Updates and refactoring to the encoder to fix data inconsistencies in…

… writer
rcsb · Apr 13, 2016 · eb712d5 · eb712d5
1 parent ddb0955
commit eb712d5
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Showing 12 changed files with 39 additions and 19 deletions.
diff --git a/mmtf-api/src/main/java/org/rcsb/mmtf/api/DataTransferInterface.java b/mmtf-api/src/main/java/org/rcsb/mmtf/api/DataTransferInterface.java
@@ -47,9 +47,9 @@ void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, int
 	 * @param chainIndices the indices of the chain this refers to.
 	 * @param sequence the full sequence of the entity
 	 * @param description the text description of the entity
-	 * @param title
+	 * @param type as a string (POLYMER/NON-POLYMER and WATER)
 	 */
-	void setEntityInfo(int[] chainIndices, String sequence, String description, String title);
+	void setEntityInfo(int[] chainIndices, String sequence, String description, String type);
 
 	/**
 	 * Sets the information for a given group / residue with atomic data.

diff --git a/mmtf-common/pom.xml b/mmtf-common/pom.xml
@@ -26,6 +26,18 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>uk.co.jemos.podam</groupId>
+			<artifactId>podam</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.unitils</groupId>
+			<artifactId>unitils-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-beanutils</groupId>
+			<artifactId>commons-beanutils</artifactId>
+		</dependency>
 	</dependencies>
 	<build>
 		<plugins>

diff --git a/mmtf-common/src/main/java/org/rcsb/mmtf/dataholders/Entity.java b/mmtf-common/src/main/java/org/rcsb/mmtf/dataholders/Entity.java
@@ -24,7 +24,6 @@ public class Entity implements Serializable {
 	private String sequence;
 
 
-
 	public String getDescription() {
 		return description;
 	}

diff --git a/mmtf-decoder/pom.xml b/mmtf-decoder/pom.xml
@@ -20,7 +20,6 @@
 		<dependency>
 			<groupId>commons-beanutils</groupId>
 			<artifactId>commons-beanutils</artifactId>
-			<version>1.8.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.rcsb</groupId>

diff --git a/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DefaultDecoder.java b/mmtf-decoder/src/main/java/org/rcsb/mmtf/decoder/DefaultDecoder.java
@@ -70,8 +70,10 @@ public DefaultDecoder(MmtfBean inputData) throws IOException {
 		// Get the group map (all the unique groups in the structure).
 		groupMap = inputData.getGroupList();
 		// Get the seqRes groups
-		seqResGroupList = ArrayConverters.convertFourByteToIntegers(
-				inputData.getSequenceIndexList());
+		seqResGroupList = ArrayDecoders.deltaDecode(
+				ArrayDecoders.runlengthDecode(
+						ArrayConverters.convertFourByteToIntegers(
+								inputData.getSequenceIndexList())));
 		// Get the number of chains per model
 		chainsPerModel = inputData.getChainsPerModel();
 		groupsPerChain = inputData.getGroupsPerChain();
@@ -97,7 +99,7 @@ public DefaultDecoder(MmtfBean inputData) throws IOException {
 		// Now get the relase information
 		depositionDate = inputData.getDepositionDate();
 		releaseDate = inputData.getReleaseDate();
-		secStructInfo = ArrayConverters.convertFourByteToIntegers(inputData.getSecStructList());
+		secStructInfo = ArrayConverters.convertByteToIntegers(inputData.getSecStructList());
 	}
 
 	/** The X coordinates */
@@ -195,10 +197,10 @@ public DefaultDecoder(MmtfBean inputData) throws IOException {
 
 	/** The deposition date of the structure */
 	private String depositionDate;
-	
+
 	/** The release date of the  structure */
 	private String releaseDate;
-	
+
 	private int[] secStructInfo;
 
 

diff --git a/mmtf-decoder/src/test/java/org/rcsb/mmtf/decoder/TestDefaultDecoder.java b/mmtf-decoder/src/test/java/org/rcsb/mmtf/decoder/TestDefaultDecoder.java
@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 
-import org.junit.Before;
 import org.junit.Test;
 import org.rcsb.mmtf.api.DataTransferInterface;
 import org.rcsb.mmtf.dataholders.MmtfBean;

diff --git a/mmtf-encoder/pom.xml b/mmtf-encoder/pom.xml
@@ -68,7 +68,6 @@
 		<dependency>
 			<groupId>commons-beanutils</groupId>
 			<artifactId>commons-beanutils</artifactId>
-			<version>1.8.3</version>
 		</dependency>
 	</dependencies>
 	<reporting>

diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DefaultEncoder.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/DefaultEncoder.java
@@ -73,12 +73,12 @@ public DefaultEncoder(DecodedDataInterface decodedDataInterface) throws IOExcept
 		// Run length encoded
 		mmtfBean.setAltLocList(ArrayConverters.convertIntegersToFourByte(
 				ArrayEncoders.runlengthEncode(
-				ArrayConverters.convertCharToIntegers(
-						decodedDataInterface.getAltLocIds()))));
+						ArrayConverters.convertCharToIntegers(
+								decodedDataInterface.getAltLocIds()))));
 		mmtfBean.setInsCodeList(ArrayConverters.convertIntegersToFourByte(
 				ArrayEncoders.runlengthEncode(
-				ArrayConverters.convertCharToIntegers(
-						decodedDataInterface.getInsCodes()))));
+						ArrayConverters.convertCharToIntegers(
+								decodedDataInterface.getInsCodes()))));
 
 		// Set the groupNumber
 		mmtfBean.setGroupIdList(ArrayConverters.convertIntegersToFourByte(
@@ -90,7 +90,9 @@ public DefaultEncoder(DecodedDataInterface decodedDataInterface) throws IOExcept
 		mmtfBean.setGroupList(EncoderUtils.generateGroupMap(decodedDataInterface));
 		// Set the indices for the groups mapping to the sequence
 		mmtfBean.setSequenceIndexList(ArrayConverters.convertIntegersToFourByte(
-				decodedDataInterface.getGroupSequenceIndices()));
+				ArrayEncoders.runlengthEncode(
+						ArrayEncoders.deltaEncode(
+								decodedDataInterface.getGroupSequenceIndices()))));
 		// Set the number of chains per model
 		mmtfBean.setChainsPerModel(decodedDataInterface.getChainsPerModel());
 		mmtfBean.setGroupsPerChain(decodedDataInterface.getGroupsPerChain());
@@ -124,7 +126,7 @@ public DefaultEncoder(DecodedDataInterface decodedDataInterface) throws IOExcept
 		mmtfBean.setExperimentalMethods(decodedDataInterface.getExperimentalMethods());
 		mmtfBean.setDepositionDate(decodedDataInterface.getDepositionDate());
 		mmtfBean.setReleaseDate(decodedDataInterface.getReleaseDate());
-		mmtfBean.setSecStructList(ArrayConverters.convertIntegersToFourByte(decodedDataInterface.getSecStructList()));
+		mmtfBean.setSecStructList(ArrayConverters.convertIntegersToBytes(decodedDataInterface.getSecStructList()));
 	}
 
 	public MmtfBean getMmtfBean() {

diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToEncoder.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/WriterToEncoder.java
@@ -491,7 +491,7 @@ public void setGroupInfo(String groupName, int groupNumber, char insertionCode,
 		pdbGroup.setChemCompType(polymerType);
 		pdbGroup.setElementList(new String[atomCount]);
 		pdbGroup.setGroupName(groupName);
-		pdbGroup.setSingleLetterCode(insertionCode);
+		pdbGroup.setSingleLetterCode(singleAtomCode);
 		groupAtomIndex=0;
 		groupBondIndex=0;
 		// Store the group level data

diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/serializers/MessagePackSerializer.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/serializers/MessagePackSerializer.java
@@ -3,6 +3,7 @@
 import org.msgpack.jackson.dataformat.MessagePackFactory;
 import org.rcsb.mmtf.dataholders.MmtfBean;
 
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -15,7 +16,9 @@
 public class MessagePackSerializer {
 
 	public byte[] serialize(MmtfBean object) {
+
 		ObjectMapper objectMapper = new ObjectMapper(new MessagePackFactory());
+		objectMapper.setSerializationInclusion(Include.NON_NULL);
 		byte[] byteArray;
 		try {
 			byteArray = objectMapper.writeValueAsBytes(object);

diff --git a/mmtf-encoder/src/test/java/org/rcsb/mmtf/encoder/TestDefaultEncoder.java b/mmtf-encoder/src/test/java/org/rcsb/mmtf/encoder/TestDefaultEncoder.java
@@ -18,7 +18,6 @@ public void testEncodeAllFields() throws IOException {
 		DummyApiImpl dummyApiImpl = new DummyApiImpl();
 		DefaultEncoder defaultEncoder = new DefaultEncoder(dummyApiImpl);
 		ReflectionAssert.assertPropertiesNotNull("Some properties null after encoding", defaultEncoder.getMmtfBean());
-
 	}
 
 

diff --git a/pom.xml b/pom.xml
@@ -345,6 +345,12 @@
 				<version>4.12</version>
 				<scope>test</scope>
 			</dependency>
+			<dependency>
+				<groupId>commons-beanutils</groupId>
+				<artifactId>commons-beanutils</artifactId>
+				<version>1.9.2</version>
+				<scope>test</scope>
+			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-api</artifactId>