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otter606otter606
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remove GenbankProxySequenceReader main
1 parent 195d3da commit c1e7610

1 file changed

Lines changed: 1 addition & 104 deletions

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‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java‎

Lines changed: 1 addition & 104 deletions
Original file line numberDiff line numberDiff line change
@@ -25,13 +25,7 @@
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package org.biojava.nbio.core.sequence.loader;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.AccessionID;
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import org.biojava.nbio.core.sequence.DNASequence;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
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import org.biojava.nbio.core.sequence.features.*;
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import org.biojava.nbio.core.sequence.io.GenbankSequenceParser;
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import org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser;
@@ -183,102 +177,5 @@ public Map<String, List<DBReferenceInfo>> getDatabaseReferences() {
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public List<String> getKeyWords() {
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return genbankParser.getKeyWords();
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}
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public static void main(String[] args) throws Throwable {
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GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
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= new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
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ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
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genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
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logger.info("Sequence ({},{})={}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankProteinReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankProteinReader.getDatabaseReferences());
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proteinSequence.getFeatures();
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GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
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DNASequence dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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dnaSequence.setAccession(new AccessionID("NM_001126"));
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_000266", DNACompoundSet.getDNACompoundSet());
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dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "AV254721", DNACompoundSet.getDNACompoundSet());
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dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "AV254721.2", DNACompoundSet.getDNACompoundSet());
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dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "U49845", DNACompoundSet.getDNACompoundSet());
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dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "GI:1293613", DNACompoundSet.getDNACompoundSet());
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dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "14109166", DNACompoundSet.getDNACompoundSet());
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dnaSequence = new DNASequence(genbankDNAReader);
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genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
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logger.info("Sequence ({},{})={}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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logger.info("Keywords: {}", genbankDNAReader.getKeyWords());
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logger.info("DatabaseReferences: {}", genbankDNAReader.getDatabaseReferences());
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/*
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GenbankProxySequenceReader genbankProxyReader = new GenbankProxySequenceReader("/tmp");
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Sequence<?> sequence;
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sequence = genbankProxyReader.getDNASequence(new AccessionID("NM_001126"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getDNASequence(new AccessionID("NM_000266"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getProteinSequence(new AccessionID("NP_000257"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getProteinSequence(new AccessionID("AV254721"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getProteinSequence(new AccessionID("AV254721.2"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getProteinSequence(new AccessionID("U49845"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getProteinSequence(new AccessionID("GI:1293613"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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sequence = genbankProxyReader.getProteinSequence(new AccessionID("14109166"));
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System.out.println("Sequence" + "(" + sequence.getLength() + ")=" + sequence.getSequenceAsString().substring(0, 10) + "...");
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*/
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}
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}

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