public SequenceFeature[] _rnasecstr = null;
/**
- * position of annotation resulting in invalid WUSS parsing or -1
+ * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+ * there was no RNA structure in this annotation
*/
- private long invalidrnastruc = -1;
+ private long invalidrnastruc = -2;
/**
* Updates the _rnasecstr field Determines the positions that base pair and
private void _markRnaHelices()
{
+ int mxval = 0;
// Figure out number of helices
// Length of rnasecstr is the number of pairs of positions that base pair
// with each other in the secondary structure
try
{
val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
} catch (NumberFormatException q)
{
}
annotations[_rnasecstr[x].getBegin()].value = val;
annotations[_rnasecstr[x].getEnd()].value = val;
- annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
- annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
}
+ setScore(mxval);
}
/**
* map of positions in the associated annotation