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Merge branch 'master' into phylo
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‎biojava-aa-prop/pom.xml‎

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<name>biojava-aa-prop</name>
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<url>http://www.biojava.org</url>
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<licenses>
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<license>
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<name>GNU LGPL v2</name>
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<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<build>
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<plugins>
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<plugin>

‎biojava-alignment/pom.xml‎

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<artifactId>biojava-alignment</artifactId>
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<name>biojava-alignment</name>
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<url>http://maven.apache.org</url>
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<licenses>
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<license>
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<name>GNU LGPL v2</name>
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<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<url>http://www.biojava.org</url>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<dependency>
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<groupId>org.biojava.thirdparty</groupId>
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<artifactId>forester</artifactId>
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<version>1.005</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>

‎biojava-core/pom.xml‎

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<name>BioJava</name>
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<url>http://www.biojava.org</url>
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</organization>
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<licenses>
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<license>
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<name>GNU LGPL v2</name>
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<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<build>
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<plugins>
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<plugin>

‎biojava-core/src/main/java/demo/DemoSixFrameTranslation.java‎

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package demo;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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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.AmbiguityDNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
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import org.biojava.nbio.core.sequence.io.DNASequenceCreator;
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import org.biojava.nbio.core.sequence.io.FastaReader;
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import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import org.biojava.nbio.core.sequence.template.Sequence;
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import org.biojava.nbio.core.sequence.transcription.Frame;
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import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine;
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import java.io.ByteArrayInputStream;
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import java.io.InputStream;
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import java.util.LinkedHashMap;
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import java.util.Map;
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/**
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* Created by andreas on 8/10/15.
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*/
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public class DemoSixFrameTranslation {
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public static void main(String[] args){
