From: kiramt Date: Mon, 28 Aug 2017 11:15:35 +0000 (+0100) Subject: Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch' X-Git-Tag: Release_2_10_2b1~11^2~9^2~4^2~2 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9e2b4ccd9c95ffa75130bf808b0037ea6a1054ca;hp=-c Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch' into bug/JAL-2665-2.10.2b Conflicts: src/jalview/gui/SeqCanvas.java --- 9e2b4ccd9c95ffa75130bf808b0037ea6a1054ca diff --combined src/jalview/datamodel/SequenceGroup.java index c060ef0,6964b53..e2f15e1 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@@ -27,8 -27,6 +27,8 @@@ import jalview.renderer.ResidueShaderI import jalview.schemes.ColourSchemeI; import java.awt.Color; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; import java.util.ArrayList; import java.util.List; import java.util.Map; @@@ -41,26 -39,6 +41,26 @@@ */ public class SequenceGroup implements AnnotatedCollectionI { + // TODO ideally this event notification functionality should be separated into + // a + // subclass of ViewportProperties similarly to ViewportRanges. Done here as + // quick fix for JAL-2665 + public static final String SEQ_GROUP_CHANGED = "Sequence group changed"; + + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + // end of event notification functionality initialisation + String groupName; String description; @@@ -518,8 -496,6 +518,8 @@@ if (s != null && !sequences.contains(s)) { sequences.add(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() - 1, sequences.size()); } if (recalc) @@@ -644,8 -620,10 +644,10 @@@ conservation.description = "Conservation for group " + getName() + " less than " + consPercGaps + "% gaps"; // preserve width if already set - int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length - : endRes + 1) + int aWidth = (conservation.annotations != null) + ? (endRes < conservation.annotations.length + ? conservation.annotations.length + : endRes + 1) : endRes + 1; conservation.annotations = null; conservation.annotations = new Annotation[aWidth]; // should be alignment @@@ -665,8 -643,10 +667,10 @@@ consensus.description = "Percent Identity"; consensusData = cnsns; // preserve width if already set - int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length - : endRes + 1) + int aWidth = (consensus.annotations != null) + ? (endRes < consensus.annotations.length + ? consensus.annotations.length + : endRes + 1) : endRes + 1; consensus.annotations = null; consensus.annotations = new Annotation[aWidth]; // should be alignment width @@@ -713,8 -693,6 +717,8 @@@ synchronized (sequences) { sequences.remove(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() + 1, sequences.size()); if (recalc) { @@@ -751,9 -729,7 +755,9 @@@ */ public void setStartRes(int i) { + int before = startRes; startRes = i; + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes); } /** @@@ -763,9 -739,7 +767,9 @@@ */ public void setEndRes(int i) { + int before = endRes; endRes = i; + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes); } /** @@@ -1334,11 -1308,12 +1338,12 @@@ ArrayList aa = new ArrayList<>(); for (AlignmentAnnotation ann : getAlignmentAnnotation()) { - if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId() - .equals(calcId))) - && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq)) - && (label == null || (ann.label != null && ann.label - .equals(label)))) + if ((calcId == null || (ann.getCalcId() != null + && ann.getCalcId().equals(calcId))) + && (seq == null || (ann.sequenceRef != null + && ann.sequenceRef == seq)) + && (label == null + || (ann.label != null && ann.label.equals(label)))) { aa.add(ann); } @@@ -1374,10 -1349,7 +1379,10 @@@ { synchronized (sequences) { + int before = sequences.size(); sequences.clear(); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, + sequences.size()); } } @@@ -1465,7 -1437,8 +1470,8 @@@ @Override public boolean isNucleotide() { - if (context != null) { + if (context != null) + { return context.isNucleotide(); } return false; diff --combined src/jalview/gui/AlignmentPanel.java index c4eb26a,922e481..7cd8b50 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@@ -70,8 -70,7 +70,7 @@@ import javax.swing.SwingUtilities * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable, AlignmentViewPanel, - ViewportListenerI + AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; @@@ -157,8 -156,8 +156,8 @@@ // is initialised if (av.getWrapAlignment()) { - int widthInRes = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); + int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( + getSeqPanel().seqCanvas.getWidth()); vpRanges.setViewportWidth(widthInRes); } else @@@ -167,7 -166,7 +166,7 @@@ / av.getCharWidth(); int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - + vpRanges.setViewportWidth(widthInRes); vpRanges.setViewportHeight(heightInSeq); } @@@ -226,10 -225,10 +225,10 @@@ // 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())); + scalePanelHolder.