X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=c03b56dacd0fa6d9d5933940d001f577775255a1;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=fe216c07622fca5b240d593b6e094aba605ac236;hpb=ca106e8dd8c6bd849356c3a75cecc1d7eabd7230;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index fe216c0..c03b56d 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -30,12 +30,13 @@ 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; @@ -46,7 +47,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; -import java.awt.Insets; +import java.awt.Graphics2D; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; @@ -74,8 +75,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { public AlignViewport av; - ViewportRanges vpRanges; - OverviewPanel overviewPanel; private SeqPanel seqPanel; @@ -95,9 +94,6 @@ public class AlignmentPanel extends GAlignmentPanel implements private AnnotationLabels alabels; - // this value is set false when selection area being dragged - boolean fastPaint = true; - private int hextent = 0; private int vextent = 0; @@ -122,7 +118,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { alignFrame = af; this.av = av; - vpRanges = av.getRanges(); setSeqPanel(new SeqPanel(av, this)); setIdPanel(new IdPanel(av, this)); @@ -154,11 +149,12 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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()); - vpRanges.setViewportWidth(widthInRes); + ranges.setViewportWidth(widthInRes); } else { @@ -167,8 +163,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - vpRanges.setViewportWidth(widthInRes); - vpRanges.setViewportHeight(heightInSeq); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } } @@ -212,7 +208,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -229,7 +226,8 @@ public class AlignmentPanel extends GAlignmentPanel implements 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(); @@ -240,11 +238,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (this.alignFrame.getSplitViewContainer() != null) - { - ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); - } - repaint(); } @@ -340,19 +333,11 @@ 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); } /** @@ -370,8 +355,10 @@ 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 @@ -381,116 +368,118 @@ 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); + ViewportRanges ranges = av.getRanges(); - 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 = (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.absoluteToVisibleColumn(start); + end = hidden.absoluteToVisibleColumn(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 = ranges.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 = ranges.getEndRes()) <= end) { - vpRanges.scrollToWrappedVisible(start); + /* + * 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); - paintAlignment(redrawOverview); - return true; + return scrollNeeded; } /** @@ -545,7 +534,9 @@ 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); } /** @@ -555,40 +546,10 @@ public class AlignmentPanel extends GAlignmentPanel implements protected void validateAnnotationDimensions(boolean adjustPanelHeight) { int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + annotationHeight = getAnnotationPanel() + .adjustForAlignFrame(adjustPanelHeight, annotationHeight); - 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)); @@ -612,7 +573,8 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - vpRanges.setStartSeq(0); + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -626,6 +588,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); + validateAnnotationDimensions(false); } int canvasWidth = getSeqPanel().seqCanvas.getWidth(); @@ -635,16 +598,16 @@ public class AlignmentPanel extends GAlignmentPanel implements { int widthInRes = getSeqPanel().seqCanvas .getWrappedCanvasWidth(canvasWidth); - vpRanges.setViewportWidth(widthInRes); + ranges.setViewportWidth(widthInRes); } else { - int widthInRes = (canvasWidth / av.getCharWidth()) - 1; + int widthInRes = (canvasWidth / av.getCharWidth()); int heightInSeq = (getSeqPanel().seqCanvas.getHeight() - / av.getCharHeight()) - 1; + / av.getCharHeight()); - vpRanges.setViewportWidth(widthInRes); - vpRanges.setViewportHeight(heightInSeq); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } } @@ -685,7 +648,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { // reset the width to exclude hidden columns width = av.getAlignment().getHiddenColumns() - .findColumnPosition(width); + .absoluteToVisibleColumn(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@ -743,10 +706,12 @@ public class AlignmentPanel extends GAlignmentPanel implements return; } + ViewportRanges ranges = av.getRanges(); + if (evt.getSource() == hscroll) { - int oldX = vpRanges.getStartRes(); - int oldwidth = vpRanges.getViewportWidth(); + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); int x = hscroll.getValue(); int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@ -757,12 +722,12 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - vpRanges.setViewportStartAndWidth(x, width); + ranges.setViewportStartAndWidth(x, width); } else if (evt.getSource() == vscroll) { - int oldY = vpRanges.getStartSeq(); - int oldheight = vpRanges.getViewportHeight(); + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); int y = vscroll.getValue(); int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -773,12 +738,9 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - vpRanges.setViewportStartAndHeight(y, height); - } - if (!fastPaint) - { - repaint(); + ranges.setViewportStartAndHeight(y, height); } + repaint(); } /** @@ -793,6 +755,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; // no horizontal scroll when wrapped } + final ViewportRanges ranges = av.getRanges(); + if (evt.getSource() == vscroll) { int newY = vscroll.getValue(); @@ -802,8 +766,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * this prevents infinite recursion of events when the scroll/viewport * ranges values are the same */ - int oldX = vpRanges.getStartRes(); - int oldY = vpRanges.getWrappedScrollPosition(oldX); + int oldX = ranges.getStartRes(); + int oldY = ranges.getWrappedScrollPosition(oldX); if (oldY == newY) { return; @@ -813,9 +777,9 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * limit page up/down to one width's worth of positions */ - int rowSize = vpRanges.getViewportWidth(); + int rowSize = ranges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; - vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); + ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } else @@ -836,20 +800,20 @@ public class AlignmentPanel extends GAlignmentPanel implements "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel - vpRanges.setStartRes(0); - vpRanges.setStartSeq(0); + ranges.setStartRes(0); + ranges.setStartSeq(0); } }); } 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()); @@ -857,10 +821,12 @@ 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) { @@ -878,17 +844,20 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void paintComponent(Graphics g) { - invalidate(); + invalidate(); // needed so that the id width adjuster works correctly Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); - validate(); + + validate(); // needed so that the id width adjuster works correctly /* - * set scroll bar positions + * set scroll bar positions - tried to remove but necessary for split panel to resize correctly + * though I still think this call should be elsewhere. */ - setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); + ViewportRanges ranges = av.getRanges(); + setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); } /** @@ -900,8 +869,9 @@ public class AlignmentPanel extends GAlignmentPanel implements */ private void setScrollingForWrappedPanel(int topLeftColumn) { - int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn); - int maxScroll = vpRanges.getWrappedMaxScroll(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) @@ -946,30 +916,16 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! - * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! - * - * @return DOCUMENT ME! - * - * @throws PrinterException - * DOCUMENT ME! - */ - /** * Draws the alignment image, including sequence ids, sequences, and * annotation labels and annotations if shown, on either one or two Graphics - * context. + * contexts. * * @param pageWidth + * in pixels * @param pageHeight - * @param pi + * in pixels + * @param pageIndex + * (0, 1, ...) * @param idGraphics * the graphics context for sequence ids and annotation labels * @param alignmentGraphics @@ -978,7 +934,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return * @throws PrinterException */ - public int printUnwrapped(int pageWidth, int pageHeight, int pi, + public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex, Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { @@ -992,8 +948,8 @@ public class AlignmentPanel extends GAlignmentPanel implements : idWidth; FontMetrics fm = getFontMetrics(av.getFont()); - int charHeight = av.getCharHeight(); - int scaleHeight = charHeight + fm.getDescent(); + final int charHeight = av.getCharHeight(); + final int scaleHeight = charHeight + fm.getDescent(); idGraphics.setColor(Color.white); idGraphics.fillRect(0, 0, pageWidth, pageHeight); @@ -1002,29 +958,20 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * How many sequences and residues can we fit on a printable page? */ - int totalRes = (pageWidth - idWidth) / av.getCharWidth(); + final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; + final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - int alignmentWidth = av.getAlignment().getWidth(); - int pagesWide = (alignmentWidth / totalRes) + 1; + final int alignmentWidth = av.getAlignment().getWidth(); + final 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 startRes = (pageIndex % pagesWide) * totalRes; + final int endRes = Math.min(startRes + totalRes - 1, + alignmentWidth - 1); - final int startSeq = (pi / pagesWide) * totalSeq; - int endSeq = startSeq + totalSeq; - - int alignmentHeight = av.getAlignment().getHeight(); - if (endSeq > alignmentHeight) - { - endSeq = alignmentHeight; - } + final int startSeq = (pageIndex / pagesWide) * totalSeq; + final int alignmentHeight = av.getAlignment().getHeight(); + final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight); int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; @@ -1035,7 +982,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pagesHigh /= pageHeight; - if (pi >= (pagesWide * pagesHigh)) + if (pageIndex >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } @@ -1054,47 +1001,12 @@ public class AlignmentPanel extends GAlignmentPanel implements * then reset to top