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emckee2006emckee2006
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Merge branch 'pr/44'
# Conflicts: # biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
2 parents 6c6cdaa + 715fce4 commit c819e5a

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-813
lines changed

32 files changed

+895
-813
lines changed

‎.travis.yml‎

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@@ -2,4 +2,5 @@ language: java
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jdk:
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- oraclejdk8
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sudo: false
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#after_success:
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# - mvn clean cobertura:cobertura coveralls:report

‎biojava-aa-prop/src/test/resources/log4j2.xml‎

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@@ -6,7 +6,7 @@
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</Console>
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</appenders>
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<loggers>
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<root level="info">
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<root level="warn">
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<appender-ref ref="Console"/>
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</root>
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</loggers>

‎biojava-alignment/src/test/java/org/biojava/nbio/alignment/NeedlemanWunschTest.java‎

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@@ -77,7 +77,7 @@ public void testComplex() throws Exception {
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PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(a, b, Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(gop, gep), mx);
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SequencePair<DNASequence, NucleotideCompound> pair = aligner.getPair();
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System.out.println(pair); // prints the alignment above
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int nMatches = "--CGTATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA".length() - 2 - 4;
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double expectedScore = nMatches * match

‎biojava-alignment/src/test/resources/log4j2.xml‎

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@@ -6,7 +6,7 @@
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</Console>
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</appenders>
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<loggers>
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<root level="info">
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<root level="warn">
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<appender-ref ref="Console"/>
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</root>
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</loggers>

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java‎

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@@ -74,13 +74,13 @@ public void testProcess() throws Throwable {
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= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "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("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
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GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
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= new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "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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logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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//logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
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/*
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* Method 2: With the GenbankReaderHelper
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*/
@@ -92,12 +92,12 @@ public void testProcess() throws Throwable {
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LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(dnaResource.getInputStream());
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for (DNASequence sequence : dnaSequences.values()) {
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logger.info("DNA Sequence: {}", sequence.getSequenceAsString());
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logger.debug("DNA Sequence: {}", sequence.getSequenceAsString());
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}
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LinkedHashMap<String, ProteinSequence> protSequences = GenbankReaderHelper.readGenbankProteinSequence(protResource.getInputStream());
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for (ProteinSequence sequence : protSequences.values()) {
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logger.info("Protein Sequence: {}", sequence.getSequenceAsString());
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logger.debug("Protein Sequence: {}", sequence.getSequenceAsString());
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}
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/*
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* Method 3: With the GenbankReader Object
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);
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dnaSequences = dnaReader.process();
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logger.info("DNA Sequence: {}", dnaSequences);
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logger.debug("DNA Sequence: {}", dnaSequences);
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GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
@@ -121,7 +121,7 @@ public void testProcess() throws Throwable {
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);
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protSequences = protReader.process();
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logger.info("Protein Sequence: {}", protSequences);
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logger.debug("Protein Sequence: {}", protSequences);
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}
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‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java‎

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@@ -128,7 +128,7 @@ public void CDStest() throws Exception {
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Assert.assertTrue(proteinSequences.size() == 1);
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logger.info("protein sequences: {}", proteinSequences);
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logger.debug("protein sequences: {}", proteinSequences);
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ProteinSequence protein = new ArrayList<ProteinSequence>(proteinSequences.values()).get(0);
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‎biojava-core/src/test/resources/log4j2.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Configuration status="WARN">
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<Appenders>
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<configuration status="WARN">
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<appenders>
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<Console name="Console" target="SYSTEM_ERR">
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<PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
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</Console>
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</Appenders>
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<Loggers>
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<!--
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<Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
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<AppenderRef ref="Console"/>
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</Logger>
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-->
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<!--
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<Logger name="org.biojava.nbio.core.sequence.location.InsdcParserTest" level="debug" />
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-->
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<Root level="info">
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<AppenderRef ref="Console"/>
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</Root>
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</Loggers>
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</Configuration>
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</appenders>
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<loggers>
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<root level="warn">
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<appender-ref ref="Console"/>
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</root>
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</loggers>
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</configuration>

‎biojava-genome/src/test/resources/log4j2.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Configuration status="WARN">
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<Appenders>
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<configuration status="WARN">
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<appenders>
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<Console name="Console" target="SYSTEM_ERR">
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<PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
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</Console>
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</Appenders>
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<Loggers>
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<!--
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<Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
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<AppenderRef ref="Console"/>
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</Logger>
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-->
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<Root level="info">
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<AppenderRef ref="Console"/>
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</Root>
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</Loggers>
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</Configuration>
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</appenders>
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<loggers>
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<root level="warn">
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<appender-ref ref="Console"/>
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</root>
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</loggers>
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</configuration>

‎biojava-integrationtest/src/test/resources/log4j2.xml‎

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</Console>
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</appenders>
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<loggers>
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<root level="info">
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<root level="warn">
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<appender-ref ref="Console"/>
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</root>
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</loggers>

‎biojava-modfinder/src/test/resources/log4j2.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<Configuration status="WARN">
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<Appenders>
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<configuration status="WARN">
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<appenders>
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<Console name="Console" target="SYSTEM_ERR">
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<PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
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</Console>
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</Appenders>
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<Loggers>
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<!--
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<Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
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<AppenderRef ref="Console"/>
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</Logger>
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-->
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<Root level="info">
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<AppenderRef ref="Console"/>
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</Root>
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</Loggers>
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</Configuration>
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</appenders>
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<loggers>
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<root level="warn">
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<appender-ref ref="Console"/>
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</root>
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</loggers>
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</configuration>

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