getWidth(); if (canvasWidth > 0) { // may not yet be laid out if (wrap) { int widthInRes = getSeqPanel().seqCanvas .getWrappedCanvasWidth(canvasWidth); ranges.setViewportWidth(widthInRes); } else { int widthInRes = (canvasWidth / av.getCharWidth()); int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()); ranges.setViewportWidth(widthInRes); ranges.setViewportHeight(heightInSeq); } } idSpaceFillerPanel1.setVisible(!wrap); repaint(); } /** * Adjust row/column scrollers to show a visible position in the alignment. * * @param x * visible column to scroll to * @param y * visible row to scroll to * */ public void setScrollValues(int xpos, int ypos) { int x = xpos; int y = ypos; if (av == null || av.getAlignment() == null) { return; } if (av.getWrapAlignment()) { setScrollingForWrappedPanel(x); } else { int width = av.getAlignment().getWidth(); int height = av.getAlignment().getHeight(); if (av.hasHiddenColumns()) { // reset the width to exclude hidden columns width = av.getAlignment().getHiddenColumns() .findColumnPosition(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); 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; } // update the scroll values hscroll.setValues(x, hextent, 0, width); vscroll.setValues(y, vextent, 0, height); } } /** * Respond to adjustment event when horizontal or vertical scrollbar is * changed * * @param evt * adjustment event encoding whether hscroll or vscroll changed */ @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (av.getWrapAlignment()) { adjustScrollingWrapped(evt); return; } ViewportRanges ranges = av.getRanges(); if (evt.getSource() == hscroll) { int oldX = ranges.getStartRes(); int oldwidth = ranges.getViewportWidth(); int x = hscroll.getValue(); int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); // 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 if ((x == oldX) && (width == oldwidth)) { return; } ranges.setViewportStartAndWidth(x, width); } else if (evt.getSource() == vscroll) { int oldY = ranges.getStartSeq(); int oldheight = ranges.getViewportHeight(); 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 if ((y == oldY) && (height == oldheight)) { return; } ranges.setViewportStartAndHeight(y, height); } repaint(); } /** * Responds to a scroll change by setting the start position of the viewport. * Does * * @param evt */ protected void adjustScrollingWrapped(AdjustmentEvent evt) { if (evt.getSource() == hscroll) { return; // no horizontal scroll when wrapped } final ViewportRanges ranges = av.getRanges(); if (evt.getSource() == vscroll) { int newY = vscroll.getValue(); /* * 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 */ int oldX = ranges.getStartRes(); int oldY = ranges.getWrappedScrollPosition(oldX); if (oldY == newY) { return; } if (newY > -1) { /* * limit page up/down to one width's worth of positions */ int rowSize = ranges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; ranges.setViewportStartAndWidth(Math.max(0, newX), 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() { @Override public void run() { // When updating scrolling to use ViewportChange events, this code // 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( "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel ranges.setStartRes(0); ranges.setStartSeq(0); } }); } repaint(); } /* (non-Javadoc) * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean) */ @Override public void paintAlignment(boolean updateOverview, boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); sorter.sort(getAlignment().getAlignmentAnnotation(), av.getSortAnnotationsBy()); repaint(); if (updateStructures) { av.getStructureSelectionManager().sequenceColoursChanged(this); } if (updateOverview) { if (overviewPanel != null) { overviewPanel.updateOverviewImage(); } } } /** * DOCUMENT ME! * * @param g * DOCUMENT ME! */ @Override public void paintComponent(Graphics g) { invalidate(); Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); validate(); /* * set scroll bar positions */ ViewportRanges ranges = av.getRanges(); setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); } /** * Set vertical scroll bar position, and number of increments, for wrapped * panel * * @param topLeftColumn * the column position at top left (0..) */ private void setScrollingForWrappedPanel(int topLeftColumn) { ViewportRanges ranges = av.getRanges(); int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); /* * a scrollbar's value can be set to at most (maximum-extent) * so we add extent (1) to the maxScroll value */ vscroll.setUnitIncrement(1); vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1); } /** * DOCUMENT ME! * * @param pg * DOCUMENT ME! * @param pf * DOCUMENT ME! * @param pi * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException * DOCUMENT ME! */ @Override 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(pwidth, pheight, pi, pg); } else { return printUnwrapped(pwidth, pheight, pi, pg, pg); } } /** * 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. * * @param pageWidth * @param pageHeight * @param pi * @param idGraphics * the graphics context for sequence ids and annotation labels * @param alignmentGraphics * the graphics context for sequences and annotations (may or may not * be the same context as idGraphics) * @return * @throws PrinterException */ public int printUnwrapped(int pageWidth, int pageHeight, int pi, Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { final int idWidth = getVisibleIdWidth(false); /* * Get the horizontal offset to where we draw the sequences. * This is idWidth if using a single Graphics context, else zero. */ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth; FontMetrics fm = getFontMetrics(av.getFont()); int charHeight = av.getCharHeight(); int scaleHeight = charHeight + fm.getDescent(); idGraphics.setColor(Color.white); idGraphics.fillRect(0, 0, pageWidth, pageHeight); idGraphics.setFont(av.getFont()); /* * How many sequences and residues can we fit on a printable page? */ int totalRes = (pageWidth - idWidth) / av.getCharWidth(); int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; int alignmentWidth = av.getAlignment().getWidth(); 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; int alignmentHeight = av.getAlignment().getHeight(); if (endSeq > alignmentHeight) { endSeq = alignmentHeight; } int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; if (av.isShowAnnotation()) { pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; } pagesHigh /= pageHeight; if (pi >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; /* * draw the Scale at horizontal offset, then reset to top left (0, 0) */ alignmentGraphics.translate(alignmentGraphicsOffset, 0); getScalePanel().drawScale(alignmentGraphics, startRes, endRes, pageWidth - idWidth, scaleHeight); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); /* * Draw the sequence ids, offset for scale height, * 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); 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); /* * draw the sequences, offset for scale height, and id width (if using a * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, endRes, startSeq, endSeq); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) { /* * draw annotation labels; drawComponent() translates by * getScrollOffset(), so compensate for that first; * then reset to (0, scale height) */ int offset = getAlabels().getScrollOffset(); idGraphics.translate(0, -offset); idGraphics.translate(0, alignmentDrawnHeight); getAlabels().drawComponent(idGraphics, idWidth); idGraphics.translate(0, -alignmentDrawnHeight); /* * draw the annotations starting at * (idOffset, alignmentHeight) from (0, scaleHeight) */ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, 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(int pwidth, int pheight, int pi, Graphics pg) throws PrinterException { int annotationHeight = 0; AnnotationLabels labels = null; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); if (av.getScaleAboveWrapped()) { hgap += av.getCharHeight(); } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + annotationHeight; int idWidth = getVisibleIdWidth(false); int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() .findColumnPosition(maxwidth) - 1; } int resWidth = getSeqPanel().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.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())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); pg.translate(+3, -ypos - (av.getAlignment().getHeight() * av.getCharHeight())); } ypos += cHeight; } while (ypos < totalHeight); pg.translate(idWidth, 0); getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) { return Printable.PAGE_EXISTS; } else { return Printable.NO_SUCH_PAGE; } } /** * get current sequence ID panel width, or nominal value if panel were to be * displayed using default settings * * @return */ public int getVisibleIdWidth() { return getVisibleIdWidth(true); } /** * get current sequence ID panel width, or nominal value if panel were to be * displayed using default settings * * @param onscreen * indicate if the Id width for onscreen or offscreen display should * be returned * @return */ public 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; } Integer idwidth = null; if (onscreen || (idwidth = Cache .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { int w = getIdPanel().getWidth(); return (w > 0 ? w : calculateIdWidth().width + 4); } return idwidth.intValue() + 4; } void makeAlignmentImage(jalview.util.