X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=c9f1fcf7defd1489d50188909e1b785a63f154af;hb=8e640547def8e151db1fafafe93a2a0bb8078369;hp=3feae5d740ca6f9c9eead8bd044b800ffbf957cc;hpb=4550191c87ce9e044ce35980d4c926684fe4f04a;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 3feae5d..c9f1fcf 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -59,22 +59,19 @@ public class JnetAnnotationMaker
// 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))
{
- throw (new Exception(
- MessageManager
- .formatMessage(
- "exception.number_of_residues_in_query_sequence_differ_from_prediction",
- new String[] {
- (delMap == null ? "" : MessageManager
- .getString("label.mapped")),
- al.getSequenceAt(firstSeq).getName(),
- al.getSequenceAt(firstSeq)
- .getSequenceAsString(),
- Integer.valueOf(width).toString() })));
+ throw (new Exception(MessageManager.formatMessage(
+ "exception.number_of_residues_in_query_sequence_differ_from_prediction",
+ new String[]
+ { (delMap == null ? ""
+ : MessageManager.getString("label.mapped")),
+ al.getSequenceAt(firstSeq).getName(),
+ al.getSequenceAt(firstSeq).getSequenceAsString(),
+ Integer.valueOf(width).toString() })));
}
AlignmentAnnotation annot;
@@ -98,7 +95,8 @@ public class JnetAnnotationMaker
{
if (id.startsWith("JNETSOL"))
{
- float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f);
+ float amnt = (id.endsWith("25") ? 3f
+ : id.endsWith("5") ? 6f : 9f);
for (int spos = 0; spos < width; spos++)
{
int sposw = (delMap == null) ? gapmap[spos]
@@ -222,8 +220,7 @@ public class JnetAnnotationMaker
if (!firstsol)
{
// add the solvent accessibility
- annot = new AlignmentAnnotation(
- "Jnet Burial",
+ annot = new AlignmentAnnotation("Jnet Burial",
"Prediction of Solvent Accessibility
levels are