* @version $Revision: 1.161 $
*/
public class AlignmentPanel extends GAlignmentPanel implements
- AdjustmentListener, Printable, AlignmentViewPanel,
- ViewportListenerI
+ AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
{
public AlignViewport av;
// is initialised
if (av.getWrapAlignment())
{
- int widthInRes = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
vpRanges.setViewportWidth(widthInRes);
}
else
/ av.getCharWidth();
int heightInSeq = getSeqPanel().seqCanvas.getHeight()
/ av.getCharHeight();
-
+
vpRanges.setViewportWidth(widthInRes);
vpRanges.setViewportHeight(heightInSeq);
}
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight() + fm.getDescent()));
+ scalePanelHolder.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
{
Container c = new Container();
- FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
- Font.ITALIC, av.font.getSize()));
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
AlignmentI al = av.getAlignment();
int i = 0;
}
}
- return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
- idWidth), 12);
+ return new Dimension(
+ maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
}
/**
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
- + 1);
+ setScrollValues(vpRanges.getStartRes(),
+ starts + seqIndex - ends + 1);
}
/*
* Else results are already visible - no need to scroll
*/
if (annotationHeight + alignmentHeight > availableHeight)
{
- annotationHeight = Math.min(annotationHeight, availableHeight - 2
- * rowHeight);
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
}
}
else
}
hscroll.addNotify();
- annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), annotationHeight));
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), annotationHeight));
Dimension e = idPanel.getSize();
alabels.setSize(new Dimension(e.width, annotationHeight));
else
{
int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
- int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
- .getCharHeight()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight()) - 1;
vpRanges.setViewportWidth(widthInRes);
vpRanges.setViewportHeight(heightInSeq);
repaint();
}
-
/**
* Adjust row/column scrollers to show a visible position in the alignment.
*
if (av.hasHiddenColumns())
{
// reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+ width = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(width);
}
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
{
@Override
public void run()
- {
+ {
// When updating scrolling to use ViewportChange events, this code
// could not be validated and it is not clear if it is now being
// called. Log warning here in case it is called and unforeseen
// problems occur
- Cache.log
- .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+ Cache.log.warn(
+ "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
// scroll to start of panel
vpRanges.setStartRes(0);
* Get the horizontal offset to where we draw the sequences.
* This is idWidth if using a single Graphics context, else zero.
*/
- final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
+ : idWidth;
FontMetrics fm = getFontMetrics(av.getFont());
int charHeight = av.getCharHeight();
endSeq = alignmentHeight;
}
- int pagesHigh = ((alignmentHeight / totalSeq) + 1)
- * pageHeight;
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
if (av.isShowAnnotation())
{
{
return Printable.NO_SUCH_PAGE;
}
- final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
- + 3;
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
/*
* draw the Scale at horizontal offset, then reset to top left (0, 0)
if (av.isRightAlignIds())
{
fm = idGraphics.getFontMetrics();
- xPos = idWidth
- - fm.stringWidth(displayId)
- - 4;
+ xPos = idWidth - fm.stringWidth(displayId) - 4;
}
idGraphics.drawString(displayId, xPos,
* single graphics context), then reset to (0, scale height)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
- getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
- startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanelForPrint(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq);
alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
if (av.isShowAnnotation() && (endSeq == alignmentHeight))
* draw the annotations starting at
* (idOffset, alignmentHeight) from (0, scaleHeight)
*/
- alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
+ alignmentGraphics.translate(alignmentGraphicsOffset,
+ alignmentDrawnHeight);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
alignmentGraphics, -1, startRes, endRes + 1);
}
.findColumnPosition(maxwidth) - 1;
}
- int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
- - idWidth);
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pwidth - idWidth);
int totalHeight = cHeight * (maxwidth / resWidth + 1);
}
if (labels != null)
{
- pg.translate(-3,
- ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
+ pg.translate(-3, ypos
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(
- +3,
- -ypos
- - (av.getAlignment().getHeight() * av
- .getCharHeight()));
+ pg.translate(+3, -ypos
+ - (av.getAlignment().getHeight() * av.getCharHeight()));
}
ypos += cHeight;
return calculateIdWidth(-1).width + 4;
