/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
private boolean dontScrollComplement;
+ private PropertyChangeListener propertyChangeListener;
+
/**
* Creates a new AlignmentPanel object.
*
vscroll.addAdjustmentListener(this);
final AlignmentPanel ap = this;
- av.addPropertyChangeListener(new PropertyChangeListener()
+ propertyChangeListener = new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
alignmentChanged();
}
}
- });
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
fontChanged();
adjustAnnotationHeight();
updateLayout();
* automatically adjust annotation panel height for new annotation whilst
* ensuring the alignment is still visible.
*/
+ @Override
public void adjustAnnotationHeight()
{
// TODO: display vertical annotation scrollbar if necessary
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
int oldX = av.getStartRes();
// as preference setting
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
setScrollValues(av.getStartRes(), av.getStartSeq());
* Repaint the alignment including the annotations and overview panels (if
* shown).
*/
+ @Override
public void paintAlignment(boolean updateOverview)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
invalidate();
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
if (av.getWrapAlignment())
{
- return printWrappedAlignment(pg, pwidth, pheight, pi);
+ return printWrappedAlignment(pwidth, pheight, pi, pg);
}
else
{
- return printUnwrapped(pg, pwidth, pheight, pi);
+ return printUnwrapped(pwidth, pheight, pi, pg);
}
}
* @throws PrinterException
* DOCUMENT ME!
*/
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ public int printUnwrapped(int pwidth, int pheight, int pi,
+ Graphics... pg)
throws PrinterException
{
+ boolean isMultiGraphics = pg.length > 1;
+ int G0 = 0; // Graphic index of idPanel graphics in multi-graphics mode or
+ // entire graphics for non mulit-graphics mode
+ int G1 = 0; // Graphic index of alignmentPanel graphics for multi-graphics
+ // mode
+ if (isMultiGraphics)
+ {
+ G0 = 0;
+ G1 = 1;
+ }
+
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
int scaleHeight = av.getCharHeight() + fm.getDescent();
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
+ pg[G0].setColor(Color.white);
+ pg[G0].fillRect(0, 0, pwidth, pheight);
+ pg[G0].setFont(av.getFont());
// //////////////////////////////////
// / How many sequences and residues can we fit on a printable page?
}
// draw Scale
- pg.translate(idWidth, 0);
- getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth,
- scaleHeight);
- pg.translate(-idWidth, scaleHeight);
+ if (isMultiGraphics)
+ {
+ pg[G1].translate(0, 0);
+ getScalePanel().drawScale(pg[G1], startRes, endRes,
+ pwidth - idWidth, scaleHeight);
+ pg[G1].translate(-idWidth, scaleHeight);
+ }
+ else
+ {
+ pg[G0].translate(idWidth, 0);
+ getScalePanel().drawScale(pg[G0], startRes, endRes, pwidth - idWidth,
+ scaleHeight);
+ pg[G0].translate(-idWidth, scaleHeight);
+ }
// //////////////
// Draw the ids
Color currentColor = null;
Color currentTextColor = null;
- pg.setFont(getIdPanel().getIdCanvas().getIdfont());
+ if (isMultiGraphics)
+ {
+ pg[G0].translate(0, scaleHeight);
+ }
+ pg[G0].setFont(getIdPanel().getIdCanvas().getIdfont());
SequenceI seq;
for (int i = startSeq; i < endSeq; i++)
currentTextColor = Color.black;
}
- pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
+ pg[G0].setColor(currentColor);
+ pg[G0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
av.getCharHeight());
- pg.setColor(currentTextColor);
+ pg[G0].setColor(currentTextColor);
int xPos = 0;
if (av.isRightAlignIds())
{
- fm = pg.getFontMetrics();
+ fm = pg[G0].getFontMetrics();
xPos = idWidth
- fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
- 4;
}
- pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+ pg[G0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
- pg.setFont(av.getFont());
+ pg[G0].setFont(av.getFont());
+
// draw main sequence panel
- pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
- endSeq, 0);
+ pg[G0].translate(idWidth, 0);
+ if (isMultiGraphics)
+ {
+ pg[G1].translate(idWidth, 0);
+ getSeqPanel().seqCanvas.drawPanel(pg[G1], startRes, endRes,
+ startSeq, endSeq, 0);
+ }
+ else
+ {
+ getSeqPanel().seqCanvas.drawPanel(pg[G0], startRes, endRes, startSeq,
+ endSeq, 0);
+ }
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
- // draw annotation - need to offset for current scroll position
+ // draw annotation label - need to offset for current scroll position
int offset = -getAlabels().getScrollOffset();
- pg.translate(0, offset);
- pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
- + 3);
