- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
treeSelectionChanged((Sequence) ob);
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
treeSelectionChanged((Sequence) ob);
PaintRefresher.Refresh(this, av.getSequenceSetId());
repaint();
- Color col = new Color((int) (Math.random() * 255), (int) (Math
- .random() * 255), (int) (Math.random() * 255));
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
.getWidth(), ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
.getWidth(), ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
-
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
- .getIgnoreGapsConsensus());
+ // cs is null if shading is an annotationColourGradient
+ if (cs!=null)
+ {
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+ av.getIgnoreGapsConsensus());
+ }
}
SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
}
SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
&& av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
&& av.getGlobalColourScheme().conservationApplied())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null), sg
- .getStartRes(), sg.getEndRes());
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());