AlignmentAnnotation[] tmp;
for (int s = 0; s < command.seqs.length; s++)
{
- if (modifyVisibility)
+ if (modifyVisibility)
{
// Rows are only removed or added to sequence object.
if (!insert) {
if (insert)
{
temp = new Annotation[aSize + command.number];
+ if(annotations[a].padGaps)
+ for (int aa = 0; aa < temp.length; aa++)
+ {
+ temp[aa] = new Annotation(
+ command.al.getGapCharacter()+"",
+ null, ' ', 0);
+ }
}
else
{
public int graphHeight = 40;
+ public boolean padGaps = true;
+
public static final int NO_GRAPH = 0;
public static final int BAR_GRAPH = 1;
{
if (annotations[i] == null)
{
+ padGaps = false;
continue;
}
{
hasText = true;
}
+ else
+ padGaps = false;
}
if (nonSSLabel)
}
}
-
}
annotationId = this.hashCode() + "";