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; @@@ -289,8 -288,8 +288,8 @@@ { Container c = new Container(); - FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), - Font.ITALIC, av.font.getSize())); + FontMetrics fm = c.getFontMetrics( + new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); int i = 0; @@@ -331,8 -330,8 +330,8 @@@ } } - return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, - idWidth), 12); + return new Dimension( + maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** @@@ -477,8 -476,8 +476,8 @@@ /* * Scroll down to make end of search results visible */ - setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends - + 1); + setScrollValues(vpRanges.getStartRes(), + starts + seqIndex - ends + 1); } /* * Else results are already visible - no need to scroll @@@ -579,8 -578,8 +578,8 @@@ */ if (annotationHeight + alignmentHeight > availableHeight) { - annotationHeight = Math.min(annotationHeight, availableHeight - 2 - * rowHeight); + annotationHeight = Math.min(annotationHeight, + availableHeight - 2 * rowHeight); } } else @@@ -590,8 -589,8 +589,8 @@@ } hscroll.addNotify(); - annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), annotationHeight)); + annotationScroller.setPreferredSize( + new Dimension(annotationScroller.getWidth(), annotationHeight)); Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); @@@ -641,8 -640,8 +640,8 @@@ else { int widthInRes = (canvasWidth / av.getCharWidth()) - 1; - int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av - .getCharHeight()) - 1; + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()) - 1; vpRanges.setViewportWidth(widthInRes); vpRanges.setViewportHeight(heightInSeq); @@@ -654,7 -653,6 +653,6 @@@ repaint(); } - /** * Adjust row/column scrollers to show a visible position in the alignment. * @@@ -686,7 -684,8 +684,8 @@@ if (av.hasHiddenColumns()) { // reset the width to exclude hidden columns - width = av.getAlignment().getHiddenColumns().findColumnPosition(width); + width = av.getAlignment().getHiddenColumns() + .findColumnPosition(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@@ -828,13 -827,13 +827,13 @@@ { @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"); + Cache.log.warn( + "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel vpRanges.setStartRes(0); @@@ -989,7 -988,8 +988,8 @@@ * 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; + final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 + : idWidth; FontMetrics fm = getFontMetrics(av.getFont()); int charHeight = av.getCharHeight(); @@@ -1026,8 -1026,7 +1026,7 @@@ endSeq = alignmentHeight; } - int pagesHigh = ((alignmentHeight / totalSeq) + 1) - * pageHeight; + int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; if (av.isShowAnnotation()) { @@@ -1040,8 -1039,7 +1039,7 @@@ { return Printable.NO_SUCH_PAGE; } - final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight - + 3; + final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; /* * draw the Scale at horizontal offset, then reset to top left (0, 0) @@@ -1090,9 -1088,7 +1088,7 @@@ if (av.isRightAlignIds()) { fm = idGraphics.getFontMetrics(); - xPos = idWidth - - fm.stringWidth(displayId) - - 4; + xPos = idWidth - fm.stringWidth(displayId) - 4; } idGraphics.drawString(displayId, xPos, @@@ -1107,8 -1103,8 +1103,8 @@@ * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, - startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanelForPrint(alignmentGraphics, startRes, + endRes, startSeq, endSeq); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@@ -1128,7 -1124,8 +1124,8 @@@ * draw the annotations starting at * (idOffset, alignmentHeight) from (0, scaleHeight) */ - alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + alignmentGraphics.translate(alignmentGraphicsOffset, + alignmentDrawnHeight); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, startRes, endRes + 1); } @@@ -1182,8 -1179,8 +1179,8 @@@ .findColumnPosition(maxwidth) - 1; } - int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(pwidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@@ -1220,16 -1217,13 +1217,13 @@@ } if (labels != null) { - pg.translate(-3, - ypos + (av.getAlignment().getHeight() * av.getCharHeight())); + 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())); + pg.translate(+3, -ypos + - (av.getAlignment().getHeight() * av.getCharHeight())); } ypos += cHeight; @@@ -1279,8 -1273,8 +1273,8 @@@ return calculateIdWidth(-1).width + 4; } Integer idwidth = null; - if (onscreen - || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + if (onscreen || (idwidth = Cache + .