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 { AlignmentDimension aDimension = getAlignmentDimension(); try { 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(); } } else { if (graphics != null) { printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, graphics, graphics); 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(); } } finally { } } public AlignmentDimension getAlignmentDimension() { int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() .findColumnPosition(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + getScalePanel().getHeight(); int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); if (av.getWrapAlignment()) { height = getWrappedHeight(); if (headless) { // need to obtain default alignment width and then add in any // additional allowance for id margin // this duplicates the calculation in getWrappedHeight but adjusts for // offscreen idWith width = alignFrame.getWidth() - vscroll.getPreferredSize().width - alignFrame.getInsets().left - alignFrame.getInsets().right - getVisibleIdWidth() + getVisibleIdWidth(false); } else { width = getSeqPanel().getWidth() + getVisibleIdWidth(false); } } else if (av.isShowAnnotation()) { height += getAnnotationPanel().adjustPanelHeight() + 3; } return new AlignmentDimension(width, height); } /** * 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 // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.getCharHeight() + fm.getDescent(); // Gen image map // //////////////////////////////// if (imgMapFile != null) { try { int sSize = av.getAlignment().getHeight(); int alwidth = av.getAlignment().getWidth(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(HTMLOutput.getImageMapHTML()); out.println("" + ""); for (int s = 0; s < sSize; s++) { int sy = s * av.getCharHeight() + scaleHeight; SequenceI seq = av.getAlignment().getSequenceAt(s); SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (int column = 0; column < alwidth; column++) { StringBuilder text = new StringBuilder(512); String triplet = null; if (av.getAlignment().isNucleotide()) { triplet = ResidueProperties.nucleotideName.get(seq .getCharAt(column) + ""); } else { triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) + ""); } if (triplet == null) { continue; } int seqPos = seq.findPosition(column); int gSize = groups.length; for (int g = 0; g < gSize; g++) { if (text.length() < 1) { text.append(" column) { text.append("
").append(groups[g].getName()) .append(""); } } if (text.length() < 1) { text.append(" features = seq.findFeatures(column, column); for (SequenceFeature sf : features) { if (sf.isContactFeature()) { text.append("
").append(sf.getType()).append(" ") .append(sf.getBegin()).append(":") .append(sf.getEnd()); } else { text.append("
"); text.append(sf.getType()); String description = sf.getDescription(); if (description != null && !sf.getType().equals(description)) { description = description.replace("\"", """); text.append(" ").append(description); } } String status = sf.getStatus(); if (status != null && !"".equals(status)) { text.append(" (").append(status).append(")"); } } 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 = getSeqPanel().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 = getSeqPanel().seqCanvas .getWrappedCanvasWidth(seqPanelWidth); int hgap = av.getCharHeight(); if (av.getScaleAboveWrapped()) { hgap += av.getCharHeight(); } int annotationHeight = 0; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + annotationHeight; int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() .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(getSeqPanel().seqCanvas); PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); closeChildFrames(); /* * try to ensure references are nulled */ if (annotationPanel != null) { annotationPanel.dispose(); annotationPanel = null; } if (av != null) { av.removePropertyChangeListener(propertyChangeListener); propertyChangeListener = null; StructureSelectionManager ssm = av.getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); ssm.removeCommandListener(av); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); av.dispose(); av = null; } else { if (Cache.log.isDebugEnabled()) { Cache.log.warn("Closing alignment panel which is already closed."); } } } /** * Close any open dialogs that would be orphaned when this one is closed */ protected void closeChildFrames() { if (overviewPanel != null) { overviewPanel.dispose(); overviewPanel = null; } if (calculationDialog != null) { calculationDialog.closeFrame(); calculationDialog = null; } } /** * hides or shows dynamic annotation rows based on groups and av state flags */ public void updateAnnotation() { updateAnnotation(false, false); } public void updateAnnotation(boolean applyGlobalSettings) { updateAnnotation(applyGlobalSettings, false); } public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings) { av.updateGroupAnnotationSettings(applyGlobalSettings, preserveNewGroupSettings); adjustAnnotationHeight(); } @Override public AlignmentI getAlignment() { return av == null ? null : av.getAlignment(); } @Override public String getViewName() { return av.viewName; } /** * Make/Unmake this