*/
package jalview.datamodel;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-
import java.util.AbstractList;
import java.util.ArrayList;
import java.util.List;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
{
return mapping;
}
+
+ /**
+ * Returns true if the mapping covers the full length of the given sequence.
+ * This allows us to distinguish the CDS that codes for a protein from
+ * another overlapping CDS in the parent dna sequence.
+ *
+ * @param seq
+ * @return
+ */
+ public boolean covers(SequenceI seq)
+ {
+ List<int[]> mappedRanges = null;
+ MapList mapList = mapping.getMap();
+ if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
+ {
+ mappedRanges = mapList.getFromRanges();
+ }
+ else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
+ {
+ mappedRanges = mapList.getToRanges();
+ }
+ else
+ {
+ return false;
+ }
+
+ /*
+ * check that each mapped range lies within the sequence range
+ * (necessary for circular CDS - example EMBL:J03321:AAA91567)
+ * and mapped length covers (at least) sequence length
+ */
+ int length = 0;
+ for (int[] range : mappedRanges)
+ {
+ int from = Math.min(range[0], range[1]);
+ int to = Math.max(range[0], range[1]);
+ if (from < seq.getStart() || to > seq.getEnd())
+ {
+ return false;
+ }
+ length += (to - from + 1);
+ }
+ // add 1 to mapped length to allow for a mapped stop codon
+ if (length + 1 < (seq.getEnd() - seq.getStart() + 1))
+ {
+ return false;
+ }
+ return true;
+ }
}
private List<SequenceToSequenceMapping> mappings;
}
/**
+ * Return the corresponding aligned or dataset dna sequence for given amino
+ * acid sequence, or null if not found. returns the sequence from the first
+ * mapping found that involves the protein sequence.
*
- * @param sequenceRef
- * @return null or corresponding aaSeq entry for dnaSeq entry
+ * @param aaSeqRef
+ * @return
*/
public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
{
* Two AlignedCodonFrame objects are equal if they hold the same ordered list
* of mappings
*
- * @see SequenceToSequenceMapping#
+ * @see SequenceToSequenceMapping#equals
*/
@Override
public boolean equals(Object obj)
{
return mappings;
}
+
+ /**
+ * Returns the first mapping found which is between the two given sequences,
+ * and covers the full extent of both.
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
+ SequenceI seq2)
+ {
+ for (SequenceToSequenceMapping mapping : mappings)
+ {
+ if (mapping.covers(seq2) && mapping.covers(seq1))
+ {
+ return mapping;
+ }
+ }
+ return null;
+ }
}