File | Line |
---|
uk/ac/ebi/intenz/tools/release/helper/EnzymeClassHelper.java | 50 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubSubclassHelper.java | 51 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubclassHelper.java | 51 |
xmlStringBuffer.append(encoding.xml2Display(removeFormatting(enzymeClass.getDescription()), EncodingType.SWISSPROT_CODE));
xmlStringBuffer.append("</description>");
}
xmlStringBuffer.append("<reactions>");
xmlStringBuffer.append("</reactions>");
xmlStringBuffer.append("<syst_name>");
xmlStringBuffer.append("</syst_name>");
xmlStringBuffer.append("<synonyms>");
xmlStringBuffer.append("</synonyms>");
xmlStringBuffer.append("<comments>");
xmlStringBuffer.append("</comments>");
xmlStringBuffer.append("<links>");
xmlStringBuffer.append("</links>");
xmlStringBuffer.append("<references>");
xmlStringBuffer.append("<reference>");
xmlStringBuffer.append("<reference>");
xmlStringBuffer.append("<number>");
xmlStringBuffer.append("</number>");
xmlStringBuffer.append("<authors>");
xmlStringBuffer.append("</auhors>");
xmlStringBuffer.append("<title>");
xmlStringBuffer.append("</title>");
xmlStringBuffer.append("<year>");
xmlStringBuffer.append("</year>");
xmlStringBuffer.append("<issue>");
xmlStringBuffer.append("</issue>");
xmlStringBuffer.append("<patent_no>");
xmlStringBuffer.append("</patent_no>");
xmlStringBuffer.append("<first_page>");
xmlStringBuffer.append("</first_page>");
xmlStringBuffer.append("<last_page>");
xmlStringBuffer.append("</last_page>");
xmlStringBuffer.append("<edition>");
xmlStringBuffer.append("</edition>");
xmlStringBuffer.append("<editor>");
xmlStringBuffer.append("</editor>");
xmlStringBuffer.append("<volume>");
xmlStringBuffer.append("</volume>");
xmlStringBuffer.append("<pub_place>");
xmlStringBuffer.append("</pub_place>");
xmlStringBuffer.append("<pub_company>");
xmlStringBuffer.append("</pub_company>");
xmlStringBuffer.append("<pub_med>");
xmlStringBuffer.append("</pub_med>");
xmlStringBuffer.append("<medline>");
xmlStringBuffer.append("</medline>");
xmlStringBuffer.append("</reference>");
xmlStringBuffer.append("</reference>");
xmlStringBuffer.append("</references>");
xmlStringBuffer.append("<history>");
xmlStringBuffer.append("</history>");
xmlStringBuffer.append("</enzyme>");
return xmlStringBuffer.toString();
}
private static String removeFormatting(String text) {
text = text.replaceAll("\\<small\\>", "");
text = text.replaceAll("\\<\\/small\\>", "");
text = text.replaceAll("\\<b\\>", "");
text = text.replaceAll("\\<\\/b\\>", "");
text = text.replaceAll("\\<i\\>", "");
text = text.replaceAll("\\<\\/i\\>", "");
return text;
}
} |
File | Line |
---|
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 103 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 323 |
xmlStringBuffer.append("<reference>");
xmlStringBuffer.append("<number>");
xmlStringBuffer.append("</number>");
xmlStringBuffer.append("<authors>");
xmlStringBuffer.append("</authors>");
xmlStringBuffer.append("<title>");
xmlStringBuffer.append("</title>");
xmlStringBuffer.append("<year>");
xmlStringBuffer.append("</year>");
xmlStringBuffer.append("<issue>");
xmlStringBuffer.append("</issue>");
xmlStringBuffer.append("<patent_no>");
xmlStringBuffer.append("</patent_no>");
xmlStringBuffer.append("<first_page>");
xmlStringBuffer.append("</first_page>");
xmlStringBuffer.append("<last_page>");
xmlStringBuffer.append("</last_page>");
xmlStringBuffer.append("<edition>");
xmlStringBuffer.append("</edition>");
xmlStringBuffer.append("<editor>");
xmlStringBuffer.append("</editor>");
xmlStringBuffer.append("<volume>");
xmlStringBuffer.append("</volume>");
xmlStringBuffer.append("<pub_place>");
xmlStringBuffer.append("</pub_place>");
xmlStringBuffer.append("<pub_company>");
xmlStringBuffer.append("</pub_company>");
xmlStringBuffer.append("<pub_med>");
xmlStringBuffer.append("</pub_med>");
xmlStringBuffer.append("<medline>");
xmlStringBuffer.append("</medline>");
xmlStringBuffer.append("</reference>"); |
File | Line |
---|
uk/ac/ebi/intenz/tools/release/helper/EnzymeClassHelper.java | 75 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 107 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubSubclassHelper.java | 76 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubclassHelper.java | 76 |
xmlStringBuffer.append("</auhors>");
xmlStringBuffer.append("<title>");
xmlStringBuffer.append("</title>");
xmlStringBuffer.append("<year>");
