/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
/**
// do we need to scroll the panel?
// TODO: tons of nullpointereexceptions raised here.
if (results != null && results.getSize() > 0 && av != null
- && av.alignment != null)
+ && av.getAlignment() != null)
{
- int seqIndex = av.alignment.findIndex(results);
+ int seqIndex = av.getAlignment().findIndex(results);
if (seqIndex == -1)
{
return false;
}
- SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
- int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+ int[] r=results.getResults(seq, 0, av.getAlignment().getWidth());
if (r == null)
{
return false;
{
return false;
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
start = av.getColumnSelection().findColumnPosition(start);
end = av.getColumnSelection().findColumnPosition(end);
if (start==end)
{
- if (!av.colSel.isVisible(r[0]))
+ if (!av.getColumnSelection().isVisible(r[0]))
{
// don't scroll - position isn't visible
return false;
public void setScrollValues(int x, int y)
{
// System.err.println("Scroll to "+x+","+y);
- if (av == null || av.alignment == null)
+ if (av == null || av.getAlignment() == null)
{
return;
}
- int width = av.alignment.getWidth();
- int height = av.alignment.getHeight();
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
width = av.getColumnSelection().findColumnPosition(width);
}
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
+ int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
endSeq = av.getAlignment().getHeight();
}
- int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+ int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight;
if (av.showAnnotation)
{
pg.translate(idWidth, 0);
seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
- if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+ if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
{
pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
alabels.drawComponent((Graphics2D) pg, idWidth);
pg.translate(idWidth + 3, 0);
- annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+ annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
int idWidth = getVisibleIdWidth(false);
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
do
{
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
pg.setFont(idPanel.idCanvas.idfont);
- SequenceI s = av.alignment.getSequenceAt(i);
+ SequenceI s = av.getAlignment().getSequenceAt(i);
String string = s.getDisplayId(av.getShowJVSuffix());
int xPos = 0;
if (av.rightAlignIds)
void makeAlignmentImage(int type, File file)
{
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+ int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ scalePanel.getHeight();
int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
{
try
{
- int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+ 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));
{
sy = s * av.charHeight + scaleHeight;
- SequenceI seq = av.alignment.getSequenceAt(s);
+ SequenceI seq = av.getAlignment().getSequenceAt(s);
SequenceFeature[] features = seq.getDatasetSequence()
.getSequenceFeatures();
- SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
text = new StringBuffer();
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+ "");
int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ annotationHeight;
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
ssm.removeStructureViewerListener(seqPanel, null);
ssm.removeSelectionListener(seqPanel);
- av.alignment = null;
+ av.setAlignment(null);
av = null;
}
else
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
- Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.getAlignment().getSequencesArray());
// intersect alignment annotation with alignment groups
- AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
Hashtable oldrfs = new Hashtable();
if (aan != null)
{
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.put(aan[an].groupRef, aan[an].groupRef);
- av.alignment.deleteAnnotation(aan[an]);
+ av.getAlignment().deleteAnnotation(aan[an]);
aan[an] = null;
}
}
// set defaults for this group's conservation/consensus
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
+ sg.setNormaliseSequenceLogo(normLogo);
}
if (conv)
{
updateCalcs = true;
- av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
}
if (cons)
{
updateCalcs = true;
- av.alignment.addAnnotation(sg.getConsensus(), 0);
+ av.getAlignment().addAnnotation(sg.getConsensus(), 0);
}
// refresh the annotation rows
if (updateCalcs)
@Override
public AlignmentI getAlignment()
{
- return av.alignment;
+ return av.getAlignment();
}
/**
{
return av.getStructureSelectionManager();
}
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
}