*/
public boolean covers(SequenceI seq)
{
- return covers(seq,false,false);
+ return covers(seq, false, false);
}
+
/**
*
* @param seq
- * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
- * @param either - when true coverage is required for either seq or the mapped sequence
- * @return true if mapping covers full length of given sequence (or the other if either==true)
+ * @param localCover
+ * - when true - compare extent of seq's dataset sequence rather
+ * than the local extent
+ * @param either
+ * - when true coverage is required for either seq or the mapped
+ * sequence
+ * @return true if mapping covers full length of given sequence (or the
+ * other if either==true)
*/
- public boolean covers(SequenceI seq, boolean localCover,boolean either)
+ public boolean covers(SequenceI seq, boolean localCover, boolean either)
{
- List<int[]> mappedRanges = null,otherRanges=null;
+ List<int[]> mappedRanges = null, otherRanges = null;
MapList mapList = mapping.getMap();
- int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
- ;
+ int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend;
+ ;
if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
{
- if (localCover && fromSeq !=seq)
+ if (localCover && fromSeq != seq)
{
- mstart=fromSeq.getStart();
- mend=fromSeq.getEnd();
+ mstart = fromSeq.getStart();
+ mend = fromSeq.getEnd();
}
mappedRanges = mapList.getFromRanges();
- otherRanges=mapList.getToRanges();
- ostart=mapping.to.getStart();
- oend=mapping.to.getEnd();
+ otherRanges = mapList.getToRanges();
+ ostart = mapping.to.getStart();
+ oend = mapping.to.getEnd();
}
else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
{
- if (localCover && mapping.to !=seq)
+ if (localCover && mapping.to != seq)
{
- mstart=mapping.to.getStart();
- mend=mapping.to.getEnd();
+ mstart = mapping.to.getStart();
+ mend = mapping.to.getEnd();
}
mappedRanges = mapList.getToRanges();
- otherRanges=mapList.getFromRanges();
- ostart=fromSeq.getStart();
- oend=fromSeq.getEnd();
+ otherRanges = mapList.getFromRanges();
+ ostart = fromSeq.getStart();
+ oend = fromSeq.getEnd();
}
else
{
* (necessary for circular CDS - example EMBL:J03321:AAA91567)
* and mapped length covers (at least) sequence length
*/
- int length = countRange(mappedRanges,mstart,mend);
+ int length = countRange(mappedRanges, mstart, mend);
if (length != -1)
{
}
return false;
}
- private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+
+ private int countRange(List<int[]> mappedRanges, int mstart, int mend)
{
- int length=0;
+ int length = 0;
for (int[] range : mappedRanges)
{
int from = Math.min(range[0], range[1]);
/**
* Adds any regions mapped to or from position {@code pos} in sequence
- * {@code seq} to the given search results
- * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
+ * {@code seq} to the given search results Note: recommend first using the
+ * .covers(,true,true) to ensure mapping covers both sequences
+ *
* @param seq
* @param pos
* @param sr
{
ds = seq;
}
-
+
if (this.fromSeq == seq || this.fromSeq == ds)
{
codon = this.mapping.map.locateInTo(pos, pos);
}
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.covers(seq,true,true)) {
+ if (ssm.covers(seq, true, true))
+ {
ssm.markMappedRegion(ds, index, results);
}
}