http://rest.pdbj.org/strnavi?
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
'
org.embl.ebi.escience.scuflworkers.java.StringConcat
/ENTRY/DAD/primary-accession = '
org.embl.ebi.escience.scuflworkers.java.StringConcat
'
org.embl.ebi.escience.scuflworkers.java.StringConcat
/ENTRY/PDB/header/idcode = '
org.embl.ebi.escience.scuflworkers.java.StringConcat
pdb:
org.embl.ebi.escience.scuflworkers.java.StringConcat
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
String definition = "hypothetical protein";
BufferedReader br = new BufferedReader(new StringReader(output));
br.readLine();
br.readLine();
String l = br.readLine();
if(l.indexOf("hypothetical") == -1 && l.indexOf("unidentified") == -1) {
definition = l;
break;
}
output
definition
String pdbid = "";
String chain = "";
String url = "";
boolean hasHit = false;
for(Iterator it = blastResult.iterator(); it.hasNext(); ) {
String l = (String)it.next();
BufferedReader br = new BufferedReader(new StringReader(l));
String ll;
while((ll = br.readLine()) != null) {
String[] lll = ll.split("\t");
if(lll[1].indexOf("|") == -1) {
continue;
}
String s = lll[1].substring(0, lll[1].indexOf("|"));
pdbid = s.substring(0, 4);
chain = s.substring(5);
if(!pdbid.equals("")) {
hasHit = true;
break;
}
}
br.close();
if(hasHit) {
break;
}
}
url = "/strnavi?pdbid=" + pdbid + "&chain=" + chain + "&fmt=simple";
blastResult
url
String definition = "hypothetical protein";
for(Iterator it = definitionList.iterator(); it.hasNext();) {
String s = (String)it.next();
BufferedReader br = new BufferedReader(new StringReader(s));
br.readLine();
br.readLine();
String l = br.readLine();
if(l.indexOf("hypothetical") == -1 && l.indexOf("unidentified") == -1) {
definition = l;
break;
}
}
definitionList
definition
List accession = new ArrayList();
BufferedReader br = new BufferedReader(new StringReader(blastResult));
String l;
while((l = br.readLine()) != null) {
String[] ll = l.split("\t");
String ddbj = ll[1].substring(0, ll[1].indexOf("|"));
accession.add(ddbj);
}
blastResult
accession
String pdbid = "";
for(Iterator it = pdbidlist.iterator(); it.hasNext();) {
String l = (String)it.next();
pdbid = l.substring(0, 4);
break;
}
pdbidlist
pdbid
Execute Blast with parameter
blastp
PDB
-e 1 -m 8
http://xml.nig.ac.jp/wsdl/Blast.wsdl
searchParam
Execute Blast with parameter
blastp
DAD
-m 8 -e 0.00000000001 -v 10
http://xml.nig.ac.jp/wsdl/Blast.wsdl
searchParam
Get DAD entry of FASTA Format by Accession Number
http://xml.nig.ac.jp/wsdl/GetEntry.wsdl
getFASTA_DADEntry
http://soap.genome.jp/KEGG.wsdl
btit
/ENTRY/DAD/definition
1
1
http://xml.nig.ac.jp/wsdl/ARSA.wsdl
searchByXMLPath
/ENTRY/PDB/title
1
1
http://xml.nig.ac.jp/wsdl/ARSA.wsdl
searchByXMLPath
genes
1
10
http://soap.genome.jp/KEGG.wsdl
get_linkdb_by_entry
text/html
text/xml