Java Code Examples for org.biojava.nbio.structure.Structure#getJournalArticle()

The following examples show how to use org.biojava.nbio.structure.Structure#getJournalArticle() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.

Example 1

Source File: PDBFileParserTest.java From biojava with GNU Lesser General Public License v2.1

6 votes

@Test
public void testMultiLineJRNL() throws IOException {
	//            System.out.println("Testing JRNL record parsing from 3pfk");
	String jrnlString =
			"JRNL        AUTH   P.R.EVANS,G.W.FARRANTS,P.J.HUDSON                            " + newline +
			"JRNL        TITL   PHOSPHOFRUCTOKINASE: STRUCTURE AND CONTROL.                  " + newline +
			"JRNL        REF    PHILOS.TRANS.R.SOC.LONDON,    V. 293    53 1981              " + newline +
			"JRNL        REF  2 SER.B                                                        " + newline +
			"JRNL        REFN                   ISSN 0080-4622                               " + newline +
			"JRNL        PMID   6115424                                                      ";


	BufferedReader br = new BufferedReader(new StringReader(jrnlString));
	Structure s = null;

	s = parser.parsePDBFile(br);

	// String jrnl = s.getJournalArticle().toString();
	//            System.out.println(jrnl);
	JournalArticle journalArticle = s.getJournalArticle();
	assertEquals("293", journalArticle.getVolume());
	assertEquals("53", journalArticle.getStartPage());
	assertEquals(1981, journalArticle.getPublicationDate());
	assertEquals("PHILOS.TRANS.R.SOC.LONDON, SER.B", journalArticle.getJournalName());
}

Example 2

Source File: PDBFileParserTest.java From biojava with GNU Lesser General Public License v2.1

6 votes

@Test
public void testIncorrectDateFormatMultiLineJRNL() throws IOException{
	//            System.out.println("Testing JRNL record parsing from 3pfk");
	String jrnlString =
			"JRNL        AUTH   P.R.EVANS,G.W.FARRANTS,P.J.HUDSON                            " + newline +
			"JRNL        TITL   PHOSPHOFRUCTOKINASE: STRUCTURE AND CONTROL.                  " + newline +
			"JRNL        REF    PHILOS.TRANS.R.SOC.LONDON,    V. 293    53 19SE              " + newline +
			"JRNL        REF  2 SER.B                                                        " + newline +
			"JRNL        REFN                   ISSN 0080-4622                               " + newline +
			"JRNL        PMID   6115424                                                      ";


	BufferedReader br = new BufferedReader(new StringReader(jrnlString));
	Structure s = null;
	s = parser.parsePDBFile(br);
	//    String jrnl = s.getJournalArticle().toString();
	//            System.out.println(jrnl);
	JournalArticle journalArticle = s.getJournalArticle();
	assertEquals("293", journalArticle.getVolume());
	assertEquals("53", journalArticle.getStartPage());
	assertEquals(0, journalArticle.getPublicationDate());
	assertEquals("PHILOS.TRANS.R.SOC.LONDON, SER.B", journalArticle.getJournalName());
}

Example 3

Source File: PDBFileParserTest.java From biojava with GNU Lesser General Public License v2.1

6 votes

@Test
public void testInvalidFormatREFsectionJRNL() throws IOException{
	//            System.out.println("Testing JRNL record parsing from 3pfk");
	String jrnlString =
			"JRNL        AUTH   P.R.EVANS,G.W.FARRANTS,P.J.HUDSON                            " + newline +
			//            "JRNL        TITL   PHOSPHOFRUCTOKINASE: STRUCTURE AND CONTROL.                  " + newline +
			"JRNL        REF    INTERESTING TIMES                                            " + newline +
			"JRNL        REFN                   ISSN 0080-4622                               " + newline +
			"JRNL        PMID   6115424                                                      ";


	BufferedReader br = new BufferedReader(new StringReader(jrnlString));
	Structure s = null;
	s = parser.parsePDBFile(br);
	// String jrnl = s.getJournalArticle().toString();
	//            System.out.println(jrnl);
	JournalArticle journalArticle = s.getJournalArticle();
	assertEquals("", journalArticle.getVolume());
	assertEquals("", journalArticle.getStartPage());
	assertEquals(0, journalArticle.getPublicationDate());
	assertEquals("", journalArticle.getJournalName());
}

Example 4

Source File: PDBFileParserTest.java From biojava with GNU Lesser General Public License v2.1

