/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.
*
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
* true, suppresses invoking the same method recursively.
*/
- private boolean followingComplementScroll;
+ 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();
* Highlight the given results on the alignment.
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
scrollToPosition(results);
getSeqPanel().seqCanvas.highlightSearchResults(results);
*
* @param results
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI results)
{
return scrollToPosition(results, 0, true, false);
}
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults,
+ public boolean scrollToPosition(SearchResultsI searchResults,
boolean redrawOverview)
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
* if true, try to centre the search results horizontally in the view
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
+ public boolean scrollToPosition(SearchResultsI results,
int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
* 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
annotationScroller.setPreferredSize(new Dimension(annotationScroller
.getWidth(), annotationHeight));
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), annotationHeight));
annotationScroller.validate();
x = 0;
}
+ /*
+ * each scroll adjustment triggers adjustmentValueChanged, which resets the
+ * 'do not scroll complement' flag; ensure it is the same for both
+ * operations
+ */
+ boolean flag = isDontScrollComplement();
hscroll.setValues(x, hextent, 0, width);
+ setDontScrollComplement(flag);
vscroll.setValues(y, vextent, 0, height);
}
* @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());
* If there is one, scroll the (Protein/cDNA) complementary alignment to
* match, unless we are ourselves doing that.
*/
- if (isFollowingComplementScroll())
+ if (isDontScrollComplement())
{
- setFollowingComplementScroll(false);
+ setDontScrollComplement(false);
}
else
{
* 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();
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
+ /*
+ * set scroll bar positions; first suppress this being 'followed' in any
+ * complementary split pane
+ */
+ setDontScrollComplement(true);
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
* @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;
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);
- }
+
}
}
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
* @param verticalOffset
* the number of visible sequences to show above the mapped region
*/
- public void scrollToCentre(SearchResults sr, int verticalOffset)
+ public void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
/*
* To avoid jumpy vertical scrolling (if some sequences are gapped or not
* mapped), we can make the scroll-to location a sequence above the one
* actually mapped.
*/
- SequenceI mappedTo = sr.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
}
/**
- * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
*
* @param b
*/
- protected void setFollowingComplementScroll(boolean b)
+ protected void setDontScrollComplement(boolean b)
{
- this.followingComplementScroll = b;
+ this.dontScrollComplement = b;
}
- protected boolean isFollowingComplementScroll()
+ protected boolean isDontScrollComplement()
{
- return this.followingComplementScroll;
+ return this.dontScrollComplement;
}
}
git://source.jalview.org / jalview.git / blobdiff