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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
ScoreModels.java
diff --git
a/src/jalview/analysis/scoremodels/ScoreModels.java
b/src/jalview/analysis/scoremodels/ScoreModels.java
index
7262fb8
..
ebc9a26
100644
(file)
--- a/
src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/
src/jalview/analysis/scoremodels/ScoreModels.java
@@
-41,12
+41,22
@@
public class ScoreModels
private final ScoreMatrix DNA;
private final ScoreMatrix DNA;
- private static ScoreModels instance = new ScoreModels();
+ private static ScoreModels instance;
private Map<String, ScoreModelI> models;
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()
{
public static ScoreModels getInstance()
{
+ if (instance == null)
+ {
+ instance = new ScoreModels();
+ }
return instance;
}
return instance;
}
@@
-66,11
+76,11
@@
public class ScoreModels
/*
* using LinkedHashMap keeps models ordered as added
*/
/*
* 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");
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
}
registerScoreModel(new FeatureDistanceModel());
}
@@
-139,6
+149,14
@@
public class ScoreModels
}
/**
}
/**
+ * 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
*
* Returns the default peptide or nucleotide score model, currently BLOSUM62
* or DNA
*