Merge branch 'master' of github.com:biojava/biojava

* 'master' of github.com:biojava/biojava: (211 commits)
  TestSuperPosition now tests rmsd of non-centered points.
  Documentation and minor fix
  Redo the PR #576 re-use code into a method
  Fix bug in centroid calculation SuperPositionSVD #588
  Simple integration test for superposition methods
  More complete test
  Inserts space when altLoc is null, so that the rest of fields are properly aligned.
  FileConvert fix - added empty space if altLoc is null.
  Fixing hard biounits test. Small fix in Chain docs.
  Cleanup whitespace
  Solving a compilation problem, making Grid usable for Point3d #545
  Some more work towards #545, some cleanup
  Issue #582 and some more work towards #545
  Add constructors for the MMTFFilereader
  Added caching functionality for MMTF
  Address jose comment on #558
  Also get short name when getting other protein aliases
  Fix bug with dihedral axis calculation #558
  Fix bug in superposeAndTransform method SuperPositions
  Remove tests that require String comparisons with floats
  ...

.travis.yml

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

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>

biojava-alignment/pom.xml

@@ -73,10 +73,5 @@
     		<groupId>org.apache.logging.log4j</groupId>
     		<artifactId>log4j-core</artifactId>
   		</dependency>
-  		<dependency>
-  			<groupId>org.biojava</groupId>
-  			<artifactId>biojava-phylo</artifactId>
-			<version>5.0.0-SNAPSHOT</version>
-  		</dependency>
 	</dependencies>
 </project>

biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java → biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java

@@ -391,7 +391,7 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix pamMLdi
 		// Need to import PAM1 matrix to biojava TODO
 		//SubstitutionMatrix<AminoAcidCompound> PAM1 = SubstitutionMatrixHelper.getPAM250();
 
-		return null;
+		throw new IllegalStateException("PAM ML distance calculation not implemented!");
 	}
 
 	/**
@@ -447,18 +447,4 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix structu
 		return DM;
 	}
 
-	/**
-	 * The joint sequence-structure distance (d<sub>SS</sub>) is a combination
-	 * of the sequence-based and the structure-based distances.
-	 *
-	 * @param rmsdMat
-	 *            RMSD matrix for all structure pairs (symmetric matrix)
-	 * @return DistanceMatrix
-	 */
-	public static <C extends Sequence<D>, D extends Compound> DistanceMatrix jointSeqStrucDistance(
-			double[][] rmsdMat) {
-		// TODO
-		return null;
-	}
-
 }

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

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>

biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java

@@ -26,6 +26,7 @@
 import org.biojava.nbio.core.sequence.Strand;
 import org.biojava.nbio.core.sequence.features.FeatureInterface;
 import org.biojava.nbio.core.sequence.features.Qualifier;
+import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
 import org.biojava.nbio.core.sequence.location.template.Point;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
 import org.biojava.nbio.core.sequence.template.Compound;
@@ -186,7 +187,7 @@ private String _insdc_feature_location_string(FeatureInterface<AbstractSequence<
 				if(f.getLocations().getStrand() != Strand.NEGATIVE) {
 					StringBuilder sb = new StringBuilder();
 					Formatter formatter = new Formatter(sb,Locale.US);
-					formatter.format("Inconsistent strands: %r for parent, %r for child", feature.getLocations().getStrand(), f.getLocations().getStrand());
+					formatter.format("Inconsistent strands: %s for parent, %s for child", feature.getLocations().getStrand(), f.getLocations().getStrand());
 					String output = formatter.toString();
 					formatter.close();
 					throw new RuntimeException(output);
@@ -220,7 +221,7 @@ private String _insdc_feature_location_string(FeatureInterface<AbstractSequence<
 
 	private String _insdc_location_string_ignoring_strand_and_subfeatures(
 			//SequenceLocation<AbstractSequence<C>, C> sequenceLocation,
-						org.biojava.nbio.core.sequence.location.template.AbstractLocation sequenceLocation,
+						AbstractLocation sequenceLocation,
 			int record_length) {
 	/*
 	if location.ref:

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

@@ -337,10 +337,21 @@ public ArrayList<AccessionID> getAccessions() throws XPathExpressionException {
 
