X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=654136ac0cf498007a6bdc4ef9ef5e743ee78975;hb=9c007fa50a82b3ae0f987e6454ae17c941b63563;hp=011d8baf161f84af5099d1405c05f6e2c6cdb441;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 011d8ba..654136a 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,6 @@
package jalview.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
@@ -35,10 +36,9 @@ public class ScoreModels
*
* - BLOSUM62
* - PAM250
- * - SeqSpace (identity matrix)
+ * - PID
* - DNA
* - Sequence Feature Similarity
- * - Percentage Identity
*
*/
private ScoreModels()
@@ -49,12 +49,9 @@ public class ScoreModels
models = new LinkedHashMap();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in?
- // registerScoreModel(new IdentityScoreModel());
+ registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
registerScoreModel(new FeatureDistanceModel());
- registerScoreModel(new PIDDistanceModel());
}
/**
@@ -94,9 +91,20 @@ public class ScoreModels
return models.values();
}
- public ScoreModelI forName(String s)
+ /**
+ * Returns an instance of a score model for the given name. If the model is of
+ * 'view dependent' type (e.g. feature similarity), instantiates a new
+ * instance configured for the given view. Otherwise returns a cached instance
+ * of the score model.
+ *
+ * @param name
+ * @param avp
+ * @return
+ */
+ public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
{
- return models.get(s);
+ ScoreModelI model = models.get(name);
+ return model == null ? null : model.getInstance(avp);
}
public void registerScoreModel(ScoreModelI sm)