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The IO bundle for Geneweaver.
/*-
*
* Copyright 2018, 2020 The Jackson Laboratory Inc.
*
* 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.
*
* @author Matthew Gerring
*/
package org.geneweaver.domain;
import java.util.Collection;
import java.util.Objects;
import javax.annotation.processing.Generated;
import com.fasterxml.jackson.annotation.JsonIgnore;
/**
*
HomoloGene ID Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID HGNC ID OMIM Gene ID Genetic Location Genomic Coordinates (mouse: , human: ) Nucleotide RefSeq IDs Protein RefSeq IDs SWISS_PROT IDs
3 mouse, laboratory 10090 Acadm 11364 MGI:87867 Chr3 78.77 cM Chr3:153922357-153944632(-) NM_007382 NP_031408 P45952
3 human 9606 ACADM 34 HGNC:89 OMIM:607008 Chr1 p31.1 Chr1:75724347-75763679(+) NM_001286043,NM_000016,NM_001127328,NM_001286042,NM_001286044 NP_001120800,NP_001272971,NP_001272972,NP_001272973,NP_000007 P11310
5 mouse, laboratory 10090 Acadvl 11370 MGI:895149 Chr11 42.96 cM Chr11:70010183-70015411(-) NM_017366 NP_059062 P50544
5 human 9606 ACADVL 37 HGNC:92 OMIM:609575 Chr17 p13.1 Chr17:7217125-7225267(+) NM_000018,NM_001033859,NM_001270448,NM_001270447 NP_001029031,NP_001257377,XP_006721579,XP_011522131,XP_011522132,NP_000009,XP_024306509,NP_001257376 P49748
6 mouse, laboratory 10090 Acat1 110446 MGI:87870 Chr9 29.12 cM Chr9:53580522-53610350(-) NM_144784 NP_659033 Q8QZT1
6 human 9606 ACAT1 38 HGNC:93 OMIM:607809 Chr11 q22.3 Chr11:108121531-108148168(+) NM_001386689,NM_001386688,NM_001386687,NM_001386686,NM_001386691,NM_001386678,NM_000019,NM_001386677,NM_001386685,NM_001386682,NM_001386679,NM_001386681,NM_001386690 NP_001373615,NP_001373617,NP_001373618,NP_001373619,NP_001373620,XP_016873171,XP_024304282,NP_001373607,NP_001373606,NP_000010,NP_001373608,NP_001373610,NP_001373611,NP_001373614,NP_001373616 P24752
7 mouse, laboratory 10090 Acvr1 11477 MGI:87911 Chr2 33.05 cM Chr2:58446438-58566828(-) NM_001355049,NM_001110205,NM_001355048,NM_007394,NM_001110204,XM_006497622 NP_001341978,NP_001103675,NP_001103674,NP_001341977,NP_031420,XP_006497685 P37172
7 human 9606 ACVR1 90 HGNC:171 OMIM:102576 Chr2 q24.1 Chr2:157736446-157875880(-) NM_001347667,NM_001347666,NM_001347665,NM_001347664,NM_001347663,NM_001111067,NM_001105 NP_001334594,NP_001334595,NP_001334596,XP_006712888,XP_011510410,NP_001096,NP_001104537,NP_001334592,NP_001334593 Q04771
9 mouse, laboratory 10090 Sgca 20391 MGI:894698 Chr11 59.01 cM Chr11:94962791-94976327(-) XM_011248836,NM_009161 NP_033187,XP_011247138 P82350
9 human 9606 SGCA 6442 HGNC:10805 OMIM:600119 Chr17 q21.33 Chr17:50165517-50175932(+) NM_001135697,NM_000023 XP_011523422,NP_001129169,NP_000014,XP_024306641,XP_011523426,XP_011523425,XP_011523424,XP_011523423 Q16586
12 mouse, laboratory 10090 Adsl 11564 MGI:103202 Chr15 37.95 cM Chr15:80948490-80970946(+) NM_009634 NP_033764 P54822
12 human 9606 ADSL 158 HGNC:291 OMIM:608222 Chr22 q13.1 Chr22:40346500-40387408(+) NM_000026,NM_001363840,NM_001317923,NM_001123378 XP_016884128,XP_024307934,XP_016884129,XP_016884127,XP_016884126,XP_016884125,XP_011528282,XP_011528279,NP_001350769,NP_001304852,NP_001116850,NP_000017 P30566
* @author gerrim
*
*/
@Generated("POJO")
public class HomologGene extends AbstractEntity {
private Long hid;
private String organismName;
private Long taxonId;
private String symbol;
private Long entrezId;
private String mgiId;
private String hgncId;
private String location;
private String coords;
// TODO It might not be required to parse everything in?
private Collection nucelotideSeqIds;
private Collection proteinSeqIds;
private Collection swissProtIds;
/**
* This is the ENSEMBL gene id. It must be found by mapping
* gene name and taxon to ensembl geneId, it is not in the
* original homologene file.
