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JAL-2629 update spikes/mungo to latest
[jalview.git]
/
src
/
jalview
/
schemes
/
HmmerLocalBackground.java
diff --git
a/src/jalview/schemes/HmmerLocalBackground.java
b/src/jalview/schemes/HmmerLocalBackground.java
index
d7a5e65
..
2fe775c
100644
(file)
--- a/
src/jalview/schemes/HmmerLocalBackground.java
+++ b/
src/jalview/schemes/HmmerLocalBackground.java
@@
-2,6
+2,7
@@
package jalview.schemes;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ResidueCount;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.util.HashMap;
import jalview.datamodel.SequenceI;
import java.util.HashMap;
@@
-19,15
+20,13
@@
public class HmmerLocalBackground extends HmmerColourScheme
float logTotalCount;
/**
float logTotalCount;
/**
- * Constructor given a Hidden Markov Model
+ * Constructor given a sequence collection
*
*
- * @param sg
- *
- * @param markov
+ * @param ac
*/
public HmmerLocalBackground(AnnotatedCollectionI ac)
{
*/
public HmmerLocalBackground(AnnotatedCollectionI ac)
{
- super(ac.getHmmConsensus());
+ super(ac.getHmmSequences());
countFrequencies(ac);
}
countFrequencies(ac);
}
@@
-48,9
+47,9
@@
public class HmmerLocalBackground extends HmmerColourScheme
* Counts and stores the relative frequency of every residue in the alignment
* (apart from any HMM consensus sequences)
*
* 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<>();
{
// TODO or total counts in Consensus Profile (how do we get at it?)?
Map<Character, Float> freqs = new HashMap<>();
@@
-59,10
+58,10
@@
public class HmmerLocalBackground extends HmmerColourScheme
* count symbols, excluding any HMM consensus sequences
*/
ResidueCount counts = new ResidueCount();
* 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)
{
for (SequenceI seq : seqs)
{
- if (!seq.isHMMConsensusSequence())
+ if (!seq.hasHMMProfile())
{
for (char c : seq.getSequence())
{
{
for (char c : seq.getSequence())
{