import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
/**
* A class that can register and serve instances of ScoreModelI
*/
-public class ScoreModels
+public class ScoreModels implements ApplicationSingletonI
{
- private final ScoreMatrix BLOSUM62;
-
- private final ScoreMatrix PAM250;
-
- private final ScoreMatrix DNA;
-
- private static ScoreModels instance = new ScoreModels();
-
- private Map<String, ScoreModelI> models;
-
+ /**
+ * Answers the singleton instance of this class, with lazy initialisation
+ * (built-in score models are loaded on the first call to this method)
+ *
+ * @return
+ */
public static ScoreModels getInstance()
{
- return instance;
+ return (ScoreModels) ApplicationSingletonProvider.getInstance(ScoreModels.class);
}
/**
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap<String, ScoreModelI>();
+ models = new LinkedHashMap<>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
}
+ private final ScoreMatrix BLOSUM62;
+
+ private final ScoreMatrix PAM250;
+
+ private final ScoreMatrix DNA;
+
+ private Map<String, ScoreModelI> models;
+
/**
* Tries to load a score matrix from the given resource file, and if
* successful, registers it.
}
/**
+ * Resets to just the built-in score models
+ */
+ public void reset()
+ {
+ ApplicationSingletonProvider.removeInstance(this.getClass());
+ }
+
+ /**
* Returns the default peptide or nucleotide score model, currently BLOSUM62
* or DNA
*