}
Integer idwidth = null;
- if (onscreen
- || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+ if (onscreen || (idwidth = Cache
+ .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
int w = getIdPanel().getWidth();
return (w > 0 ? w : calculateIdWidth().width + 4);
{
int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
- headless = (System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true"));
+ headless = (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
if (file != null)
{
- alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[] { type.getLabel() }),
- pSessionId);
+ alignFrame.setProgressBar(MessageManager
+ .formatMessage("status.saving_file", new Object[]
+ { type.getLabel() }), pSessionId);
}
}
try
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight()
- + boarderBottomOffset, file, imageTitle,
- alignFrame, pSessionId, headless);
+ aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, file,
+ imageTitle, alignFrame, pSessionId, headless);
Graphics graphics = im.getGraphics();
if (av.getWrapAlignment())
{
{
if (graphics != null)
{
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
- 0, graphics, graphics);
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
im.writeImage();
}
}
// this duplicates the calculation in getWrappedHeight but adjusts for
// offscreen idWith
width = alignFrame.getWidth() - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right - getVisibleIdWidth()
- + getVisibleIdWidth(false);
+ - alignFrame.getInsets().left - alignFrame.getInsets().right
+ - getVisibleIdWidth() + getVisibleIdWidth(false);
}
else
{
{
try
{
- int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
- .getAlignment().getWidth(), g, gSize, f, fSize, sy;
+ int s, sSize = av.getAlignment().getHeight(), res,
+ alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize,
+ sy;
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
String triplet = null;
if (av.getAlignment().isNucleotide())
{
- triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res) + "");
+ triplet = ResidueProperties.nucleotideName
+ .get(seq.getCharAt(res) + "");
}
else
{
- triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
- + "");
+ triplet = ResidueProperties.aa2Triplet
+ .get(seq.getCharAt(res) + "");
}
if (triplet == null)
{
text.append("<br>");
text.append(features[f].getType());
- if (features[f].getDescription() != null
- && !features[f].getType().equals(
- features[f].getDescription()))
+ if (features[f].getDescription() != null && !features[f]
+ .getType().equals(features[f].getDescription()))
{
text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (").append(features[f].getValue("status"))
+ text.append(" (")
+ .append(features[f].getValue("status"))
.append(")");
}
}
@Override
/**
- * Property change event fired when a change is made to the viewport ranges
+ * Property change event fired when a change is made to the viewport ranges
* object associated with this alignment panel's viewport
*/
public void propertyChange(PropertyChangeEvent evt)
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
{
final FeatureRenderer fr;
- final SequenceRenderer sr;
+ final SequenceRenderer seqRdr;
BufferedImage img;
Graphics2D gg;
- int imgWidth;
-
- int imgHeight;
-
AlignViewport av;
boolean fastPaint = false;
int cursorY = 0;
+ int charHeight = 0;
+
+ int charWidth = 0;
+
+ boolean fastpainting = false;
+
+ AnnotationPanel annotations;
+
/**
* Creates a new SeqCanvas object.
*
this.av = ap.av;
updateViewport();
fr = new FeatureRenderer(ap);
- sr = new SequenceRenderer(av);
+ seqRdr = new SequenceRenderer(av);
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
public SequenceRenderer getSequenceRenderer()
{
- return sr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
return fr;
}
- int charHeight = 0, charWidth = 0;
-
private void updateViewport()
{
charHeight = av.getCharHeight();
{
g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
}
- g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
- - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
- ypos - 2);
+ g.drawLine((mpos * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2),
+ (mpos * charWidth) + (charWidth / 2), ypos - 2);
}
}
}
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * charHeight))
- - (charHeight / 5));
+ g.drawString(value + "", x,
+ (ypos + (i * charHeight)) - (charHeight / 5));
}
}
}
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
- - (charHeight / 5));
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * charHeight)) - (charHeight / 5));
}
}
}
- boolean fastpainting = false;
/**
* need to make this thread safe move alignment rendering in response to
int transX = 0;
int transY = 0;
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
if (horizontal > 0) // scrollbar pulled right, image to the left
{
}
else
{
- transY = imgHeight - ((vertical + 1) * charHeight);
+ transY = img.getHeight() - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
@Override
public void paintComponent(Graphics g)
{
- updateViewport();
- BufferedImage lcimg = img; // take reference since other threads may null
- // img and call later.
