<commit_before>package org.mskcc.cbio.oncokb.model;
// Generated Dec 19, 2013 1:33:26 AM by Hibernate Tools 3.2.1.GA

import com.fasterxml.jackson.annotation.JsonIgnore;
import org.apache.commons.lang3.StringUtils;
import org.mskcc.cbio.oncokb.util.AlterationUtils;

import java.util.ArrayList;
import java.util.List;


/**
 * TumorType generated by hbm2java
 */
public class Query implements java.io.Serializable {
    private String id; //Optional, This id is passed from request. The identifier used to distinguish the query
    private String type; // Query type. Different type may return different result.
    private String hugoSymbol;
    private Integer entrezGeneId;
    private String alteration;
    private String alterationType;
    private String tumorType;
    private String consequence;
    private Integer proteinStart;
    private Integer proteinEnd;
    private String hgvs;

    public Query() {
    }

    public Query(Alteration alt) {
        if (alt != null) {
            if (alt.getGene() != null) {
                this.hugoSymbol = alt.getGene().getHugoSymbol();
                this.entrezGeneId = alt.getGene().getEntrezGeneId();
            }
            setAlteration(alt.getAlteration());
            this.alterationType = alt.getAlterationType() == null ? "MUTATION" : alt.getAlterationType().name();
            this.consequence = alt.getConsequence() == null ? null : alt.getConsequence().getTerm();
            this.proteinStart = alt.getProteinStart();
            this.proteinEnd = alt.getProteinEnd();
        }
    }

    public Query(VariantQuery variantQuery) {
        if (variantQuery != null) {
            if (variantQuery.getGene() != null) {
                this.hugoSymbol = variantQuery.getGene().getHugoSymbol();
                this.entrezGeneId = variantQuery.getGene().getEntrezGeneId();
            }
            setAlteration(variantQuery.getQueryAlteration());
            this.consequence = variantQuery.getConsequence();
            this.proteinStart = variantQuery.getProteinStart();
            this.proteinEnd = variantQuery.getProteinEnd();
        }<commit_msg>Assign tumor type when using variantQuery<commit_after>package org.mskcc.cbio.oncokb.model;
// Generated Dec 19, 2013 1:33:26 AM by Hibernate Tools 3.2.1.GA

import com.fasterxml.jackson.annotation.JsonIgnore;
import org.apache.commons.lang3.StringUtils;
import org.mskcc.cbio.oncokb.util.AlterationUtils;

import java.util.ArrayList;
import java.util.List;


/**
 * TumorType generated by hbm2java
 */
public class Query implements java.io.Serializable {
    private String id; //Optional, This id is passed from request. The identifier used to distinguish the query
    private String type; // Query type. Different type may return different result.
    private String hugoSymbol;
    private Integer entrezGeneId;
    private String alteration;
    private String alterationType;
    private String tumorType;
    private String consequence;
    private Integer proteinStart;
    private Integer proteinEnd;
    private String hgvs;

    public Query() {
    }

    public Query(Alteration alt) {
        if (alt != null) {
            if (alt.getGene() != null) {
                this.hugoSymbol = alt.getGene().getHugoSymbol();
                this.entrezGeneId = alt.getGene().getEntrezGeneId();
            }
            setAlteration(alt.getAlteration());
            this.alterationType = alt.getAlterationType() == null ? "MUTATION" : alt.getAlterationType().name();
            this.consequence = alt.getConsequence() == null ? null : alt.getConsequence().getTerm();
            this.proteinStart = alt.getProteinStart();
            this.proteinEnd = alt.getProteinEnd();
        }
    }

    public Query(VariantQuery variantQuery) {
        if (variantQuery != null) {
            if (variantQuery.getGene() != null) {
                this.hugoSymbol = variantQuery.getGene().getHugoSymbol();
                this.entrezGeneId = variantQuery.getGene().getEntrezGeneId();
            }
            setAlteration(variantQuery.getQueryAlteration());
            this.setTumorType(variantQuery.getQueryTumorType());
            this.consequence = variantQuery.getConsequence();
            this.proteinStart = variantQuery.getProteinStart();
            this.proteinEnd = variantQuery.getProteinEnd();
        }
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{'dir': 'git-commits-cleaned', 'id': '3105630', 'n_tokens_mistral': 1288, 'n_tokens_neox': 1185, 'n_words': 278}