Mercurial > hg > anteater

comparison src/de/mpiwg/anteater/xml/impl/LinnaeusParser.java @ 5:35d8c78ccd36

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include linneaus findings
author jdamerow
date Thu, 25 Oct 2012 15:26:03 -0700
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4:dcc35f89dce3 5:35d8c78ccd36
1 package de.mpiwg.anteater.xml.impl;
2
3 import java.io.InputStream;
4 import java.util.ArrayList;
5 import java.util.List;
6
7 import org.jdom2.Attribute;
8 import org.jdom2.DataConversionException;
9 import org.jdom2.Element;
10
11 import de.mpiwg.anteater.species.scientific.ScientificName;
12 import de.mpiwg.anteater.xml.ICommonNameFinderParser;
13
14 public class LinnaeusParser extends JDOMParser implements ICommonNameFinderParser {
15
16 public LinnaeusParser(String content) {
17 super(content, false);
18 }
19
20 public LinnaeusParser(InputStream stream) {
21 super(stream);
22 }
23
24 @Override
25 public List<ScientificName> parseSpeciesNames() {
26 List<Element> names = executeXPath("/linnaeus/species", null);
27
28 List<ScientificName> commonNames = new ArrayList<ScientificName>();
29 for (Element name : names) {
30 ScientificName commonName = new ScientificName();
31
32 Attribute id = name.getAttribute("id");
33 commonName.setNcbiId(id.getValue());
34 commonName.setIdentifiedName(id.getValue());
35
36 Attribute start = name.getAttribute("start");
37 try {
38 commonName.setStart(start.getIntValue());
39 } catch (DataConversionException e) {
40 // TODO Auto-generated catch block
41 e.printStackTrace();
42 }
43
44 Attribute end = name.getAttribute("end");
45 try {
46 commonName.setLength(end.getIntValue() - start.getIntValue());
47 } catch (DataConversionException e) {
48 // TODO Auto-generated catch block
49 e.printStackTrace();
50 }
51
52 Attribute text = name.getAttribute("text");
53 commonName.setScientificName(text.getValue());
54 commonName.setReferenceInText(text.getValue());
55
56 commonNames.add(commonName);
57 }
58
59 return commonNames;
60 }
61
62 }