+ public double getBitScore()
+ {
+ return bitScore;
+ }
+
+ public void setBitScore(double bitScore)
+ {
+ this.bitScore = bitScore;
+ }
+
+ public double getEValue()
+ {
+ return eValue;
+ }
+
+ public void setEValue(double eValue)
+ {
+ this.eValue = eValue;
+ }
+
+ public static AlignmentAnnotation findFirstAnnotation(
+ Iterable<AlignmentAnnotation> alignmentAnnotation, String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+
+ for (AlignmentAnnotation annot : alignmentAnnotation)
+ {
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
+ }
+ return null;
+ }
+