Now actually testing something, test doesn't pass yet

josemduarte · josemduarte · commit b7aa1bace112 · 2015-06-06T18:24:02.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/MMCIFFileTools.java
@@ -11,10 +11,20 @@
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.GroupType;
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
 import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+/**
+ * Some tools for mmCIF file writing.
+ * 
+ * See http://www.iucr.org/__data/assets/pdf_file/0019/22618/cifguide.pdf
+ * 
+ * 
+ * @author duarte_j
+ *
+ */
 public class MMCIFFileTools {
 
 	private static final Logger logger = LoggerFactory.getLogger(MMCIFFileTools.class);
@@ -32,7 +42,7 @@ public class MMCIFFileTools {
 	public static final String MMCIF_DEFAULT_VALUE = ".";
 	
 	/**
-	 * The header appearing at the beginning of a mmCIF file
+	 * The header appearing at the beginning of a mmCIF file. A "block code" can be added to it of no more than 32 chars.
 	 */
 	public static final String MMCIF_TOP_HEADER = "data_";
 	
@@ -47,7 +57,7 @@ public class MMCIFFileTools {
 	public static String toLoopMmCifHeaderString(String categoryName, String className) throws ClassNotFoundException {
 		StringBuilder str = new StringBuilder();
 		
-		str.append("loop_"+newline);
+		str.append(SimpleMMcifParser.LOOP_START+newline);
 		
 		Class<?> c = Class.forName(className);
 		
@@ -73,6 +83,8 @@ public static String toMMCIF(List<Object> list) {
 			sb.append(toSingleLineMmCifString(o, sizes));
 		}
 		
+		sb.append(SimpleMMcifParser.LOOP_END+newline);
+		
 		return sb.toString();
 	}
 	
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -23,13 +23,15 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.io.MMCIFFileReader;
+import org.biojava.nbio.structure.io.MMCIFFileTools;
 import org.biojava.nbio.structure.io.StructureIOFile;
 import org.biojava.nbio.structure.io.mmcif.model.*;
 import org.biojava.nbio.structure.jama.Matrix;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import javax.vecmath.Matrix4d;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -238,8 +240,8 @@ public void parse(BufferedReader buf)
 					if ( pos < 0 ) {
 						// looks like a chem_comp file
 						// line should start with data, otherwise something is wrong!
-						if (! line.startsWith("data_")){
-							logger.warn("this does not look like a valid MMcif file! The first line should be data_1XYZ, but is " + line);
+						if (! line.startsWith(MMCIFFileTools.MMCIF_TOP_HEADER)){
+							logger.warn("This does not look like a valid MMcif file! The first line should start with 'data_', but is '" + line+"'");
 							triggerDocumentEnd();
 							return;
 						}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
@@ -2,13 +2,19 @@
 
 import static org.junit.Assert.*;
 
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.IOException;
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.io.mmcif.MMcifParser;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
+import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
 import org.junit.Test;
 
 public class TestMMCIFWriting {
@@ -25,17 +31,35 @@ public void test1SMT() throws IOException, StructureException {
 		params.setAlignSeqRes(true);
 		cache.setFileParsingParams(params);
 		
-		Structure sCif = StructureIO.getStructure("1SMT");
+		Structure originalStruct = StructureIO.getStructure("1SMT");
+				
+		File outputFile = File.createTempFile("biojava_testing_", ".cif");
 		
-		assertNotNull(sCif);
 		
-
-		FileConvert fc = new FileConvert(sCif);
+		FileConvert fc = new FileConvert(originalStruct);
 		
-		FileWriter fw = new FileWriter("/home/jose/test.cif");
-		//System.out.println(fc.toMmCif());
+		FileWriter fw = new FileWriter(outputFile);
 		fw.write(fc.toMMCIF());
 		fw.close();
+		
+		
+		MMcifParser parser = new SimpleMMcifParser();
+
+		SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
+
+		FileParsingParameters fileParsingParams = new FileParsingParameters();
+		fileParsingParams.setAlignSeqRes(true);
+
+		consumer.setFileParsingParameters(fileParsingParams);
+
+		parser.addMMcifConsumer(consumer);
+
+		parser.parse(new BufferedReader(new FileReader(outputFile))); 
+
+		Structure readStruct = consumer.getStructure();
+		
+		assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
+		
 	}
 
 }
