biojava · sbliven · Aug 23, 2016 · Aug 11, 2016 · Aug 15, 2016 · Aug 15, 2016
diff --git a/.travis.yml b/.travis.yml
@@ -2,4 +2,5 @@ language: java
 jdk:
   - oraclejdk8
 sudo: false
-
+#after_success:
+#  - mvn clean cobertura:cobertura coveralls:report
diff --git a/biojava-aa-prop/src/test/resources/log4j2.xml b/biojava-aa-prop/src/test/resources/log4j2.xml
@@ -6,7 +6,7 @@
 		</Console>
 	</appenders>
 	<loggers>
-		<root level="info">
+		<root level="warn">
 			<appender-ref ref="Console"/>
 		</root>
 	</loggers>

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

diff --git a/biojava-alignment/src/test/resources/log4j2.xml b/biojava-alignment/src/test/resources/log4j2.xml
@@ -6,7 +6,7 @@
 		</Console>
 	</appenders>
 	<loggers>
-		<root level="info">
+		<root level="warn">
 			<appender-ref ref="Console"/>
 		</root>
 	</loggers>

diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
@@ -74,13 +74,13 @@ public void testProcess() throws Throwable {
 				= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
 		ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
 		genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
-		logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
+		//logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
 
 	GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
 	= new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
 	DNASequence dnaSequence = new DNASequence(genbankDNAReader);
 	genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-	logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
+	//logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
 		/*
 		 * Method 2: With the GenbankReaderHelper
 		 */
@@ -92,12 +92,12 @@ public void testProcess() throws Throwable {
 
 		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(dnaResource.getInputStream());
 		for (DNASequence sequence : dnaSequences.values()) {
-			logger.info("DNA Sequence: {}", sequence.getSequenceAsString());
+			logger.debug("DNA Sequence: {}", sequence.getSequenceAsString());
 		}
 
 		LinkedHashMap<String, ProteinSequence> protSequences = GenbankReaderHelper.readGenbankProteinSequence(protResource.getInputStream());
 		for (ProteinSequence sequence : protSequences.values()) {
-			logger.info("Protein Sequence: {}", sequence.getSequenceAsString());
+			logger.debug("Protein Sequence: {}", sequence.getSequenceAsString());
 		}
 		/*
 		 * Method 3: With the GenbankReader Object
@@ -111,7 +111,7 @@ public void testProcess() throws Throwable {
 		);
 		dnaSequences = dnaReader.process();
 
-		logger.info("DNA Sequence: {}", dnaSequences);
+		logger.debug("DNA Sequence: {}", dnaSequences);
 
 
 		GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
@@ -121,7 +121,7 @@ public void testProcess() throws Throwable {
 		);
 		protSequences = protReader.process();
 
-		logger.info("Protein Sequence: {}", protSequences);
+		logger.debug("Protein Sequence: {}", protSequences);
 
 	}
 

diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -128,7 +128,7 @@ public void CDStest() throws Exception {
 
 
 		Assert.assertTrue(proteinSequences.size() == 1);
-		logger.info("protein sequences: {}", proteinSequences);
+		logger.debug("protein sequences: {}", proteinSequences);
 
 		ProteinSequence protein = new ArrayList<ProteinSequence>(proteinSequences.values()).get(0);
 

diff --git a/biojava-core/src/test/resources/log4j2.xml b/biojava-core/src/test/resources/log4j2.xml
@@ -1,22 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN">
-    <Appenders>
+<configuration status="WARN">
+    <appenders>
         <Console name="Console" target="SYSTEM_ERR">
             <PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
         </Console>
-    </Appenders>
-    <Loggers>
-        <!-- 
-        <Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
-            <AppenderRef ref="Console"/>
-        </Logger>
-        -->
-        <!--
-        <Logger name="org.biojava.nbio.core.sequence.location.InsdcParserTest" level="debug" />
-        -->
-
-        <Root level="info">
-            <AppenderRef ref="Console"/>
-        </Root>
-    </Loggers>
-</Configuration>
+    </appenders>
+    <loggers>
+        <root level="warn">
+            <appender-ref ref="Console"/>
+        </root>
+    </loggers>
+</configuration>
diff --git a/biojava-genome/src/test/resources/log4j2.xml b/biojava-genome/src/test/resources/log4j2.xml
@@ -1,18 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN">
-    <Appenders>
+<configuration status="WARN">
+    <appenders>
         <Console name="Console" target="SYSTEM_ERR">
             <PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
         </Console>
-    </Appenders>
-    <Loggers>
-        <!-- 
-        <Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
-            <AppenderRef ref="Console"/>
-        </Logger>
-        -->
-        <Root level="info">
-            <AppenderRef ref="Console"/>
-        </Root>
-    </Loggers>
-</Configuration>
+    </appenders>
+    <loggers>
+        <root level="warn">
+            <appender-ref ref="Console"/>
+        </root>
+    </loggers>
+</configuration>
diff --git a/biojava-integrationtest/src/test/resources/log4j2.xml b/biojava-integrationtest/src/test/resources/log4j2.xml
@@ -6,7 +6,7 @@
 		</Console>
 	</appenders>
 	<loggers>
-		<root level="info">
+		<root level="warn">
 			<appender-ref ref="Console"/>
 		</root>
 	</loggers>