xmlStringBuffer.append("</year>");
xmlStringBuffer.append("<issue>");
xmlStringBuffer.append("</issue>");
xmlStringBuffer.append("<patent_no>");
xmlStringBuffer.append("</patent_no>");
xmlStringBuffer.append("<first_page>");
xmlStringBuffer.append("</first_page>");
xmlStringBuffer.append("<last_page>");
xmlStringBuffer.append("</last_page>");
xmlStringBuffer.append("<edition>");
xmlStringBuffer.append("</edition>");
xmlStringBuffer.append("<editor>");
xmlStringBuffer.append("</editor>");
xmlStringBuffer.append("<volume>");
xmlStringBuffer.append("</volume>");
xmlStringBuffer.append("<pub_place>");
xmlStringBuffer.append("</pub_place>");
xmlStringBuffer.append("<pub_company>");
xmlStringBuffer.append("</pub_company>");
xmlStringBuffer.append("<pub_med>");
xmlStringBuffer.append("</pub_med>");
xmlStringBuffer.append("<medline>");
xmlStringBuffer.append("</medline>");
xmlStringBuffer.append("</reference>");
xmlStringBuffer.append("</reference>"); |
File | Line |
---|
uk/ac/ebi/intenz/tools/release/helper/EnzymeClassHelper.java | 75 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 327 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubSubclassHelper.java | 76 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubclassHelper.java | 76 |
xmlStringBuffer.append("</auhors>");
xmlStringBuffer.append("<title>");
xmlStringBuffer.append("</title>");
xmlStringBuffer.append("<year>");
xmlStringBuffer.append("</year>");
xmlStringBuffer.append("<issue>");
xmlStringBuffer.append("</issue>");
xmlStringBuffer.append("<patent_no>");
xmlStringBuffer.append("</patent_no>");
xmlStringBuffer.append("<first_page>");
xmlStringBuffer.append("</first_page>");
xmlStringBuffer.append("<last_page>");
xmlStringBuffer.append("</last_page>");
xmlStringBuffer.append("<edition>");
xmlStringBuffer.append("</edition>");
xmlStringBuffer.append("<editor>");
xmlStringBuffer.append("</editor>");
xmlStringBuffer.append("<volume>");
xmlStringBuffer.append("</volume>");
xmlStringBuffer.append("<pub_place>");
xmlStringBuffer.append("</pub_place>");
xmlStringBuffer.append("<pub_company>");
xmlStringBuffer.append("</pub_company>");
xmlStringBuffer.append("<pub_med>");
xmlStringBuffer.append("</pub_med>");
xmlStringBuffer.append("<medline>");
xmlStringBuffer.append("</medline>");
xmlStringBuffer.append("</reference>"); |
File | Line |
---|
uk/ac/ebi/intenz/tools/release/helper/EnzymeClassHelper.java | 82 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 114 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 334 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeReferenceHelper.java | 189 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubSubclassHelper.java | 83 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeSubclassHelper.java | 83 |
xmlStringBuffer.append("<patent_no>");
xmlStringBuffer.append("</patent_no>");
xmlStringBuffer.append("<first_page>");
xmlStringBuffer.append("</first_page>");
xmlStringBuffer.append("<last_page>");
xmlStringBuffer.append("</last_page>");
xmlStringBuffer.append("<edition>");
xmlStringBuffer.append("</edition>");
xmlStringBuffer.append("<editor>");
xmlStringBuffer.append("</editor>");
xmlStringBuffer.append("<volume>");
xmlStringBuffer.append("</volume>");
xmlStringBuffer.append("<pub_place>");
xmlStringBuffer.append("</pub_place>");
xmlStringBuffer.append("<pub_company>");
xmlStringBuffer.append("</pub_company>");
xmlStringBuffer.append("<pub_med>");
xmlStringBuffer.append("</pub_med>");
xmlStringBuffer.append("<medline>");
xmlStringBuffer.append("</medline>"); |
File | Line |
---|
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 69 |
uk/ac/ebi/intenz/tools/release/helper/EnzymeEntryHelper.java | 166 |
String commonName = enzymeEntry.getCommonName(EnzymeViewConstant.INTENZ).getName();
if ( commonName == null ) commonName = enzymeEntry.getCommonName(EnzymeViewConstant.IUBMB).getName();
xmlStringBuffer.append("<common_name>");
xmlStringBuffer.append(removeFormatting(encoding.xml2Display(commonName)));
xmlStringBuffer.append("</common_name>");
xmlStringBuffer.append("<common_name>");
xmlStringBuffer.append(removeFormatting(encoding.xml2Display(commonName, EncodingType.SWISSPROT_CODE)));
xmlStringBuffer.append("</common_name>");
xmlStringBuffer.append("</common_names>");
// All other fields are empty.
xmlStringBuffer.append("<description>");
xmlStringBuffer.append("</description>");
xmlStringBuffer.append("<reactions>"); |