X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=6325e6136aecd54a39329628a236a580221259bc;hb=ad1a1b9167535b1f6e34d84f8d26f4c63f5d394f;hp=1753a64139aafbb7fc7b2ca940d319e03c873fbb;hpb=2c5c51911c44a653b8ed54c3cdb4500c8aca1475;p=jalview.git
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1753a64..6325e61 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -32,7 +32,6 @@ 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;
@@ -40,13 +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
@@ -54,7 +52,7 @@ 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";
@@ -89,7 +87,8 @@ 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.
@@ -110,7 +109,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
public SequenceRenderer getSequenceRenderer()
{
- return seqRdr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
@@ -196,7 +195,7 @@ 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();
@@ -232,6 +231,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
}
+
/*
* white fill the space for the scale
*/
@@ -256,6 +256,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
g.drawString(valueAsString, xOffset, y);
}
}
+
}
/**
@@ -278,7 +279,7 @@ 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;
}
@@ -298,6 +299,7 @@ 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);
@@ -338,7 +340,8 @@ 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.
@@ -352,57 +355,55 @@ 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();
-
+
ViewportRanges ranges = av.getRanges();
-
+
int width = getWidth();
int height = getHeight();
-
+
width -= (width % charWidth);
height -= (height % charHeight);
-
- // selectImage is the selection group outline image
- BufferedImage selectImage = drawSelectionGroup(
- ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq());
+
if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
{
- BufferedImage lcimg = buildLocalImage(selectImage);
- g.drawImage(lcimg, 0, 0, this);
+ g.drawImage(img, 0, 0, this);
+
+ drawSelectionGroup((Graphics2D) g, ranges.getStartRes(),
+ ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
+
fastPaint = false;
}
- else if ((width > 0) && (height > 0))
+ else if (width > 0 && height > 0)
{
- // img is a cached version of the last view we drew, if any
- // if we have no img or the size has changed, make a new one
+ /*
+ * img is a cached version of the last view we drew, if any
+ * if we have no img or the size has changed, make a new one
+ */
if (img == null || width != img.getWidth()
|| height != img.getHeight())
{
- img = setupImage();
- if (img == null)
- {
- return;
- }
- gg = (Graphics2D) img.getGraphics();
- gg.setFont(av.getFont());
+ img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
}
-
+
+ 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());
@@ -412,11 +413,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
-
- // lcimg is a local *copy* of img which we'll draw selectImage on top of
- BufferedImage lcimg = buildLocalImage(selectImage);
- g.drawImage(lcimg, 0, 0, this);
+ drawSelectionGroup(gg, ranges.getStartRes(),
+ ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
+
+ g.drawImage(img, 0, 0, this);
+ gg.dispose();
}
if (av.cursorMode)
@@ -445,14 +447,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
{
drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
- BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+ drawSelectionGroup((Graphics2D) g1, startRes, endRes,
startSeq, endSeq);
- if (selectImage != null)
- {
- ((Graphics2D) g1).setComposite(AlphaComposite
- .getInstance(AlphaComposite.SRC_OVER));
- g1.drawImage(selectImage, 0, 0, this);
- }
}
/**
@@ -470,102 +466,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
- SequenceGroup group = av.getSelectionGroup();
-
drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+ SequenceGroup group = av.getSelectionGroup();
if (group != null)
{
- BufferedImage selectImage = null;
- try
- {
- selectImage = new BufferedImage(canvasWidth, canvasHeight,
- BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
- } catch (OutOfMemoryError er)
- {
- System.gc();
- System.err.println("Print image OutOfMemory Error.\n" + er);
- new OOMWarning("Creating wrapped alignment image for printing", er);
- }
- if (selectImage != null)
- {
- Graphics2D g2 = selectImage.createGraphics();
- setupSelectionGroup(g2, selectImage);