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { int w = getIdPanel().getWidth(); return (w > 0 ? w : calculateIdWidth().width + 4); @@@ -1292,15 -1286,15 +1286,15 @@@ { int boarderBottomOffset = 5; long pSessionId = System.currentTimeMillis(); - headless = (System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true")); + 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); + alignFrame.setProgressBar(MessageManager + .formatMessage("status.saving_file", new Object[] + { type.getLabel() }), pSessionId); } } try @@@ -1327,9 -1321,9 +1321,9 @@@ } im = new jalview.util.ImageMaker(this, type, imageAction, - aDimension.getWidth(), aDimension.getHeight() - + boarderBottomOffset, file, imageTitle, - alignFrame, pSessionId, headless); + aDimension.getWidth(), + aDimension.getHeight() + boarderBottomOffset, file, + imageTitle, alignFrame, pSessionId, headless); Graphics graphics = im.getGraphics(); if (av.getWrapAlignment()) { @@@ -1345,8 -1339,8 +1339,8 @@@ { if (graphics != null) { - printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), - 0, graphics, graphics); + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + graphics, graphics); im.writeImage(); } } @@@ -1391,9 -1385,8 +1385,8 @@@ // 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); + - alignFrame.getInsets().left - alignFrame.getInsets().right + - getVisibleIdWidth() + getVisibleIdWidth(false); } else { @@@ -1444,8 -1437,9 +1437,9 @@@ { try { - int s, sSize = av.getAlignment().getHeight(), res, alwidth = av - .getAlignment().getWidth(), g, gSize, f, fSize, sy; + int s, sSize = av.getAlignment().getHeight(), res, + alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize, + sy; PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); out.println(""); text.append(features[f].getType()); - if (features[f].getDescription() != null - && !features[f].getType().equals( - features[f].getDescription())) + if (features[f].getDescription() != null && !features[f] + .getType().equals(features[f].getDescription())) { text.append(" ").append(features[f].getDescription()); } if (features[f].getValue("status") != null) { - text.append(" (").append(features[f].getValue("status")) + text.append(" (") + .append(features[f].getValue("status")) .append(")"); } } @@@ -1903,7 -1897,7 +1897,7 @@@ @Override /** - * Property change event fired when a change is made to the viewport ranges + * 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) diff --combined src/jalview/gui/SeqCanvas.java index 955a9e6,a052ae3..f0d8c3e --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@@ -30,7 -30,6 +30,7 @@@ import jalview.renderer.ScaleRenderer.S import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; +import java.awt.AlphaComposite; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; @@@ -55,12 -54,16 +55,12 @@@ public class SeqCanvas extends JCompone { final FeatureRenderer fr; - final SequenceRenderer sr; + final SequenceRenderer seqRdr; BufferedImage img; Graphics2D gg; - int imgWidth; - - int imgHeight; - AlignViewport av; boolean fastPaint = false; @@@ -73,14 -76,6 +73,14 @@@ int cursorY = 0; + int charHeight = 0; + + int charWidth = 0; + + boolean fastpainting = false; + + AnnotationPanel annotations; + /** * Creates a new SeqCanvas object. * @@@ -92,7 -87,7 +92,7 @@@ this.av = ap.av; updateViewport(); fr = new FeatureRenderer(ap); - sr = new SequenceRenderer(av); + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@@ -102,7 -97,7 +102,7 @@@ public SequenceRenderer getSequenceRenderer() { - return sr; + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@@ -110,6 -105,8 +110,6 @@@ return fr; } - int charHeight = 0, charWidth = 0; - private void updateViewport() { charHeight = av.getCharHeight(); @@@ -147,9 -144,9 +147,9 @@@ { g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2)); } - g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2) - - (charHeight / 2), (mpos * charWidth) + (charWidth / 2), - ypos - 2); + g.drawLine((mpos * charWidth) + (charWidth / 2), + (ypos + 2) - (charHeight / 2), + (mpos * charWidth) + (charWidth / 2), ypos - 2); } } } @@@ -211,8 -208,8 +211,8 @@@ { int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) - charWidth / 2; - g.drawString(value + "", x, (ypos + (i * charHeight)) - - (charHeight / 5)); + g.drawString(value + "", x, + (ypos + (i * charHeight)) - (charHeight / 5)); } } } @@@ -263,12 -260,13 +263,12 @@@ if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight)) - - (charHeight / 5)); + g.drawString(String.valueOf(value), 0, + (ypos + (i * charHeight)) - (charHeight / 5)); } } } - boolean fastpainting = false; /** * need to make this thread safe move alignment rendering in response to @@@ -297,9 -295,8 +297,9 @@@ int transX = 0; int transY = 0; - gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, - imgHeight, -horizontal * charWidth, -vertical * charHeight); + gg.copyArea(horizontal * charWidth, vertical * charHeight, + img.getWidth(), img.getHeight(), -horizontal * charWidth, + -vertical * charHeight); if (horizontal > 0) // scrollbar pulled right, image to the left { @@@ -320,7 -317,7 +320,7 @@@ } else { - transY = imgHeight - ((vertical + 1) * charHeight); + transY = img.getHeight() - ((vertical + 1) * charHeight); } } else if (vertical < 0) @@@ -354,154 -351,73 +354,154 @@@ @Override public void paintComponent(Graphics g) { - updateViewport(); - BufferedImage lcimg = img; // take reference since other threads may null - // img and call later. super.paintComponent(g); - if (lcimg != null && (fastPaint + updateViewport(); + + ViewportRanges ranges = av.getRanges(); + + int width = getWidth(); + int height = getHeight(); + + width -= (width % charWidth); + height -= (height % charHeight); + + // selectImage is the selection group outline image + BufferedImage selectImage = drawSelectionGroup( + ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq()); + + if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) { + BufferedImage lcimg = buildLocalImage(selectImage); g.drawImage(lcimg, 0, 0, this); fastPaint = false; - return; - } - - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); - - imgWidth -= (imgWidth % charWidth); - imgHeight -= (imgHeight % charHeight); - - if ((imgWidth < 1) || (imgHeight < 1)) - { - return; } - - if (lcimg == null || imgWidth != lcimg.getWidth() - || imgHeight != lcimg.getHeight()) + else if ((width > 0) && (height > 0)) { - try + // img is a cached version of the last view we drew, if any + // if we have no img or the size has changed, make a new one + if (img == null || width != img.getWidth() + || height != img.getHeight()) { - lcimg = img = new BufferedImage(imgWidth, imgHeight, - BufferedImage.TYPE_INT_RGB); + img = setupImage(); + if (img == null) + { + return; + } gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); - } catch (OutOfMemoryError er) + } + + if (av.antiAlias) { - System.gc(); - System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - return; + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); } + else + { + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); + } + + // lcimg is a local *copy* of img which we'll draw selectImage on top of + BufferedImage lcimg = buildLocalImage(selectImage); + g.drawImage(lcimg, 0, 0, this); } + } - if (av.antiAlias) + /** + * Draw an alignment panel for printing + * + * @param g1 + * Graphics object to draw with + * @param startRes + * start residue of print area + * @param endRes + * end residue of print area + * @param startSeq + * start sequence of print area + * @param endSeq + * end sequence of print area + */ + public void drawPanelForPrint(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq) + { + BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + startSeq, endSeq); + drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); + ((Graphics2D) g1).setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g1.drawImage(selectImage, 0, 0, this); + } + + /* + * Make a local image by combining the cached image img + * with any selection + */ + private BufferedImage buildLocalImage(BufferedImage selectImage) + { + // clone the cached image + BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + img.getType()); + Graphics2D g2d = lcimg.createGraphics(); + g2d.drawImage(img, 0, 0, null); + + // overlay selection group on lcimg + if (selectImage != null) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + g2d.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g2d.drawImage(selectImage, 0, 0, this); } + g2d.dispose(); + + return lcimg; + } - gg.setColor(Color.white); - gg.fillRect(0, 0, imgWidth, imgHeight); + /* + * Set up a buffered image of the correct height and size for the sequence canvas + */ + private BufferedImage setupImage() + { + BufferedImage lcimg = null; - ViewportRanges ranges = av.getRanges(); - if (av.getWrapAlignment()) + int width = getWidth(); + int height = getHeight(); + + width -= (width % charWidth); + height -= (height % charHeight); + + if ((width < 1) || (height < 1)) { - drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + return null; } - else + + try { - drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq(), 0); - } + lcimg = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println( + "Group image OutOfMemory Redraw Error.