\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
get gene information
http://xml.nig.ac.jp/wsdl/Ensembl.wsdl
getGeneInfo
\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
String[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++){
if (!(split[i].equals("")))
{
nonEmpty.add(split[i].trim());
}
}
String[] non_empty = new String[nonEmpty.size()];
for (int i = 0; i < non_empty.length; i ++)
{
non_empty[i] = nonEmpty.elementAt(i);
}
String output = "";
for (int i = 0; i < non_empty.length; i++)
{
output = output + (String) (non_empty[i] + "\n");
}
input
output
Alltext
To be added
http://phoebus.cs.man.ac.uk:1977/axis/services/uniprotsequence.uniprot
String[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
String[] trimmedSplit = trimmed.split(":");
if (trimmedSplit.length == 2){
nonEmpty.add(trimmedSplit[1].trim());
}
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
}
input
output
swiss
extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl
http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_ddbj_gene_info
Extract information from a Uniprot text file including PubMed, InterPro, Pfam and other related accession numbers
http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_uniprot
String[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
String[] trimmedSplit = trimmed.split("=");
if (trimmedSplit.length >= 1)
{
if(trimmedSplit[0].equals("GO"))
{
nonEmpty.add(trimmedSplit[1].trim());
}
}
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + (String) (nonEmpty.elementAt(i) + "\n");
}
//AC=Q5DTJ5
//EMBL=AK220525
//EMBL=BAD90524.1
//Ensembl=ENSMUSG00000002763
//MGI=MGI:2385054
//GO=GO:0005515
//InterPro=IPR003593
//InterPro=IPR003959
//Pfam=PF00004
//SMART=SM00382
input
output
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
String[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++){
if (!(split[i].equals("")))
{
nonEmpty.add(split[i].trim());
}
}
String[] non_empty = new String[nonEmpty.size()];
for (int i = 0; i < non_empty.length; i ++)
{
non_empty[i] = nonEmpty.elementAt(i);
}
String output = "";
for (int i = 0; i < non_empty.length; i++)
{
output = output + (String) (non_empty[i] + "\n");
}
input
output
Get tree information by GO ID
http://xml.nig.ac.jp/wsdl/GO.wsdl
getTree