alignment panel the current input focus * * @param b */ public void setSelected(boolean b) { try { if (alignFrame.getSplitViewContainer() != null) { /* * bring enclosing SplitFrame to front first if there is one */ ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); } alignFrame.setSelected(b); } catch (Exception ex) { } if (b) { alignFrame.setDisplayedView(this); } } @Override public StructureSelectionManager getStructureSelectionManager() { return av.getStructureSelectionManager(); } @Override public void raiseOOMWarning(String string, OutOfMemoryError error) { new OOMWarning(string, error, this); } @Override public jalview.api.FeatureRenderer cloneFeatureRenderer() { return new FeatureRenderer(this); } @Override public jalview.api.FeatureRenderer getFeatureRenderer() { return seqPanel.seqCanvas.getFeatureRenderer(); } public void updateFeatureRenderer( jalview.renderer.seqfeatures.FeatureRenderer fr) { fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer()); } public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr) { if (getSeqPanel().seqCanvas.getFeatureRenderer() != null) { getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr); } } public ScalePanel getScalePanel() { return scalePanel; } public void setScalePanel(ScalePanel scalePanel) { this.scalePanel = scalePanel; } public SeqPanel getSeqPanel() { return seqPanel; } public void setSeqPanel(SeqPanel seqPanel) { this.seqPanel = seqPanel; } public AnnotationPanel getAnnotationPanel() { return annotationPanel; } public void setAnnotationPanel(AnnotationPanel annotationPanel) { this.annotationPanel = annotationPanel; } public AnnotationLabels getAlabels() { return alabels; } public void setAlabels(AnnotationLabels alabels) { this.alabels = alabels; } public IdPanel getIdPanel() { return idPanel; } public void setIdPanel(IdPanel idPanel) { this.idPanel = idPanel; } /** * Follow a scrolling change in the (cDNA/Protein) complementary alignment. * The aim is to keep the two alignments 'lined up' on their centre columns. * * @param sr * holds mapped region(s) of this alignment that we are scrolling * 'to'; may be modified for sequence offset by this method * @param verticalOffset * the number of visible sequences to show above the mapped region */ protected void scrollToCentre(SearchResultsI sr, int verticalOffset) { /* * To avoid jumpy vertical scrolling (if some sequences are gapped or not * mapped), we can make the scroll-to location a sequence above the one * actually mapped. */ SequenceI mappedTo = sr.getResults().get(0).getSequence(); List seqs = av.getAlignment().getSequences(); /* * This is like AlignmentI.findIndex(seq) but here we are matching the * dataset sequence not the aligned sequence */ boolean matched = false; for (SequenceI seq : seqs) { if (mappedTo == seq.getDatasetSequence()) { matched = true; break; } } if (!matched) { return; // failsafe, shouldn't happen } /* * Scroll to position but centring the target residue. */ scrollToPosition(sr, verticalOffset, true, true); } /** * Set a flag to say do not scroll any (cDNA/protein) complement. * * @param b */ protected void setToScrollComplementPanel(boolean b) { this.scrollComplementaryPanel = b; } /** * Get whether to scroll complement panel * * @return true if cDNA/protein complement panels should be scrolled */ protected boolean isSetToScrollComplementPanel() { return this.scrollComplementaryPanel; } /** * Redraw sensibly. * * @adjustHeight if true, try to recalculate panel height for visible * annotations */ protected void refresh(boolean adjustHeight) { validateAnnotationDimensions(adjustHeight); addNotify(); if (adjustHeight) { // sort, repaint, update overview paintAlignment(true, false); } else { // lightweight repaint repaint(); } } @Override /** * Property change event fired when a change is made to the viewport ranges * object associated with this alignment panel's viewport */ public void propertyChange(PropertyChangeEvent evt) { // update this panel's scroll values based on the new viewport ranges values ViewportRanges ranges = av.getRanges(); int x = ranges.getStartRes(); int y = ranges.getStartSeq(); setScrollValues(x, y); // now update any complementary alignment (its viewport ranges object // is different so does not get automatically updated) if (isSetToScrollComplementPanel()) { setToScrollComplementPanel(false); av.scrollComplementaryAlignment(); setToScrollComplementPanel(true); } } /** * Set the reference to the PCA/Tree chooser dialog for this panel. This * reference should be nulled when the dialog is closed. * * @param calculationChooser */ public void setCalculationDialog(CalculationChooser calculationChooser) { calculationDialog = calculationChooser; } /** * Returns the reference to the PCA/Tree chooser dialog for this panel (null * if none is open) */ public CalculationChooser getCalculationDialog() { return calculationDialog; } }