X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7ecedf4647772df2f3934e7584b7f419f2813a18;hb=75ce39c3308a69bafc2e7c5514e44de22dd3d6f0;hp=1e1105f86d1a8413d931835502e8cd1a7e19ebb0;hpb=f5cadfa2a55d78a08268a0df9a7c3f64d1c43e8a;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 1e1105f..7ecedf4 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.VisibleContigsIterator; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.util.Comparison; @@ -42,9 +43,10 @@ import java.awt.RenderingHints; import java.awt.Shape; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; +import java.util.Iterator; import java.util.List; -import javax.swing.JComponent; +import javax.swing.JPanel; /** * The Swing component on which the alignment sequences, and annotations (if @@ -52,7 +54,7 @@ import javax.swing.JComponent; * Wrapped mode, but not the scale above in Unwrapped mode. * */ -public class SeqCanvas extends JComponent implements ViewportListenerI +public class SeqCanvas extends JPanel implements ViewportListenerI { private static final String ZEROS = "0000000000"; @@ -87,7 +89,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private int wrappedVisibleWidths; // number of wrapped widths displayed - private Graphics2D gg; + // Don't do this! Graphics handles are supposed to be transient + //private Graphics2D gg; /** * Creates a new SeqCanvas object. @@ -148,6 +151,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI for (ScaleMark mark : marks) { int mpos = mark.column; // (i - startx - 1) +// System.out.println("n " + mpos + " " + ypos); if (mpos < 0) { continue; @@ -194,12 +198,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int yPos = ypos + charHeight; int startX = startx; int endX = endx; + + //System.out.println("v " + startx + " " + endx + " " + ypos); + if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startX = hiddenColumns.adjustForHiddenColumns(startx); - endX = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -238,7 +245,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // fillRect origin is top left of rectangle g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast, charHeight + 1); - + if (value != -1) { /* @@ -252,6 +259,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int xOffset = labelSpace - labelLength; g.setColor(Color.black); g.drawString(valueAsString, xOffset, y); + + //System.out.println("v " + valueAsString + " " + xOffset + " " + y); + } } } @@ -276,7 +286,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting || gg == null || img == null) + if (fastpainting || img == null) { return; } @@ -295,7 +305,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int endSeq = ranges.getEndSeq(); int transX = 0; int transY = 0; - + + Graphics gg = img.getGraphics(); gg.copyArea(horizontal * charWidth, vertical * charHeight, img.getWidth(), img.getHeight(), -horizontal * charWidth, -vertical * charHeight); @@ -336,8 +347,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.translate(transX, transY); drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); gg.translate(-transX, -transY); - - repaint(); + gg.dispose(); + + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the + // overview window and others may be adversely affected. + av.getAlignPanel().repaint(); } finally { fastpainting = false; @@ -347,8 +362,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI @Override public void paintComponent(Graphics g) { - super.paintComponent(g); - + super.paintComponent(g); + int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); @@ -361,9 +376,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI height -= (height % charHeight); // selectImage is the selection group outline image - BufferedImage selectImage = drawSelectionGroup( - ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq()); + BufferedImage selectImage = drawSelectionGroup(ranges.getStartRes(), + ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) @@ -385,10 +399,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return; } - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); } + + Graphics2D gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, @@ -407,6 +423,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq(), 0); } + + + gg.dispose(); // lcimg is a local *copy* of img which we'll draw selectImage on top of BufferedImage lcimg = buildLocalImage(selectImage); @@ -504,8 +523,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private BufferedImage buildLocalImage(BufferedImage selectImage) { // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); + BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + img.getType()); + + // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + // img.getType()); Graphics2D g2d = lcimg.createGraphics(); g2d.drawImage(img, 0, 0, null); @@ -545,8 +567,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + lcimg = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works } catch (OutOfMemoryError er) { System.gc(); @@ -644,6 +666,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI ViewportRanges ranges = av.getRanges(); ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues); + // we need to call this again to make sure the startColumn + + // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths + // correctly. + calculateWrappedGeometry(canvasWidth, canvasHeight); + /* * draw