version = "10", url = "http://www.arabidopsis.org") @DataURL(name = "TAIR ftp", description = "ftp.arabidopsis.org", urls = {"ftp://ftp.arabidopsis.org/Genes/TAIR10_genome_release/*",
public static String getFiles(PluginDescription pb) { StringBuffer sb = new StringBuffer(); Class<?> plugin = PluginRegistry.getInstance().loadCls(pb.getCls()); sb.append("<html> <body> <font face=\"Calibri\"> "); DataURL urlAnno = plugin.getAnnotation(DataURL.class); if (urlAnno != null) { sb.append("<h1>").append(urlAnno.name()).append("</h1>"); sb.append("<p>").append(urlAnno.description()).append("</p>"); for (String url : urlAnno.urls()) { sb.append("<li type=circle><a href=\"").append(url).append("\">").append(url).append("</a></li>"); } } sb.append("</font> </body> </html>"); return sb.toString(); }
@DataURL(name = "BioCyc databases", description = "Place biopax-level2.owl or similar file in data folder with no directory structure", urls = { "" }) public class Parser extends ONDEXParser {
.getAnnotation(DataURL.class); if (dburlAnnotation != null) { String name = dburlAnnotation.name().trim(); String description = dburlAnnotation .description().trim(); String[] urls = dburlAnnotation.urls();
@DataURL(name = "AraCyc databases", description = "URL on application to AraCyc all files in data folder with no directory structure", urls = {""})
@DataURL(name = "ec2go", description = "external2go mapping file", urls = "http://www.geneontology.org/external2go/ec2go") @DataSourceRequired(ids = MetaData.cvGO) @EvidenceTypeRequired(ids = MetaData.evidence)
@Authors(authors = {"Keywan Hassani-Pak"}, emails = {"keywan at users.sourceforge.net"}) @DatabaseTarget(name = "phytozome", description = "Phytozome is a joint project of JGI and CIG to facilitate comparative genomic studies amongst green plants. This Phytozome parser creates Chromosome, Scaffold, Gene, CDS and Protein concepts.", version = "9.0", url = "http://phytozome.net/") @DataURL(name = "Phytozome annotation directory", 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/"})
@DataURL(name = "enzclass and enzyme files", description = "enzclass and enzyme, all txt and dat files in directory files", urls = {"ftp://ftp.expasy.org/databases/enzyme"}) @DataSourceRequired(ids = { MetaData.DS_EC, MetaData.DS_PROTSITE, MetaData.DS_UNIPROTKB})
@DataURL(name = "brenda zip and exception file", description = "brenda zip file and an exceptions file for data file inconsistancies", urls = {"http://www.brenda-enzymes.org/brenda_download/brenda_dl_0905.zip", "https://ondex.svn.sourceforge.net/svnroot/ondex/trunk/ondex-parent/modules/enzymatics/data/brenda/exception.txt"}) @DataSourceRequired(ids = { MetaData.CV_ec, MetaData.CV_brenda,