super.paintComponent(g);
- if (lcimg != null && (fastPaint
+ updateViewport();
+
+ 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);
fastPaint = false;
- return;
- }
-
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
-
- imgWidth -= (imgWidth % charWidth);
- imgHeight -= (imgHeight % charHeight);
-
- if ((imgWidth < 1) || (imgHeight < 1))
- {
- return;
}
-
- if (lcimg == null || imgWidth != lcimg.getWidth()
- || imgHeight != lcimg.getHeight())
+ else if ((width > 0) && (height > 0))
{
- try
+ // 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())
{
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ img = setupImage();
+ if (img == null)
+ {
+ return;
+ }
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
- } catch (OutOfMemoryError er)
+ }
+
+ if (av.antiAlias)
{
- System.gc();
- System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
- new OOMWarning("Creating alignment image for display", er);
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
- return;
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
}
+ else
+ {
+ 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);
}
+ }
- if (av.antiAlias)
+ /**
+ * Draw an alignment panel for printing
+ *
+ * @param g1
+ * Graphics object to draw with
+ * @param startRes
+ * start residue of print area
+ * @param endRes
+ * end residue of print area
+ * @param startSeq
+ * start sequence of print area
+ * @param endSeq
+ * end sequence of print area
+ */
+ public void drawPanelForPrint(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+ startSeq, endSeq);
+ drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+ ((Graphics2D) g1).setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g1.drawImage(selectImage, 0, 0, this);
+ }
+
+ /*
+ * 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());
+ Graphics2D g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
{
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ g2d.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2d.drawImage(selectImage, 0, 0, this);
}
+ g2d.dispose();
+
+ return lcimg;
+ }
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
+ /*
+ * Set up a buffered image of the correct height and size for the sequence canvas
+ */
+ private BufferedImage setupImage()
+ {
+ BufferedImage lcimg = null;
- ViewportRanges ranges = av.getRanges();
- if (av.getWrapAlignment())
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ if ((width < 1) || (height < 1))
{
- drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ return null;
}
- else
+
+ try
{
- drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq(), 0);
- }
+ 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);
- g.drawImage(lcimg, 0, 0, this);
+ return null;
+ }
+ return lcimg;
}
/**
}
gg.fillPolygon(
- new int[] { res * charWidth - charHeight / 4,
+ new int[]
+ { res * charWidth - charHeight / 4,
res * charWidth + charHeight / 4, res * charWidth },
- new int[] { ypos - (charHeight / 2),
- ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ new int[]
+ { ypos - (charHeight / 2), ypos - (charHeight / 2),
+ ypos - (charHeight / 2) + 8 },
3);
}
annotations = new AnnotationPanel(av);
}
- annotations.renderer.drawComponent(annotations, av, g, -1,
- startRes, endx + 1);
+ annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+ endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
g.setClip(clip);
}
}
- AnnotationPanel annotations;
+ /*
+ * Draw a selection group over a wrapped alignment
+ */
+ private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
+ int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ // height gap above each panel
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ int startx = startRes;
+ int endx;
+ int ypos = hgap; // vertical offset
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
+ }
+
+ // chop the wrapped alignment extent up into panel-sized blocks and treat
+ // each block as if it were a block from an unwrapped alignment
+ while ((ypos <= canvasHeight) && (startx < maxwidth))
+ {
+ // set end value to be start + width, or maxwidth, whichever is smaller
+ endx = startx + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ drawUnwrappedSelection(g, group, startx, endx, 0,
+ av.getAlignment().getHeight() - 1,
+ ypos);
+
+ g.translate(-LABEL_WEST, 0);
+
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ }
+ }
int getAnnotationHeight()
{
return annotations.adjustPanelHeight();
}
- /**
- * DOCUMENT ME!
+ /*
+ * Draw an alignment panel for printing
*
* @param g1
- * DOCUMENT ME!
+ * Graphics object to draw with
* @param startRes
- * DOCUMENT ME!
+ * start residue of print area
* @param endRes
- * DOCUMENT ME!
+ * end residue of print area
* @param startSeq
- * DOCUMENT ME!
+ * start sequence of print area
* @param endSeq
- * DOCUMENT ME!
+ * end sequence of print area
* @param offset
- * DOCUMENT ME!
