X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=6828202da66c0dda62cc07345543fb8f2bad629b;hb=700502ef808b904af9431e7eca8efe3b4c457e04;hp=c5320f1f7594457bb4e3fa9906b765464d1af43e;hpb=8002d3a28b1e21a9d89a24e4c81cf9397ecea0db;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index c5320f1..6828202 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -59,23 +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;
@@ -99,17 +95,18 @@ 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]
- : delMap[gapmap[spos]];
+ : gapmap[delMap[spos]];
if (firstsol)
{
sol[sposw] = new Annotation(0f);
}
if (preds[i].getCharAt(spos) == 'B'
- && (sol[spos].value == 0f || sol[spos].value < amnt))
+ && (sol[sposw].value == 0f || sol[sposw].value < amnt))
{
sol[sposw].value = amnt;
}
@@ -151,7 +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) + "", "",
@@ -162,7 +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) + "", "",
@@ -193,13 +190,13 @@ public class JnetAnnotationMaker
if (id.equals("JNETCONF"))
{
annot = new AlignmentAnnotation(preds[i].getName(),
- "JNet Output", annotations, 0f, 10f,
+ "JPred Output", annotations, 0f, 10f,
AlignmentAnnotation.BAR_GRAPH);
}
else
{
annot = new AlignmentAnnotation(preds[i].getName(),
- "JNet Output", annotations);
+ "JPred Output", annotations);
}
if (seqRef != null)
@@ -223,8 +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