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

sroughley · sbliven · commit 716780a550e9 · 2016-03-08T18:59:07.000+01:00
(Cherry-picked from 07de4bb by sbliven to resolve pull biojava#332)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java b/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();
 
     }
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDBRefParsing.java
@@ -0,0 +1,51 @@
+package org.biojava.nbio.structure.io;
+
+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.junit.Test;
+
+public class TestDBRefParsing {
+
+	@Test
+	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) {
+			is.close();
+			throw new AssertionError("Unable to process truncated DBRef line");
+		}
+		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());
+	}
+}
