X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=95e114e22901954119cc9c6a104b8e1681147651;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=193d5f48e7d34ea0b02b60da9f9c3f84e8e802c0;hpb=6666fd8b18b395d444e7f4c76016231f5a4d3669;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 193d5f4..95e114e 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
@@ -20,12 +41,24 @@ public class ScoreModels
private final ScoreMatrix DNA;
- private static ScoreModels instance = new ScoreModels();
+ private final ScoreMatrix FOLDSEEK3DI;
+
+ private static ScoreModels instance;
private Map 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()
{
+ if (instance == null)
+ {
+ instance = new ScoreModels();
+ }
return instance;
}
@@ -35,10 +68,9 @@ public class ScoreModels
*
* - BLOSUM62
* - PAM250
- * - SeqSpace (identity matrix)
+ * - PID
* - DNA
* - Sequence Feature Similarity
- * - Percentage Identity
*
*/
private ScoreModels()
@@ -46,13 +78,13 @@ public class ScoreModels
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap();
+ models = new LinkedHashMap<>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ FOLDSEEK3DI = loadScoreMatrix("scoreModel/foldseek_mat3di.scm");
+ registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
- // registerScoreModel(new PIDDistanceModel()); // superseded by PIDModel
}
/**
@@ -69,14 +101,15 @@ public class ScoreModels
/*
* delegate parsing to ScoreMatrixFile
*/
- FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+ FileParse fp = new FileParse(resourcePath,
+ DataSourceType.CLASSLOADER);
ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
registerScoreModel(sm);
return sm;
} catch (IOException e)
{
- System.err.println("Error reading " + resourcePath + ": "
- + e.getMessage());
+ jalview.bin.Console.errPrintln(
+ "Error reading " + resourcePath + ": " + e.getMessage());
}
return null;
}
@@ -92,9 +125,20 @@ 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)
@@ -102,12 +146,21 @@ public class ScoreModels
ScoreModelI sm2 = models.get(sm.getName());
if (sm2 != null)
{
- System.err.println("Warning: replacing score model " + sm2.getName());
+ jalview.bin.Console.errPrintln(
+ "Warning: replacing score model " + sm2.getName());
}
models.put(sm.getName(), sm);
}
/**
+ * 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
*
@@ -128,4 +181,9 @@ public class ScoreModels
{
return PAM250;
}
+ public ScoreMatrix getFOLDSEEK3DI()
+ {
+ return FOLDSEEK3DI;
+ }
+
}