+ * vertical offset
*/
- public void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
+ private void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
updateViewport();
if (!av.hasHiddenColumns())
}
- // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
- // int x1, int x2, int y1, int y2, int startx, int starty,
private void draw(Graphics g, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.isRenderGaps());
+ seqRdr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
// empty
continue;
}
- sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
startRes, endRes, offset + ((i - startSeq) * charHeight));
if (av.isShowSequenceFeatures())
{
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * charHeight), false);
+ fr.drawSequence(g, nextSeq, startRes, endRes,
+ offset + ((i - startSeq) * charHeight), false);
}
// / Highlight search Results once all sequences have been drawn
{
for (int r = 0; r < visibleResults.length; r += 2)
{
- sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1],
- (visibleResults[r] - startRes) * charWidth,
- offset + ((i - startSeq) * charHeight));
+ seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
offset + ((i - startSeq) * charHeight));
}
}
// ///////////////////////////////////
// Now outline any areas if necessary
// ///////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
- int sx = -1;
- int sy = -1;
- int ex = -1;
+ SequenceGroup group = null;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * charWidth;
- if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ if (av.getAlignment().getGroups().size() > 0)
{
group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
if (group != null)
{
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+
do
{
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
-
++
+ groupIndex++;
- for (i = startSeq; i <= endSeq; i++)
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
{
- sx = (group.getStartRes() - startRes) * charWidth;
- sy = offset + ((i - startSeq) * charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
- - 1;
+ break;
+ }
- if (sx + ex < 0 || sx > visWidth)
- {
- continue;
- }
+ group = av.getAlignment().getGroups().get(groupIndex);
- if ((sx <= (endRes - startRes) * charWidth)
- && group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i)))
- {
- if ((bottom == -1) && !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i + 1)))
- {
- bottom = sy + charHeight;
- }
-
- if (!inGroup)
- {
- if (((top == -1) && (i == 0)) || !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i - 1)))
- {
- top = sy;
- }
-
- oldY = sy;
- inGroup = true;
-
- if (group == av.getSelectionGroup())
- {
- g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
- g.setColor(Color.RED);
- }
- else
- {
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private BufferedImage drawSelectionGroup(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;
+ }
+
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+
+ // 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);
+
+ if (!av.getWrapAlignment())
+ {
+ drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
+ 0);
+ }
+ else
+ {
+ drawWrappedSelection(g, group, getWidth(), getHeight(),
+ av.getRanges().getStartRes());
+ }
+
+ g.dispose();
+ return selectionImage;
+ }
+
+ /*
+ * 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)
+ */
+ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq, int offset)
+ {
+ if (!av.hasHiddenColumns())
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
+ offset);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ 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);
+ }
+ }
+ }
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq,
+ int verticalOffset)
+ {
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ int sx = -1;
+ int sy = -1;
+ int xwidth = -1;
+
+ for (i = startSeq; i <= endSeq; i++)
+ {
+ // position of start residue of group relative to startRes, in pixels
+ sx = (group.getStartRes() - startRes) * charWidth;
+
+ // width of group in pixels
+ xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
+ - 1;
+
+ sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (sx + xwidth < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1) && !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
{
- if (inGroup)
- {
- if (sx >= 0 && sx < visWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
-
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
-
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
-
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + ex, bottom);
- bottom = -1;
- }
-
- inGroup = false;
- }
+ top = sy;
}
- }
+ oldY = sy;
+ inGroup = true;
+ }
+ }
+ else
+ {
if (inGroup)
{
- sy = offset + ((i - startSeq) * charHeight);
+ // if start position is visible, draw vertical line to left of
+ // group
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
}
- if (sx + ex < visWidth)
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
{
- g.drawLine(sx + ex, oldY, sx + ex, sy);
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
if (sx < 0)
{
- ex += sx;
+ xwidth += sx;
sx = 0;
}
- if (sx + ex > visWidth)
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
{
- ex = visWidth;
+ xwidth = (endRes - startRes + 1) * charWidth - sx;
}
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
-
+
+ // draw horizontal line at top of group
if (top != -1)
{
- g.drawLine(sx, top, sx + ex, top);
+ g.drawLine(sx, top, sx + xwidth, top);
top = -1;
}
+ // draw horizontal line at bottom of group
if (bottom != -1)
{
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+ g.drawLine(sx, bottom, sx + xwidth, bottom);
bottom = -1;
}
inGroup = false;
}
+ }
+ }
- groupIndex++;
+ if (inGroup)
+ {
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
- g.setStroke(new BasicStroke());
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
- if (groupIndex >= av.getAlignment().getGroups().size())
- {
- break;
- }
+ if (sx < 0)
+ {
+ xwidth += sx;
+ sx = 0;
+ }
- group = av.getAlignment().getGroups().get(groupIndex);
+ if (sx + xwidth > visWidth)
+ {
+ xwidth = visWidth;
+ }
+ else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth;
+ }
- } while (groupIndex < av.getAlignment().getGroups().size());
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + xwidth, top);
+ top = -1;
+ }
- }
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
+ bottom = -1;
+ }
+ inGroup = false;
+ }
}
-
+
/**
* DOCUMENT ME!