\n" + er); + new OOMWarning("Creating alignment image for display", er); - g.drawImage(lcimg, 0, 0, this); + return null; + } + return lcimg; } /** @@@ -661,10 -577,12 +661,12 @@@ } gg.fillPolygon( - new int[] { res * charWidth - charHeight / 4, + new int[] + { res * charWidth - charHeight / 4, res * charWidth + charHeight / 4, res * charWidth }, - new int[] { ypos - (charHeight / 2), - ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 }, + new int[] + { ypos - (charHeight / 2), ypos - (charHeight / 2), + ypos - (charHeight / 2) + 8 }, 3); } @@@ -694,8 -612,8 +696,8 @@@ annotations = new AnnotationPanel(av); } - annotations.renderer.drawComponent(annotations, av, g, -1, - startRes, endx + 1); + annotations.renderer.drawComponent(annotations, av, g, -1, startRes, + endx + 1); g.translate(0, -cHeight - ypos - 3); } g.setClip(clip); @@@ -707,61 -625,7 +709,61 @@@ } } - AnnotationPanel annotations; + /* + * Draw a selection group over a wrapped alignment + */ + private void drawWrappedSelection(Graphics2D g, SequenceGroup group, + int canvasWidth, + int canvasHeight, int startRes) + { + // height gap above each panel + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; + + int startx = startRes; + int endx; + int ypos = hgap; // vertical offset + int maxwidth = av.getAlignment().getWidth(); + + if (av.hasHiddenColumns()) + { + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); + } + + // chop the wrapped alignment extent up into panel-sized blocks and treat + // each block as if it were a block from an unwrapped alignment + while ((ypos <= canvasHeight) && (startx < maxwidth)) + { + // set end value to be start + width, or maxwidth, whichever is smaller + endx = startx + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.translate(LABEL_WEST, 0); + + drawUnwrappedSelection(g, group, startx, endx, 0, + av.getAlignment().getHeight() - 1, + ypos); + + g.translate(-LABEL_WEST, 0); + + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; + + // update horizontal offset + startx += cWidth; + } + } int getAnnotationHeight() { @@@ -778,24 -642,24 +780,24 @@@ return annotations.adjustPanelHeight(); } - /** - * DOCUMENT ME! + /* + * Draw an alignment panel for printing * * @param g1 - * DOCUMENT ME! + * Graphics object to draw with * @param startRes - * DOCUMENT ME! + * start residue of print area * @param endRes - * DOCUMENT ME! + * end residue of print area * @param startSeq - * DOCUMENT ME! + * start sequence of print area * @param endSeq - * DOCUMENT ME! + * end sequence of print area * @param offset - * DOCUMENT ME! + * vertical offset */ - public void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, - int endSeq, int offset) + private void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) { updateViewport(); if (!av.hasHiddenColumns()) @@@ -859,11 -723,13 +861,11 @@@ } - // int startRes, int endRes, int startSeq, int endSeq, int x, int y, - // int x1, int x2, int y1, int y2, int startx, int starty, private void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) { g.setFont(av.getFont()); - sr.prepare(g, av.isRenderGaps()); + seqRdr.prepare(g, av.isRenderGaps()); SequenceI nextSeq; @@@ -878,13 -744,13 +880,13 @@@ // empty continue; } - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), + seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), startRes, endRes, offset + ((i - startSeq) * charHeight)); if (av.isShowSequenceFeatures()) { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * charHeight), false); + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * charHeight), false); } // / Highlight search Results once all sequences have been drawn @@@ -897,10 -763,10 +899,10 @@@ { for (int r = 0; r < visibleResults.length; r += 2) { - sr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], - (visibleResults[r] - startRes) * charWidth, - offset + ((i - startSeq) * charHeight)); + seqRdr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], (visibleResults[r] - startRes) + * charWidth, offset + + ((i - startSeq) * charHeight)); } } } @@@ -908,7 -774,7 +910,7 @@@ if (av.cursorMode && cursorY == i && cursorX >= startRes && cursorX <= endRes) { - sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, + seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, offset + ((i - startSeq) * charHeight)); } } @@@ -929,11 -795,15 +931,11 @@@ // /////////////////////////////////// // Now outline any areas if necessary // /////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - int sx = -1; - int sy = -1; - int ex = -1; + SequenceGroup group = null; int groupIndex = -1; - int visWidth = (endRes - startRes + 1) * charWidth; - if ((group == null) && (av.getAlignment().getGroups().size() > 0)) + if (av.getAlignment().getGroups().size() > 0) { group = av.getAlignment().getGroups().get(0); groupIndex = 0; @@@ -941,300 -811,168 +943,300 @@@ if (group != null) { + g.setStroke(new BasicStroke()); + g.setColor(group.getOutlineColour()); + do { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, + endSeq, offset); - ++ + groupIndex++; - for (i = startSeq; i <= endSeq; i++) + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.getAlignment().getGroups().size()) { - sx = (group.getStartRes() - startRes) * charWidth; - sy = offset + ((i - startSeq) * charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - - 1; + break; + } - if (sx + ex < 0 || sx > visWidth) - { - continue; - } + group = av.getAlignment().getGroups().get(groupIndex); - if ((sx <= (endRes - startRes) * charWidth) - && group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) && !