diff --git a/biojava-modfinder/src/test/resources/log4j2.xml b/biojava-modfinder/src/test/resources/log4j2.xml
@@ -1,18 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN">
-    <Appenders>
+<configuration status="WARN">
+    <appenders>
         <Console name="Console" target="SYSTEM_ERR">
             <PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
         </Console>
-    </Appenders>
-    <Loggers>
-        <!-- 
-        <Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
-            <AppenderRef ref="Console"/>
-        </Logger>
-        -->
-        <Root level="info">
-            <AppenderRef ref="Console"/>
-        </Root>
-    </Loggers>
-</Configuration>
+    </appenders>
+    <loggers>
+        <root level="warn">
+            <appender-ref ref="Console"/>
+        </root>
+    </loggers>
+</configuration>
diff --git a/biojava-ontology/src/test/resources/log4j2.xml b/biojava-ontology/src/test/resources/log4j2.xml
@@ -11,7 +11,7 @@
             <AppenderRef ref="Console"/>
         </Logger>
         -->
-        <Root level="info">
+        <Root level="warn">
             <AppenderRef ref="Console"/>
         </Root>
     </Loggers>

diff --git a/biojava-phylo/src/test/resources/log4j2.xml b/biojava-phylo/src/test/resources/log4j2.xml
@@ -11,7 +11,7 @@
             <AppenderRef ref="Console"/>
         </Logger>
         -->
-        <Root level="info">
+        <Root level="warn">
             <AppenderRef ref="Console"/>
         </Root>
     </Loggers>

diff --git a/biojava-protein-disorder/src/test/resources/log4j2.xml b/biojava-protein-disorder/src/test/resources/log4j2.xml
@@ -1,18 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN">
-    <Appenders>
-        <Console name="Console" target="SYSTEM_ERR">
+<configuration status="WARN">
+    <appenders>
+        <console name="Console" target="SYSTEM_ERR">
             <PatternLayout pattern="%d{HH:mm:ss} [%t] %-5level %logger{36} - %msg%n"/>
-        </Console>
-    </Appenders>
-    <Loggers>
-        <!-- 
-        <Logger name="org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader" level="debug">
-            <AppenderRef ref="Console"/>
-        </Logger>
-        -->
-        <Root level="info">
-            <AppenderRef ref="Console"/>
-        </Root>
-    </Loggers>
-</Configuration>
+        </console>
+    </appenders>
+    <loggers>
+        <root level="warn">
+            <appender-ref ref="Console"/>
+        </root>
+    </loggers>
+</configuration>
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/FastqTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/FastqTest.java
@@ -31,6 +31,7 @@
 public final class FastqTest
 	extends TestCase
 {
+
 	public void testConstructor()
 	{
 		Fastq fastq = new Fastq("description", "sequence", "quality_", FastqVariant.FASTQ_SANGER);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -25,6 +25,7 @@
 
 import org.biojava.nbio.core.sequence.template.Sequence;
 import org.biojava.nbio.structure.io.FileParsingParameters;
+import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 
 import java.util.List;
 
@@ -277,7 +278,7 @@ public interface Chain {
 	/**
 	 * Returns the sequence of amino acids as it has been provided in the ATOM records.
 	 * Non-standard residues will be present in the string only if the property
-	 * {@value PDBFileReader.LOAD_CHEM_COMP_PROPERTY} has been set.
+	 * {@value org.biojava.nbio.structure.io.PDBFileReader.LOAD_CHEM_COMP_PROPERTY} has been set.
 	 * @return amino acid sequence as string
 	 * @see #getSeqResSequence()
 	 */
@@ -413,5 +414,53 @@ public interface Chain {
 	 * @return
 	 * @see EntityType
 	 */
-	EntityType getEntityType(); 
+	EntityType getEntityType();
+
+	/** Tests if a chain is consisting of water molecules only
+	 *
+	 * @return true if there are only solvent molecules in this chain.
+     */
+	 public boolean isWaterOnly();
+
+	/**  Returns true if the given chain is composed of non-polymeric (including water) groups only.
+	 *
+ 	 * @return true if only non-polymeric groups in this chain.
+     */
+	public boolean isPureNonPolymer();
+
+	/**
+	 * Get the predominant {@link GroupType} for a given Chain, following these
+	 * rules: <li>if the ratio of number of residues of a certain
+	 * {@link GroupType} to total non-water residues is above the threshold
+	 * {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL}, then that {@link GroupType} is
+	 * returned</li> <li>if there is no {@link GroupType} that is above the
+	 * threshold then the {@link GroupType} with most members is chosen, logging
+	 * it</li>
+	 * <p>
+	 * See also {@link ChemComp#getPolymerType()} and
+	 * {@link ChemComp#getResidueType()} which follow the PDB chemical component
+	 * dictionary and provide a much more accurate description of groups and
+	 * their linking.
+	 * </p>
+	 *
+	 * @return
+	 */
+	public GroupType getPredominantGroupType();
+
+	/**
+	 * Tell whether given chain is a protein chain
+	 *
+
+	 * @return true if protein, false if nucleotide or ligand
+	 * @see #getPredominantGroupType()
+	 */
+	public  boolean isProtein();
+
+	/**
+	 * Tell whether given chain is DNA or RNA
+	 *
+	 * @return true if nucleic acid, false if protein or ligand
+	 * @see #getPredominantGroupType()
+	 */
+	public  boolean isNucleicAcid();
 }