@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer implements ArgumentNames {
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Mapping extends ONDEXMapping
@Custodians(custodians = { "Jochen Weile" }, emails = { "jweile at users.sourceforge.net" }) public class Transformer extends ONDEXTransformer implements ArgumentNames {
@Custodians(custodians = { "Jochen Weile" }, emails = { "jweile at users.sourceforge.net" }) public class Filter extends ONDEXFilter implements ArgumentNames {
@Custodians(custodians = {"Jochen Weile"}, emails = {" \tjweile at users.sourceforge.net"}) public class Filter extends ONDEXFilter
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer implements ArgumentNames {
@Custodians(custodians = { "Jochen Weile" }, emails = { "jweile at users.sourceforge.net" }) public class Filter extends ONDEXFilter implements ArgumentNames {
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Filter extends ONDEXFilter implements ArgumentNames {
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) @Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) @Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport
@Authors(authors = { "Jan Taubert" }, emails = { "jantaubert at users.sourceforge.net" }) @Custodians(custodians = { "Jan Taubert" }, emails = { "jantaubert at users.sourceforge.net" }) @Status(status = StatusType.STABLE, description = "Tested October 2012 (Jan Taubert)") public class Parser extends ONDEXParser {
@Custodians(custodians = {"Matthew Hindle"}, emails = {"matthew_hindle at users.sourceforge.net"}) @Status(status = StatusType.EXPERIMENTAL) public class NT2ProteinBLASTxAlignmentMapping extends ONDEXMapping {
@Custodians(custodians = {"Victor Lesk"}, emails = {"v.lesk at imperial.ac.uk"}) public class Parser extends ONDEXParser implements ArgumentNames {
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) @Status(description = "Set to DISCONTINUED 4 May 2010 due to System.out usage. (Christian)", status = StatusType.DISCONTINUED) public class Export extends ONDEXExport
@Custodians(custodians = {"Jan Taubert"}, emails = {"jantaubert at users.sourceforge.net"}) public class Producer extends ProducerONDEXPlugin
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer implements ArgumentNames {
@DatabaseTarget(name = "GlycomeDB", description = "A carbohydrate structure metadatabase", version = "", url = "http://www.glycome-db.org") @Authors(authors = {"Jan Taubert", "Victor Lesk"}, emails = {"jantaubert at users.sourceforge.net", "v.lesk at imperial.ac.uk"}) @Custodians(custodians = {"Victor Lesk"}, emails = {"v.lesk at imperial.ac.uk"}) public class Parser extends ONDEXParser
@Custodians(custodians = {"Jochen Weile"}, emails = {"jweile at users.sourceforge.net"}) public class Transformer extends ONDEXTransformer implements ArgumentNames {
description = "This parser requires as input the annotation directory of a specific species. Do not change the file names. It parses the GFF3, peptide FASTA, CDS FASTA and Synonyms TXT file inside of the annotation directory. It was tested on Arabidopsis, rice, poplar and brachypodium.", urls = {"ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v9.0/"}) @Custodians(custodians = {"Keywan Hassani-pak"}, emails = {"keywan at users.sourceforge.net"}) @DataSourceRequired(ids = {MetaData.DS_PHYTOZOME }) @ConceptClassRequired(ids = {MetaData.CC_PROTEIN, MetaData.CC_CDS, MetaData.CC_GENE, MetaData.CHROMOSOME, MetaData.SCAFFOLD })