TASK-2242 Improve mutational signature analysis

biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java

@@ -51,13 +51,19 @@ public class Signature {
             description = FieldConstants.SIGNATURE_FILES_DESCRIPTION)
     private List<String> files;
 
+    @Deprecated
     @DataField(id = "fitting", indexed = true,
-            description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_DESCRIPTION)
+            description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION)
     private SignatureFitting fitting;
 
+    @DataField(id = "fittings", indexed = true,
+            description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORES_DESCRIPTION)
+    private List<SignatureFitting> fittings;
+
     public Signature() {
     }
 
+    @Deprecated
     public Signature(String id, String description, ObjectMap query, String type, List<GenomeContextCount> counts, List<String> files,
                      SignatureFitting fitting) {
         this.id = id;
@@ -69,6 +75,17 @@ public Signature(String id, String description, ObjectMap query, String type, Li
         this.fitting = fitting;
     }
 
+    public Signature(String id, String description, ObjectMap query, String type, List<GenomeContextCount> counts, List<String> files,
+                     List<SignatureFitting> fittings) {
+        this.id = id;
+        this.description = description;
+        this.query = query;
+        this.type = type;
+        this.counts = counts;
+        this.files = files;
+        this.fittings = fittings;
+    }
+
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("Signature{");
@@ -78,7 +95,7 @@ public String toString() {
         sb.append(", type='").append(type).append('\'');
         sb.append(", counts=").append(counts);
         sb.append(", files=").append(files);
-        sb.append(", fitting=").append(fitting);
+        sb.append(", fittings=").append(fittings);
         sb.append('}');
         return sb.toString();
     }
@@ -137,15 +154,26 @@ public Signature setFiles(List<String> files) {
         return this;
     }
 
+    @Deprecated
     public SignatureFitting getFitting() {
         return fitting;
     }
 
+    @Deprecated
     public Signature setFitting(SignatureFitting fitting) {
         this.fitting = fitting;
         return this;
     }
 
+    public List<SignatureFitting> getFittings() {
+        return fittings;
+    }
+
+    public Signature setFittings(List<SignatureFitting> fittings) {
+        this.fittings = fittings;
+        return this;
+    }
+
     public static class GenomeContextCount {
 
         @DataField(id = "context", indexed = true,

biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java

@@ -27,6 +27,9 @@
 
 public class SignatureFitting {
 
+    @DataField(id = "id", indexed = true,
+            description = FieldConstants.SIGNATURE_FITTING_ID_DESCRIPTION)
+    private String id;
 
     @DataField(id = "method", indexed = true,
             description = FieldConstants.SIGNATURE_FITTING_METHOD_DESCRIPTION)
@@ -42,7 +45,7 @@ public class SignatureFitting {
 
     @DataField(id = "scores", indexed = true, uncommentedClasses = {"Score"},
             description = FieldConstants.SIGNATURE_FITTING_SCORES_DESCRIPTION)
-    private List<Score> scores;
+    private List<SignatureFittingScore> scores;
 
     @Deprecated
     @DataField(id = "coeff", indexed = true,
@@ -66,7 +69,8 @@ public SignatureFitting() {
     }
 
     @Deprecated
-    public SignatureFitting(String method, String signatureSource, String signatureVersion, List<Score> scores, double coeff, String file) {
+    public SignatureFitting(String method, String signatureSource, String signatureVersion, List<SignatureFittingScore> scores,
+                            double coeff, String file) {
         this.method = method;
         this.signatureSource = signatureSource;
         this.signatureVersion = signatureVersion;
@@ -75,8 +79,21 @@ public SignatureFitting(String method, String signatureSource, String signatureV
         this.file = file;
     }
 
-    public SignatureFitting(String method, String signatureSource, String signatureVersion, List<Score> scores, double coeff, String file,
-                            List<String> files, ObjectMap params) {
+    @Deprecated
+    public SignatureFitting(String method, String signatureSource, String signatureVersion, List<SignatureFittingScore> scores,
+                            double coeff, String file, List<String> files, ObjectMap params) {
+        this.method = method;
+        this.signatureSource = signatureSource;
+        this.signatureVersion = signatureVersion;
+        this.scores = scores;
+        this.coeff = coeff;
+        this.file = file;
+        this.files = files;
+        this.params = params;
+    }
+
+    public SignatureFitting(String id, String method, String signatureSource, String signatureVersion, List<SignatureFittingScore> scores,
+                            double coeff, String file, List<String> files, ObjectMap params) {
         this.method = method;
         this.signatureSource = signatureSource;
         this.signatureVersion = signatureVersion;
@@ -89,7 +106,8 @@ public SignatureFitting(String method, String signatureSource, String signatureV
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("SignatureFitting{");
+        final StringBuilder sb = new StringBuilder("SignatureFittingScore{");
+        sb.append("id='").append(id).append('\'');
         sb.append("method='").append(method).append('\'');
         sb.append(", signatureSource='").append(signatureSource).append('\'');
         sb.append(", signatureVersion='").append(signatureVersion).append('\'');
@@ -102,6 +120,15 @@ public String toString() {
         return sb.toString();
     }
 
