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NCBIQBlastService replaced with the new implementation.
(For usage example see NCBIQBlastServiceDemo) git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9533 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent 31eb18d commit e3a8dcd

20 files changed

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‎biojava3-core/src/test/java/org/biojava3/core/sequence/DNATest.java‎

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package org.biojava3.core.sequence;
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import org.biojava3.core.sequence.template.SequenceReader;
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import static org.hamcrest.CoreMatchers.is;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.assertTrue;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import junit.framework.Assert;
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import org.biojava3.core.exceptions.CompoundNotFoundError;
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import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
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import org.biojava3.core.sequence.compound.DNACompoundSet;
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import org.biojava3.core.sequence.compound.NucleotideCompound;
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import org.biojava3.core.sequence.storage.BitSequenceReader;
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import org.biojava3.core.sequence.storage.FourBitSequenceReader;
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import org.biojava3.core.sequence.storage.SingleCompoundSequenceReader;
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import org.biojava3.core.sequence.storage.TwoBitSequenceReader;
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import org.biojava3.core.sequence.template.CompoundSet;
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import org.biojava3.core.sequence.template.ProxySequenceReader;
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import org.biojava3.core.sequence.template.SequenceMixin;
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import org.biojava3.core.sequence.template.SequenceReader;
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import org.biojava3.core.sequence.template.SequenceView;
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import org.biojava3.core.sequence.transcription.Frame;
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import org.biojava3.core.sequence.views.ComplementSequenceView;

‎biojava3-ws/src/main/java/demo/NCBIQBlastService2Demo.java‎

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This file was deleted.

‎biojava3-ws/src/main/java/demo/NCBIQBlastServiceDemo.java‎

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package demo;
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import static org.biojava3.ws.alignment.qblast.BlastAlignmentParameterEnum.ENTREZ_QUERY;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import org.biojava3.core.sequence.io.util.IOUtils;
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import org.biojava3.ws.alignment.qblast.BlastProgramEnum;
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import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
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import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
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import org.biojava3.ws.alignment.qblast.NCBIQBlastService;
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/**
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* A simple demo showing {@link NCBIQBlastService} usage
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*
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* @author Gediminas Rimsa
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*/
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public class NCBIQBlastServiceDemo {
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private static final String BLAST_OUTPUT_FILE = "blastOutput.xml";
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private static final String SEQUENCE = "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKS";
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public static void main(String[] args) {
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NCBIQBlastService service = new NCBIQBlastService();
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// set alignment options
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NCBIQBlastAlignmentProperties props = new NCBIQBlastAlignmentProperties();
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props.setBlastProgram(BlastProgramEnum.blastp);
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props.setBlastDatabase("swissprot");
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props.setAlignmentOption(ENTREZ_QUERY, "\"serum albumin\"[Protein name] AND mammals[Organism]");
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// set output options
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NCBIQBlastOutputProperties outputProps = new NCBIQBlastOutputProperties();
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// Example of two possible ways of setting output options (in this case, it was already set by constructor)
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// outputProps.setAlignmentNumber(100);
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// outputProps.setOutputOption(BlastOutputParameterEnum.ALIGNMENTS, "100");
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String rid = null;
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FileWriter writer = null;
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BufferedReader reader = null;
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try {
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// send blast request and save request id
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rid = service.sendAlignmentRequest(SEQUENCE, props);
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while (!service.isReady(rid)) {
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System.out.println("Waiting for results. Sleeping for 5 seconds");
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Thread.sleep(5000);
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}
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// read results when they are ready
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InputStream in = service.getAlignmentResults(rid, outputProps);
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reader = new BufferedReader(new InputStreamReader(in));
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File f = new File(BLAST_OUTPUT_FILE);
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System.out.println("Saving query results in file " + f.getAbsolutePath());
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writer = new FileWriter(f);
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String line;
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while ((line = reader.readLine()) != null) {
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writer.write(line + System.getProperty("line.separator"));
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}
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} catch (Exception e) {
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System.out.println(e.getMessage());
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e.printStackTrace();
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} finally {
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IOUtils.close(writer);
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IOUtils.close(reader);
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service.sendDeleteRequest(rid);
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}
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}
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}

‎biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastAlignmentParameterEnum.java‎

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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
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* be distributed with the code. If you do not have a copy,
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* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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* Created on 2012-02-11
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*
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*/
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package org.biojava3.ws.alignment.qblast;
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/**
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* Alignment request parameters accepted by QBlast service.<br/>
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* Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
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* <p/>
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* Taken from <a href=http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
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*
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* @author Gediminas Rimsa
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*/
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public enum BlastAlignmentParameterEnum {
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CMD,
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TOOL,
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EMAIL,
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ALIGNMENTS,
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BLAST_PROGRAM,
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CDD_SEARCH,
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COMPOSITION_BASED_STATISTICS,
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DATABASE_PREFIX,
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DATABASE,
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DB_GENETIC_CODE,
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DESCRIPTIONS,
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ENTREZ_QUERY,
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EXPECT,
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FILTER,
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FIRST_QUERY_NUM,
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GAPCOSTS,
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GENETIC_CODE,
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HITLIST_SIZE,
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I_THRESH,
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LCASE_MASK,
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MATCH_SCORES,
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MATRIX_NAME,
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MAX_NUM_SEQ,
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MEGABLAST,
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NUM_OVERVIEW,
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OTHER_ADVANCED,
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PERC_IDENT,
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PHI_PATTERN,
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PROGRAM,
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PSSM,
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QUERY,
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QUERY_BELIEVE_DEFLINE,
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QUERY_FROM,
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QUERY_TO,
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REPEATS,
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SHORT_QUERY_ADJUST,
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SEARCHSP_EFF,
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TEMPLATE_LENTH,
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TEMPLATE_TYPE,
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THRESHOLD,
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TWO_HITS,
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WORD_SIZE,
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WWW_BLAST_TYPE
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}

biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast2/NCBIQBlastJob.java renamed to biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastJob.java

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*
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*/
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package org.biojava3.ws.alignment.qblast2;
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package org.biojava3.ws.alignment.qblast;
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/**
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* Used to store information about QBlast search job, namely: request ID, start
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* time, expected execution time
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* Information about QBlast search job
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*
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* @author Gediminas Rimsa
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*/
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public class NCBIQBlastJob {
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public class BlastJob {
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private String id;
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private long startTimestamp;
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private long expectedExecutionTime;
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/**
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* Request id (RID) as received from QBlast server
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* @return
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*/
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public String getId() {
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return id;
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}
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public void setExpectedExecutionTime(long expectedExecutionTime) {
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this.expectedExecutionTime = expectedExecutionTime;
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}
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@Override
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public String toString() {
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StringBuilder builder = new StringBuilder();
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builder.append("BlastJob [id=");
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builder.append(id);
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builder.append(", startTimestamp=");
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builder.append(startTimestamp);
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builder.append(", expectedExecutionTime=");
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builder.append(expectedExecutionTime);
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builder.append("]");
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return builder.toString();
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}
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}

biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast2/enums/BlastMatrix.java renamed to biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastMatrixEnum.java

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*
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*/
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package org.biojava3.ws.alignment.qblast2.enums;
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package org.biojava3.ws.alignment.qblast;
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/**
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* Enum representing blast matrices supported by QBlast
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* Enum representing matrices supported by QBlast
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*
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* @author Gediminas Rimsa
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*/
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public enum BlastMatrix {
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public enum BlastMatrixEnum {
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BLOSUM45,
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BLOSUM50,
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BLOSUM62,
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PAM250,
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PAM30,
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PAM70
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}

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