X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=6828202da66c0dda62cc07345543fb8f2bad629b;hb=f4990f6e5cedd6d2277cb5edbd1ecd14d9a80184;hp=2a8a00ffbe3873507e8daa3e3cbce0e311e9113c;hpb=ff450fad8709ae81919af7a15ea382af7292794c;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 2a8a00f..6828202 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -64,17 +64,14 @@ public class JnetAnnotationMaker
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]
@@ -150,7 +148,7 @@ public class JnetAnnotationMaker
{
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) + "", "",
@@ -161,7 +159,7 @@ public class JnetAnnotationMaker
{
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) + "", "",
@@ -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- 0 - Exposed
- 3 - 25% or more S.A. accessible
- 6 - 5% or more S.A. accessible
- 9 - Buried (<5% exposed)
",
sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
@@ -234,8 +231,8 @@ public class JnetAnnotationMaker
seqRef.addAlignmentAnnotation(annot);
}
al.addAnnotation(annot);
- al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
+ al.setAnnotationIndex(annot,
+ al.getAlignmentAnnotation().length - existingAnnotations - 1);
}
// Hashtable scores = prediction.getScores();