001package com.hfg.bio; 002 003 004//------------------------------------------------------------------------------ 005/** 006 XML tag and attribute names for bio classes. 007 <div> 008 @author J. Alex Taylor, hairyfatguy.com 009 </div> 010 */ 011//------------------------------------------------------------------------------ 012// com.hfg Library 013// 014// This library is free software; you can redistribute it and/or 015// modify it under the terms of the GNU Lesser General Public 016// License as published by the Free Software Foundation; either 017// version 2.1 of the License, or (at your option) any later version. 018// 019// This library is distributed in the hope that it will be useful, 020// but WITHOUT ANY WARRANTY; without even the implied warranty of 021// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 022// Lesser General Public License for more details. 023// 024// You should have received a copy of the GNU Lesser General Public 025// License along with this library; if not, write to the Free Software 026// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 027// 028// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com 029// jataylor@hairyfatguy.com 030//------------------------------------------------------------------------------ 031 032public class HfgBioXML 033{ 034 public static final String HFGBIOSEQ_TAG = "HfgBioSeq"; 035 public static final String DESCRIPTION_TAG = "Description"; 036 public static final String PROTEIN_TAG = "Protein"; 037 public static final String CHAINS_TAG = "Chains"; 038 public static final String AASET_TAG = "AASet"; 039 public static final String AMINO_ACIDS_TAG = "AminoAcids"; 040 public static final String AA_TAG = "AA"; 041 public static final String NTERM_TAG = "NTerm"; 042 public static final String CTERM_TAG = "CTerm"; 043 public static final String MOL_TAG = "Mol"; 044 public static final String KAS_TAG = "Kas"; 045 public static final String SIDECHAIN_KAS_TAG = "SidechainKAs"; 046 public static final String ELEMENTAL_COMP_TAG = "ElementalComp"; 047 public static final String XLINKS_TAG = "XLinks"; 048 public static final String XLINK_TAG = "XLink"; 049 public static final String XLINK_TYPE_TAG = "XLinkType"; 050 public static final String DONORS_TAG = "Donors"; 051 public static final String ACCEPTORS_TAG = "Acceptors"; 052 public static final String DONOR_TAG = "Donor"; 053 public static final String ACCEPTOR_TAG = "Acceptor"; 054 public static final String ATTRIBUTES_TAG = "Attributes"; 055 public static final String ATTRIBUTE_TAG = "Attr"; 056 public static final String STRAND_TAG = "Strand"; 057 public static final String GENOMIC_LOC_TAG = "GenomicLoc"; 058 public static final String AA_GROUPING_SCHEME_TAG = "AAGroupingScheme"; 059 public static final String ALIGNED_QUERY = "AlignedQuery"; 060 public static final String ALIGNED_SUBJECT = "AlignedSubject"; 061 public static final String ALIGNMENT = "Alignment"; 062 public static final String ALIGNMENT_SCORING = "AlignmentScoring"; 063 public static final String QUERY = "Query"; 064 public static final String SUBJECT = "Subject"; 065 public static final String KA_SET_TAG = "KaSet"; 066 public static final String PKA_TAG = "pKa"; 067 public static final String N_TERM_PKA_TAG = "NTerm_pKa"; 068 public static final String C_TERM_PKA_TAG = "CTerm_pKa"; 069 public static final String C_TERM_AA_PKA_TAG = "CTermAA_pKa"; 070 public static final String PROTEIN_ANALYSIS_MODE_TAG = "ProteinAnalysisMode"; 071 public static final String INTRON_TAG = "Intron"; 072 public static final String DNA_TAG = "DNA"; 073 074 public static final String AA_ATT = "aa"; 075 public static final String ASSEMBLY_ATT = "assembly"; 076 public static final String BUILD_ATT = "build"; 077 public static final String C_TERM_ATT = "cTerm"; 078 public static final String CHROMOSOME_ATT = "chromosome"; 079 public static final String CLASS_ATT = "class"; 080 public static final String CONTIG_ATT = "contig"; 081 public static final String CONTIG_LENGTH_ATT = "contigLength"; 082 public static final String ID_ATT = "id"; 083 public static final String NAME_ATT = "name"; 084 public static final String MONO_MASS_ATT = "monoMass"; 085 public static final String AVG_MASS_ATT = "avgMass"; 086 public static final String SHORT_NAME_ATT = "shortName"; 087 public static final String DEFAULT_ANALYSIS_MODE_ATT = "defaultAnalysisMode"; 088 public static final String DISULFIDE_CNT_ATT = "disulfideBonds"; 089 public static final String LOCKED_ATT = "locked"; 090 public static final String MAPPING_ATT = "mapping"; 091 public static final String N_TERM_ATT = "nTerm"; 092 public static final String THREE_LTR_CODE_ATT = "threeLtrCode"; 093 public static final String ONE_LTR_CODE_ATT = "oneLtrCode"; 094 public static final String IS_APPROX_ATT = "isApprox"; 095 public static final String IS_NULL_ATT = "isNull"; 096 public static final String CHAIN_ID_ATT = "chainId"; 097 public static final String RESIDUE_ATT = "residue"; 098 public static final String SCORE_ATT = "score"; 099 public static final String SEQ_LENGTH_ATT = "seqLength"; 100 public static final String START_ATT = "start"; 101 public static final String STRAND_ATT = "strand"; 102 public static final String COMPARISON_LENGTH_ATT = "comparisionLength"; 103 public static final String NUM_IDENTITIES_ATT = "numIdentitites"; 104 public static final String PROTONATED_FORM_ATT = "protonatedForm"; 105 public static final String TAXON_ATT = "taxon"; 106 public static final String VALUE_ATT = "value"; 107 public static final String MONOSACCHARIDE_ATT = "monosaccharide"; 108 public static final String DONOR_SITE_ATT = "donorSite"; 109 public static final String ACCEPTOR_SITE_ATT = "acceptorSite"; 110}