Merge 69fd815 into 2512f2e

rcsb · May 3, 2016 · a808813 · a808813
2 parents 2512f2e + 69fd815
commit a808813
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Showing 7 changed files with 184 additions and 19 deletions.
diff --git a/mmtf-api/src/main/java/org/rcsb/mmtf/api/StructureDataInterface.java b/mmtf-api/src/main/java/org/rcsb/mmtf/api/StructureDataInterface.java
@@ -297,9 +297,36 @@ public interface StructureDataInterface {
 	/**
 	 * Returns the sequence for the entity specified by the index.
 	 * @param entityInd the index of the specified entity.
-	 * @return the one letter sequence for this entity. Empty string if no sequence is applicable.
+	 * @return the one letter sequence for this entity. Empty string 
+	 * if no sequence is applicable.
 	 */
     String getEntitySequence(int entityInd);
+
+    /**
+	 * Returns the entity description (as defined in mmCIF dictionary) 
+	 * for the entity specified by the chain index.
+     * @param chainInd the index of the specified chain
+     * @return the entity description
+     */
+    String getChainEntityDescription(int chainInd);
+
+	/**
+	 * Returns the entity type (polymer, non-polymer, water)
+	 * for the entity specified by the chain index.
+     * @param chainInd the index of the specified chain
+	 * @return the entity type (polymer, non-polymer, water) for 
+	 * the specified chain
+	 */ 
+    String getChainEntityType(int chainInd);
+
+	/**
+	 * Returns the sequence for the entity specified by the chain index.
+     * @param chainInd the index of the specified chain
+	 * @return the one letter sequence for this chain. Empty string if 
+	 * no sequence is applicable.
+	 */
+    String getChainEntitySequence(int chainInd);
+
 
 	/**
 	 * Returns the identifier of the structure.

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
@@ -1,7 +1,9 @@
 package org.rcsb.mmtf.decoder;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.dataholders.BioAssemblyData;
@@ -104,6 +106,8 @@ public DefaultDecoder(MmtfStructure inputData) {
 		depositionDate = inputData.getDepositionDate();
 		releaseDate = inputData.getReleaseDate();
 		secStructInfo = ArrayConverters.convertByteToIntegers(inputData.getSecStructList());
+		// Now  generate this map
+		generateChanEntityIndexMap();
 	}
 
 	/** The X coordinates */
@@ -205,7 +209,11 @@ public DefaultDecoder(MmtfStructure inputData) {
 	/** The release date of the  structure */
 	private String releaseDate;
 
+	/** The secondary structure info */
 	private int[] secStructInfo;
+
+	/** The map of chain indices to the entity */
+	private Map<Integer, Integer> chainToEntityIndexMap;
 
 
 	@Override
@@ -490,5 +498,54 @@ public String getReleaseDate() {
 		return releaseDate;
 	}
 
+	@Override
+	public String getChainEntityDescription(int chainInd) {
+		if(chainToEntityIndexMap==null){
+			generateChanEntityIndexMap();
+		}
+		Integer entityInd = chainToEntityIndexMap.get(chainInd);
+		if(entityInd==null){
+			return null;
+		}
+		return getEntityDescription(entityInd);
+	}
+
+	@Override
+	public String getChainEntityType(int chainInd) {
+		if(chainToEntityIndexMap==null){
+			generateChanEntityIndexMap();
+		}
+		Integer entityInd = chainToEntityIndexMap.get(chainInd);
+		if(entityInd==null){
+			return null;
+		}
+		return getEntityType(entityInd);
+	}
+
+	@Override
+	public String getChainEntitySequence(int chainInd) {
+		if(chainToEntityIndexMap==null){
+			generateChanEntityIndexMap();
+		}
+		Integer entityInd = chainToEntityIndexMap.get(chainInd);
+		if(entityInd==null){
+			return null;
+		}
+		return getEntitySequence(entityInd);
+	}
+
+	/**
+	 * Utility function to generate a map, mapping chain index to
+	 * entity index.
+	 */
+	private void generateChanEntityIndexMap() {
+		chainToEntityIndexMap = new HashMap<>();
+		for(int i=0; i<entityList.length; i++) {
+			for(int chainInd : entityList[i].getChainIndexList()){
+				chainToEntityIndexMap.put(chainInd, i);
+			}
+		}
+	}
+
 
 }
diff --git a/mmtf-decoder/src/test/java/org/rcsb/mmtf/decoder/DummyApiImpl.java b/mmtf-decoder/src/test/java/org/rcsb/mmtf/decoder/DummyApiImpl.java
@@ -289,4 +289,19 @@ public int[] getSecStructList() {
 		return new int[numGroups];
 	}
 
+	@Override
+	public String getChainEntityDescription(int chainInd) {
+		return "DESC";
+	}
+
+	@Override
+	public String getChainEntityType(int chainInd) {
+		return "TYPE";
+	}
+
+	@Override
+	public String getChainEntitySequence(int chainInd) {
+		return "SEQUENCE";
+	}
+
 }
diff --git a/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/AdapterToStructureData.java b/mmtf-encoder/src/main/java/org/rcsb/mmtf/encoder/AdapterToStructureData.java
@@ -1,8 +1,10 @@
 package org.rcsb.mmtf.encoder;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 
 import org.rcsb.mmtf.api.StructureDataInterface;
 import org.rcsb.mmtf.api.StructureAdapterInterface;
@@ -124,26 +126,27 @@ public class AdapterToStructureData implements StructureDataInterface, Structure
 	private int[] secStructInfo;
 