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i + 1))) - { - bottom = sy + charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) || !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - if (group == av.getSelectionGroup()) - { - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - g.setColor(Color.RED); - } - else - { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - } - } - } - else + } while (groupIndex < av.getAlignment().getGroups().size()); + + } + + } + + + /* + * Draw the selection group as a separate image and overlay + */ + private BufferedImage drawSelectionGroup(int startRes, int endRes, + int startSeq, int endSeq) + { + // get a new image of the correct size + BufferedImage selectionImage = setupImage(); + + if (selectionImage == null) + { + return null; + } + + SequenceGroup group = av.getSelectionGroup(); + if (group == null) + { + // nothing to draw + return null; + } + + // set up drawing colour + Graphics2D g = (Graphics2D) selectionImage.getGraphics(); + + // set background to transparent + g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); + g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + + // set up foreground to draw red dashed line + g.setComposite(AlphaComposite.Src); + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); + + if (!av.getWrapAlignment()) + { + drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, + 0); + } + else + { + drawWrappedSelection(g, group, getWidth(), getHeight(), + av.getRanges().getStartRes()); + } + + g.dispose(); + return selectionImage; + } + + /* + * Draw a selection group over an unwrapped alignment + * @param g graphics object to draw with + * @param group selection group + * @param startRes start residue of area to draw + * @param endRes end residue of area to draw + * @param startSeq start sequence of area to draw + * @param endSeq end sequence of area to draw + * @param offset vertical offset (used when called from wrapped alignment code) + */ + private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, int offset) + { + if (!av.hasHiddenColumns()) + { + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, + offset); + } + else + { + // package into blocks of visible columns + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int[] region : av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy()) + { + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } + + blockEnd = hideStart - 1; + + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, + blockStart, blockEnd, startSeq, endSeq, offset); + + g.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + + if (screenY > (endRes - startRes)) + { + // already rendered last block + break; + } + } + + if (screenY <= (endRes - startRes)) + { + // remaining visible region to render + blockEnd = blockStart + (endRes - startRes) - screenY; + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, + blockStart, blockEnd, startSeq, endSeq, offset); + + g.translate(-screenY * charWidth, 0); + } + } + } + + /* + * Draw the selection group as a separate image and overlay + */ + private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, + int verticalOffset) + { + int visWidth = (endRes - startRes + 1) * charWidth; + + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; + + int sx = -1; + int sy = -1; + int xwidth = -1; + + for (i = startSeq; i <= endSeq; i++) + { + // position of start residue of group relative to startRes, in pixels + sx = (group.getStartRes() - startRes) * charWidth; + + // width of group in pixels + xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) + - 1; + + sy = verticalOffset + (i - startSeq) * charHeight; + + if (sx + xwidth < 0 || sx > visWidth) + { + continue; + } + + if ((sx <= (endRes - startRes) * charWidth) + && group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i))) + { + if ((bottom == -1) && !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i + 1))) + { + bottom = sy + charHeight; + } + + if (!inGroup) + { + if (((top == -1) && (i == 0)) || !