boolean validCharWidth;
int wrappedWidth;
Font font;
+ boolean seqNameItalics;
AlignmentI alignment;
ColumnSelection colSel = new ColumnSelection();
int threshold;
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
int style = 0;
if (fontStyle.equals("bold"))
11f,
AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
+ conservation.autoCalculated = true;
if (Cache.getDefault("SHOW_CONSERVATION", true))
11f,
AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
+ quality.autoCalculated = true;
alignment.addAnnotation(quality);
}
new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
+ consensus.autoCalculated = true;
if (Cache.getDefault("SHOW_IDENTITY", true))
{
resetAllColourSchemes();
- alignment.adjustSequenceAnnotations();
+ // alignment.adjustSequenceAnnotations();
}