{\r
int i = 0;\r
SequenceI[] preds = prediction.getSeqsAsArray();\r
+ // in the future we could search for the query\r
+ // sequence in the alignment before calling this function.\r
SequenceI seqRef = al.getSequenceAt(FirstSeq);\r
int width = preds[0].getSequence().length();\r
int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
{\r
for (int j = 0; j < width; j++)\r
{\r
- float value = Float.parseFloat(preds[i].getCharAt(\r
- j) + "");\r
+ float value = new Float(preds[i].getCharAt(\r
+ j) + "").floatValue();\r
annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
j) + "", "", preds[i].getCharAt(j),\r
value);\r