 	/**
 	 * Pull uniprot protein aliases associated with this sequence
+	 * Provided for backwards compatibility now that we support both
+	 * gene and protein aliases via separate methods.
 	 * @return
 	 * @throws XPathExpressionException
 	 */
 	public ArrayList<String> getAliases() throws XPathExpressionException {
+
+		return getProteinAliases();
+	}
+	/**
+	 * Pull uniprot protein aliases associated with this sequence
+	 * @return
+	 * @throws XPathExpressionException
+	 */
+	public ArrayList<String> getProteinAliases() throws XPathExpressionException {
 		ArrayList<String> aliasList = new ArrayList<String>();
 		if (uniprotDoc == null) {
 			return aliasList;
@@ -353,6 +364,39 @@ public ArrayList<String> getAliases() throws XPathExpressionException {
 			Element fullNameElement = XMLHelper.selectSingleElement(element, "fullName");
 			aliasList.add(fullNameElement.getTextContent());
 		}
+		keyWordElementList = XMLHelper.selectElements(proteinElement, "recommendedName");
+		for (Element element : keyWordElementList) {
+			Element fullNameElement = XMLHelper.selectSingleElement(element, "fullName");
+			aliasList.add(fullNameElement.getTextContent());
+			Element shortNameElement = XMLHelper.selectSingleElement(element, "shortName");
+			if(null != shortNameElement) {
+				String shortName = shortNameElement.getTextContent();
+				if(null != shortName && !shortName.trim().isEmpty()) {
+					aliasList.add(shortName);
+				}
+			}
+		}
+
+		return aliasList;
+	}
+
+	/**
+	 * Pull uniprot gene aliases associated with this sequence
+	 * @return
+	 * @throws XPathExpressionException
+	 */
+	public ArrayList<String> getGeneAliases() throws XPathExpressionException {
+		ArrayList<String> aliasList = new ArrayList<String>();
+		if (uniprotDoc == null) {
+			return aliasList;
+		}
+		Element uniprotElement = uniprotDoc.getDocumentElement();
+		Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
+		Element proteinElement = XMLHelper.selectSingleElement(entryElement, "gene");
+		ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "name");
+		for (Element element : keyWordElementList) {
+			aliasList.add(element.getTextContent());
+		}
 
 		return aliasList;
 	}

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);
 
 	}
 

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);
 

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>

biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java

@@ -286,34 +286,41 @@ public Location union( Location other )
 	}
 
 	/**
-	* Return the intersection, or null if no overlap.
-	*
-	 * @param other The location to intersect.
-	 * @return The maximal location that is contained by both. Returns null if no overlap!
-	 * @throws IllegalArgumentException Locations are on opposite strands.
-	*/
-	public Location intersection( Location other )
-	{
-		if( isSameStrand( other ) )
-		{
-			int start= ( mStart > other.mStart)? mStart: other.mStart;	//pick larger
-			int end= ( mEnd < other.mEnd)? mEnd: other.mEnd;	//pick smaller
-
-			if( start <= end )
-			{
-				return new Location( start, end );
-			}
-			else
-			{
-				return null;
-			}
-		}
-		else
-		{
-			throw new IllegalArgumentException( "Locations are on opposite strands." );
-		}
+	 * Return the intersection, or null if no overlap.
+	 *
+	 * @param other
+	 *            The location to intersect.
+	 * @return The maximal location that is contained by both. Returns null if
+	 *         no overlap!
+	 * @throws IllegalArgumentException
+	 *             Locations are on opposite strands.
+	 */
+	public Location intersection(Location other) {
+		if (isSameStrand(other)) {
+			return intersect(mStart, mEnd, other.mStart, other.mEnd);
+		} else {
+			throw new IllegalArgumentException("Locations are on opposite strands.");
+		}
+	}
+
+	private Location intersect(int a1, int a2, int b1, int b2) {
+		if (a1 > b1) {
+			return intersect(b1, b2, a1, a2);
+		}
+		// Safe to assume a1 <= b1
+		if (b1 >= a2) {
+			// b starts after a ends
+			return null;
+		} else if (b1 < a2 && b2 <= a2) {
+			// b starts after a starts and ends before or at where a ends
+			return new Location(b1, b2);
+		} else if (b1 >= a1 && a2 <= b2) {
+			// b starts after a but extends after the end of a
+			return new Location(b1, a2);
+		}
+		return null;
+	}	
 
-	}
 
 	/**
 	 * Get starting index (origin 0).