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josemduartejosemduarte
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Updating genenames.org url to https
1 parent 67ca7f2 commit 39d8c24

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4 files changed

+32
-34
lines changed

4 files changed

+32
-34
lines changed

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/ChromPos.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,8 @@
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*/
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public class ChromPos {
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int pos;
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int phase;
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private int pos;
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private int phase;
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public int getPhase() {
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return phase;

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.java‎

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Original file line numberDiff line numberDiff line change
@@ -27,21 +27,19 @@
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import java.util.List;
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public class GeneChromosomePosition implements Comparable<GeneChromosomePosition>, Serializable{
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/**
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*
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*/
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private static final long serialVersionUID = -6886306238993367835L;
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String geneName;
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String genebankId;
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String chromosome;
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Character orientation;
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Integer transcriptionStart;
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Integer transcriptionEnd;
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Integer cdsStart;
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Integer cdsEnd;
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private String geneName;
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private String genebankId;
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private String chromosome;
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private Character orientation;
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private Integer transcriptionStart;
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private Integer transcriptionEnd;
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private Integer cdsStart;
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private Integer cdsEnd;
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int exonCount;
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List<Integer> exonStarts;
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List<Integer> exonEnds;
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private List<Integer> exonStarts;
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private List<Integer> exonEnds;
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public String getGeneName() {
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return geneName;

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneName.java‎

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Original file line numberDiff line numberDiff line change
@@ -25,7 +25,8 @@
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import java.io.Serializable;
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/** A simple bean that contains gene name information as available from www.genenames.org
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/**
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* A simple bean that contains gene name information as available from www.genenames.org
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*
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* @author Andreas Prlic
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*
@@ -34,23 +35,21 @@ public class GeneName implements Serializable, Comparable<GeneName>{
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//[HGNC ID, Approved Symbol, Approved Name, Status, Previous Symbols, Previous Names, Synonyms,
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// Chromosome, Accession Numbers, RefSeq IDs,Uniprot]
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/**
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*
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*/
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private static final long serialVersionUID = -7163977639324764020L;
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String hgncId;
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String approvedSymbol;
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String approvedName;
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String status;
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String previousSymbols;
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String previousNames;
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String synonyms;
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String chromosome;
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String accessionNr;
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String refseqIds;
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String uniprot;
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String omimId;
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String ensemblGeneId;
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private String hgncId;
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private String approvedSymbol;
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private String approvedName;
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private String status;
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private String previousSymbols;
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private String previousNames;
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private String synonyms;
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private String chromosome;
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private String accessionNr;
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private String refseqIds;
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private String uniprot;
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private String omimId;
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private String ensemblGeneId;
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public String getHgncId() {
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return hgncId;

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,8 @@
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import java.util.ArrayList;
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import java.util.List;
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/** Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
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/**
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* Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
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*
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* @author Andreas Prlic
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*
@@ -44,7 +45,7 @@ public class GeneNamesParser {
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private static final Logger logger = LoggerFactory.getLogger(GeneNamesParser.class);
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public static final String DEFAULT_GENENAMES_URL = "http://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id" +
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public static final String DEFAULT_GENENAMES_URL = "https://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id" +
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"&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag";
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/** parses a file from the genenames website

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