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authorPaul-Christian Volkmer2024-09-21 22:10:24 +0200
committerPaul-Christian Volkmer2024-09-21 22:10:24 +0200
commitcc27edc544cec1b892e7c224aec9e6e42342aa39 (patch)
tree3036b92f84a707d769782d63c2b018166623abf5 /src/main/java/DNPM/dto/Variant.java
parent93215825f5c8aec0912d562b544f370cffe9cda7 (diff)
refactor: use package name following Java guidelines
Diffstat (limited to 'src/main/java/DNPM/dto/Variant.java')
-rw-r--r--src/main/java/DNPM/dto/Variant.java110
1 files changed, 0 insertions, 110 deletions
diff --git a/src/main/java/DNPM/dto/Variant.java b/src/main/java/DNPM/dto/Variant.java
deleted file mode 100644
index d3fab9e..0000000
--- a/src/main/java/DNPM/dto/Variant.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package DNPM.dto;
-
-import de.itc.onkostar.api.Procedure;
-
-import java.util.Optional;
-
-/**
- * Ein Auszug der Variante aus dem NGS-Bericht zur Übertragung an das Frontend zur Auswahl der stützenden molekularen Alteration
- *
- * @since 0.2.0
- */
-public class Variant {
- private final Integer id;
-
- private final String ergebnis;
-
- private final String gen;
-
- private final String exon;
-
- private final String pathogenitaetsklasse;
-
- private Variant(
- final int id,
- final String ergebnis,
- final String gen,
- final String exon,
- final String pathogenitaetsklasse
- ) {
- this.id = id;
- this.ergebnis = ergebnis;
- this.gen = gen;
- this.exon = exon;
- this.pathogenitaetsklasse = pathogenitaetsklasse;
- }
-
- public Integer getId() {
- return id;
- }
-
- public String getErgebnis() {
- return ergebnis;
- }
-
- public String getGen() {
- return gen;
- }
-
- public String getExon() {
- return exon;
- }
-
- public String getPathogenitaetsklasse() {
- return pathogenitaetsklasse;
- }
-
- /**
- * Erstellt ein Optional einer Variante aus einer Prozedur
- * @param procedure Die zu verwendende Prozedur
- * @return Das Optional, wenn die Prozedur verwendet werden kann, ansonsten ein leeres Optional
- */
- public static Optional<Variant> fromProcedure(Procedure procedure) {
- if (!"OS.Molekulargenetische Untersuchung".equals(procedure.getFormName())) {
- return Optional.empty();
- }
-
- var ergebnis = procedure.getValue("Ergebnis");
- var gene = procedure.getValue("Untersucht");
- var exon = procedure.getValue("ExonInt");
- var pathogenitaetsklasse = procedure.getValue("Pathogenitaetsklasse");
-
- if (null == gene) {
- return Optional.empty();
- }
-
- if (ergebnis.getString().equals("P")) {
- return Optional.of(
- new Variant(
- procedure.getId(),
- "Einfache Variante (Mutation)",
- gene.getString().isBlank() ? "-" : gene.getString(),
- null == exon || exon.getString().isBlank() ? "-" : exon.getString(),
- null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString()
- )
- );
- } else if (ergebnis.getString().equals("CNV")) {
- return Optional.of(
- new Variant(
- procedure.getId(),
- "Copy Number Variation (CNV)",
- gene.getString().isBlank() ? "-" : gene.getString(),
- null == exon || exon.getString().isBlank() ? "-" : exon.getString(),
- null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString()
- )
- );
- } else if (ergebnis.getString().equals("F")) {
- return Optional.of(
- new Variant(
- procedure.getId(),
- "Fusion (Translokation Inversion Insertion)",
- gene.getString().isBlank() ? "-" : gene.getString(),
- null == exon || exon.getString().isBlank() ? "-" : exon.getString(),
- null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString()
- )
- );
- } else {
- return Optional.empty();
- }
- }
-}