Updates to Biojava to remove any mention of the Messagepack serializer /deserializer

abradle · abradle · commit aaf33b09f0f9 · 2016-04-12T15:37:49.000-07:00
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfReader.java b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
@@ -15,8 +15,7 @@
 public class DemoMmtfReader {
 
 	public static void main(String[] args) throws IOException, StructureException {
-		MmtfUtils.setUpBioJava();
-		Structure structure = MmtfActions.getBiojavaStruct("4cup");
+		Structure structure = MmtfActions.readBiojavaStruct("/path/to/file");
 		System.out.println(structure.getChains().size());
 	}
 	
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfRoundTrip.java b/biojava-structure/src/main/java/demo/DemoMmtfRoundTrip.java
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfWriter.java b/biojava-structure/src/main/java/demo/DemoMmtfWriter.java
@@ -13,8 +13,7 @@ public class DemoMmtfWriter {
 	public static void main(String[] args) throws IOException, StructureException {
 		MmtfUtils.setUpBioJava();
 		Structure structure = StructureIO.getStructure("4cup");
-		// TODO write the byte array to a file
-		MmtfActions.getByteArray(structure);
+		MmtfActions.writeBiojavaStruct(structure, "/tmp/4cup.mmtf");
 	}
 	
 	
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java
@@ -3,144 +3,51 @@
 import java.io.IOException;
 
 import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
-import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
-import org.rcsb.mmtf.dataholders.MmtfBean;
 import org.rcsb.mmtf.decoder.BeanToDataApi;
 import org.rcsb.mmtf.decoder.DataApiToReader;
-import org.rcsb.mmtf.deserializers.MessagePackDeserializer;
-import org.rcsb.mmtf.encoder.DataApiToBean;
+import org.rcsb.mmtf.decoder.ReaderUtils;
 import org.rcsb.mmtf.encoder.WriterToDataApi;
-import org.rcsb.mmtf.serializers.MessagePackSerializer;
-import org.rcsb.mmtf.utils.DownloadUtils;
+import org.rcsb.mmtf.encoder.WriterUtils;
 
+/**
+ * A class of functions for reading and writing Biojava structures using MMTF
+ * @author Anthony Bradley
+ *
+ */
 public class MmtfActions {
-
-	/**
-	 * Utility function to get a Biojava structure from a PDB code.
-	 * @param pdbCode the pdb code of the structure you desire
-	 * @return a Biojava structure object relating to the input PDB code
-	 * @throws IOException 
-	 */
-	public static Structure getBiojavaStruct(String pdbCode) throws IOException {
-		return getBiojavaStruct(DownloadUtils.getDataFromUrl(pdbCode));
-	}
 	
 	/**
 	 * Utility function to get a Biojava structure from a byte array.
 	 * @param inputByteArray Must be uncompressed (i.e. with entropy compression methods like gzip)
 	 * @return a Biojava structure object relating to the input byte array.
 	 * @throws IOException 
 	 */
-	public static Structure getBiojavaStruct(byte[] inputByteArray) throws IOException {
+	public static Structure readBiojavaStruct(String filePath) throws IOException {
 		// Get the reader - this is the bit that people need to implement.
 		MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
-		// Set up the deserializer
-		MessagePackDeserializer messagePackDeserializer = new MessagePackDeserializer();
-		// Get the data
-		MmtfBean mmtfBean = messagePackDeserializer.deserialize(inputByteArray);
-		// Set up the data API
-		BeanToDataApi beanToGet = new BeanToDataApi(mmtfBean);
 		// Set up the inflator
 		DataApiToReader getToInflator = new DataApiToReader();
 		// Do the inflation
-		getToInflator.read(beanToGet, mmtfStructureReader);
+		getToInflator.read(new BeanToDataApi(ReaderUtils.getDataFromFile(filePath)), mmtfStructureReader);
 		// Get the structue
 		return mmtfStructureReader.getStructure();
 	}
-
-	/**
-	 * Get the byte array (messagepack encoded) of the PDB code you desire.
-	 * @param pdbId the input PDB id for the structure you want
-	 * @return the byte array of the structure compressed and message pack encoded
-	 * @throws IOException
-	 * @throws StructureException
-	 */
-	public static byte[] getByteArray(String pdbId) throws IOException, StructureException {
-		MmtfUtils.setUpBioJava();
-		return getByteArray(StructureIO.getStructure(pdbId));
-	}
-
-	/**
-	 * Utility function to get a byte array from a Biojava structure.
-	 * @param structure the input Biojava structure object
-	 * @return the byte array of the structure compressed and message pack encoded
-	 * @throws IOException 
-	 */
-	public static byte[] getByteArray(Structure structure) throws IOException {
-		MessagePackSerializer messagePackSerializer = new MessagePackSerializer();
-		return messagePackSerializer.serialize(getBean(structure));
-	}
-
-	/**
-	 * Utility function to get an mmtf bean from a Biojava structure.
-	 * @param structure the input Biojava structure object
-	 * @return the raw (compressed) data as an MmtfBean object
-	 * @throws IOException 
-	 */
-	public static MmtfBean getBean(Structure structure) throws IOException {
-		// Get to bean
-		DataApiToBean getToBean = new DataApiToBean(getApi(structure));
-		return getToBean.getMmtfBean();
-	}
 	