*
{
String eventName = evt.getPropertyName();
- if (av.getWrapAlignment())
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ }
+ else if (av.getWrapAlignment())
{
if (eventName.equals(ViewportRanges.STARTRES))
{
* @author $author$
* @version $Revision: 1.130 $
*/
- public class SeqPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener, SequenceListener,
- SelectionListener
+ public class SeqPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener,
+ SequenceListener, SelectionListener
{
/** DOCUMENT ME!! */
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
- .getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.getAlignment().getHeight() - 1);
}
else
{
- seq = Math.min((y / av.getCharHeight())
- + av.getRanges().getStartSeq(),
- av
- .getAlignment().getHeight() - 1);
+ seq = Math.min(
+ (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+ av.getAlignment().getHeight() - 1);
}
return seq;
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null, av.getAlignment()
- .getSequences());
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
}
} finally
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- if (av.hasHiddenColumns()
- && !hidden.isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
Point p = lastp;
if (!event.isShiftDown() || p == null)
{
- p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
- event.getX() + wdth, event.getY() - 20) : null;
+ p = (tooltipText != null && tooltipText.length() > 6)
+ ? new Point(event.getX() + wdth, event.getY() - 20)
+ : null;
}
/*
* TODO: try to modify position region is not obcured by tooltip
}
else
{
- residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
- .equals(displayChar) ? "STOP"
- : ResidueProperties.aa2Triplet.get(displayChar));
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ("*".equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
}
text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
.append(": ").append(residue == null ? displayChar : residue);
int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
- if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
- .getX() - lastMousePress.getX()))
+ if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
+ .abs(evt.getX() - lastMousePress.getX()))
{
/*
* on drag up or down, decrement or increment font size
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage(
- "label.edit_params", new String[] { label }));
+ editCommand = new EditCommand(MessageManager
+ .formatMessage("label.edit_params", new String[]
+ { label }));
}
}
ap.alignFrame.statusBar.setText(message.toString());
// Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.getHiddenRepSequences())
- .contains(seq)))
+ if (groupEditing || (sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
{
fixedColumns = true;
}
else
{
- appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
- - lastres);
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres);
}
}
else
}
else
{
- appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
- - startres);
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres);
}
}
* highlight the first feature at the position on the alignment
*/
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features.get(0).getBegin(), features
- .get(0).getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(),
+ features.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
/*
if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.cannot_edit_annotations_in_wrapped_view"),
MessageManager.getString("label.wrapped_view_no_edit"),
JvOptionPane.WARNING_MESSAGE);
return;
if (stretchGroup == null)
{
- // Only if left mouse button do we want to change group sizes
+ createStretchGroup(res, sequence);
+ }
- // define a new group here
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(res);
- sg.setEndRes(res);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
- stretchGroup = sg;
+ if (stretchGroup != null)
+ {
+ stretchGroup.addPropertyChangeListener(seqCanvas);
+ }
- if (av.getConservationSelected())
- {
- SliderPanel.setConservationSlider(ap, av.getResidueShading(),
- ap.getViewName());
- }
+ seqCanvas.repaint();
+ }
- if (av.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
- ap.getViewName());
- }
- // TODO: stretchGroup will always be not null. Is this a merge error ?
- if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if ((stretchGroup != null)
- && (stretchGroup.getStartRes() == res))
- {
- // Edit end res position of selected group
- changeStartRes = true;
- }
- stretchGroup.getWidth();
+ private void createStretchGroup(int res, SequenceI sequence)
+ {
+ // Only if left mouse button do we want to change group sizes
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
}
- seqCanvas.repaint();
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
+ // or is there a threading issue here?
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+ {
+ // Edit end res position of selected group
+ changeStartRes = true;
+ }
+ stretchGroup.getWidth();
+
}
/**
{
return;
}
+
+ stretchGroup.removePropertyChangeListener(seqCanvas);
+
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
boolean vischange = stretchGroup.recalcConservation(true);
stretchGroup.cs.alignmentChanged(stretchGroup,
av.getHiddenRepSequences());
- ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
+ ResidueShaderI groupColourScheme = stretchGroup
+ .getGroupColourScheme();
String name = stretchGroup.getName();
if (stretchGroup.cs.conservationApplied())
{
{
scrollThread.setEvent(evt);
}
-
- seqCanvas.repaint();
}
void scrollCanvas(MouseEvent evt)
running = av.getRanges().scrollUp(true);
}
- if (mouseDragging && (evt.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getRanges()
- .getEndSeq()))
+ if (mouseDragging && (evt.getY() >= getHeight()) && (av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
running = av.getRanges().scrollUp(false);
}
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
- boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
- .getSequenceSetId().equals(av.getSequenceSetId())));
+ boolean iSentTheSelection = (av == source
+ || (source instanceof AlignViewport
+ && ((AlignmentViewport) source).getSequenceSetId()
+ .equals(av.getSequenceSetId())));
if (iSentTheSelection)
{
repaint = true;
}
- if (copycolsel
- && av.hasHiddenColumns()
+ if (copycolsel && av.hasHiddenColumns()
&& (av.getAlignment().getHiddenColumns() == null))
{
System.err.println("Bad things");
git://source.jalview.org / jalview.git / commitdiff