one width at a time (including any scales or annotation shown), * until we have run out of either alignment or vertical space available @@ -838,6 +865,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.getScaleRightWrapped()) { int x = labelWidthWest + viewportWidth * charWidth; + + //System.out.println("shifting " + x); g.translate(x, 0); drawVerticalScale(g, startCol, endColumn, ypos, false); g.translate(-x, 0); @@ -890,11 +919,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int charWidth = av.getCharWidth(); g.setColor(Color.blue); + int res; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + + Iterator it = hidden.getStartRegionIterator(startColumn, + endColumn); + while (it.hasNext()) { - int res = pos - startColumn; + res = it.next() - startColumn; if (res < 0 || res > endColumn - startColumn + 1) { @@ -943,7 +975,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); + .absoluteToVisibleColumn(maxwidth); } // chop the wrapped alignment extent up into panel-sized blocks and treat @@ -1021,29 +1053,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI else { int screenY = 0; - final int screenYMax = endRes - startRes; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) - { - int hideStart = region[0]; - int hideEnd = region[1]; + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + while (regions.hasNext()) + { + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; /* * draw up to just before the next hidden region, or the end of * the visible region, whichever comes first */ - blockEnd = Math.min(hideStart - 1, blockStart + screenYMax - - screenY); - g1.translate(screenY * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); @@ -1052,7 +1078,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * draw the downline of the hidden column marker (ScalePanel draws the * triangle on top) if we reached it */ - if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1) + if (av.getShowHiddenMarkers() + && (regions.hasNext() || regions.endsAtHidden())) { g1.setColor(Color.blue); @@ -1063,23 +1090,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > screenYMax) - { - // already rendered last block - return; - } - } - - if (screenY <= screenYMax) - { - // remaining visible region to render - blockEnd = blockStart + screenYMax - screenY; - g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); - - g1.translate(-screenY * charWidth, 0); } } @@ -1137,16 +1147,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasSearchResults()) { SearchResultsI searchResults = av.getSearchResults(); - int[] visibleResults = searchResults.getResults(nextSeq, - startRes, endRes); + int[] visibleResults = searchResults.getResults(nextSeq, startRes, + endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { seqRdr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * charWidth, offset - + ((i - startSeq) * charHeight)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); } } } @@ -1181,10 +1191,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (group != null) { g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); do { + g.setColor(group.getOutlineColour()); drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, offset); @@ -1278,7 +1288,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // convert the cursorX into a position on the visible alignment int cursor_xpos = av.getAlignment().getHiddenColumns() - .findColumnPosition(cursorX); + .absoluteToVisibleColumn(cursorX); if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) { @@ -1377,22 +1387,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { // package into blocks of visible columns int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; g.translate(screenY * charWidth, 0); drawPartialGroupOutline(g, group, @@ -1400,24 +1405,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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); } } } @@ -1580,20 +1567,42 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * Highlights search results in the visible region by rendering as white text * on a black background. Any previous highlighting is removed. Answers true * if any highlight was left on the visible alignment (so status bar should be + * set to match), else false. This method does _not_ set the 'fastPaint' flag, + * so allows the next repaint to update the whole display. + * + * @param results + * @return + */ + public boolean highlightSearchResults(SearchResultsI results) + { + return highlightSearchResults(results, false); + + } + + /** + * Highlights search results in the visible region by rendering as white text + * on a black background. Any previous highlighting is removed. Answers true + * if any highlight was left on the visible alignment (so status bar should be * set to match), else false. *

- * Currently fastPaint is not implemented for wrapped alignments. If a wrapped - * alignment had to be scrolled to show the highlighted region, then it should - * be fully redrawn, otherwise a fast paint can be performed. This argument - * could be removed if fast paint of scrolled wrapped alignment is coded in - * future (JAL-2609). + * Optionally, set the 'fastPaint' flag for a faster redraw if only the + * highlighted regions are modified. This speeds up highlighting across linked + * alignments. + *

