/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
+ ana = new AlignmentAnnotation(ana);
ana.liftOver(sequence, shadowMap);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
}
else
{
- if (sequence != null && sequence.getAnnotation() != null)
- {
- for (AlignmentAnnotation ana : sequence.getAnnotation())
+ if (sequence != null && sequence.getAnnotation() != null)
{
- List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
- ana.getCalcId(), ana.label);
- if (transfer == null || transfer.size() == 0)
- {
- ana.liftOver(dsq, sqmpping);
- // mapping.transfer(ana);
- }
- else
+ for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- continue;
+ List<AlignmentAnnotation> transfer = sq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana = new AlignmentAnnotation(ana);
+ ana.liftOver(dsq, sqmpping);
+ // mapping.transfer(ana);
+ }
+ else
+ {
+ continue;
+ }
}
}
}
- }
- float min = -1, max = 0;
- Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
- for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+ if (false)
{
- int prn = mapping.getPDBResNum(k + 1);
-
- an[k] = new Annotation(prn);
- if (min == -1)
+ // Useful for debugging mappings - adds annotation for mapped position
+ float min = -1, max = 0;
+ Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+ for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
{
- min = k;
- max = k;
- }
- else
- {
- if (min > k)
+ int prn = mapping.getPDBResNum(k + 1);
+
+ an[k] = new Annotation(prn);
+ if (min == -1)
{
min = k;
+ max = k;
}
- else if (max < k)
+ else
{
- max = k;
+ if (min > k)
+ {
+ min = k;
+ }
+ else if (max < k)
+ {
+ max = k;
+ }
}
}
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+ an, min, max, AlignmentAnnotation.LINE_GRAPH));
}
- sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
- "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
- an, min, max, AlignmentAnnotation.LINE_GRAPH));
-
}
}
}