import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.util.HashMap;
float logTotalCount;
/**
- * Constructor given a Hidden Markov Model
+ * Constructor given a sequence collection
*
- * @param sg
- *
- * @param markov
+ * @param ac
*/
public HmmerLocalBackground(AnnotatedCollectionI ac)
{
- super(ac.getHmmConsensus());
+ super(ac.getHmmSequences());
countFrequencies(ac);
}
* Counts and stores the relative frequency of every residue in the alignment
* (apart from any HMM consensus sequences)
*
- * @param sg
+ * @param sc
*/
- public void countFrequencies(AnnotatedCollectionI sg)
+ public void countFrequencies(SequenceCollectionI sc)
{
// TODO or total counts in Consensus Profile (how do we get at it?)?
Map<Character, Float> freqs = new HashMap<>();
* count symbols, excluding any HMM consensus sequences
*/
ResidueCount counts = new ResidueCount();
- List<SequenceI> seqs = sg.getSequences();
+ List<SequenceI> seqs = sc.getSequences();
for (SequenceI seq : seqs)
{
if (!seq.hasHMMProfile())