+ * Currently fastPaint is not implemented for scrolled wrapped alignments. If + * a wrapped alignment had to be scrolled to show the highlighted region, then + * it should be fully redrawn, otherwise a fast paint can be performed. This + * argument could be removed if fast paint of scrolled wrapped alignment is + * coded in future (JAL-2609). * * @param results - * @param noFastPaint + * @param doFastPaint + * if true, sets a flag so the next repaint only redraws the modified + * image * @return */ public boolean highlightSearchResults(SearchResultsI results, - boolean noFastPaint) + boolean doFastPaint) { if (fastpainting) { @@ -1602,7 +1611,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean wrapped = av.getWrapAlignment(); try { - fastPaint = !noFastPaint; + fastPaint = doFastPaint; fastpainting = fastPaint; /* @@ -1659,7 +1668,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositions(SearchResultsI results) { - if ((results == null) || (gg == null)) // JAL-2784 check gg is not null + if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } @@ -1681,9 +1690,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } for (int seqNo = ranges.getStartSeq(); seqNo <= ranges @@ -1726,14 +1735,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstCol = alignment.getHiddenColumns() - .findColumnPosition(firstCol); - lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol); + .absoluteToVisibleColumn(firstCol); + lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol); } int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth(); int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight(); + Graphics gg = img.getGraphics(); gg.translate(transX, transY); drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0); gg.translate(-transX, -transY); + gg.dispose(); } return matchFound; @@ -1784,14 +1795,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI scrollX = -range; } } - // Both scrolling and resizing change viewport ranges: scrolling changes - // both start and end points, but resize only changes end values. - // Here we only want to fastpaint on a scroll, with resize using a normal - // paint, so scroll events are identified as changes to the horizontal or - // vertical start value. - if (eventName.equals(ViewportRanges.STARTRES)) - { - if (av.getWrapAlignment()) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } + } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); } @@ -1811,14 +1838,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { fastPaintWrapped(scrollX); } - else - { - fastPaint(scrollX, 0); - } - // bizarrely, we only need to scroll on the x value here as fastpaint - // copies the full height of the image anyway. Passing in the y value - // causes nasty repaint artefacts, which only disappear on a full - // repaint. } } @@ -1835,9 +1854,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { ViewportRanges ranges = av.getRanges(); - // if (Math.abs(scrollX) > ranges.getViewportWidth()) - // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3 - if (true) + if (Math.abs(scrollX) > ranges.getViewportWidth()) { /* * shift of more than one view width is @@ -1848,7 +1865,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } - if (fastpainting || gg == null) + if (fastpainting || img == null) { return; } @@ -1858,6 +1875,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { + + Graphics gg = img.getGraphics(); + calculateWrappedGeometry(getWidth(), getHeight()); /* @@ -1886,6 +1906,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ drawWrappedDecorators(gg, ranges.getStartRes()); + gg.dispose(); + repaint(); } finally { @@ -1909,6 +1931,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } + Graphics gg = img.getGraphics(); + ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int charWidth = av.getCharWidth(); @@ -1935,6 +1959,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI /* * white fill first to erase annotations */ + + gg.translate(xOffset, 0); gg.setColor(Color.white); gg.fillRect(labelWidthWest, ypos, @@ -1942,6 +1968,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.translate(-xOffset, 0); drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } /* @@ -1985,7 +2012,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); } - } + gg.dispose(); + } /** * Shifts the visible alignment by the specified number of columns - left if @@ -2001,6 +2029,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return; } + + Graphics gg = img.getGraphics(); + int charWidth = av.getCharWidth(); int canvasHeight = getHeight(); @@ -2067,11 +2098,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * charWidth, heightToCopy, widthToCopy, -wrappedRepeatHeightPx); } - y += wrappedRepeatHeightPx; xpos += viewportWidth; } } + gg.dispose(); } @@ -2087,7 +2118,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositionsWrapped(SearchResultsI results) { - if ((results == null) || (gg == null)) // JAL-2784 check gg is not null + if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } @@ -2115,13 +2146,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + + Graphics gg = img.getGraphics(); + for (int seqNo = ranges.getStartSeq(); seqNo <= ranges .getEndSeq(); seqNo++) { @@ -2156,7 +2190,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /* @@ -2192,6 +2226,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } + gg.dispose(); + return matchFound; }