Fixed DBRef#toPDB() method to give 80 characters line

Author: sroughley

biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java

@@ -131,13 +131,13 @@ public void toPDB(StringBuffer buf){
 //        DBREF  3EH2 A    2   767  UNP    P53992   SC24C_HUMAN    329   1094
 //        DBREF 3EH2 A    2   767     UNP   P53992  SC24C_HUMAN   329   1094
 //        DBREF  3ETA A  990  1295  UNP    P06213   INSR_HUMAN    1017   1322
-        formatter.format("DBREF  %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c",
+        formatter.format("DBREF  %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c            ",
                 idCode, chainId,seqbegin,insertBegin,seqEnd,insertEnd,
                 database,dbAccession,dbIdCode,
                 dbSeqBegin,idbnsBegin,dbSeqEnd,idbnsEnd
                 );
 
-        buf.append(formatter.toString().trim());
+        buf.append(formatter.toString());
         formatter.close();
 
     }

biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java

@@ -1,50 +1,51 @@
 package org.biojava.nbio.structure.io;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 
 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.junit.Test;
 
 public class TestDBRefParsing {
-	@Test
-	public void test2W6E() throws IOException, StructureException {
-
-		// an entry with a title in multiple lines in PDB file
-
-		AtomCache cache = new AtomCache();
-
-		StructureIO.setAtomCache(cache);
-
-		cache.setUseMmCif(false);
-		Structure sPdb = StructureIO.getStructure("2W6E");
-		// System.out.println(sPdb.getName());
-		System.out.println(sPdb.getDBRefs().get(0).toPDB());
-	}
 
 	@Test
-	public void testShortLine() throws IOException,StructureException{
+	public void testShortLine() throws IOException, StructureException {
 		String shortLine = "DBREF  2W6E A  -42   510  UNP    P19483   ATPA1_BOVIN      1    553";
 		InputStream is = new ByteArrayInputStream(shortLine.getBytes());
 		PDBFileParser pdbPars = new PDBFileParser();
 		Structure s;
-		try{
-			s=pdbPars.parsePDBFile(is);
-		}catch (Exception e){
+		try {
+			s = pdbPars.parsePDBFile(is);
+		} catch (Exception e) {
 			is.close();
 			throw new AssertionError("Unable to process truncated DBRef line");
 		}
-		
-		
-		is = new ByteArrayInputStream(String.format("%1$-80s", shortLine).getBytes());
+		is = new ByteArrayInputStream(String.format("%1$-80s", shortLine)
+				.getBytes());
 		Structure ref = pdbPars.parsePDBFile(is);
 		is.close();
 		assertEquals(ref.getDBRefs().get(0), s.getDBRefs().get(0));
 	}
+
+	@Test
+	public void testToPdbLength() throws IOException {
+		String shortLine = "DBREF  2W6E A  -42   510  UNP    P19483   ATPA1_BOVIN      1    553";
+		InputStream is = new ByteArrayInputStream(shortLine.getBytes());
+		PDBFileParser pdbPars = new PDBFileParser();
+		Structure s;
+		try {
+			s = pdbPars.parsePDBFile(is);
+		} catch (Exception e) {
+			is.close();
+			throw new AssertionError("Unable to process truncated DBRef line");
+		}
+		//Make sure that the record is true to the input
+		assertEquals(shortLine, s.getDBRefs().get(0).toPDB().trim());
+		//And is padded to the correct lenght
+		assertEquals(80, s.getDBRefs().get(0).toPDB().length());
+	}
 }