X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=3228372617c5880eb3bba6daeb4d3b265d86f8c9;hb=9c96547bd26c1cfb65877bc3bc1941c3c5d5fe76;hp=a732527b7688876772e94e8665d51066b717e1e6;hpb=e54df488cd82761bfb0e9372aeae2acc5a1324d7;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index a732527..3228372 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -30,10 +30,12 @@ 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; @@ -70,8 +72,7 @@ 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 +158,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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 +168,7 @@ public class AlignmentPanel extends GAlignmentPanel implements / av.getCharWidth(); int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - + vpRanges.setViewportWidth(widthInRes); vpRanges.setViewportHeight(heightInSeq); } @@ -213,7 +214,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -226,11 +228,12 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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())); + idwidthAdjuster.invalidate(); + scalePanelHolder.invalidate(); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; getAnnotationPanel().adjustPanelHeight(); @@ -241,11 +244,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (this.alignFrame.getSplitViewContainer() != null) - { - ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); - } - repaint(); } @@ -289,8 +287,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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 +329,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, - idWidth), 12); + return new Dimension( + maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** @@ -341,19 +339,11 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void highlightSearchResults(SearchResultsI results) { - scrollToPosition(results); - getSeqPanel().seqCanvas.highlightSearchResults(results); - } + boolean scrolled = scrollToPosition(results, 0, true, false); - /** - * Scroll the view to show the position of the highlighted region in results - * (if any) and redraw the overview - * - * @param results - */ - public boolean scrollToPosition(SearchResultsI results) - { - return scrollToPosition(results, 0, true, false); + boolean noFastPaint = scrolled && av.getWrapAlignment(); + + getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint); } /** @@ -371,8 +361,10 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Scroll the view to show the position of the highlighted region in results - * (if any) + * 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 @@ -382,116 +374,117 @@ public class AlignmentPanel extends GAlignmentPanel implements * - when set, the overview will be recalculated (takes longer) * @param centre * if true, try to centre the search results horizontally in the view - * @return false if results were not found + * @return */ - public boolean scrollToPosition(SearchResultsI results, + protected boolean scrollToPosition(SearchResultsI results, int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; - // 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 nullpointerexceptions raised here. - if (results != null && results.getSize() > 0 && av != null - && av.getAlignment() != null) - { - 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]; + 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); - /* - * To centre results, scroll to positions half the visible width - * left/right of the start/end positions - */ - if (centre) - { - int offset = (vpRanges.getEndRes() - vpRanges.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()) + 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 = (vpRanges.getEndRes() - vpRanges.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) { - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - start = hidden.findColumnPosition(start); - end = hidden.findColumnPosition(end); - if (start == end) + if (!hidden.isVisible(r[0])) { - if (!hidden.isVisible(r[0])) - { - // don't scroll - position isn't visible - return false; - } + // 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); + /* + * 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 (!av.getWrapAlignment()) + { + if ((startv = vpRanges.getStartRes()) >= start) { - if ((startv = vpRanges.getStartRes()) >= start) - { - /* - * Scroll left to make start of search results visible - */ - setScrollValues(start, seqIndex); - } - else if ((endv = vpRanges.getEndRes()) <= end) - { - /* - * Scroll right to make end of search results visible - */ - setScrollValues(startv + end - endv, seqIndex); - } - else if ((starts = vpRanges.getStartSeq()) > seqIndex) - { - /* - * Scroll up to make start of search results visible - */ - setScrollValues(vpRanges.getStartRes(), seqIndex); - } - else if ((ends = vpRanges.getEndSeq()) <= seqIndex) - { - /* - * Scroll down to make end of search results visible - */ - setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends - + 1); - } /* - * Else results are already visible - no need to scroll + * Scroll left to make start of search results visible */ + setScrollValues(start, seqIndex); } - else + else if ((endv = vpRanges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + end - endv, seqIndex); + } + else if ((starts = vpRanges.getStartSeq()) > seqIndex) { - vpRanges.scrollToWrappedVisible(start); + /* + * Scroll up to make start of search results visible + */ + setScrollValues(vpRanges.getStartRes(), seqIndex); } + else if ((ends = vpRanges.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends + + 1); + } + /* + * Else results are already visible - no need to scroll + */ + scrollNeeded = false; + } + else + { + scrollNeeded = vpRanges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); - return true; + paintAlignment(redrawOverview, false); + + return scrollNeeded; } /** @@ -546,7 +539,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } validateAnnotationDimensions(true); addNotify(); - paintAlignment(true); + // TODO: many places call this method and also paintAlignment with various + // different settings. this means multiple redraws are triggered... + paintAlignment(true, false); } /** @@ -579,8 +574,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ if (annotationHeight + alignmentHeight > availableHeight) { - annotationHeight = Math.min(annotationHeight, availableHeight - 2 - * rowHeight); + annotationHeight = Math.min(annotationHeight, + availableHeight - 2 * rowHeight); } } else @@ -590,8 +585,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } 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)); @@ -640,9 +635,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - int widthInRes = (canvasWidth / av.getCharWidth()) - 1; - int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av - .getCharHeight()) - 1; + int widthInRes = (canvasWidth / av.getCharWidth()); + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()); vpRanges.setViewportWidth(widthInRes); vpRanges.setViewportHeight(heightInSeq); @@ -654,7 +649,6 @@ public class AlignmentPanel extends GAlignmentPanel implements repaint(); } - /** * Adjust row/column scrollers to show a visible position in the alignment. * @@ -686,7 +680,8 @@ public class AlignmentPanel extends GAlignmentPanel implements 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(); @@ -809,14 +804,14 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - else if (newY > -1) + if (newY > -1) { /* * limit page up/down to one width's worth of positions */ int rowSize = vpRanges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; - vpRanges.setViewportStartAndWidth(newX, rowSize); + vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } else @@ -828,13 +823,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { @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); @@ -845,12 +840,12 @@ public class AlignmentPanel extends GAlignmentPanel implements repaint(); } - /** - * Repaint the alignment including the annotations and overview panels (if - * shown). + /* (non-Javadoc) + * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean) */ @Override - public void paintAlignment(boolean updateOverview) + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); @@ -858,10 +853,12 @@ public class AlignmentPanel extends GAlignmentPanel implements av.getSortAnnotationsBy()); repaint(); - if (updateOverview) + if (updateStructures) { - // TODO: determine if this paintAlignment changed structure colours av.getStructureSelectionManager().sequenceColoursChanged(this); + } + if (updateOverview) + { if (overviewPanel != null) { @@ -989,7 +986,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * 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 +1024,7 @@ public class AlignmentPanel extends GAlignmentPanel implements endSeq = alignmentHeight; } - int pagesHigh = ((alignmentHeight / totalSeq) + 1) - * pageHeight; + int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; if (av.isShowAnnotation()) { @@ -1040,8 +1037,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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 +1086,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.isRightAlignIds()) { fm = idGraphics.getFontMetrics(); - xPos = idWidth - - fm.stringWidth(displayId) - - 4; + xPos = idWidth - fm.stringWidth(displayId) - 4; } idGraphics.drawString(displayId, xPos, @@ -1107,8 +1101,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, - startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, + endRes, startSeq, endSeq); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1128,7 +1122,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * 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 +1177,8 @@ public class AlignmentPanel extends GAlignmentPanel implements .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 +1215,13 @@ public class AlignmentPanel extends GAlignmentPanel implements } 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; @@ -1237,7 +1229,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) @@ -1279,8 +1271,8 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 +1284,15 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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 +1319,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } 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 +1337,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (graphics != null) { - printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), - 0, graphics, graphics); + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + graphics, graphics); im.writeImage(); } } @@ -1391,9 +1383,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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 { @@ -1444,33 +1435,32 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.getAlignment().getHeight(), res, alwidth = av - .getAlignment().getWidth(), g, gSize, f, fSize, sy; + int sSize = av.getAlignment().getHeight(); + int alwidth = av.getAlignment().getWidth(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); - out.println(jalview.io.HTMLOutput.getImageMapHTML()); + out.println(HTMLOutput.getImageMapHTML()); out.println("" + ""); - for (s = 0; s < sSize; s++) + for (int s = 0; s < sSize; s++) { - sy = s * av.getCharHeight() + scaleHeight; + int sy = s * av.getCharHeight() + scaleHeight; SequenceI seq = av.getAlignment().getSequenceAt(s); - SequenceFeature[] features = seq.getSequenceFeatures(); SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); - for (res = 0; res < alwidth; res++) + for (int column = 0; column < alwidth; column++) { - StringBuilder text = new StringBuilder(); + StringBuilder text = new StringBuilder(512); String triplet = null; if (av.getAlignment().isNucleotide()) { triplet = ResidueProperties.nucleotideName.get(seq - .getCharAt(res) + ""); + .getCharAt(column) + ""); } else { - triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) + ""); } @@ -1479,84 +1469,73 @@ public class AlignmentPanel extends GAlignmentPanel implements continue; } - int alIndex = seq.findPosition(res); - gSize = groups.length; - for (g = 0; g < gSize; g++) + int seqPos = seq.findPosition(column); + int gSize = groups.length; + for (int g = 0; g < gSize; g++) { if (text.length() < 1) { text.append(" res) + if (groups[g].getStartRes() < column + && groups[g].getEndRes() > column) { text.append("
").append(groups[g].getName()) .append(""); } } - if (features != null) + if (text.length() < 1) { - if (text.length() < 1) - { - text.append(" features = seq.findFeatures(column, column); + for (SequenceFeature sf : features) { - - if ((features[f].getBegin() <= seq.findPosition(res)) - && (features[f].getEnd() >= seq.findPosition(res))) + if (sf.isContactFeature()) { - if (features[f].isContactFeature()) - { - if (features[f].getBegin() == seq.findPosition(res) - || features[f].getEnd() == seq - .findPosition(res)) - { - text.append("
").append(features[f].getType()) - .append(" ").append(features[f].getBegin()) - .append(":").append(features[f].getEnd()); - } - } - else + 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)) { - text.append("
"); - text.append(features[f].getType()); - 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")) - .append(")"); - } + 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()); } - } - if (text.length() > 1) - { - text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); - out.println(text.toString()); } } } @@ -1825,7 +1804,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResultsI sr, int verticalOffset) + protected void scrollToCentre(SearchResultsI sr, int verticalOffset) { /* * To avoid jumpy vertical scrolling (if some sequences are gapped or not @@ -1892,7 +1871,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (adjustHeight) { // sort, repaint, update overview - paintAlignment(true); + paintAlignment(true, false); } else { @@ -1903,7 +1882,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @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)