*/
private String geneId;
/*
* Something like 'Homologene'from http://www.informatics.jax.org/homology.shtml
*/
private String source;
/**
* @return the hid
*/
public Long getHid() {
return hid;
}
/**
* @param hid the hid to set
*/
public void setHid(Long hid) {
this.hid = hid;
}
/**
* @return the organismName
*/
public String getOrganismName() {
return organismName;
}
/**
* @param organismName the organismName to set
*/
public void setOrganismName(String organismName) {
this.organismName = organismName;
}
/**
* @return the taxonId
*/
public Long getTaxonId() {
return taxonId;
}
/**
* @param taxonId the taxonId to set
*/
public void setTaxonId(Long taxonId) {
this.taxonId = taxonId;
}
/**
* @return the symbol
*/
public String getSymbol() {
return symbol;
}
/**
* @param symbol the symbol to set
*/
public void setSymbol(String symbol) {
this.symbol = symbol;
}
/**
* @return the entrezId
*/
public Long getEntrezId() {
return entrezId;
}
/**
* @param entrezId the entrezId to set
*/
public void setEntrezId(Long entrezId) {
this.entrezId = entrezId;
}
/**
* @return the hgncId
*/
public String getHgncId() {
return hgncId;
}
/**
* @param hgncId the hgncId to set
*/
public void setHgncId(String hgncId) {
this.hgncId = hgncId;
}
/**
* @return the location
*/
public String getLocation() {
return location;
}
/**
* @param location the location to set
*/
public void setLocation(String location) {
this.location = location;
}
/**
* @return the coords
*/
public String getCoords() {
return coords;
}
/**
* @param coords the coords to set
*/
public void setCoords(String coords) {
this.coords = coords;
}
/**
* @return the nucelotideSeqIds
*/
public Collection getNucelotideSeqIds() {
return nucelotideSeqIds;
}
/**
* @param nucelotideSeqIds the nucelotideSeqIds to set
*/
public void setNucelotideSeqIds(Collection nucelotideSeqIds) {
this.nucelotideSeqIds = nucelotideSeqIds;
}
/**
* @return the proteinSeqIds
*/
public Collection getProteinSeqIds() {
return proteinSeqIds;
}
/**
* @param proteinSeqIds the proteinSeqIds to set
*/
public void setProteinSeqIds(Collection proteinSeqIds) {
this.proteinSeqIds = proteinSeqIds;
}
/**
* @return the swissProtIds
*/
public Collection getSwissProtIds() {
return swissProtIds;
}
/**
* @param swissProtIds the swissProtIds to set
*/
public void setSwissProtIds(Collection swissProtIds) {
this.swissProtIds = swissProtIds;
}
/**
* @return the mgiId
*/
public String getMgiId() {
return mgiId;
}
/**
* @param mgiId the mgiId to set
*/
public void setMgiId(String mgiId) {
this.mgiId = mgiId;
}
@Override
public int hashCode() {
final int prime = 31;
int result = super.hashCode();
result = prime * result + Objects.hash(coords, entrezId, geneId, hgncId, hid, location, mgiId, nucelotideSeqIds,
organismName, proteinSeqIds, source, swissProtIds, symbol, taxonId);
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (!super.equals(obj))
return false;
if (!(obj instanceof HomologGene))
return false;
HomologGene other = (HomologGene) obj;
return Objects.equals(coords, other.coords) && Objects.equals(entrezId, other.entrezId)
&& Objects.equals(geneId, other.geneId) && Objects.equals(hgncId, other.hgncId)
&& Objects.equals(hid, other.hid) && Objects.equals(location, other.location)
&& Objects.equals(mgiId, other.mgiId) && Objects.equals(nucelotideSeqIds, other.nucelotideSeqIds)
&& Objects.equals(organismName, other.organismName)
&& Objects.equals(proteinSeqIds, other.proteinSeqIds) && Objects.equals(source, other.source)
&& Objects.equals(swissProtIds, other.swissProtIds) && Objects.equals(symbol, other.symbol)
&& Objects.equals(taxonId, other.taxonId);
}
/**
* @return the source
*/
public String getSource() {
return source;
}
/**
* @param source the source to set
*/
public void setSource(String source) {
this.source = source;
}
/**
* @return the geneId
*/
public String getGeneId() {
return geneId;
}
/**
* @param geneId the geneId to set
*/
public HomologGene setGeneId(String geneId) {
this.geneId = geneId;
return this;
}
@JsonIgnore
public String getGeneNameKey() {
return getTaxonId()+":"+getSymbol();
}
}