Additional testing of the reader and writer.

abradle · abradle · commit 68ccb6909f83 · 2016-04-19T12:05:03.000-07:00
Altered the demo function.
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfReader.java b/biojava-structure/src/main/java/demo/DemoMmtfReader.java
@@ -5,7 +5,6 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.io.mmtf.MmtfActions;
-import org.biojava.nbio.structure.io.mmtf.MmtfUtils;
 
 /**
  * Class to show how to read a Biojava structure using MMTF
@@ -14,8 +13,14 @@
  */
 public class DemoMmtfReader {
 
+	/**
+	 * Main function to run the demo
+	 * @param args no args to specify
+	 * @throws IOException 
+	 * @throws StructureException
+	 */
 	public static void main(String[] args) throws IOException, StructureException {
-		Structure structure = MmtfActions.readFromFile("/path/to/file");
+		Structure structure = MmtfActions.readFromWeb("4cup");
 		System.out.println(structure.getChains().size());
 	}
 	
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
@@ -152,7 +152,13 @@ private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
 	private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> entityInfos) {
 		for (EntityInfo entityInfo : entityInfos) {
 			String description = entityInfo.getDescription();
-			String type = entityInfo.getType().getEntityType();
+			String type;
+			if (entityInfo.getType()==null){
+				type = null;
+			}
+			else{
+				type = entityInfo.getType().getEntityType();
+			}
 			List<Chain> entityChains = entityInfo.getChains();
 			if (entityChains.isEmpty()){
 				// Error mapping chain to entity
@@ -181,7 +187,7 @@ private void storeBioassemblyInformation(Map<String, Integer> chainIdToIndexMap,
 			for(Entry<double[], int[]> transformEntry : transformMap.entrySet()) {
 				mmtfDecoderInterface.setBioAssemblyTrans(bioAssemblyIndex, transformEntry.getValue(), transformEntry.getKey());
 			}
-			 bioAssemblyIndex+=1;
+			bioAssemblyIndex+=1;
 		}
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -185,6 +185,9 @@ public static float[] getUnitCellAsArray(PDBCrystallographicInfo xtalInfo) {
 	 * @return the array of strings describing the methods used.
 	 */
 	public static String[] techniquesToStringArray(Set<ExperimentalTechnique> experimentalTechniques) {
+		if(experimentalTechniques==null){
+			return new String[0];
+		}
 		String[] outArray = new String[experimentalTechniques.size()];
 		int index = 0;
 		for (ExperimentalTechnique experimentalTechnique : experimentalTechniques) {
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
@@ -0,0 +1,79 @@
+package org.biojava.nbio.structure.io.mmtf;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import org.biojava.nbio.structure.AminoAcidImpl;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.AtomImpl;
+import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.ChainImpl;
+import org.biojava.nbio.structure.Element;
+import org.biojava.nbio.structure.EntityInfo;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.PDBHeader;
+import org.biojava.nbio.structure.ResidueNumber;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureImpl;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
+/**
+ * Test that Biojava can read and write MMTF data.
+ * @author Anthony Bradley
+ *
+ */
+public class TestBasicMmtf {
+
+    /**
+     * A test folder for testing writing files.
+     */
+    @Rule
+    public TemporaryFolder testFolder = new TemporaryFolder();
+	
+	
+	/**
+	 * Test that Biojava can read a file from the file system.
+	 * @throws IOException
+	 */
+	@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()));
+		assertEquals(structure.getPDBCode(),"4CUP");
+		assertEquals(structure.getChains().size(),6);
+	}
+	
+	/**
+	 * Test the writing of Structure objects to a file.
+	 * @throws IOException 
+	 */
+	@Test
+	public void testWrite() throws IOException {
+		Structure structure = new StructureImpl();
+		PDBHeader pdbHeader = new PDBHeader();
+		pdbHeader.setExperimentalTechnique("X-RAY DIFFRACTION");
+		structure.setEntityInfos(new ArrayList<EntityInfo>());
+		structure.setPDBHeader(pdbHeader);
+		Chain chain = new ChainImpl();
+		Group group = new AminoAcidImpl(); 
+		group.setPDBName("FKF");
+		Atom atom = new AtomImpl();
+		atom.setName("A");
+		atom.setElement(Element.Ag);
+		atom.setCoords(new double[] {1.0,2.0,3.0});
+		chain.addGroup(group);
+		group.addAtom(atom);
+		ResidueNumber residueNumber = new ResidueNumber();
+		residueNumber.setInsCode('A');
+		residueNumber.setSeqNum(100);
+		group.setResidueNumber(residueNumber);
+		structure.addChain(chain);
+		File tempFile = testFolder.newFile("tmpfile");
+		MmtfActions.writeToFile(structure, tempFile.getAbsolutePath());		
+	}
+}
diff --git a/biojava-structure/src/test/resources/org/biojava/nbio/structure/io/mmtf/4CUP.mmtf b/biojava-structure/src/test/resources/org/biojava/nbio/structure/io/mmtf/4CUP.mmtf
