X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;fp=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=7262fb81925396f1ee4ce0dd5198a68f6de8ff53;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
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+/*
+ * 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;
+import jalview.io.ScoreMatrixFile;
+
+import java.io.IOException;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+/**
+ * A class that can register and serve instances of ScoreModelI
+ */
+public class ScoreModels
+{
+ private final ScoreMatrix BLOSUM62;
+
+ private final ScoreMatrix PAM250;
+
+ private final ScoreMatrix DNA;
+
+ private static ScoreModels instance = new ScoreModels();
+
+ private Map models;
+
+ public static ScoreModels getInstance()
+ {
+ return instance;
+ }
+
+ /**
+ * Private constructor to enforce use of singleton. Registers Jalview's
+ * "built-in" score models:
+ *
+ * - BLOSUM62
+ * - PAM250
+ * - PID
+ * - DNA
+ * - Sequence Feature Similarity
+ *
+ */
+ private ScoreModels()
+ {
+ /*
+ * using LinkedHashMap keeps models ordered as added
+ */
+ models = new LinkedHashMap();
+ BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
+ PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
+ registerScoreModel(new PIDModel());
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new FeatureDistanceModel());
+ }
+
+ /**
+ * Tries to load a score matrix from the given resource file, and if
+ * successful, registers it.
+ *
+ * @param string
+ * @return
+ */
+ ScoreMatrix loadScoreMatrix(String resourcePath)
+ {
+ try
+ {
+ /*
+ * delegate parsing to ScoreMatrixFile
+ */
+ 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());
+ }
+ return null;
+ }
+
+ /**
+ * Answers an iterable set of the registered score models. Currently these are
+ * returned in the order in which they were registered.
+ *
+ * @return
+ */
+ public Iterable getModels()
+ {
+ return models.values();
+ }
+
+ /**
+ * 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)
+ {
+ ScoreModelI model = models.get(name);
+ return model == null ? null : model.getInstance(avp);
+ }
+
+ public void registerScoreModel(ScoreModelI sm)
+ {
+ ScoreModelI sm2 = models.get(sm.getName());
+ if (sm2 != null)
+ {
+ System.err.println("Warning: replacing score model " + sm2.getName());
+ }
+ models.put(sm.getName(), sm);
+ }
+
+ /**
+ * Returns the default peptide or nucleotide score model, currently BLOSUM62
+ * or DNA
+ *
+ * @param forPeptide
+ * @return
+ */
+ public ScoreMatrix getDefaultModel(boolean forPeptide)
+ {
+ return forPeptide ? BLOSUM62 : DNA;
+ }
+
+ public ScoreMatrix getBlosum62()
+ {
+ return BLOSUM62;
+ }
+
+ public ScoreMatrix getPam250()
+ {
+ return PAM250;
+ }
+}