org.embl.ebi.escience.scuflworkers.java.DecodeBase64
content
import org.apache.xml.serialize.XMLSerializer;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
String OutObj="";
String skel="<?xml version='1.0' encoding='ISO-8859-1'?><moby:MOBY xmlns='http://www.biomoby.org/moby' xmlns:moby='http://www.biomoby.org/moby'><moby:mobyContent><moby:mobyData queryID='one'><moby:Collection></moby:Collection></moby:mobyData></moby:mobyContent></moby:MOBY>";
skel="<?xml version='1.0' encoding='ISO-8859-1'?><moby:MOBY xmlns='http://www.biomoby.org/moby' xmlns:moby='http://www.biomoby.org/moby'><moby:mobyContent><moby:mobyData queryID='one'><moby:Collection></moby:Collection></moby:mobyData></moby:mobyContent></moby:MOBY>";
skel="<moby:MOBY xmlns='http://www.biomoby.org/moby' xmlns:moby='http://www.biomoby.org/moby'><moby:mobyContent><moby:mobyData queryID='one'><moby:Collection></moby:Collection></moby:mobyData></moby:mobyContent></moby:MOBY>";
DocumentBuilderFactory dbf=DocumentBuilderFactory.newInstance();
DocumentBuilder db = null;
db = dbf.newDocumentBuilder();
InputSource Source1 = new InputSource(new StringReader(MobyA));
InputSource Source2 = new InputSource(new StringReader(MobyB));
InputSource Source3 = new InputSource(new StringReader(MobyC));
InputSource SourceSkel = new InputSource(new StringReader(skel));
Document doc1 = null;
Document doc2 = null;
Document doc3 = null;
Document docsalida = null;
doc1 = db.parse(Source1);
doc2 = db.parse(Source2);
doc3 = db.parse(Source3);
docsalida=db.parse(SourceSkel);
XMLSerializer serializer = new XMLSerializer();
StringWriter sw=new StringWriter();
// First, Simples
NodeList nodelist1an = doc1.getElementsByTagName("moby:Simple");
NodeList nodelist1a = doc1.getElementsByTagName("Simple");
NodeList nodelist2an = doc2.getElementsByTagName("moby:Simple");
NodeList nodelist2a = doc2.getElementsByTagName("Simple");
NodeList nodelist3an = doc3.getElementsByTagName("moby:Simple");
NodeList nodelist3a = doc3.getElementsByTagName("Simple");
// Second, Collection
NodeList nodelist1bn = doc1.getElementsByTagName("moby:Collection");
NodeList nodelist1b = doc1.getElementsByTagName("Collection");
NodeList nodelist2bn = doc2.getElementsByTagName("moby:Collection");
NodeList nodelist2b = doc2.getElementsByTagName("Collection");
NodeList nodelist3bn = doc3.getElementsByTagName("moby:Collection");
NodeList nodelist3b = doc3.getElementsByTagName("Collection");
// We will iterate over these lists
NodeList[] globalS={
nodelist1an,
nodelist1a,
nodelist2an,
nodelist2a,
nodelist3an,
nodelist3a
};
NodeList[] globalC={
nodelist1bn,
nodelist1b,
nodelist2bn,
nodelist2b,
nodelist3bn,
nodelist3b
};
NodeList nodelistfinal = docsalida.getElementsByTagName("moby:Collection");
serializer.setOutputCharStream(sw);
Node comienzo = nodelistfinal.item(0);
// Common index variable for all this work
int gi;
int maxgi;
// We are skipping over Collected Simples
for(gi=0,maxgi=globalS.length;gi<maxgi;gi++) {
int i;
int maxi;
for(i=0,maxi=globalS[gi].getLength();i<maxi;i++) {
Node found=globalS[gi].item(i);
String nname=found.getParentNode().getNodeName();
if(! (nname.equals("moby:Collection") || nname.equals("Collection"))) {
// Remove the articleName from the Simple element
// As it's got to be attached now to the Colelction element
// NB: Let Taverna attach it automatically to the Collection element
found.getAttributes().removeNamedItem("moby:articleName");
comienzo.appendChild(docsalida.importNode(found,true));
}
}
}
for(gi=0,maxgi=globalC.length;gi<maxgi;gi++) {
int i;
int maxi;
for(i=0,maxi=globalC[gi].getLength();i<maxi;i++) {
Node found=globalC[gi].item(i);
comienzo.appendChild(docsalida.importNode(found,true));
}
}
// Last step!!!
serializer.serialize(docsalida);
OutObj = sw.toString();
MobyOutput = OutObj;
MobyA
MobyB
MobyC
MobyOutput
Converts a DNA FASTA sequence into a DNA sequence
http://moby.ucalgary.ca/moby/MOBY-Central.pl
fromFASTAToDNASequence
genome.imim.es
Converts a DNA FASTA sequence into a DNA sequence
http://moby.ucalgary.ca/moby/MOBY-Central.pl
fromFASTAToDNASequence
genome.imim.es
Ab initio gene prediction tool that returns the gene predictions in GFF format (GFF version 2).
http://moby.ucalgary.ca/moby/MOBY-Central.pl
runGeneIDGFF
genome.imim.es
Both
Homo sapiens (suitable for mammals)
Normal
None
None
Ab initio gene prediction service. It runs geneid with synteny evidences to improve the accuracy of the results and returns the output predictions in GFF format. To generate the synteny evidences, use a service that provides tblastx.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
runSGP2GFF
genome.imim.es
Human Vs Mouse
Processor to parse the datatype GFF
http://moby.ucalgary.ca/moby/MOBY-Central.pl
GFF
geneid_predictions
Processor to parse the datatype GFF
Processor to parse the datatype b64_encoded_jpeg
http://moby.ucalgary.ca/moby/MOBY-Central.pl
b64_encoded_jpeg
image
Processor to parse the datatype b64_encoded_jpeg
It compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence (used as a database) using the Washington University BLAST algorithm.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
runWUTBlastx_2Seqs
inb.bsc.es
off
9
none
sump
3
15
blosum62
10.0
25
2
a string
http://moby.ucalgary.ca/moby/MOBY-Central.pl
String
Runs gff2ps software to vizualize a set of GFF annotations maps. It returns an encoded image in JPEG format.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
runGFF2JPEG
genome.imim.es
a string
http://moby.ucalgary.ca/moby/MOBY-Central.pl
String
Processor to parse the datatype BLAST-Text
http://moby.ucalgary.ca/moby/MOBY-Central.pl
BLAST-Text
wutblastx_report
Processor to parse the datatype BLAST-Text
NA sequence in FASTA format
http://moby.ucalgary.ca/moby/MOBY-Central.pl
FASTA_NA
Processor to parse the datatype GFF
http://moby.ucalgary.ca/moby/MOBY-Central.pl
GFF
geneid_predictions
Processor to parse the datatype GFF
NA sequence in FASTA format
http://moby.ucalgary.ca/moby/MOBY-Central.pl
FASTA_NA
a string
http://moby.ucalgary.ca/moby/MOBY-Central.pl
String
Generic Feature Format File (of any subtype)
http://moby.ucalgary.ca/moby/MOBY-Central.pl
GFF
text/xml
image/*