- drawWrappedSelection(g2, group, canvasWidth, canvasHeight,
+ drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight,
startRes);
-
- g2.setComposite(
- AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
- g.drawImage(selectImage, 0, 0, this);
- g2.dispose();
- }
- }
- }
-
- /*
- * Make a local image by combining the cached image img
- * with any selection
- */
- 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());
- Graphics2D g2d = lcimg.createGraphics();
- g2d.drawImage(img, 0, 0, null);
-
- // overlay selection group on lcimg
- if (selectImage != null)
- {
- g2d.setComposite(
- AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
- g2d.drawImage(selectImage, 0, 0, this);
- }
-
- g2d.dispose();
-
- return lcimg;
- }
-
- /*
- * Set up a buffered image of the correct height and size for the sequence canvas
- */
- private BufferedImage setupImage()
- {
- BufferedImage lcimg = null;
-
- int charWidth = av.getCharWidth();
- int charHeight = av.getCharHeight();
-
- int width = getWidth();
- int height = getHeight();
-
- width -= (width % charWidth);
- height -= (height % charHeight);
-
- if ((width < 1) || (height < 1))
- {
- return null;
}
-
- try
- {
- lcimg = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
- } catch (OutOfMemoryError er)
- {
- System.gc();
- System.err.println(
- "Group image OutOfMemory Redraw Error.\n" + er);
- new OOMWarning("Creating alignment image for display", er);
-
- return null;
- }
-
- return lcimg;
}
/**
@@ -773,21 +681,8 @@ 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
@@ -814,7 +709,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
startColumn, endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
- g.setClip(clip);
g.translate(-xOffset, 0);
}
@@ -830,6 +724,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
int charWidth = av.getCharWidth();
g.setFont(av.getFont());
+
g.setColor(Color.black);
int ypos = wrappedSpaceAboveAlignment;
@@ -851,6 +746,7 @@ 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);
@@ -964,6 +860,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
// chop the wrapped alignment extent up into panel-sized blocks and treat
// each block as if it were a block from an unwrapped alignment
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
while ((ypos <= canvasHeight) && (startx < maxwidth))
{
// set end value to be start + width, or maxwidth, whichever is smaller
@@ -988,6 +888,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
// update horizontal offset
startx += cWidth;
}
+ g.setStroke(new BasicStroke());
}
int getAnnotationHeight()
@@ -1154,14 +1055,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
+ /**
+ * Draws the outlines of any groups defined on the alignment (excluding the
+ * current selection group, if any)
+ *
+ * @param g1
+ * @param startRes
+ * @param endRes
+ * @param startSeq
+ * @param endSeq
+ * @param offset
+ */
void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
Graphics2D g = (Graphics2D) g1;
- //
- // ///////////////////////////////////
- // Now outline any areas if necessary
- // ///////////////////////////////////
SequenceGroup group = null;
int groupIndex = -1;
@@ -1174,58 +1082,44 @@ 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);
groupIndex++;
-
- g.setStroke(new BasicStroke());
-
if (groupIndex >= av.getAlignment().getGroups().size())
{
break;
}
-
group = av.getAlignment().getGroups().get(groupIndex);
-
} while (groupIndex < av.getAlignment().getGroups().size());
-
}
-
}
-
- /*
- * Draw the selection group as a separate image and overlay
+ /**
+ * Draws the outline of the current selection group (if any)
+ *
+ * @param g
+ * @param startRes
+ * @param endRes
+ * @param startSeq
+ * @param endSeq
*/
- private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ private void drawSelectionGroup(Graphics2D g, int startRes, int endRes,
int startSeq, int endSeq)
{
- // get a new image of the correct size
- BufferedImage selectionImage = setupImage();
-
- if (selectionImage == null)
- {
- return null;
- }
-
SequenceGroup group = av.getSelectionGroup();
if (group == null)
{
- // nothing to draw
- return null;
+ return;
}
- // set up drawing colour
- Graphics2D g = (Graphics2D) selectionImage.getGraphics();
-
- setupSelectionGroup(g, selectionImage);
-
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
if (!av.getWrapAlignment())
