X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=2139b6b78814830eeaed2742911a6142f2f70b6a;hb=b8196b19d8f419759df704d0f016de59b0c6ead0;hp=928ce41f1b90007c6dbe55b7c8d5380aee692faf;hpb=bb5ca6096768a8e57a3c3158469e5eba7cabcfdb;p=jalview.git
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 928ce41..2139b6b 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -39,13 +39,12 @@ import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
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
@@ -53,8 +52,13 @@ 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
{
+ /*
+ * pixels gap between sequences and annotations when in wrapped mode
+ */
+ static final int SEQS_ANNOTATION_GAP = 3;
+
private static final String ZEROS = "0000000000";
final FeatureRenderer fr;
@@ -82,13 +86,14 @@ 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.
@@ -109,7 +114,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
public SequenceRenderer getSequenceRenderer()
{
- return seqRdr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
@@ -195,7 +200,7 @@ 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();
@@ -231,6 +236,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
}
+
/*
* white fill the space for the scale
*/
@@ -255,6 +261,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
g.drawString(valueAsString, xOffset, y);
}
}
+
}
/**
@@ -277,7 +284,7 @@ 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;
}
@@ -297,6 +304,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
int transX = 0;
int transY = 0;
+ Graphics gg = img.getGraphics();
gg.copyArea(horizontal * charWidth, vertical * charHeight,
img.getWidth(), img.getHeight(), -horizontal * charWidth,
-vertical * charHeight);
@@ -337,7 +345,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
gg.translate(transX, transY);
drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
gg.translate(-transX, -transY);
-
+ 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.
@@ -351,22 +360,19 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
@Override
public void paintComponent(Graphics g)
{
- super.paintComponent(g);
-
+ //super.paintComponent(g); // BH 2019
+
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
-
+
ViewportRanges ranges = av.getRanges();
-
+
int width = getWidth();
int height = getHeight();
-
+
width -= (width % charWidth);
height -= (height % charHeight);
-
- drawSelectionGroup((Graphics2D) g,
- ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq());
+
if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
@@ -389,19 +395,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
|| height != img.getHeight())
{
img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
- 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,
RenderingHints.VALUE_ANTIALIAS_ON);
}
-
+
gg.setColor(Color.white);
gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-
+
if (av.getWrapAlignment())
{
drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
@@ -416,6 +423,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
g.drawImage(img, 0, 0, this);
+ gg.dispose();
}
if (av.cursorMode)
@@ -563,7 +571,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
calculateWrappedGeometry(canvasWidth, canvasHeight);
/*
- * draw one width at a time (including any scales or annotation shown),
+ * draw one width at a time (excluding any scales shown),
* until we have run out of either alignment or vertical space available
*/
int ypos = wrappedSpaceAboveAlignment;
@@ -610,14 +618,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
* (av.getScaleAboveWrapped() ? 2 : 1);
/*
- * height in pixels of the wrapped widths
+ * compute height in pixels of the wrapped widths
+ * - start with space above plus sequences
*/
wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
- // add sequences
- wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
+ wrappedRepeatHeightPx += av.getAlignment().getHeight()
* charHeight;
- // add annotations panel height if shown
- wrappedRepeatHeightPx += getAnnotationHeight();
+
+ /*
+ * add annotations panel height if shown
+ * also gap between sequences and annotations
+ */
+ if (av.isShowAnnotation())
+ {
+ wrappedRepeatHeightPx += getAnnotationHeight();
+ wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px
+ }
/*
* number of visible widths (the last one may be part height),
@@ -661,8 +677,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
* @param endColumn
* @param canvasHeight
*/
- protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
- int endColumn, int canvasHeight)
+ protected void drawWrappedWidth(Graphics g, final int ypos,
+ final int startColumn, final int endColumn,
+ final int canvasHeight)
{
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
@@ -678,21 +695,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
int xOffset = labelWidthWest
+ ((startColumn - ranges.getStartRes()) % viewportWidth)
* charWidth;
