import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
private IdPanel idPanel;
private boolean headless;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
* 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();
{
return av;
}
+
public void alignmentChanged()
{
av.alignmentChanged(this);
scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight()
- + fm.getDescent()));
+ .getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+ public boolean scrollToPosition(SearchResults searchResults,
+ boolean redrawOverview)
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
}
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResults results,
- int verticalOffset,
- boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
// TODO: properly locate search results in view when large numbers of hidden
}
int start = r[0];
int end = r[1];
- // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
// DEBUG
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
{
int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
- end = Math.min(end + offset, seq.getEnd() - 1);
+ end = end + offset - 1;
}
if (start < 0)
{
*/
seqIndex = Math.max(0, seqIndex - verticalOffset);
+ // System.out.println("start=" + start + ", end=" + end + ", startv="
+ // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+ // + av.getStartSeq() + ", ends=" + av.getEndSeq());
if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
* 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
/*
* Estimate available height in the AlignFrame for alignment +
- * annotations. Deduct an estimate of 75 for menu bar, scale panel,
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
* hscroll, status bar (as these are not laid out we can't inspect their
- * actual heights). Insets gives borders including title bar.
+ * actual heights). Insets gives frame borders.
*/
+ int stuff = Platform.isAMac() ? 80 : 100;
Insets insets = alignFrame.getInsets();
- int availableHeight = alignFrame.getHeight() - 75 - insets.top
+ int availableHeight = alignFrame.getHeight() - stuff - insets.top
- insets.bottom;
/*
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();
* Adjust row/column scrollers to show a visible position in the alignment.
*
* @param x
- * visible column to scroll to DOCUMENT ME!
+ * visible column to scroll to
* @param y
* visible row to scroll to
*
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll to "+x+","+y);
+ // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
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();
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
// 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(),
av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment()
- .getAlignmentAnnotation(),
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
+ // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
* @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
{
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
// draw main sequence panel
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+ endSeq, 0);
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
}
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
+ pg.translate(
+ +3,
+ -ypos
- (av.getAlignment().getHeight() * av
.getCharHeight()));
}
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
if ((pi * pheight) < totalHeight)
{
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);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
im.writeImage();
}
}
+
} catch (OutOfMemoryError err)
{
// Be noisy here.
}
} finally
{
- if (alignFrame != null && !headless)
- {
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
- }
+
}
}
{
makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
}
+
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
if (av.getAlignment().isNucleotide())
{
triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res)
- + "");
+ .getCharAt(res) + "");
}
else
{
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
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
@Override
public AlignmentI getAlignment()
{
- return av.getAlignment();
+ return av == null ? null : av.getAlignment();
}
-
@Override
public String getViewName()
{
return new FeatureRenderer(this);
}
- @Override
+
+ @Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.getFeatureRenderer();
}
- public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
{
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}
}
/**
- * 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;
}
}