{
drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
@@ -1236,9 +1130,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
drawWrappedSelection(g, group, getWidth(), getHeight(),
av.getRanges().getStartRes());
}
-
- g.dispose();
- return selectionImage;
+ g.setStroke(new BasicStroke());
}
/**
@@ -1329,33 +1221,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
- /*
- * Set up graphics for selection group
- */
- private void setupSelectionGroup(Graphics2D g,
- BufferedImage selectionImage)
- {
- // set background to transparent
- g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
- g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
-
- // set up foreground to draw red dashed line
- g.setComposite(AlphaComposite.Src);
- g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
- g.setColor(Color.RED);
- }
-
- /*
+ /**
* Draw a selection group over an unwrapped alignment
- * @param g graphics object to draw with
- * @param group selection group
- * @param startRes start residue of area to draw
- * @param endRes end residue of area to draw
- * @param startSeq start sequence of area to draw
- * @param endSeq end sequence of area to draw
- * @param offset vertical offset (used when called from wrapped alignment code)
+ *
+ * @param g
+ * graphics object to draw with
+ * @param group
+ * selection group
+ * @param startRes
+ * start residue of area to draw
+ * @param endRes
+ * end residue of area to draw
+ * @param startSeq
+ * start sequence of area to draw
+ * @param endSeq
+ * end sequence of area to draw
+ * @param offset
+ * vertical offset (used when called from wrapped alignment code)
*/
private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
int startRes, int endRes, int startSeq, int endSeq, int offset)
@@ -1393,8 +1275,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
}
- /*
- * Draw the selection group as a separate image and overlay
+ /**
+ * Draws part of a selection group outline
+ *
+ * @param g
+ * @param group
+ * @param startRes
+ * @param endRes
+ * @param startSeq
+ * @param endSeq
+ * @param verticalOffset
*/
private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
int startRes, int endRes, int startSeq, int endSeq,
@@ -1551,20 +1441,42 @@ 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)
{
@@ -1573,7 +1485,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
boolean wrapped = av.getWrapAlignment();
try
{
- fastPaint = !noFastPaint;
+ fastPaint = doFastPaint;
fastpainting = fastPaint;
/*
@@ -1630,7 +1542,7 @@ 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;
}
@@ -1702,9 +1614,11 @@ 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;
@@ -1825,7 +1739,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
return;
}
- if (fastpainting || gg == null)
+ if (fastpainting || img == null)
{
return;
}
@@ -1835,6 +1749,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
try
{
+
+ Graphics gg = img.getGraphics();
+
calculateWrappedGeometry(getWidth(), getHeight());
/*
@@ -1863,6 +1780,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
*/
drawWrappedDecorators(gg, ranges.getStartRes());
+ gg.dispose();
+
repaint();
} finally
{
@@ -1886,6 +1805,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
return;
}
+ Graphics gg = img.getGraphics();
+
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
int charWidth = av.getCharWidth();
@@ -1912,6 +1833,8 @@ 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,
@@ -1919,6 +1842,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
gg.translate(-xOffset, 0);
drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
+
}
/*
@@ -1962,7 +1886,8 @@ 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
@@ -1978,6 +1903,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
{
return;
}
+
+ Graphics gg = img.getGraphics();
+
int charWidth = av.getCharWidth();
int canvasHeight = getHeight();
@@ -2044,11 +1972,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
* charWidth, heightToCopy, widthToCopy,
-wrappedRepeatHeightPx);
}
-
y += wrappedRepeatHeightPx;
xpos += viewportWidth;
}
}
+ gg.dispose();
}
@@ -2064,7 +1992,7 @@ 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;
}
@@ -2099,6 +2027,9 @@ 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++)
{
@@ -2169,6 +2100,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
}
}
+ gg.dispose();
+
return matchFound;
}