1 package uk.ac.ebi.intenz.tools.release.helper;
2
3 import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass;
4 import uk.ac.ebi.xchars.SpecialCharacters;
5 import uk.ac.ebi.xchars.domain.EncodingType;
6
7
8
9
10
11
12
13 public class EnzymeSubclassHelper {
14
15
16
17 private EnzymeSubclassHelper() {}
18
19 public static String toXML(EnzymeSubclass enzymeSubclass, SpecialCharacters encoding) {
20 StringBuffer xmlStringBuffer = new StringBuffer();
21
22 xmlStringBuffer.append("<enzyme>");
23
24 xmlStringBuffer.append("<ec>");
25 xmlStringBuffer.append("EC " + enzymeSubclass.getEc().toString());
26 xmlStringBuffer.append("</ec>");
27
28 xmlStringBuffer.append("<deleted_text>");
29 xmlStringBuffer.append("</deleted_text>");
30
31 xmlStringBuffer.append("<common_name>");
32 if (!enzymeSubclass.getName().equals("")) {
33 xmlStringBuffer.append(encoding.xml2Display(removeFormatting(enzymeSubclass.getName())));
34 }
35 xmlStringBuffer.append("</common_name>");
36
37 if (!enzymeSubclass.getName().equals("")) {
38 xmlStringBuffer.append("<common_name>");
39 xmlStringBuffer.append(encoding.xml2Display(removeFormatting(enzymeSubclass.getName()), EncodingType.SWISSPROT_CODE));
40 xmlStringBuffer.append("</common_name>");
41 }
42
43 xmlStringBuffer.append("<description>");
44 if (!enzymeSubclass.getDescription().equals("")) {
45 xmlStringBuffer.append(encoding.xml2Display(removeFormatting(enzymeSubclass.getDescription())));
46 }
47 xmlStringBuffer.append("</description>");
48
49 if (!enzymeSubclass.getDescription().equals("")) {
50 xmlStringBuffer.append("<description>");
51 xmlStringBuffer.append(encoding.xml2Display(removeFormatting(enzymeSubclass.getDescription()), EncodingType.SWISSPROT_CODE));
52 xmlStringBuffer.append("</description>");
53 }
54
55 xmlStringBuffer.append("<reactions>");
56 xmlStringBuffer.append("</reactions>");
57
58 xmlStringBuffer.append("<syst_name>");
59 xmlStringBuffer.append("</syst_name>");
60
61 xmlStringBuffer.append("<synonyms>");
62 xmlStringBuffer.append("</synonyms>");
63
64 xmlStringBuffer.append("<comments>");
65 xmlStringBuffer.append("</comments>");
66
67 xmlStringBuffer.append("<links>");
68 xmlStringBuffer.append("</links>");
69
70 xmlStringBuffer.append("<references>");
71 xmlStringBuffer.append("<reference>");
72 xmlStringBuffer.append("<reference>");
73 xmlStringBuffer.append("<number>");
74 xmlStringBuffer.append("</number>");
75 xmlStringBuffer.append("<authors>");
76 xmlStringBuffer.append("</auhors>");
77 xmlStringBuffer.append("<title>");
78 xmlStringBuffer.append("</title>");
79 xmlStringBuffer.append("<year>");
80 xmlStringBuffer.append("</year>");
81 xmlStringBuffer.append("<issue>");
82 xmlStringBuffer.append("</issue>");
83 xmlStringBuffer.append("<patent_no>");
84 xmlStringBuffer.append("</patent_no>");
85 xmlStringBuffer.append("<first_page>");
86 xmlStringBuffer.append("</first_page>");
87 xmlStringBuffer.append("<last_page>");
88 xmlStringBuffer.append("</last_page>");
89 xmlStringBuffer.append("<edition>");
90 xmlStringBuffer.append("</edition>");
91 xmlStringBuffer.append("<editor>");
92 xmlStringBuffer.append("</editor>");
93 xmlStringBuffer.append("<volume>");
94 xmlStringBuffer.append("</volume>");
95 xmlStringBuffer.append("<pub_place>");
96 xmlStringBuffer.append("</pub_place>");
97 xmlStringBuffer.append("<pub_company>");
98 xmlStringBuffer.append("</pub_company>");
99 xmlStringBuffer.append("<pub_med>");
100 xmlStringBuffer.append("</pub_med>");
101 xmlStringBuffer.append("<medline>");
102 xmlStringBuffer.append("</medline>");
103 xmlStringBuffer.append("</reference>");
104 xmlStringBuffer.append("</reference>");
105 xmlStringBuffer.append("</references>");
106
107 xmlStringBuffer.append("<history>");
108 xmlStringBuffer.append("</history>");
109
110 xmlStringBuffer.append("</enzyme>");
111
112 return xmlStringBuffer.toString();
113 }
114
115 private static String removeFormatting(String text) {
116 text = text.replaceAll("\\<small\\>", "");
117 text = text.replaceAll("\\<\\/small\\>", "");
118 text = text.replaceAll("\\<b\\>", "");
119 text = text.replaceAll("\\<\\/b\\>", "");
120 text = text.replaceAll("\\<i\\>", "");
121 text = text.replaceAll("\\<\\/i\\>", "");
122 return text;
123 }
124 }