*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
// in the future we could search for the query
// sequence in the alignment before calling this function.
SequenceI seqRef = al.getSequenceAt(firstSeq);
- int width = preds[0].getSequence().length;
+ int width = preds[0].getLength();
int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
if ((delMap != null && delMap.length > width)
|| (delMap == null && gapmap.length != width))
while (i < preds.length)
{
- String id = preds[i].getName().toUpperCase();
+ String id = preds[i].getName().toUpperCase(Locale.ROOT);
if (id.startsWith("LUPAS") || id.startsWith("JNET")
|| id.startsWith("JPRED"))
{
for (int j = 0; j < width; j++)
{
- float value = new Float(preds[i].getCharAt(j) + "")
+ float value = Float.valueOf(preds[i].getCharAt(j) + "")
.floatValue();
annotations[gapmap[j]] = new Annotation(
preds[i].getCharAt(j) + "", "",
{
for (int j = 0; j < width; j++)
{
- float value = new Float(preds[i].getCharAt(j) + "")
+ float value = Float.valueOf(preds[i].getCharAt(j) + "")
.floatValue();
annotations[gapmap[delMap[j]]] = new Annotation(
preds[i].getCharAt(j) + "", "",