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1 package JSci.biology;
2
3 import java.lang.Double  ;
4 import java.io.IOException ;
5 import java.util.Collections ;
6 import java.util.Map ;
7 import java.util.HashMap ;
8 import javax.xml.parsers.*;
9 import org.w3c.dom.*;
10 import org.xml.sax.SAXException ;
11 import JSci.chemistry.Molecule;
12
13
19 public final class AminoAcids {
20 private static final Map table = new HashMap ();
21 private static Map symbols;
22
23 private AminoAcids() {}
24
27 public static String getName(String symbol) {
28 if(symbols == null)
29 symbols = loadIndex();
30 return (String )symbols.get(symbol);
31 }
32
35 public static AminoAcid getAminoAcid(String name) {
36 name=name.toLowerCase();
37 AminoAcid aminoacid = (AminoAcid) table.get(name);
38 if(aminoacid==null) {
39 aminoacid=loadAminoAcid("aminoacids/"+name.replace(' ', '-')+".xml");
40 if(aminoacid != null)
41 table.put(name,aminoacid);
42 }
43 return aminoacid;
44 }
45
48 private static Map loadIndex() {
49 DocumentBuilderFactory docFactory=DocumentBuilderFactory.newInstance();
50 try {
51 DocumentBuilder docBuilder=docFactory.newDocumentBuilder();
52 Document doc=docBuilder.parse(AminoAcids.class.getResource("aminoacids/index.xml").toString());
53 Node root=doc.getDocumentElement();
54 NodeList nl=root.getChildNodes();
55 Map index = new HashMap ();
56 for(int i=0; i<nl.getLength(); i++) {
57 Node node = nl.item(i);
58 if(node.getNodeName().equals("amino-acid")) {
59 NamedNodeMap attr = node.getAttributes();
60 index.put(attr.getNamedItem("symbol").getNodeValue(), attr.getNamedItem("name").getNodeValue());
61 }
62 }
63 return index;
64 } catch(ParserConfigurationException e) {
65 return Collections.EMPTY_MAP;
66 } catch(IOException e) {
67 return Collections.EMPTY_MAP;
68 } catch(SAXException e) {
69 return Collections.EMPTY_MAP;
70 }
71 }
72
75 private static AminoAcid loadAminoAcid(String resname) {
76 DocumentBuilderFactory docFactory=DocumentBuilderFactory.newInstance();
77 try {
78 DocumentBuilder docBuilder=docFactory.newDocumentBuilder();
79 Document doc=docBuilder.parse(AminoAcids.class.getResource(resname).toString());
80 Node root=doc.getDocumentElement();
81 NodeList nl=root.getChildNodes();
82 String name=findStringValue(nl,"name");
83 String abbreviation=findStringValue(nl,"abbreviation");
84 String symbol=findStringValue(nl,"symbol");
85 String formula=findStringValue(nl,"molecular-formula");
86 AminoAcid aminoacid=new AminoAcid(name, abbreviation, symbol, formula);
87 aminoacid.setMolecularWeight(findDoubleValue(nl,"molecular-weight"));
88 aminoacid.setIsoelectricPoint(findDoubleValue(nl,"isoelectric-point"));
89 aminoacid.setCASRegistryNumber(findStringValue(nl,"CAS-registry-number"));
90 return aminoacid;
91 } catch(ParserConfigurationException e) {
92 return null;
93 } catch(IOException e) {
94 return null;
95 } catch(SAXException e) {
96 return null;
97 }
98 }
99 private static String findStringValue(NodeList nl,String name) {
100 Node item;
101 for(int i=0;i<nl.getLength();i++) {
102 item=nl.item(i);
103 if(item.getNodeName().equals(name))
104 return item.getFirstChild().getNodeValue();
105 }
106 return "";
107 }
108 private static double findDoubleValue(NodeList nl,String name) {
109 Node item;
110 for(int i=0;i<nl.getLength();i++) {
111 item=nl.item(i);
112 if(item.getNodeName().equals(name))
113 return Double.parseDouble(item.getFirstChild().getNodeValue());
114 }
115 return Double.NaN;
116 }
117 }
118 |
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