Merge branch 'issue-panel' into develop

biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Cancer.java

@@ -0,0 +1,107 @@
+package org.opencb.biodata.models.clinical.interpretation;
+
+import org.opencb.biodata.models.clinical.interpretation.ClinicalProperty.RoleInCancer;
+
+import java.util.List;
+
+public class Cancer {
+
+    private boolean somatic;
+    private boolean germline;
+    private RoleInCancer role;
+    private List<String> tissues;
+    private List<String> somaticTumourTypes;
+    private List<String> germlineTumourTypes;
+    private List<String> fusionPartners;
+
+    public Cancer() {
+    }
+
+    public Cancer(boolean somatic, boolean germline, RoleInCancer role, List<String> tissues,
+                  List<String> somaticTumourTypes, List<String> germlineTumourTypes, List<String> fusionPartners) {
+        this.somatic = somatic;
+        this.germline = germline;
+        this.role = role;
+        this.tissues = tissues;
+        this.somaticTumourTypes = somaticTumourTypes;
+        this.germlineTumourTypes = germlineTumourTypes;
+        this.fusionPartners = fusionPartners;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("Cancer{");
+        sb.append("somatic=").append(somatic);
+        sb.append(", germline=").append(germline);
+        sb.append(", role=").append(role);
+        sb.append(", tissues=").append(tissues);
+        sb.append(", somaticTumourTypes=").append(somaticTumourTypes);
+        sb.append(", germlineTumourTypes=").append(germlineTumourTypes);
+        sb.append(", fusionPartners=").append(fusionPartners);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public boolean isSomatic() {
+        return somatic;
+    }
+
+    public Cancer setSomatic(boolean somatic) {
+        this.somatic = somatic;
+        return this;
+    }
+
+    public boolean isGermline() {
+        return germline;
+    }
+
+    public Cancer setGermline(boolean germline) {
+        this.germline = germline;
+        return this;
+    }
+
+    public RoleInCancer getRole() {
+        return role;
+    }
+
+    public Cancer setRole(RoleInCancer role) {
+        this.role = role;
+        return this;
+    }
+
+    public List<String> getTissues() {
+        return tissues;
+    }
+
+    public Cancer setTissues(List<String> tissues) {
+        this.tissues = tissues;
+        return this;
+    }
+
+    public List<String> getSomaticTumourTypes() {
+        return somaticTumourTypes;
+    }
+
+    public Cancer setSomaticTumourTypes(List<String> somaticTumourTypes) {
+        this.somaticTumourTypes = somaticTumourTypes;
+        return this;
+    }
+
+    public List<String> getGermlineTumourTypes() {
+        return germlineTumourTypes;
+    }
+
+    public Cancer setGermlineTumourTypes(List<String> germlineTumourTypes) {
+        this.germlineTumourTypes = germlineTumourTypes;
+        return this;
+    }
+
+    public List<String> getFusionPartners() {
+        return fusionPartners;
+    }
+
+    public Cancer setFusionPartners(List<String> fusionPartners) {
+        this.fusionPartners = fusionPartners;
+        return this;
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalProperty.java

@@ -22,22 +22,22 @@
 public class ClinicalProperty {
 
     public enum ModeOfInheritance {
-        MONOALLELIC,
+        AUTOSOMAL_DOMINANT,
         MONOALLELIC_NOT_IMPRINTED,
         MONOALLELIC_MATERNALLY_IMPRINTED,
         MONOALLELIC_PATERNALLY_IMPRINTED,
-        BIALLELIC,
+        AUTOSOMAL_RECESSIVE,
         MONOALLELIC_AND_BIALLELIC,
         MONOALLELIC_AND_MORE_SEVERE_BIALLELIC,
-        XLINKED_BIALLELIC,
-        XLINKED_MONOALLELIC,
-        YLINKED,
+        X_LINKED_DOMINANT,
+        X_LINKED_RECESSIVE,
+        Y_LINKED,
         MITOCHONDRIAL,
 
         // Not modes of inheritance, but...
         DE_NOVO,
         COMPOUND_HETEROZYGOUS,
-
+        MENDELIAN_ERROR,
         UNKNOWN
     }
 
@@ -55,6 +55,13 @@ public enum Penetrance {
         INCOMPLETE
     }
 
+    public enum Confidence {
+        HIGH,
+        MEDIUM,
+        LOW,
+        REJECTED
+    }
+
     public enum RoleInCancer {
         ONCOGENE,
         TUMOR_SUPPRESSOR_GENE,