- getAlabels().drawComponent(pg, idWidth);
- pg.translate(idWidth + 3, 0);
- getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
- pg, -1, startRes, endRes + 1);
- pg.translate(0, -offset);
+ pg[G0].translate(0, offset);
+ pg[G0].translate(-idWidth - 3,
+ (endSeq - startSeq) * av.getCharHeight() + 3);
+ getAlabels().drawComponent(pg[G0], idWidth);
+ pg[G0].translate(idWidth + 3, 0);
+ pg[G0].translate(0, -offset);
+ if (isMultiGraphics)
+ {
+ // draw annotation - need to offset for current scroll position
+ pg[G1].translate(0, offset);
+ pg[G1].translate(-idWidth - 3,
+ (endSeq - startSeq) * av.getCharHeight() + 3);
+ pg[G1].translate(idWidth + 3, 0);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(),
+ av, pg[G1], -1, startRes, endRes + 1);
+ pg[G1].translate(0, -offset);
+ }
+ else
+ {
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(),
+ av, pg[G0], -1, startRes, endRes + 1);
+ pg[G0].translate(0, -offset);
+ }
}
return Printable.PAGE_EXISTS;
* @throws PrinterException
* DOCUMENT ME!
*/
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi) throws PrinterException
+ public int printWrappedAlignment(int pwidth, int pheight, int pi,
+ Graphics pg) throws PrinterException
{
int annotationHeight = 0;
AnnotationLabels labels = null;
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
- : calculateIdWidth().width + 4);
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
- long progress = System.currentTimeMillis();
+ int boarderBottomOffset = 5;
+ long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[] { type.getLabel() }),
- progress);
+ if (file != null)
+ {
+ 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(), file,
- imageTitle);
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file, imageTitle,
+ alignFrame, pSessionId, headless);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
- printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, 0,
+ im.getGraphics());
im.writeImage();
}
}
{
if (im.getGraphics() != null)
{
- printUnwrapped(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
+ 0, im.getGraphics());
im.writeImage();
}
}
+
} catch (OutOfMemoryError err)
{
// Be noisy here.
}
} finally
{
- if (alignFrame != null && !headless)
- {
- alignFrame.setProgressBar(
- MessageManager.getString("status.export_complete"),
- progress);
- }
+
}
}
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
{
int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
.getAlignment().getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
- text = new StringBuffer();
+ StringBuilder text = new StringBuilder();
String triplet = null;
if (av.getAlignment().isNucleotide())
{
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.getCharWidth()) + "," + sy
- + "," + (idWidth + (res + 1) * av.getCharWidth())
- + "," + (av.getCharHeight() + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
}
if (groups[g].getStartRes() < res
&& groups[g].getEndRes() > res)
{
- text.append("<br><em>" + groups[g].getName() + "</em>");
+ text.append("<br><em>").append(groups[g].getName())
+ .append("</em>");
}
}
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.getCharWidth()) + "," + sy
- + "," + (idWidth + (res + 1) * av.getCharWidth())
- + "," + (av.getCharHeight() + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
}
fSize = features.length;
for (f = 0; f < fSize; f++)
if ((features[f].getBegin() <= seq.findPosition(res))
&& (features[f].getEnd() >= seq.findPosition(res)))
{
- if (features[f].getType().equals("disulfide bond"))
+ if (features[f].isContactFeature())
{
if (features[f].getBegin() == seq.findPosition(res)
|| features[f].getEnd() == seq
.findPosition(res))
{
- text.append("<br>disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
+ text.append("<br>").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
}
}
else
&& !features[f].getType().equals(
features[f].getDescription()))
{
- text.append(" " + features[f].getDescription());
+ text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (" + features[f].getValue("status")
- + ")");
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
}
}
}
PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+
+ /*
+ * try to ensure references are nulled
+ */
+ if (annotationPanel != null)
+ {
+ annotationPanel.dispose();
+ }
+
if (av != null)
{
+ av.removePropertyChangeListener(propertyChangeListener);
jalview.structure.StructureSelectionManager ssm = av
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeCommandListener(av);
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
- av.setAlignment(null);
+ av.dispose();
av = null;
}
else
git://source.jalview.org / jalview.git / blobdiff