- annotations[j]=new Annotation(s==null ? ""+val:null,s==null ? ""+val:null,(char) val,val*1f,val >= 0 && val < colors.length ? colors[val] : Color.white);
+ if (s!=null && jalview.util.Comparison.isGap(s.getCharAt(j)))
+ {
+ annotations[j]=null;
+ if (val>0)
+ {
+ System.err.println("Warning: non-zero value for positional T-COFFEE score for gap at "+j+" in sequence "+s.getName());
+ }
+ } else {
+ annotations[j]=new Annotation(s==null ? ""+val:null,s==null ? ""+val:null,'\0',val*1f,val >= 0 && val < colors.length ? colors[val] : Color.white);
+ }