if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
{
+ // draw annotation - need to offset for current scroll position
+ int offset=-alabels.scrollOffset;
+ pg.translate(0, offset);
pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
alabels.drawComponent((Graphics2D) pg, idWidth);
pg.translate(idWidth + 3, 0);
annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
+ pg.translate(0, -offset);
}
return Printable.PAGE_EXISTS;
void makeAlignmentImage(int type, File file)
{
+ long progress=System.currentTimeMillis();
+ if (alignFrame!=null) {
+ alignFrame.setProgressBar("Saving "+(type == jalview.util.ImageMaker.PNG ? "PNG image":"EPS file") , progress);
+ }
+ try {
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
{
jalview.util.ImageMaker im;
+ final String imageAction,imageTitle;
if (type == jalview.util.ImageMaker.PNG)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Create PNG image from alignment", width, height, file,
- null);
- }
- else
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Create EPS file from alignment", width, height, file,
- alignFrame.getTitle());
+ imageAction="Create PNG image from alignment";
+ imageTitle=null;
+ } else {
+ imageAction="Create EPS file from alignment";
+ imageTitle=alignFrame.getTitle();
}
-
+ im = new jalview.util.ImageMaker(this, type, imageAction, width, height, file,
+ imageTitle);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
ex.printStackTrace();
}
+ }
+ finally {
+ if (alignFrame!=null)
+ {
+ alignFrame.setProgressBar("Export complete.", progress);
+ }
+ }
}
/**
*/
public void updateAnnotation()
{
- updateAnnotation(false);
+ updateAnnotation(false, false);
}
-
public void updateAnnotation(boolean applyGlobalSettings)
{
- // TODO: this should be merged with other annotation update stuff - that
- // sits on AlignViewport
- boolean updateCalcs = false;
- boolean conv = av.isShowGroupConservation();
- boolean cons = av.isShowGroupConsensus();
- boolean showprf = av.isShowSequenceLogo();
- boolean showConsHist = av.isShowConsensusHistogram();
- boolean normLogo = av.isNormaliseSequenceLogo();
-
- boolean sortg = true;
-
- // remove old automatic annotation
- // add any new annotation
-
- // intersect alignment annotation with alignment groups
-
- AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
- Hashtable oldrfs = new Hashtable();
- if (aan != null)
- {
- for (int an = 0; an < aan.length; an++)
- {
- if (aan[an].autoCalculated && aan[an].groupRef != null)
- {
- oldrfs.put(aan[an].groupRef, aan[an].groupRef);
- av.getAlignment().deleteAnnotation(aan[an]);
- aan[an] = null;
- }
- }
- }
- if (av.getAlignment().getGroups()!=null)
- {
- for (SequenceGroup sg:av.getAlignment().getGroups())
- {
- updateCalcs = false;
- if (applyGlobalSettings || !oldrfs.containsKey(sg))
- {
- // set defaults for this group's conservation/consensus
- sg.setshowSequenceLogo(showprf);
- sg.setShowConsensusHistogram(showConsHist);
- sg.setNormaliseSequenceLogo(normLogo);
- }
- if (conv)
- {
- updateCalcs = true;
- av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
- }
- if (cons)
- {
- updateCalcs = true;
- av.getAlignment().addAnnotation(sg.getConsensus(), 0);
- }
- // refresh the annotation rows
- if (updateCalcs)
- {
- sg.recalcConservation();
- }
- }
- }
- oldrfs.clear();
+ updateAnnotation(applyGlobalSettings,false);
+ }
+ public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings, preserveNewGroupSettings);
adjustAnnotationHeight();
}