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lafitalafita
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Port TreeConstructor.main to demo
1 parent 04a9adb commit 4485ea6

2 files changed

Lines changed: 33 additions & 65 deletions

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‎biojava-phylo/src/main/java/demo/DemoTreeConstructor.java‎

Lines changed: 33 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1,49 +1,66 @@
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package demo;
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3+
import java.io.InputStream;
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import java.util.LinkedHashMap;
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import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
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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.io.FastaReader;
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import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
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import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
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import org.biojava.nbio.phylo.TreeConstructionAlgorithm;
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import org.biojava.nbio.phylo.ProgressListenerStub;
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import org.biojava.nbio.phylo.TreeConstructor;
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import org.biojava.nbio.phylo.TreeType;
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/**
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* This demo contains the CookBook examples to create a phylogenetic tree from a
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* This demo contains the CookBook example to create a phylogenetic tree from a
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* given multiple sequence alignment (MSA).
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*
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* @author Scooter Willis
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* @author Aleix Lafita
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*
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*/
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public class DemoTreeConstructor {
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public static void main(String[] args) throws Exception {
2129

22-
MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = new
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MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
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InputStream inStream = TreeConstructor.class
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.getResourceAsStream("/PF00104_small.fasta");
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ProteinSequence pSeq1 = new ProteinSequence(
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"RER-RDGGGNSRKYDDRRSPRDGE---IDYDERTVSHYQRQFQDERISDGM"
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+ "LNTLKQSLKGLDCQPIHLKDSKANRSIMIDEIHTGTADSVTFEQKLPDGEMKL");
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ProteinSequence pSeq2 = new ProteinSequence(
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"RDRHRD---DRHRYDEDRDHRRDQRNVSDYDSEELRKFEEDYKSDRLGQYV"
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+ "FSDLNSAVKGLVVQPIHL-NKEVNRTVIIDSICKESAEKVRFEFGKGEDAREI");
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ProteinSequence pSeq3 = new ProteinSequence(
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"RPTH---GGLSLNIDVSTTMILEPGPVIEF-----LKANQSVETPRQIDWI"
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+ "-----KAAKML--KHMRVKATHRNMEFKIIGLSSKPCNQQLFSMKIKDGEREV");
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FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
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new FastaReader<ProteinSequence, AminoAcidCompound>(
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inStream, new GenericFastaHeaderParser<ProteinSequence,
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AminoAcidCompound>(), new ProteinSequenceCreator(
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AminoAcidCompoundSet.getAminoAcidCompoundSet()));
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LinkedHashMap<String, ProteinSequence> proteinSequences =
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fastaReader.process();
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inStream.close();
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35-
msa.addAlignedSequence(pSeq1);
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msa.addAlignedSequence(pSeq2);
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msa.addAlignedSequence(pSeq3);
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MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa =
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new MultipleSequenceAlignment<ProteinSequence,
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AminoAcidCompound>();
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for (ProteinSequence proteinSequence : proteinSequences.values()) {
49+
msa.addAlignedSequence(proteinSequence);
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}
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long readTime = System.currentTimeMillis();
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TreeConstructor<ProteinSequence, AminoAcidCompound> treeConstructor =
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new TreeConstructor<ProteinSequence, AminoAcidCompound>(
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msa, TreeType.NJ, TreeConstructionAlgorithm.PID,
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msa, TreeType.NJ, TreeConstructionAlgorithm.PID,
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new ProgressListenerStub());
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treeConstructor.process();
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long treeTime = System.currentTimeMillis();
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String newick = treeConstructor.getNewickString(true, true);
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System.out.println(newick);
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System.out.println("Tree time {" + (treeTime - readTime) + "}");
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}
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}

‎biojava-phylo/src/main/java/org/biojava/nbio/phylo/TreeConstructor.java‎

Lines changed: 0 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -25,12 +25,6 @@
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package org.biojava.nbio.phylo;
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import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
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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.io.FastaReader;
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import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
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import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
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import org.biojava.nbio.core.sequence.template.AbstractSequence;
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import org.biojava.nbio.core.sequence.template.Compound;
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import org.forester.evoinference.distance.NeighborJoining;
@@ -41,13 +35,10 @@
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.InputStream;
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import java.io.PrintStream;
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import java.text.DecimalFormat;
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import java.util.ArrayList;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Vector;
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@@ -267,44 +258,4 @@ public void updateProgress(String state, int currentCount, int totalCount) {
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}
268259
}
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270-
public static void main(String[] args) {
271-
272-
try {
273-
274-
275-
InputStream inStream = TreeConstructor.class.getResourceAsStream("/PF00104_small.fasta");
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277-
278-
279-
FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence,AminoAcidCompound>(inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
280-
LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process();
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inStream.close();
282-
283-
284-
MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> multipleSequenceAlignment = new MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
285-
for (ProteinSequence proteinSequence : proteinSequences.values()) {
286-
287-
multipleSequenceAlignment.addAlignedSequence(proteinSequence);
288-
}
289-
290-
long readTime = System.currentTimeMillis();
291-
TreeConstructor<ProteinSequence, AminoAcidCompound> treeConstructor = new TreeConstructor<ProteinSequence, AminoAcidCompound>(multipleSequenceAlignment, TreeType.NJ, TreeConstructionAlgorithm.PID, new ProgressListenerStub());
292-
treeConstructor.process();
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long treeTime = System.currentTimeMillis();
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String newick = treeConstructor.getNewickString(true, true);
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296-
297-
298-
299-
logger.info("Tree time {}", (treeTime - readTime));
300-
logger.info(newick);
301-
302-
// treeConstructor.outputPhylipDistances("/Users/Scooter/mutualinformation/project/nuclear_receptor/PF00104_small.fasta.phylip");
303-
304-
} catch (FileNotFoundException ex) {
305-
logger.error("Can't find file specified by args[0]", ex);
306-
} catch (Exception e) {
307-
logger.error("Exception: ", e);
308-
}
309-
}
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}

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