import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
+import jalview.util.Platform;
import java.io.IOException;
import java.util.LinkedHashMap;
private final ScoreMatrix DNA;
- private static ScoreModels instance = new ScoreModels();
-
- private Map<String, ScoreModelI> models;
+ private static ScoreModels instance;
+ /**
+ * 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;
+ ScoreModels m = instance;
+ @SuppressWarnings("unused")
+ ThreadGroup g = null;
+ if (Platform.isJS())
+ {
+ g = Thread.currentThread().getThreadGroup();
+ /**
+ * @j2sNative m = g._jalviewScoreModelsInstance;
+ *
+ */
+ }
+ if (m == null)
+ {
+ m = new ScoreModels();
+ if (Platform.isJS())
+ {
+ /**
+ * @j2sNative g._jalviewScoreModelsInstance = m;
+ *
+ */
+ }
+ else
+ {
+ instance = m;
+ }
+ }
+ return m;
}
+ private Map<String, ScoreModelI> models;
+
/**
* Private constructor to enforce use of singleton. Registers Jalview's
* "built-in" score models:
/*
* 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());
}
}
/**
+ * Resets to just the built-in score models
+ */
+ public void reset()
+ {
+ instance = new ScoreModels();
+ }
+
+ /**
* Returns the default peptide or nucleotide score model, currently BLOSUM62
* or DNA
*