 	/**
-	 * Utility function to get an mmtf bean from a PDB id.
-	 * @param pdbId the input PDB id for the structure you want
-	 * @return the byte array of the structure compressed and message pack encoded
-	 * @throws IOException 
-	 * @throws StructureException 
-	 */
-	public static MmtfBean getBean(String pdbId) throws IOException, StructureException {
-		// Get to bean
-		DataApiToBean getToBean = new DataApiToBean(getApi(pdbId));
-		return getToBean.getMmtfBean();
-	}
-	
-	/**
-	 * Utility function to get an API to the data  from a Biojava structure
-	 * @param structure the input Biojava structure object
-	 * @return the API to the data in the form of an MmtfDecodedDataInterface
-	 * @throws IOException 
+	 * Utility function to write a Biojava structure object to a path.
+	 * @param structure the structure to write
+	 * @param path the full path of the file to write
+	 * @throws IOException
 	 */
-	public static MmtfDecodedDataInterface getApi(Structure structure) throws IOException {
-		// Set up the transform from the inflator to the get api
+	public static void writeBiojavaStruct(Structure structure, String path) throws IOException {
+		// Set up this writer
 		WriterToDataApi inflatorToGet = new WriterToDataApi();
 		// Get the writer - this is what people implement
 		MmtfStructureWriter mmtfStructureWriter = new MmtfStructureWriter(structure);
-		// Now deflate
+		// Now pass to the get API
 		mmtfStructureWriter.write(inflatorToGet);
-		// Return the API
-		return inflatorToGet;
+		// Now write this dat to file
+		WriterUtils.writeDataToFile(inflatorToGet, path);
 	}
 
-	/**
-	 * Utility function to get an API to the data from a PDB code.
-	 * @param pdbId the input PDB id for the structure you want
-	 * @return the API to the data in the form of an MmtfDecodedDataInterface
-	 * @throws IOException 
-	 * @throws StructureException 
-	 */
-	public static MmtfDecodedDataInterface getApi(String pdbId) throws IOException, StructureException {
-		// Set up the transform from the inflator to the get api
-		WriterToDataApi inflatorToGet = new WriterToDataApi();
-		// Get the writer - this is what people implement
-		MmtfStructureWriter mmtfStructureWriter = new MmtfStructureWriter(
-				StructureIO.getStructure(pdbId));
-		// Now deflate
-		mmtfStructureWriter.write(inflatorToGet);
-		// Get to bean
-		return inflatorToGet;
-	}
-
-	/**
-	 * Round trip a given structure. Mainly for testing purposes.
-	 * @param structure the input Biojava structure object
-	 * @return the round tripped structure (conversion to messge pack mmtf and back).
-	 * @throws IOException
-	 */
-	public static Structure roundTrip(Structure structure) throws IOException {
-		return getBiojavaStruct(getByteArray(structure));
-	}
-}
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
@@ -55,7 +55,7 @@ public void write(MmtfDecoderInterface decoder) {
 		PDBHeader pdbHeader = structure.getPDBHeader();
 		PDBCrystallographicInfo xtalInfo = pdbHeader.getCrystallographicInfo();
 		// TODO Get release date information
-		String releaseDate = "";
+		String releaseDate = "NA";
 		mmtfDecoderInterface.setHeaderInfo(pdbHeader.getRfree(), 1.0f, pdbHeader.getResolution(), pdbHeader.getTitle(), MmtfUtils.dateToIsoString(pdbHeader.getDepDate()), 
 				releaseDate, MmtfUtils.techniquesToStringArray(pdbHeader.getExperimentalTechniques()));
 		mmtfDecoderInterface.setXtalInfo(MmtfUtils.getSpaceGroupAsString(xtalInfo.getSpaceGroup()), MmtfUtils.getUnitCellAsArray(xtalInfo));
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/mmtf/TestMmtfParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/mmtf/TestMmtfParser.java

Original file line number	Diff line number	Diff line change
`@@ -15,8 +15,7 @@`
`15`	`15`	`public class DemoMmtfReader {`
`16`	`16`
`17`	`17`	`public static void main(String[] args) throws IOException, StructureException {`
`18`		`- MmtfUtils.setUpBioJava();`
`19`		`- Structure structure = MmtfActions.getBiojavaStruct("4cup");`
	`18`	`+ Structure structure = MmtfActions.readBiojavaStruct("/path/to/file");`
`20`	`19`	`System.out.println(structure.getChains().size());`
`21`	`20`	`}`
`22`	`21`
Original file line number	Diff line number	Diff line change
`@@ -13,8 +13,7 @@ public class DemoMmtfWriter {`
`13`	`13`	`public static void main(String[] args) throws IOException, StructureException {`
`14`	`14`	`MmtfUtils.setUpBioJava();`
`15`	`15`	`Structure structure = StructureIO.getStructure("4cup");`
`16`		`- // TODO write the byte array to a file`
`17`		`- MmtfActions.getByteArray(structure);`
	`16`	`+ MmtfActions.writeBiojavaStruct(structure, "/tmp/4cup.mmtf");`
`18`	`17`	`}`
`19`	`18`
`20`	`19`