Better docs and an empty test

josemduarte · josemduarte · commit 35ff5a43015c · 2016-03-08T18:42:24.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java
@@ -0,0 +1,59 @@
+package org.biojava.nbio.structure.test.io;
+
+//import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+
+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.FileParsingParameters;
+import org.junit.Ignore;
+import org.junit.Test;
+
+/**
+ * Test for a difficult large mmCIF file (a ribosome) with many 2-letter chain ids.
+ * Both tests are set to Ignore because the parsing of the file takes too long.
+ * 
+ * @author Jose Duarte
+ *
+ */
+public class Test4v5a {
+
+	@Test @Ignore
+	public void test4v5a() throws StructureException, IOException {
+		AtomCache cache = new AtomCache();
+		
+		FileParsingParameters params = cache.getFileParsingParams();
+		params.setUseInternalChainId(false);
+		params.setCreateAtomBonds(true);
+		StructureIO.setAtomCache(cache);
+		
+		StructureIO.getStructure("4v5a");
+		
+		
+	}
+
+	@Test @Ignore
+	public void test4v5aInternalChainIds() throws StructureException, IOException {
+		AtomCache cache = new AtomCache();
+		
+		FileParsingParameters params = cache.getFileParsingParams();
+		params.setUseInternalChainId(true);
+		params.setCreateAtomBonds(true);
+		StructureIO.setAtomCache(cache);
+		
+		
+		// this would throw an exception when making ss bonds from struct_conn because 
+		// chain id "AD" is both an author chain id and an asym chain id and the chains were 
+		// getting mixed
+		StructureIO.getStructure("4v5a");
+		
+		//for (Chain c : s.getChains()) {
+		//	System.out.println(c.getChainID()+" "+c.getInternalChainID()+" "+c.getAtomLength());
+		//}
+
+		
+	}
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -287,11 +287,11 @@ else if (aminoCode1 != null ) {
 		return  group ;
 	}
 	
-	/** test if the chain is already known (is in current_model
-	 * ArrayList) and if yes, returns the chain
-	 * if no -> returns null
+	/** 
+	 * Test if the given chainID is already present in the list of chains given. If yes, returns the chain
+	 * otherwise returns null. 
 	 */
-	private Chain isKnownChain(String chainID, List<Chain> chains){
+	private static Chain isKnownChain(String chainID, List<Chain> chains){
 
 		for (int i = 0; i< chains.size();i++){
 			Chain testchain =  chains.get(i);