left (0, 0) */ idGraphics.translate(0, scaleHeight); - idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont()); - Color currentColor = null; - Color currentTextColor = null; + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + List selection = av.getSelectionGroup() == null ? null + : av.getSelectionGroup().getSequences(null); + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, + selection); - 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); @@ -1104,7 +1016,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, - endRes, startSeq, endSeq); + endRes, startSeq, endSeq - 1); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1134,31 +1046,27 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Prints one page of an alignment in wrapped mode. Returns + * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if + * no page could be drawn (page number out of range). * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! + * @param pageWidth + * @param pageHeight + * @param pageNumber + * (0, 1, ...) + * @param g * - * @return DOCUMENT ME! + * @return * * @throws PrinterException - * DOCUMENT ME! */ - public int printWrappedAlignment(int pwidth, int pheight, int pi, - Graphics pg) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, + Graphics g) throws PrinterException { int annotationHeight = 0; - AnnotationLabels labels = null; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); - labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); @@ -1176,68 +1084,43 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + .absoluteToVisibleColumn(maxwidth) - 1; } int resWidth = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(pwidth - idWidth); + .getWrappedCanvasWidth(pageWidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); - - // ////////////// - // Draw the ids - pg.setColor(Color.black); + g.setColor(Color.white); + g.fillRect(0, 0, pageWidth, pageHeight); + g.setFont(av.getFont()); + g.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())); + /* + * method: print the whole wrapped alignment, but with a clip region that + * is restricted to the requested page; this supports selective print of + * single pages or ranges, (at the cost of some repeated processing in + * the 'normal' case, when all pages are printed) + */ + g.translate(0, -pageNumber * pageHeight); - pg.setFont(av.getFont()); - labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.getCharHeight())); - } + g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); - ypos += cHeight; - } while (ypos < totalHeight); + /* + * draw sequence ids and annotation labels (if shown) + */ + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight); - pg.translate(idWidth, 0); + g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, totalHeight, 0); - if ((pi * pheight) < totalHeight) + if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; - } else { @@ -1368,7 +1251,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); + .absoluteToVisibleColumn(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) @@ -1437,35 +1320,33 @@ 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) + ""); + triplet = ResidueProperties.nucleotideName.get(seq + .getCharAt(column) + ""); } else { - triplet = ResidueProperties.aa2Triplet - .get(seq.getCharAt(res) + ""); + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) + + ""); } if (triplet == null) @@ -1473,84 +1354,73 @@ 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()); } } } @@ -1599,7 +1469,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + .absoluteToVisibleColumn(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; @@ -1625,13 +1495,14 @@ public class AlignmentPanel extends GAlignmentPanel implements if (annotationPanel != null) { annotationPanel.dispose(); + annotationPanel = null; } if (av != null) { av.removePropertyChangeListener(propertyChangeListener); - jalview.structure.StructureSelectionManager ssm = av - .getStructureSelectionManager(); + propertyChangeListener = null; + StructureSelectionManager ssm = av.getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); ssm.removeCommandListener(av); @@ -1654,9 +1525,15 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void closeChildFrames() { + if (overviewPanel != null) + { + overviewPanel.dispose(); + overviewPanel = null; + } if (calculationDialog != null) { calculationDialog.closeFrame(); + calculationDialog = null; } } @@ -1690,7 +1567,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public String getViewName() { - return av.viewName; + return av.getViewName(); } /** @@ -1819,37 +1696,8 @@ 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 - * 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); } @@ -1886,7 +1734,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (adjustHeight) { // sort, repaint, update overview - paintAlignment(true); + paintAlignment(true, false); } else { @@ -1903,8 +1751,9 @@ public class AlignmentPanel extends GAlignmentPanel implements public void propertyChange(PropertyChangeEvent evt) { // update this panel's scroll values based on the new viewport ranges values - int x = vpRanges.getStartRes(); - int y = vpRanges.getStartSeq(); + ViewportRanges ranges = av.getRanges(); + int x = ranges.getStartRes(); + int y = ranges.getStartSeq(); setScrollValues(x, y); // now update any complementary alignment (its viewport ranges object