models: add some data models from opencga, #187

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

@@ -0,0 +1,88 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.biodata.models.clinical.qc.individual;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+public class InferredSexReport {
+
+    private String method;
+    private String inferredKaryotypicSex;
+    private Map<String, Object> values;
+    private List<String> files;
+
+    public InferredSexReport() {
+        this("CoverageRatio", "", new LinkedHashMap<>(), new ArrayList<>());
+    }
+
+    public InferredSexReport(String method, String inferredKaryotypicSex, Map<String, Object> values, List<String> files) {
+        this.method = method;
+        this.inferredKaryotypicSex = inferredKaryotypicSex;
+        this.values = values;
+        this.files = files;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("InferredSexReport{");
+        sb.append("method='").append(method).append('\'');
+        sb.append(", inferredKaryotypicSex='").append(inferredKaryotypicSex).append('\'');
+        sb.append(", values=").append(values);
+        sb.append(", files=").append(files);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getMethod() {
+        return method;
+    }
+
+    public InferredSexReport setMethod(String method) {
+        this.method = method;
+        return this;
+    }
+
+    public String getInferredKaryotypicSex() {
+        return inferredKaryotypicSex;
+    }
+
+    public InferredSexReport setInferredKaryotypicSex(String inferredKaryotypicSex) {
+        this.inferredKaryotypicSex = inferredKaryotypicSex;
+        return this;
+    }
+
+    public Map<String, Object> getValues() {
+        return values;
+    }
+
+    public InferredSexReport setValues(Map<String, Object> values) {
+        this.values = values;
+        return this;
+    }
+
+    public List<String> getFiles() {
+        return files;
+    }
+
+    public InferredSexReport setFiles(List<String> files) {
+        this.files = files;
+        return this;
+    }
+}

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

@@ -0,0 +1,180 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.biodata.models.clinical.qc.individual;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+//-------------------------------------------------------------------------
+// M E N D E L I A N     E R R O R S     R E P O R T
+//-------------------------------------------------------------------------
+
+public class MendelianErrorReport {
+
+    // Number total of errors for that family
+    private int numErrors;
+
+    private List<SampleAggregation> sampleAggregation;
+
+    //-------------------------------------------------------------------------
+    // S A M P L E     A G G R E G A T I O N
+    //-------------------------------------------------------------------------
+
+    public static class SampleAggregation {
+
+        // Sample
+        private String sample;
+
+        // Number of errors
+        private int numErrors;
+
+        // Ratio for that sample = total / number_of_variants
+        private double ratio;
+
+
+        // Aggregation per chromosome
+        private List<ChromosomeAggregation> chromAggregation;
+
+        public SampleAggregation() {
+            chromAggregation = new ArrayList<>();
+        }
+
+        public SampleAggregation(String sample, int numErrors, double ratio, List<ChromosomeAggregation> chromAggregation) {
+            this.sample = sample;
+            this.numErrors = numErrors;
+            this.ratio = ratio;
+            this.chromAggregation = chromAggregation;
+        }
+
+        public String getSample() {
+            return sample;
+        }
+
+        public SampleAggregation setSample(String sample) {
+            this.sample = sample;
+            return this;
+        }
+
+        public int getNumErrors() {
+            return numErrors;
+        }
+
+        public SampleAggregation setNumErrors(int numErrors) {
+            this.numErrors = numErrors;
+            return this;
+        }
+
+        public double getRatio() {
+            return ratio;
+        }
+
+        public SampleAggregation setRatio(double ratio) {
+            this.ratio = ratio;
+            return this;
+        }
+
+        public List<ChromosomeAggregation> getChromAggregation() {
+            return chromAggregation;
+        }
+
+        public SampleAggregation setChromAggregation(List<ChromosomeAggregation> chromAggregation) {
+            this.chromAggregation = chromAggregation;
+            return this;
+        }
+
+        //-------------------------------------------------------------------------
+        // C H R O M O S O M E     A G G R E G A T I O N
+        //-------------------------------------------------------------------------
+
+        public static class ChromosomeAggregation {
+
+            // Chromosome
+            private String chromosome;
+
+            // Number of errors
+            private int numErrors;
+
+            // Aggregation per error code for that chromosome
+            private Map<String, Integer> errorCodeAggregation;
+
+            public ChromosomeAggregation() {
+            }
+
+            public ChromosomeAggregation(String chromosome, int numErrors, Map<String, Integer> errorCodeAggregation) {
+                this.chromosome = chromosome;
+                this.numErrors = numErrors;
+                this.errorCodeAggregation = errorCodeAggregation;
+            }
+
+            public String getChromosome() {
+                return chromosome;
+            }
+
+            public ChromosomeAggregation setChromosome(String chromosome) {
+                this.chromosome = chromosome;
+                return this;
+            }
+
+            public int getNumErrors() {
+                return numErrors;
+            }
+
+            public ChromosomeAggregation setNumErrors(int numErrors) {
+                this.numErrors = numErrors;
+                return this;
+            }
+
+            public Map<String, Integer> getErrorCodeAggregation() {
+                return errorCodeAggregation;
+            }
+
+            public ChromosomeAggregation setErrorCodeAggregation(Map<String, Integer> errorCodeAggregation) {
+                this.errorCodeAggregation = errorCodeAggregation;
+                return this;
+            }
+        }
+    }
+
+    public MendelianErrorReport() {
+        this.numErrors = 0;
+        this.sampleAggregation = new ArrayList<>();
+    }
+
+    public MendelianErrorReport(int numErrors, List<SampleAggregation> sampleAggregation) {
+        this.numErrors = numErrors;
+        this.sampleAggregation = sampleAggregation;
+    }
+
+    public int getNumErrors() {
+        return numErrors;
+    }
+
+    public MendelianErrorReport setNumErrors(int numErrors) {
+        this.numErrors = numErrors;
+        return this;
+    }
+
+    public List<SampleAggregation> getSampleAggregation() {
+        return sampleAggregation;
+    }
+
+    public MendelianErrorReport setSampleAggregation(List<SampleAggregation> sampleAggregation) {
+        this.sampleAggregation = sampleAggregation;
+        return this;
+    }
+}