 	/** The atom counter */
-	int atomIndex = 0;
+	private int atomIndex = 0;
 	/** The atom counter within a group*/
-	int groupAtomIndex = 0;
+	private int groupAtomIndex = 0;
 	/** The current group bond */
-	int groupBondIndex = 0;
+	private int groupBondIndex = 0;
 	/** The group counter */
-	int groupIndex = 0;
+	private int groupIndex = 0;
 	/** The chain counter */
-	int chainIndex = 0;
+	private int chainIndex = 0;
 	/** The model counter */
-	int modelIndex = 0;
-	/** The entity counter */
-	int entityIndex = 0;
+	private int modelIndex = 0;
 	/** Add the atom information for the current group */
-	Group pdbGroup;
+	private Group pdbGroup;
 	/** A List for Entities as the number of entities is not defined*/
-	List<Entity> entities;
-	int totalNumBonds;
-	List<Group> pdbGroupList;
-
+	private List<Entity> entities;
+	/** The total number of bonds*/
+	private int totalNumBonds;
+	/** The list of {@link Group} objects */
+	private List<Group> pdbGroupList;
+	/** The map of chain indices to the entity */
+	private Map<Integer, Integer> chainToEntityIndexMap;
 
 	@Override
 	public float[] getxCoords() {
@@ -404,6 +407,55 @@ public String getDepositionDate() {
 		return depositionDate;
 	}
 
+
+	@Override
+	public String getChainEntityDescription(int chainInd) {
+		if(chainToEntityIndexMap==null){
+			generateChanEntityIndexMap();
+		}
+		Integer entityInd = chainToEntityIndexMap.get(chainInd);
+		if(entityInd==null){
+			return null;
+		}
+		return getEntityDescription(entityInd);
+	}
+
+	@Override
+	public String getChainEntityType(int chainInd) {
+		if(chainToEntityIndexMap==null){
+			generateChanEntityIndexMap();
+		}
+		Integer entityInd = chainToEntityIndexMap.get(chainInd);
+		if(entityInd==null){
+			return null;
+		}
+		return getEntityType(entityInd);
+	}
+
+	@Override
+	public String getChainEntitySequence(int chainInd) {
+		if(chainToEntityIndexMap==null){
+			generateChanEntityIndexMap();
+		}
+		Integer entityInd = chainToEntityIndexMap.get(chainInd);
+		if(entityInd==null){
+			return null;
+		}
+		return getEntitySequence(entityInd);
+	}
+
+	/**
+	 * Utility function to generate a map, mapping chain index to
+	 * entity index.
+	 */
+	private void generateChanEntityIndexMap() {
+		chainToEntityIndexMap = new HashMap<>();
+		for(int i=0; i<entityList.length; i++) {
+			for(int chainInd : entityList[i].getChainIndexList()){
+				chainToEntityIndexMap.put(chainInd, i);
+			}
+		}
+	}
 
 	@Override
 	public void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, 
@@ -451,6 +503,8 @@ public void finalizeStructure() {
 			// Find the index of this groups information.
 			groupList[i] = groupMap.indexOf(pdbGroupList.get(i));
 		}
+		// Now  generate this map
+		generateChanEntityIndexMap();
 	}
 
 	@Override
@@ -476,7 +530,6 @@ public void setEntityInfo(int[] chainIndices, String sequence, String descriptio
 		entity.setType(title);
 		// Add this entity
 		entities.add(entity);
-		entityIndex++;
 	}
 
 	@Override

diff --git a/mmtf-encoder/src/test/java/org/rcsb/mmtf/encoder/DummyApiImpl.java b/mmtf-encoder/src/test/java/org/rcsb/mmtf/encoder/DummyApiImpl.java
@@ -289,5 +289,18 @@ public String getReleaseDate() {
 	public int[] getSecStructList() {
 		return new int[numGroups];
 	}
+	@Override
+	public String getChainEntityDescription(int chainInd) {
+		return "DESC";
+	}
 
+	@Override
+	public String getChainEntityType(int chainInd) {
+		return "TYPE";
+	}
+
+	@Override
+	public String getChainEntitySequence(int chainInd) {
+		return "SEQUENCE";
+	}
 }
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
@@ -51,12 +51,12 @@ public void testEncodeAllFields() throws IOException {
 	 */
 	@Test
 	public void testWriter() throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, IntrospectionException {
-		AdapterToStructureData AdapterToStructureData = getWriterEncoder();
-		ReflectionAssert.assertPropertiesNotNull("Some properties null after writing", AdapterToStructureData);
+		AdapterToStructureData adapterToStructureData = getWriterEncoder();
+		ReflectionAssert.assertPropertiesNotNull("Some properties null after writing", adapterToStructureData);
 		for(PropertyDescriptor propertyDescriptor : 
 			Introspector.getBeanInfo(AdapterToStructureData.class).getPropertyDescriptors()){
 			if(propertyDescriptor.getReadMethod()!=null){
-				assertNotNull(propertyDescriptor.getReadMethod().invoke(AdapterToStructureData));
+				assertNotNull(propertyDescriptor.getReadMethod().invoke(adapterToStructureData));
 			}
 		}
 	}

diff --git a/pom.xml b/pom.xml
@@ -309,7 +309,7 @@
 			<plugin>
 				<groupId>com.versioneye</groupId>
 				<artifactId>versioneye-maven-plugin</artifactId>
-				<version>3.9.1</version>
+				<version>3.9.2</version>
 			</plugin>
 
 		</plugins>