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String dnaFastaS = ">gb:GQ903697|Organism:Arenavirus H0030026 H0030026|Segment:S|Host:Rat\n" +
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"CGCACAGAGGATCCTAGGCGTTACTGACTTGCGCTAATAACAGATACTGTTTCATATTTAGATAAAGACC\n" +
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"CAGCCAACTGATTGGTCAGCATGGGACAACTTGTGTCCCTCTTCAGTGAAATTCCATCAATCATACACGA\n" +
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"AGCTCTCAATGTTGCTCTCGTAGCTGTTAGCATCATTGCAATATTGAAAGGGGTTGTGAATGTTTGGAAG\n" +
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"AGTGGAGTTTTGCAGCTTTTGGCCTTCTTGCTCCTGGCGGGAAGATCCTGCTCAGTCATAATTGGTCATC\n" +
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"ATCTCGAACTGCAGCATGTGATCTTCAATGGGTCATCAATCACACCCTTTTTACCAGTTACATGTAAGAT\n" +
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"CAATGATACCTACTTCCTACTAAGAGGCCCCTATGAAGCTGATTGGGCAGTTGAATTGAGTGTAACTGAA\n" +
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"ACCACAGTCTTGGTTGATCTTGAAGGTGGCAGCTCAATGAAGCTGAAAGCCGGAAACATCTCAGGTTGTC\n" +
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"TTGGAGACAACCCCCATCTGAGATCAGTGGTCTTCACATTGAATTGGTTGCTAACAGGATTAGATCATGT\n" +
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"TATTGATTCTGACCCGAAAATTCTCTGTGATCTTAAAGACAGTGGGCACTTTCGTCTCCAGATGAACTTA\n" +
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"ACAGAAAAGCACTATTGTGACAAGTTTCACATCAAAATGGGCAAGGTCTTTGGCGTATTCAAAGATCCGT\n" +
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"GCATGGCTGGTGGTAAAATGTTTGCCATACTAAAAAATACCTCTTGGTCGAACCAGTGCCAAGGAAACCA\n" +
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"TGTCAGCACCATTCATCTTGTCCTTCAGAGTAATTTCAAACAGGTCCTCAGTAGCAGGAAACTGTTGAAC\n" +
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"TTTTTCAGCTGGTCATTGTCTGATGCCACAGGGGCTGATATGCCTGGTGGTTTTTGTCTGGAAAAATGGA\n" +
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"TGTTGATTTCAAGTGAACTGAAATGCTTTGGAAACACAGCTGTGGCAAAGTGCAACTTAAATCATGACTC\n" +
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"AGAGTTCTGTGACATGCTTAGGCTTTTTGATTTCAACAAAAAGGCAATAGTCACTCTTCAGAACAAAACA\n" +
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"AAGCATCGGCTGGACACAGTAATTACTGCTATCAATTCATTGATCTCTGATAATATTCTTATGAAGAACA\n" +
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"GGATTAAAGAATTGATAGATGTTCCTTACTGTAATTACACCAAATTTTGGTATGTCAATCACACAGGTCT\n" +
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"AAATCTGCACACCCTTCCAAGATGTTGGCTTGTTAAAAATGGTAGCTACTTGAATGTGTCTGACTTCAGG\n" +
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"AATGAGTGGATATTGGAGAGTGATCATCTTGTTTCGGAGATCCTTTCAAAGGAGTATGAGGAAAGGCAAA\n" +
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"ATCGTACACCACTCTCACTGGTTGACATCTGTTTCTGGAGTACATTGTTTTACACAGCATCAATTTTCCT\n" +
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"ACACCTCTTGAGAATTCCAACCCACAGACACATTGTTGGTGAGGGCTGCCCGAAGCCTCATAGGCTAAAC\n" +
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"AGGCACTCAATATGTGCTTGTGGCCTTTTCAAACAAGAAGGCAGACCCTTGAGATGGGTAAGAAAGGTGT\n" +
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"GAACAATGGTTGCTTGGTGGCCTCCATTGCTGCACCCCCCTAGGGGGGTGCAGCAATGGAGGTTCTCGYT\n" +
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"GAGCCTAGAGAACAACTGTTGAATCGGGTTCTCTAAAGAGAACATCGATTGGTAGTACCCTTTTTGGTTT\n" +
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"TTCATTGGTCACTGACCCTGAAAGCACAGCACTGAACATCAAACAGTCCAAAAGTGCACAGTGTGCATTT\n" +
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"GTTGTGGCTGGTGCTGATCCTTTCTTCTTACTTTTAATGACTATTCCCTTATGTCTGTCACACAGATGTT\n" +
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"CAAATCTCTTCCAAACAAGATCTTCAAAGAGCCGTGACTGTTCTGCGGTCAGTTTGACATCAACAATCTT\n" +
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"CAAATCCTGTCTTCCATGCATATCAAAGAGCCTCCTAATATCATCAGCACCTTGCGCAGTGAAAACCATG\n" +
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"GATTTAGGCAGACTCCTTATTATGCTTGTGATGAGGCCAGGTCGTGCATGTTCAACATCCTTCAGCAATA\n" +
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"TCCCATGACAATATTTACTTTGGTCCTTAAAAGATTTTATGTCATTGGGTTTTCTGTAGCAGTGGATGAA\n" +
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"TTTTTGTGATTCAGGCTGGTAAATTGCAAACTCAACAGGGTCATGTGGCGGGCCTTCAATGTCAATCCAT\n" +
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"GTTGTGTCACTGACCATCAACGACTCTACACTTCTCTTCACCTGAGCCTCCACCTCAGGCTTGAGCGTGG\n" +