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i - 1))) { - if (inGroup) - { - if (sx >= 0 && sx < visWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > visWidth) - { - ex = visWidth; - } - - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - inGroup = false; - } + top = sy; } - } + oldY = sy; + inGroup = true; + } + } + else + { if (inGroup) { - sy = offset + ((i - startSeq) * charHeight); + // if start position is visible, draw vertical line to left of + // group if (sx >= 0 && sx < visWidth) { g.drawLine(sx, oldY, sx, sy); } - if (sx + ex < visWidth) + // if end position is visible, draw vertical line to right of + // group + if (sx + xwidth < visWidth) { - g.drawLine(sx + ex, oldY, sx + ex, sy); + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); } if (sx < 0) { - ex += sx; + xwidth += sx; sx = 0; } - if (sx + ex > visWidth) + // don't let width extend beyond current block, or group extent + // fixes JAL-2672 + if (sx + xwidth >= (endRes - startRes + 1) * charWidth) { - ex = visWidth; + xwidth = (endRes - startRes + 1) * charWidth - sx; } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } - + + // draw horizontal line at top of group if (top != -1) { - g.drawLine(sx, top, sx + ex, top); + g.drawLine(sx, top, sx + xwidth, top); top = -1; } + // draw horizontal line at bottom of group if (bottom != -1) { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + g.drawLine(sx, bottom, sx + xwidth, bottom); bottom = -1; } inGroup = false; } + } + } - groupIndex++; + if (inGroup) + { + sy = verticalOffset + ((i - startSeq) * charHeight); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } - g.setStroke(new BasicStroke()); + if (sx + xwidth < visWidth) + { + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); + } - if (groupIndex >= av.getAlignment().getGroups().size()) - { - break; - } + if (sx < 0) + { + xwidth += sx; + sx = 0; + } - group = av.getAlignment().getGroups().get(groupIndex); + if (sx + xwidth > visWidth) + { + xwidth = visWidth; + } + else if (sx + xwidth >= (endRes - startRes + 1) * charWidth) + { + xwidth = (endRes - startRes + 1) * charWidth; + } - } while (groupIndex < av.getAlignment().getGroups().size()); + if (top != -1) + { + g.drawLine(sx, top, sx + xwidth, top); + top = -1; + } - } + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1); + bottom = -1; + } + inGroup = false; + } } - + /** * DOCUMENT ME! * @@@ -1255,12 -993,7 +1257,12 @@@ { String eventName = evt.getPropertyName(); - if (av.getWrapAlignment()) + if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + { + fastPaint = true; + repaint(); + } + else if (av.getWrapAlignment()) { if (eventName.equals(ViewportRanges.STARTRES)) { diff --combined src/jalview/gui/SeqPanel.java index c863117,056a602..328dfdc --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@@ -74,9 -74,9 +74,9 @@@ import javax.swing.ToolTipManager * @author $author$ * @version $Revision: 1.130 $ */ - public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener, SequenceListener, - SelectionListener + public class SeqPanel extends JPanel + implements MouseListener, MouseMotionListener, MouseWheelListener, + SequenceListener, SelectionListener { /** DOCUMENT ME!! */ @@@ -263,15 -263,14 +263,14 @@@ y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() - .getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), + av.getAlignment().getHeight() - 1); } else { - seq = Math.min((y / av.getCharHeight()) - + av.getRanges().getStartSeq(), - av - .getAlignment().getHeight() - 1); + seq = Math.min( + (y / av.getCharHeight()) + av.getRanges().getStartSeq(), + av.getAlignment().getHeight() - 1); } return seq; @@@ -288,8 -287,8 +287,8 @@@ if (editCommand != null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } } finally { @@@ -347,8 -346,7 +346,7 @@@ HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - if (av.hasHiddenColumns() - && !hidden.isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); @@@ -847,8 -845,9 +845,9 @@@ Point p = lastp; if (!event.isShiftDown() || p == null) { - p = (tooltipText != null && tooltipText.length() > 6) ? new Point( - event.getX() + wdth, event.getY() - 20) : null; + p = (tooltipText != null && tooltipText.length() > 6) + ? new Point(event.getX() + wdth, event.getY() - 20) + : null; } /* * TODO: try to modify position region is not obcured by tooltip @@@ -918,9 -917,9 +917,9 @@@ } else { - residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" - .equals(displayChar) ? "STOP" - : ResidueProperties.aa2Triplet.get(displayChar)); + residue = "X".equalsIgnoreCase(displayChar) ? "X" + : ("*".equals(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar)); } text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") .append(": ").append(residue == null ? displayChar : residue); @@@ -982,8 -981,8 +981,8 @@@ int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? - if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt - .getX() - lastMousePress.getX())) + if (Math.abs(evt.getY() - lastMousePress.getY()) > Math + .abs(evt.getX() - lastMousePress.getX())) { /* * on drag up or down, decrement or increment font size @@@ -1143,8 -1142,9 +1142,9 @@@ } if (editCommand == null) { - editCommand = new EditCommand(MessageManager.formatMessage( - "label.edit_params", new String[] { label })); + editCommand = new EditCommand(MessageManager + .formatMessage("label.edit_params", new String[] + { label })); } } @@@ -1161,9 -1161,8 +1161,8 @@@ ap.alignFrame.statusBar.setText(message.toString()); // Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.getSequences(av.getHiddenRepSequences()) - .contains(seq))) + if (groupEditing || (sg != null + && sg.getSequences(av.getHiddenRepSequences()).contains(seq))) { fixedColumns = true; @@@ -1351,8 -1350,8 +1350,8 @@@ } else { - appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres - - lastres); + appendEdit(Action.INSERT_GAP, groupSeqs, startres, + startres - lastres); } } else @@@ -1367,8 -1366,8 +1366,8 @@@ } else { - appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres - - startres); + appendEdit(Action.DELETE_GAP, groupSeqs, startres, + lastres - startres); } } @@@ -1589,8 -1588,8 +1588,8 @@@ * highlight the first feature at the position on the alignment */ SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequence, features.get(0).getBegin(), features - .get(0).getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); /* @@@ -1652,8 -1651,9 +1651,9 @@@ if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.cannot_edit_annotations_in_wrapped_view"), + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString( + "label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), JvOptionPane.WARNING_MESSAGE); return; @@@ -1710,53 -1710,43 +1710,53 @@@ if (stretchGroup == null) { - // Only if left mouse button do we want to change group sizes + createStretchGroup(res, sequence); + } - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + if (stretchGroup != null) + { + stretchGroup.addPropertyChangeListener(seqCanvas); + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, av.getResidueShading(), - ap.getViewName()); - } + seqCanvas.repaint(); + } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), - ap.getViewName()); - } - // TODO: stretchGroup will always be not null. Is this a merge error ? - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if ((stretchGroup != null) - && (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } - stretchGroup.getWidth(); + private void createStretchGroup(int res, SequenceI sequence) + { + // Only if left mouse button do we want to change group sizes + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } - seqCanvas.repaint(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); + } + // TODO: stretchGroup will always be not null. Is this a merge error ? + // or is there a threading issue here? + if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); + } /** @@@ -1805,9 -1795,6 +1805,9 @@@ { return; } + + stretchGroup.removePropertyChangeListener(seqCanvas); + // always do this - annotation has own state // but defer colourscheme update until hidden sequences are passed in boolean vischange = stretchGroup.recalcConservation(true); @@@ -1818,7 -1805,8 +1818,8 @@@ stretchGroup.cs.alignmentChanged(stretchGroup, av.getHiddenRepSequences()); - ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme(); + ResidueShaderI groupColourScheme = stretchGroup + .getGroupColourScheme(); String name = stretchGroup.getName(); if (stretchGroup.cs.conservationApplied()) { @@@ -1952,6 -1940,8 +1953,6 @@@ { scrollThread.setEvent(evt); } - - seqCanvas.repaint(); } void scrollCanvas(MouseEvent evt) @@@ -2015,9 -2005,8 +2016,8 @@@ running = av.getRanges().scrollUp(true); } - if (mouseDragging && (evt.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getRanges() - .getEndSeq())) + if (mouseDragging && (evt.getY() >= getHeight()) && (av + .getAlignment().getHeight() > av.getRanges().getEndSeq())) { running = av.getRanges().scrollUp(false); } @@@ -2053,8 -2042,10 +2053,10 @@@ // handles selection messages... // TODO: extend config options to allow user to control if selections may be // shared between viewports. - boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) - .getSequenceSetId().equals(av.getSequenceSetId()))); + boolean iSentTheSelection = (av == source + || (source instanceof AlignViewport + && ((AlignmentViewport) source).getSequenceSetId() + .equals(av.getSequenceSetId()))); if (iSentTheSelection) { @@@ -2156,8 -2147,7 +2158,7 @@@ repaint = true; } - if (copycolsel - && av.hasHiddenColumns() + if (copycolsel && av.hasHiddenColumns() && (av.getAlignment().getHiddenColumns() == null)) { System.err.println("Bad things");