X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=a9b9d4d3413c6b2677867443a4afb512348dc8da;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=29874045bf428ecdd19188b6d8fb8655361371da;hpb=2e9f692c73eebcd3f09f4762bc86acb5b5058202;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 2987404..a9b9d4d 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -25,26 +25,27 @@ 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; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; -import java.awt.AlphaComposite; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; +import java.awt.Rectangle; 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 @@ -52,8 +53,14 @@ import javax.swing.JComponent; * Wrapped mode, but not the scale above in Unwrapped mode. * */ -public class SeqCanvas extends JComponent implements ViewportListenerI +@SuppressWarnings("serial") +public class SeqCanvas extends JPanel implements ViewportListenerI { + /** + * vertical gap in pixels between sequences and annotations when in wrapped mode + */ + static final int SEQS_ANNOTATION_GAP = 3; + private static final String ZEROS = "0000000000"; final FeatureRenderer fr; @@ -68,7 +75,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private final SequenceRenderer seqRdr; - private boolean fastPaint = false; + boolean fastPaint = false; private boolean fastpainting = false; @@ -81,13 +88,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private int labelWidthWest; // label left width in pixels if shown - private int wrappedSpaceAboveAlignment; // gap between widths + int wrappedSpaceAboveAlignment; // gap between widths - private int wrappedRepeatHeightPx; // height in pixels of wrapped width + int wrappedRepeatHeightPx; // height in pixels of wrapped width 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. @@ -108,7 +116,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return seqRdr; + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -194,12 +202,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int yPos = ypos + charHeight; int startX = startx; int endX = endx; - + 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()); @@ -230,6 +238,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } + /* * white fill the space for the scale */ @@ -254,6 +263,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g.drawString(valueAsString, xOffset, y); } } + } /** @@ -267,6 +277,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI *
- * 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) { @@ -1512,7 +1527,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean wrapped = av.getWrapAlignment(); try { - fastPaint = !noFastPaint; + fastPaint = doFastPaint; fastpainting = fastPaint; /* @@ -1569,7 +1584,7 @@ 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; } @@ -1591,9 +1606,9 @@ 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 @@ -1636,14 +1651,16 @@ 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; @@ -1653,22 +1670,39 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public void propertyChange(PropertyChangeEvent evt) { String eventName = evt.getPropertyName(); - + // System.err.println(">>SeqCanvas propertyChange " + eventName); if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) { fastPaint = true; repaint(); return; } + else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) + { + fastPaint = false; + // System.err.println("!!!! fastPaint false from MOVE_VIEWPORT"); + repaint(); + return; + } int scrollX = 0; - if (eventName.equals(ViewportRanges.STARTRES)) + if (eventName.equals(ViewportRanges.STARTRES) + || eventName.equals(ViewportRanges.STARTRESANDSEQ)) { // Make sure we're not trying to draw a panel // larger than the visible window + if (eventName.equals(ViewportRanges.STARTRES)) + { + scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + } + else + { + scrollX = ((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]; + } ViewportRanges vpRanges = av.getRanges(); - scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); - int range = vpRanges.getViewportWidth(); + + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; if (scrollX > range) { scrollX = range; @@ -1678,14 +1712,11 @@ 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. - - // scroll - startres and endres both change if (eventName.equals(ViewportRanges.STARTRES)) { if (av.getWrapAlignment()) @@ -1702,6 +1733,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // scroll fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + 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); + } + } } /** @@ -1717,10 +1771,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { ViewportRanges ranges = av.getRanges(); - if (Math.abs(scrollX) > ranges.getViewportWidth()) + if (Math.abs(scrollX) >= ranges.getViewportWidth()) { /* - * shift of more than one view width is + * shift of one view width or more is * overcomplicated to handle in this method */ fastPaint = false; @@ -1728,7 +1782,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } - if (fastpainting || gg == null) + if (fastpainting || img == null) { return; } @@ -1738,6 +1792,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { + + Graphics gg = img.getGraphics(); + calculateWrappedGeometry(getWidth(), getHeight()); /* @@ -1766,6 +1823,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ drawWrappedDecorators(gg, ranges.getStartRes()); + gg.dispose(); + repaint(); } finally { @@ -1789,6 +1848,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } + Graphics gg = img.getGraphics(); + ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int charWidth = av.getCharWidth(); @@ -1815,6 +1876,8 @@ 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, @@ -1822,6 +1885,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.translate(-xOffset, 0); drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } /* @@ -1865,7 +1929,8 @@ 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 @@ -1881,6 +1946,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return; } + + Graphics gg = img.getGraphics(); + int charWidth = av.getCharWidth(); int canvasHeight = getHeight(); @@ -1911,10 +1979,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI while (y >= 0) { + /* + * shift 'widthToCopy' residues by 'positions' places to the right + */ gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy, positions * charWidth, 0); if (y > 0) { + /* + * copy 'positions' residue from the row above (right hand end) + * to this row's left hand end + */ gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx, positions * charWidth, heightToCopy, -widthToCopy, wrappedRepeatHeightPx); @@ -1947,11 +2022,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * charWidth, heightToCopy, widthToCopy, -wrappedRepeatHeightPx); } - y += wrappedRepeatHeightPx; xpos += viewportWidth; } } + gg.dispose(); } @@ -1967,7 +2042,7 @@ 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; } @@ -1995,13 +2070,16 @@ 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++) { @@ -2036,7 +2114,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /* @@ -2072,6 +2150,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } + gg.dispose(); + return matchFound; } @@ -2084,4 +2164,5 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return labelWidthWest; } + }