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"ACAAGAGTGGGGCACCACCGTTCCGGATGGGGACTGGTGTTTTGCTTGGTAAACTCTCAAATTCCACAAC\n" +
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"TGTATTGTCCCATGCTCTCCCTTTGATCTGTGATCTTGATGAAATGTAAGGCCAGCCCTCACCAGAGAGA\n" +
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"CACACCTTATAAAGTATGTTTTCATAAGGATTCCTCTGTCCTGGTATGGCACTGATGAACATGTTTTCCC\n" +
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"TCTTTTTGATCTCCAAGAGGGTTTTTATAATGGTTGTGAATGTGGACTCCTCAATCTTTATTGTTTCCAG\n" +
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"CATGTTGCCACCATCAATCAGGCAAGCACCGGCTTTCACAGCAGCTGATAAACTAAGGTTGTAGCCTGAT\n" +
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"ATGTTAATTTGAGAATCCTCCTGAGTGATTACCTTTAGAGAAGGATGCTTCTCCATCAAAGCATCTAAGT\n" +
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"CACTTAAATTAGGGTATTTTGCTGTGTATAGCAACCCCAGATCTGTGAGGGCCTGAACCACATCATTTAG\n" +
69+
"AGTTTCCCCTCCCTGTTCAGTCATACAGGAAATTGTGAGTGCTGGCATCGATCCAAATTGGTTGATCATA\n" +
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"AGTGATGAGTCTTTAACGTCCCAGACTTTGACCACCCCTCCAGTTCTAGCCAACCCAGGTCTCTGAATAC\n" +
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"CAACAAGTTGCAGAATTTCGGACCTCCTGGTGAGCTGTGTTGTAGAGAGGTTCCCTAGATACTGGCCACC\n" +
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"TGTGGCTGTCAACCTCTCTGTTCTTTGAACTTTTTGCCTTAATTTGTCCAAGTCACTGGAGAGTTCCATT\n" +
73+
"AGCTCTTCCTTTGACAATGATCCTATCTTAAGGAACATGTTCTTTTGGGTTGACTTCATGACCATCAATG\n" +
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"AGTCAACTTCCTTATTCAAGTCCCTCAAACTAACAAGATCACTGTCATCTCTTTTAGACCTCCTCATCAT\n" +
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"GCGTTGCACACTTGCAACCTTTGAAAAATCTAAGCCGGACAGAAGAGCCCTCGCGTCAGTTAGGACATCT\n" +
76+
"GCCTTAACAGCAGTTGTCCAGTTCGAGAGTCCTCTCCTGAGAGACTGTGTCCATCTGAATGATGGGATTG\n" +
77+
"GTTGTTCGCTCATAGTGATGAAATTGCGCAGAGTTATCCAAAAGCCTAGGATCCTCTGTGCG";
78+
79+
80+
try {
81+
82+
// parse the raw sequence from the string
83+
InputStream stream = new ByteArrayInputStream(dnaFastaS.getBytes());
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// define the Ambiguity Compound Sets
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AmbiguityDNACompoundSet ambiguityDNACompoundSet = AmbiguityDNACompoundSet.getDNACompoundSet();
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CompoundSet<NucleotideCompound> nucleotideCompoundSet = AmbiguityRNACompoundSet.getRNACompoundSet();
88+
89+
FastaReader<DNASequence, NucleotideCompound> proxy =
90+
new FastaReader<DNASequence, NucleotideCompound>(
91+
stream,
92+
new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
93+
new DNASequenceCreator(ambiguityDNACompoundSet));
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95+
// has only one entry in this example, but could be easily extended to parse a FASTA file with multiple sequences
96+
LinkedHashMap<String, DNASequence> dnaSequences = proxy.process();
97+
98+
// Initialize the Transcription Engine
99+
TranscriptionEngine engine = new
100+
TranscriptionEngine.Builder().dnaCompounds(ambiguityDNACompoundSet).rnaCompounds(nucleotideCompoundSet).build();
101+
102+
Frame[] sixFrames = Frame.getAllFrames();
103+
104+
105+
106+
for (DNASequence dna : dnaSequences.values()) {
107+
108+
Map<Frame, Sequence<AminoAcidCompound>> results = engine.multipleFrameTranslation(dna, sixFrames);
109+
110+
for (Frame frame : sixFrames){
111+
System.out.println("Translated Frame:" + frame +" : " + results.get(frame));
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//System.out.println(dna.getRNASequence(frame).getProteinSequence(engine));
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ProteinSequence ps = new ProteinSequence(results.get(frame).getSequenceAsString());
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System.out.println(ps);
116+
try {
117+
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} catch (Exception e){
119+
System.err.println(e.getMessage() + " when trying to translate frame " + frame);
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}
121+
}
122+
123+
}
124+
} catch (Exception e){
125+
e.printStackTrace();
126+
}
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}
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}

