/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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;
/**
* Creates a new AlignmentPanel object.
{
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];
// DEBUG
-// System.err.println(this.av.viewName + " Seq : " + seqIndex
-// + " Scroll to " + start + "," + end);
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
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);
}
{
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)
* 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
{
{
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)
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();
- 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)
{
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[]
- { type.getLabel() }), progress);
+ "status.saving_file", new Object[] { type.getLabel() }),
+ progress);
}
try
{
{
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+ 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);
}
@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;
}
}
git://source.jalview.org / jalview.git / blobdiff