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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.ronn;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
import org.junit.Test;
import java.io.IOException;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
/**
* Tests the following UniProt IDs:
*
* Methyltransferase mtmB1, UniProt O30642
* Sec (U), Selenoprotein V, UniProt P59797
* Asx (B), 5-hydroxytryptamine receptor 1F, UniProt Q9N2D9
* Xaa (X), DNA-3-methyladenine glycosylase (Fragment), UniProt P23571
* Glx (Z), 14-3-3 protein gamma-1, UniProt Q6UFZ3
*
*
*/
public class NonstandardProteinCompoundTest {
@Test
public void test() throws IOException, InterruptedException {
String[] uniprotIDs = new String[]{"O30642","P59797","Q9N2D9","Q9N2D9","Q6UFZ3","O30642"};
for ( String id: uniprotIDs){
try {
testUniprot(id);
// throttle load on uniprot server
Thread.sleep(1000);
} catch (CompoundNotFoundException e){
fail(e.getMessage());
}
}
}
private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
}
/**
* Fetch a protein sequence from the UniProt web site
*
* @param uniProtID
* @return a Protein Sequence
* @throws IOException
* @throws CompoundNotFoundException
*/
private static ProteinSequence getUniprot(String uniProtID) throws CompoundNotFoundException, IOException {
AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence =
new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
ProteinSequence seq = new ProteinSequence(uniprotSequence);
return seq;
}
}
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