‎biojava-core/src/main/java/demo/ParseFastaFileDemo.java‎

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package demo;
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3+
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
7+
import java.io.InputStream;
8+
import java.util.LinkedHashMap;
9+
import java.util.logging.Level;
10+
import java.util.logging.Logger;
11+
import org.biojava.nbio.core.sequence.ProteinSequence;
12+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
13+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.io.FastaReader;
15+
import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
16+
import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
17+
import org.biojava.nbio.core.util.InputStreamProvider;
18+
19+
20+
/**
21+
* Created by andreas on 6/17/15.
22+
*/
23+
public class ParseFastaFileDemo {
24+
25+
26+
public ParseFastaFileDemo(){
27+
28+
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}
30+
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/** e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
32+
* and pass in path to local location of file
33+
*
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* @param args
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*/
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public static void main(String[] args) {
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int mb = 1024*1024;
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//Getting the runtime reference from system
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Runtime runtime = Runtime.getRuntime();
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System.out.println("##### Heap utilization statistics [MB] #####");
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//Print used memory
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System.out.println("Used Memory:"
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+ (runtime.totalMemory() - runtime.freeMemory()) / mb);
48+
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//Print free memory
50+
System.out.println("Free Memory:"
51+
+ runtime.freeMemory() / mb);
52+
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//Print total available memory
54+
System.out.println("Total Memory:" + runtime.totalMemory() / mb);
55+
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//Print Maximum available memory
57+
System.out.println("Max Memory:" + runtime.maxMemory() / mb);
58+
59+
60+
if ( args.length < 1) {
61+
System.err.println("First argument needs to be path to fasta file");
62+
return;
63+
}
64+
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File f = new File(args[0]);
66+
67+
if ( ! f.exists()) {
68+
System.err.println("File does not exist " + args[0]);
69+
return;
70+
}
71+
72+
long timeS = System.currentTimeMillis();
73+
74+
try {
75+
76+
// automatically uncompress files using InputStreamProvider
77+
InputStreamProvider isp = new InputStreamProvider();
78+
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InputStream inStream = isp.getInputStream(f);
80+
81+
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FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
83+
inStream,
84+
new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
85+
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
86+
87+
LinkedHashMap<String, ProteinSequence> b;
88+
89+
int nrSeq = 0;
90+
91+
while ((b = fastaReader.process(100)) != null) {
92+
for (String key : b.keySet()) {
93+
nrSeq++;
94+
//System.out.println(nrSeq + " : " + key + " " + b.get(key));
95+
if ( nrSeq % 100000 == 0)
96+
System.out.println(nrSeq );
97+
}
98+
99+
}
100+
long timeE = System.currentTimeMillis();
101+
System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
102+
} catch (Exception ex) {
103+
Logger.getLogger(ParseFastaFileDemo.class.getName()).log(Level.SEVERE, null, ex);
104+
}
105+
}
106+
}

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.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
6+
* 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,
15+
* 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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*/
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package org.biojava.nbio.core.search.io;
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import java.util.Iterator;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.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
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
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* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
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* at:
17+
*
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* http://www.biojava.org/
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*
20+
*/
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package org.biojava.nbio.core.search.io;
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import java.util.ArrayList;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.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
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
19+
*
20+
*/
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package org.biojava.nbio.core.search.io;
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import java.util.HashMap;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.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
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
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*
20+
*/
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package org.biojava.nbio.core.search.io;
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import java.io.File;

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