Some refactoring and docs

josemduarte · josemduarte · commit 63ebeed70a0f · 2016-04-19T17:01:13.000-07:00
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfWriter.java b/biojava-structure/src/main/java/demo/DemoMmtfWriter.java
@@ -1,6 +1,7 @@
 package demo;
 
 import java.io.IOException;
+import java.nio.file.Paths;
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
@@ -13,7 +14,7 @@ public class DemoMmtfWriter {
 	public static void main(String[] args) throws IOException, StructureException {
 		MmtfUtils.setUpBioJava();
 		Structure structure = StructureIO.getStructure("4cup");
-		MmtfActions.writeToFile(structure, "/tmp/4cup.mmtf");
+		MmtfActions.writeToFile(structure, Paths.get("/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
@@ -1,6 +1,7 @@
 package org.biojava.nbio.structure.io.mmtf;
 
 import java.io.IOException;
+import java.nio.file.Path;
 
 import org.biojava.nbio.structure.Structure;
 import org.rcsb.mmtf.decoder.DefaultDecoder;
@@ -17,12 +18,12 @@
 public class MmtfActions {
 	
 	/**
-	 * Utility function to get a Biojava structure from a file.
-	 * @param inputByteArray Must be uncompressed (i.e. with entropy compression methods like gzip)
-	 * @return a Biojava structure object relating to the input byte array.
+	 * Utility function to get a Structure object from a mmtf file.
+	 * @param filePath the mmtf file
+	 * @return a Structure object relating to the input byte array.
 	 * @throws IOException 
 	 */
-	public static Structure readFromFile(String filePath) throws IOException {
+	public static Structure readFromFile(Path filePath) throws IOException {
 		// Get the reader - this is the bit that people need to implement.
 		MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
 		// Do the inflation
@@ -32,12 +33,12 @@ public static Structure readFromFile(String filePath) 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
+	 * Utility function to write a Structure object to a file.
+	 * @param structure the Structure to write
+	 * @param path the file to write
 	 * @throws IOException
 	 */
-	public static void writeToFile(Structure structure, String path) throws IOException {
+	public static void writeToFile(Structure structure, Path path) throws IOException {
 		// Set up this writer
 		WriterToEncoder writerToEncoder = new WriterToEncoder();
 		// Get the writer - this is what people implement
@@ -48,9 +49,9 @@ public static void writeToFile(Structure structure, String path) throws IOExcept
 
 	
 	/**
-	 * Utility function to get a Biojava structure from the REST service.
+	 * Utility function to get a Biojava structure from the mmtf REST service.
 	 * @param pdbId the PDB code of the required structure
-	 * @return a Biojava structure object relating to the input byte array
+	 * @return a Structure object relating to the input byte array
 	 * @throws IOException 
 	 */
 	public static Structure readFromWeb(String pdbId) throws IOException {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBasicMmtf.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBasicMmtf.java
@@ -4,6 +4,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 
 import org.biojava.nbio.structure.AminoAcidImpl;
@@ -43,7 +44,7 @@ public class TestBasicMmtf {
 	@Test
 	public void testRead() throws IOException {
 		ClassLoader classLoader = getClass().getClassLoader();
-		Structure structure = MmtfActions.readFromFile((classLoader.getResource("org/biojava/nbio/structure/io/mmtf/4CUP.mmtf").getPath()));
+		Structure structure = MmtfActions.readFromFile((Paths.get(classLoader.getResource("org/biojava/nbio/structure/io/mmtf/4CUP.mmtf").getPath())));
 		assertEquals(structure.getPDBCode(),"4CUP");
 		assertEquals(structure.getChains().size(),6);
 	}
@@ -74,6 +75,6 @@ public void testWrite() throws IOException {
 		group.setResidueNumber(residueNumber);
 		structure.addChain(chain);
 		File tempFile = testFolder.newFile("tmpfile");
-		MmtfActions.writeToFile(structure, tempFile.getAbsolutePath());		
+		MmtfActions.writeToFile(structure, tempFile.toPath());		
 	}
 }