+    public String getId() {
+        return id;
+    }
+
+    public SignatureFitting setId(String id) {
+        this.id = id;
+        return this;
+    }
+
     public String getMethod() {
         return method;
     }
@@ -129,11 +156,11 @@ public SignatureFitting setSignatureVersion(String signatureVersion) {
         return this;
     }
 
-    public List<Score> getScores() {
+    public List<SignatureFittingScore> getScores() {
         return scores;
     }
 
-    public SignatureFitting setScores(List<Score> scores) {
+    public SignatureFitting setScores(List<SignatureFittingScore> scores) {
         this.scores = scores;
         return this;
     }
@@ -173,45 +200,4 @@ public SignatureFitting setParams(ObjectMap params) {
         this.params = params;
         return this;
     }
-
-    public static class Score {
-
-        private String signatureId;
-        private double value;
-
-        public Score() {
-        }
-
-        public Score(String signatureId, double value) {
-            this.signatureId = signatureId;
-            this.value = value;
-        }
-
-        @Override
-        public String toString() {
-            final StringBuilder sb = new StringBuilder("Score{");
-            sb.append("signatureId='").append(signatureId).append('\'');
-            sb.append(", value=").append(value);
-            sb.append('}');
-            return sb.toString();
-        }
-
-        public String getSignatureId() {
-            return signatureId;
-        }
-
-        public Score setSignatureId(String signatureId) {
-            this.signatureId = signatureId;
-            return this;
-        }
-
-        public double getValue() {
-            return value;
-        }
-
-        public Score setValue(double value) {
-            this.value = value;
-            return this;
-        }
-    }
 }

biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java

@@ -0,0 +1,42 @@
+package org.opencb.biodata.models.clinical.qc;
+
+public class SignatureFittingScore {
+
+    private String signatureId;
+    private double value;
+
+    public SignatureFittingScore() {
+    }
+
+    public SignatureFittingScore(String signatureId, double value) {
+        this.signatureId = signatureId;
+        this.value = value;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("SignatureFittingScore{");
+        sb.append("signatureId='").append(signatureId).append('\'');
+        sb.append(", value=").append(value);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getSignatureId() {
+        return signatureId;
+    }
+
+    public SignatureFittingScore setSignatureId(String signatureId) {
+        this.signatureId = signatureId;
+        return this;
+    }
+
+    public double getValue() {
+        return value;
+    }
+
+    public SignatureFittingScore setValue(double value) {
+        this.value = value;
+        return this;
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java

@@ -8,9 +8,12 @@ public class FieldConstants {
     public static final String SIGNATURE_TYPE_DESCRIPTION = "Signature type SNV, INDEL...";
     public static final String SIGNATURE_COUNTS_DESCRIPTION = "List of GenomeContextCount";
     public static final String SIGNATURE_FILES_DESCRIPTION = "List of files of signature";
-    public static final String SIGNATURE_SIGNATURE_FITTING_DESCRIPTION = "Signature fitting";
+    @Deprecated
+    public static final String SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION = "Signature fitting";
+    public static final String SIGNATURE_SIGNATURE_FITTING_SCORES_DESCRIPTION = "List of signature fitting scores";
     public static final String GENOME_CONTEXT_COUNT_CONTEXT_DESCRIPTION = "Genome context to count";
     public static final String GENOME_CONTEXT_COUNT_TOTAL_DESCRIPTION = "Counted integer";
+    public static final String SIGNATURE_FITTING_ID_DESCRIPTION = "Signature fitting ID";
     public static final String SIGNATURE_FITTING_METHOD_DESCRIPTION = "Method used to fit the signature";
     public static final String SIGNATURE_FITTING_SOURCE_DESCRIPTION = "Source of the fitting signature";
     public static final String SIGNATURE_FITTING_SIGNATURE_VERSION_DESCRIPTION = "Signature version of the fitting signature";