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JAL-674 futzing with bugs
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
PDBFileWithJmol.java
diff --git
a/src/jalview/ext/jmol/PDBFileWithJmol.java
b/src/jalview/ext/jmol/PDBFileWithJmol.java
index
6553e26
..
009b9e8
100644
(file)
--- a/
src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/
src/jalview/ext/jmol/PDBFileWithJmol.java
@@
-157,7
+157,7
@@
public class PDBFileWithJmol extends AlignFile implements
{
char newseq[] = new char[len];
System.arraycopy(seq, 0, newseq, 0, len);
{
char newseq[] = new char[len];
System.arraycopy(seq, 0, newseq, 0, len);
- Annotation asecstr[] = new Annotation[len];
+ Annotation asecstr[] = new Annotation[len+firstrnum-1];
for (int p = 0; p < len; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
for (int p = 0; p < len; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
@@
-181,8
+181,13
@@
public class PDBFileWithJmol extends AlignFile implements
AlignmentAnnotation ann = new AlignmentAnnotation(
"Secondary Structure",
"Secondary Structure from PDB File", asecstr);
AlignmentAnnotation ann = new AlignmentAnnotation(
"Secondary Structure",
"Secondary Structure from PDB File", asecstr);
+ ann.belowAlignment=true;
+ ann.visible=true;
+ ann.autoCalculated=false;
ann.setCalcId(getClass().getName());
sq.addAlignmentAnnotation(ann);
ann.setCalcId(getClass().getName());
sq.addAlignmentAnnotation(ann);
+ ann.adjustForAlignment();
+ ann.validateRangeAndDisplay();
annotations.add(ann);
}
}
annotations.add(ann);
}
}