6 votes

@Test
public void testSecondMultiLineJRNL() throws IOException{
	//            System.out.println("Testing JRNL record parsing from 1gpb");
	String jrnlString =
			"JRNL        AUTH   K.R.ACHARYA,D.I.STUART,K.M.VARVILL,L.N.JOHNSON               " + newline +
			"JRNL        TITL   GLYCOGEN PHOSPHORYLASE B: DESCRIPTION OF THE                 " + newline +
			"JRNL        TITL 2 PROTEIN STRUCTURE                                            " + newline +
			"JRNL        REF    GLYCOGEN PHOSPHORYLASE B:                1 1991              " + newline +
			"JRNL        REF  2 DESCRIPTION OF THE PROTEIN                                   " + newline +
			"JRNL        REF  3 STRUCTURE                                                    " + newline +
			"JRNL        PUBL   WORLD SCIENTIFIC PUBLISHING CO.,SINGAPORE                    " + newline +
			"JRNL        REFN                                                                ";


	BufferedReader br = new BufferedReader(new StringReader(jrnlString));
	Structure s = null;
	s = parser.parsePDBFile(br);
	// String jrnl = s.getJournalArticle().toString();
	//            System.out.println(jrnl);
	JournalArticle journalArticle = s.getJournalArticle();
	assertEquals("", journalArticle.getVolume());
	assertEquals("1", journalArticle.getStartPage());
	assertEquals(1991, journalArticle.getPublicationDate());
	assertEquals("GLYCOGEN PHOSPHORYLASE B: DESCRIPTION OF THE PROTEIN STRUCTURE", journalArticle.getJournalName());
}

Example 5

Source File: PDBFileParserTest.java From biojava with GNU Lesser General Public License v2.1

6 votes

@Test
public void testToBePublishedJRNL() throws IOException{
	//            System.out.println("Testing JRNL record parsing from 1i2c");
	String jrnlString =
			"JRNL        AUTH   M.J.THEISEN,S.L.SANDA,S.L.GINELL,C.BENNING,                  " + newline +
			"JRNL        AUTH 2 R.M.GARAVITO                                                 " + newline +
			"JRNL        TITL   CHARACTERIZATION OF THE ACTIVE SITE OF                       " + newline +
			"JRNL        TITL 2 UDP-SULFOQUINOVOSE SYNTHASE: FORMATION OF THE                " + newline +
			"JRNL        TITL 3 SULFONIC ACID PRODUCT IN THE CRYSTALLINE STATE.              " + newline +
			"JRNL        REF    TO BE PUBLISHED                                              " + newline +
			"JRNL        REFN                                                                ";


	BufferedReader br = new BufferedReader(new StringReader(jrnlString));
	Structure s = null;
	s = parser.parsePDBFile(br);

	JournalArticle journalArticle = s.getJournalArticle();
	assertNull(journalArticle.getVolume());
	assertNull(journalArticle.getStartPage());
	assertEquals(0,journalArticle.getPublicationDate());
	assertEquals("TO BE PUBLISHED", journalArticle.getJournalName());
}

Example 6

Source File: PDBFileParserTest.java From biojava with GNU Lesser General Public License v2.1

5 votes

@Test
public void testSingleLineJRNL() throws IOException{
	//            System.out.println("Testing JRNL record parsing from 2bln");
	String jrnlString =
			"JRNL        AUTH   G.J.WILLIAMS,S.D.BREAZEALE,C.R.H.RAETZ,J.H.NAISMITH          " + newline +
			"JRNL        TITL   STRUCTURE AND FUNCTION OF BOTH DOMAINS OF ARNA, A            " + newline +
			"JRNL        TITL 2 DUAL FUNCTION DECARBOXYLASE AND A                            " + newline +
			"JRNL        TITL 3 FORMYLTRANSFERASE, INVOLVED IN 4-AMINO-4-DEOXY-L-            " + newline +
			"JRNL        TITL 4 ARABINOSE BIOSYNTHESIS.                                      " + newline +
			"JRNL        REF    J.BIOL.CHEM.                  V. 280 23000 2005              " + newline +
			"JRNL        REFN                   ISSN 0021-9258                               " + newline +
			"JRNL        PMID   15809294                                                     " + newline +
			"JRNL        DOI    10.1074/JBC.M501534200                                       ";


	BufferedReader br = new BufferedReader(new StringReader(jrnlString));
	Structure s = null;
	s = parser.parsePDBFile(br);
	//   String jrnl = s.getJournalArticle().toString();
	//            System.out.println(jrnl);
	JournalArticle journalArticle = s.getJournalArticle();
	//            System.out.println(journalArticle.getRef());
	assertEquals("280", journalArticle.getVolume());
	assertEquals("23000", journalArticle.getStartPage());
	assertEquals(2005, journalArticle.getPublicationDate());
	assertEquals("J.BIOL.CHEM.", journalArticle.getJournalName());
}