- g.translate(xOffset, 0);
- // When printing we have an extra clipped region,
- // the Printable page which we need to account for here
- Shape clip = g.getClip();
-
- if (clip == null)
- {
- g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
- }
- else
- {
- g.setClip(0, (int) clip.getBounds().getY(),
- viewportWidth * charWidth, (int) clip.getBounds().getHeight());
- }
+ g.translate(xOffset, 0);
/*
* white fill the region to be drawn (so incremental fast paint doesn't
@@ -709,7 +713,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
if (av.isShowAnnotation())
{
- g.translate(0, cHeight + ypos + 3);
+ final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP;
+ g.translate(0, yShift);
if (annotations == null)
{
annotations = new AnnotationPanel(av);
@@ -717,9 +722,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
annotations.renderer.drawComponent(annotations, av, g, -1,
startColumn, endx + 1);
- g.translate(0, -cHeight - ypos - 3);
+ g.translate(0, -yShift);
}
- g.setClip(clip);
g.translate(-xOffset, 0);
}
@@ -735,6 +739,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
int charWidth = av.getCharWidth();
g.setFont(av.getFont());
+
g.setColor(Color.black);
int ypos = wrappedSpaceAboveAlignment;
@@ -756,6 +761,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
if (av.getScaleRightWrapped())
{
int x = labelWidthWest + viewportWidth * charWidth;
+
g.translate(x, 0);
drawVerticalScale(g, startCol, endColumn, ypos, false);
g.translate(-x, 0);
@@ -859,13 +865,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
int startx = startRes;
int endx;
int ypos = hgap; // vertical offset
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
// chop the wrapped alignment extent up into panel-sized blocks and treat
// each block as if it were a block from an unwrapped alignment
@@ -1094,23 +1094,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
do
{
g.setColor(group.getOutlineColour());
-
drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
endSeq, offset);
groupIndex++;
-
if (groupIndex >= av.getAlignment().getGroups().size())
{
break;
}
-
group = av.getAlignment().getGroups().get(groupIndex);
-
} while (groupIndex < av.getAlignment().getGroups().size());
-
}
-
}
/**
@@ -1456,20 +1450,42 @@ 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)
{
@@ -1478,7 +1494,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
boolean wrapped = av.getWrapAlignment();
try
{
- fastPaint = !noFastPaint;
+ fastPaint = doFastPaint;
fastpainting = fastPaint;
/*
@@ -1535,7 +1551,7 @@ 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;
}
@@ -1607,9 +1623,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
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;
@@ -1650,7 +1668,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
ViewportRanges vpRanges = av.getRanges();
- int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1;
if (scrollX > range)
{
scrollX = range;
@@ -1719,10 +1737,10 @@ 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;
@@ -1730,7 +1748,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
return;
}
- if (fastpainting || gg == null)
+ if (fastpainting || img == null)
{
return;
}
@@ -1740,6 +1758,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
try
{
+
+ Graphics gg = img.getGraphics();
+
calculateWrappedGeometry(getWidth(), getHeight());
/*
@@ -1768,6 +1789,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
*/
drawWrappedDecorators(gg, ranges.getStartRes());
+ gg.dispose();
+
repaint();
} finally
{
@@ -1791,6 +1814,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
return;
}
+ Graphics gg = img.getGraphics();
+
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
int charWidth = av.getCharWidth();
@@ -1817,6 +1842,8 @@ 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,
@@ -1824,6 +1851,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
gg.translate(-xOffset, 0);
drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
+
}
/*
@@ -1867,7 +1895,8 @@ 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
@@ -1883,6 +1912,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
{
return;
}
+
+ Graphics gg = img.getGraphics();
+
int charWidth = av.getCharWidth();
int canvasHeight = getHeight();
@@ -1913,10 +1945,17 @@ 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);
@@ -1949,11 +1988,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
* charWidth, heightToCopy, widthToCopy,
-wrappedRepeatHeightPx);
}
-
y += wrappedRepeatHeightPx;
xpos += viewportWidth;
}
}
+ gg.dispose();
}
@@ -1969,7 +2008,7 @@ 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;
}
@@ -2004,6 +2043,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ Graphics gg = img.getGraphics();
+
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
.getEndSeq(); seqNo++)
{
@@ -2074,6 +2116,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
}
+ gg.dispose();
+
return matchFound;
}