*/
public class AlignmentUtils
{
-
private static final int CODON_LENGTH = 3;
private static final String SEQUENCE_VARIANT = "sequence_variant:";
- private static final String ID = "ID";
+ /*
+ * the 'id' attribute is provided for variant features fetched from
+ * Ensembl using its REST service with JSON format
+ */
+ public static final String VARIANT_ID = "id";
/**
* A data model to hold the 'normal' base value at a position, and an optional
}
/**
- * Returns the index (zero-based position) of a sequence in an alignment, or
- * -1 if not found.
- *
- * @param al
- * @param seq
- * @return
- */
- public static int getSequenceIndex(AlignmentI al, SequenceI seq)
- {
- int result = -1;
- int pos = 0;
- for (SequenceI alSeq : al.getSequences())
- {
- if (alSeq == seq)
- {
- result = pos;
- break;
- }
- pos++;
- }
- return result;
- }
-
- /**
* Returns a map of lists of sequences in the alignment, keyed by sequence
* name. For use in mapping between different alignment views of the same
* sequences.
peptidePos, var.getSource());
StringBuilder attributes = new StringBuilder(32);
- String id = (String) var.variant.getValue(ID);
+ String id = (String) var.variant.getValue(VARIANT_ID);
if (id != null)
{
if (id.startsWith(SEQUENCE_VARIANT))
{
id = id.substring(SEQUENCE_VARIANT.length());
}
- sf.setValue(ID, id);
- attributes.append(ID).append("=").append(id);
+ sf.setValue(VARIANT_ID, id);
+ attributes.append(VARIANT_ID).append("=").append(id);
// TODO handle other species variants JAL-2064
StringBuilder link = new StringBuilder(32);
try