return;
}
- final int gapped = profile.getGapped();
+ final int gapped = profile.getNonGapped();
String description = String.valueOf(gapped);
- consensus.annotations[i] = new Annotation("", description, '0',
+ consensus.annotations[i] = new Annotation(description, description,
+ '\0',
gapped);
}
}
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
- gapcounts = new AlignmentAnnotation("Gaps", "Number of Gaps",
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ "Number of aligned positions",
new Annotation[1], 0f, alignment.getHeight(),
AlignmentAnnotation.BAR_GRAPH);
initGapCounts(gapcounts);