X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1ac553668f2a9230ae5af6b1c3cb40fd6835755d;hb=b2829c5d7e7815e5e261d39964ade91ed5225510;hp=9b74007e88f40821c37159904dcb119d33ade368;hpb=0d3cf98a79df1eb920f71b3093afb150b046f9eb;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 9b74007..1ac5536 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -48,7 +48,7 @@ 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; @@ -95,9 +95,6 @@ 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; @@ -212,7 +209,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -241,11 +239,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (this.alignFrame.getSplitViewContainer() != null) - { - ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); - } - repaint(); } @@ -426,8 +419,8 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - start = hidden.findColumnPosition(start); - end = hidden.findColumnPosition(end); + start = hidden.absoluteToVisibleColumn(start); + end = hidden.absoluteToVisibleColumn(end); if (start == end) { if (!hidden.isVisible(r[0])) @@ -485,7 +478,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); + paintAlignment(redrawOverview, false); return scrollNeeded; } @@ -542,7 +535,9 @@ 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); } /** @@ -561,13 +556,10 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * 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. + * hscroll, status bar, insets. */ - int stuff = Platform.isAMac() ? 80 : 100; - Insets insets = alignFrame.getInsets(); - int availableHeight = alignFrame.getHeight() - stuff - insets.top - - insets.bottom; + int stuff = Platform.isAMac() ? 120 : 140; + int availableHeight = alignFrame.getHeight() - stuff; /* * If not enough vertical space, maximize annotation height while keeping @@ -637,9 +629,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - int widthInRes = (canvasWidth / av.getCharWidth()) - 1; + int widthInRes = (canvasWidth / av.getCharWidth()); int heightInSeq = (getSeqPanel().seqCanvas.getHeight() - / av.getCharHeight()) - 1; + / av.getCharHeight()); ranges.setViewportWidth(widthInRes); ranges.setViewportHeight(heightInSeq); @@ -683,7 +675,7 @@ 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(); @@ -775,10 +767,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } ranges.setViewportStartAndHeight(y, height); } - if (!fastPaint) - { - repaint(); - } + repaint(); } /** @@ -846,12 +835,12 @@ 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()); @@ -859,10 +848,12 @@ 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) { @@ -880,15 +871,17 @@ 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. */ ViewportRanges ranges = av.getRanges(); setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); @@ -950,30 +943,16 @@ 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 @@ -982,7 +961,7 @@ 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 { @@ -996,8 +975,8 @@ 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); @@ -1006,29 +985,20 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * How many sequences and residues can we fit on a printable page? */ - int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - - int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; + final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - int alignmentWidth = av.getAlignment().getWidth(); - int pagesWide = (alignmentWidth / totalRes) + 1; + final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - final int startRes = (pi % pagesWide) * totalRes; - int endRes = (startRes + totalRes) - 1; + final int alignmentWidth = av.getAlignment().getWidth(); + final int pagesWide = (alignmentWidth / 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; @@ -1039,7 +1009,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pagesHigh /= pageHeight; - if (pi >= (pagesWide * pagesHigh)) + if (pageIndex >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } @@ -1058,47 +1028,12 @@ 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; - - 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; - } + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + List selection = av.getSelectionGroup() == null ? null + : av.getSelectionGroup().getSequences(null); + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, + selection); - idGraphics.drawString(displayId, xPos, - (((i - startSeq) * charHeight) + charHeight) - - (charHeight / 5)); - } idGraphics.setFont(av.getFont()); idGraphics.translate(0, -scaleHeight); @@ -1108,7 +1043,7 @@ 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)) @@ -1180,7 +1115,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + .absoluteToVisibleColumn(maxwidth) - 1; } int resWidth = getSeqPanel().seqCanvas @@ -1372,7 +1307,7 @@ 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()) @@ -1590,7 +1525,7 @@ 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; @@ -1616,13 +1551,14 @@ 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); @@ -1645,9 +1581,15 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void closeChildFrames() { + if (overviewPanel != null) + { + overviewPanel.dispose(); + overviewPanel = null; + } if (calculationDialog != null) { calculationDialog.closeFrame(); + calculationDialog = null; } } @@ -1812,35 +1754,6 @@ public class AlignmentPanel extends GAlignmentPanel implements */ 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); } @@ -1877,7 +1790,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (adjustHeight) { // sort, repaint, update overview - paintAlignment(true); + paintAlignment(true, false); } else {