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