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com.hfg xml, html, svg, and bioinformatics utility library
package com.hfg.bio;
//------------------------------------------------------------------------------
/**
XML tag and attribute names for bio classes.
@author J. Alex Taylor, hairyfatguy.com
*/
//------------------------------------------------------------------------------
// com.hfg Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------
public class HfgBioXML
{
public static final String HFGBIOSEQ_TAG = "HfgBioSeq";
public static final String DESCRIPTION_TAG = "Description";
public static final String PROTEIN_TAG = "Protein";
public static final String CHAINS_TAG = "Chains";
public static final String AASET_TAG = "AASet";
public static final String AMINO_ACIDS_TAG = "AminoAcids";
public static final String AA_TAG = "AA";
public static final String NTERM_TAG = "NTerm";
public static final String CTERM_TAG = "CTerm";
public static final String MOL_TAG = "Mol";
public static final String KAS_TAG = "Kas";
public static final String SIDECHAIN_KAS_TAG = "SidechainKAs";
public static final String ELEMENTAL_COMP_TAG = "ElementalComp";
public static final String XLINKS_TAG = "XLinks";
public static final String XLINK_TAG = "XLink";
public static final String XLINK_TYPE_TAG = "XLinkType";
public static final String DONORS_TAG = "Donors";
public static final String ACCEPTORS_TAG = "Acceptors";
public static final String DONOR_TAG = "Donor";
public static final String ACCEPTOR_TAG = "Acceptor";
public static final String ATTRIBUTES_TAG = "Attributes";
public static final String ATTRIBUTE_TAG = "Attr";
public static final String STRAND_TAG = "Strand";
public static final String GENOMIC_LOC_TAG = "GenomicLoc";
public static final String AA_GROUPING_SCHEME_TAG = "AAGroupingScheme";
public static final String ALIGNED_QUERY = "AlignedQuery";
public static final String ALIGNED_SUBJECT = "AlignedSubject";
public static final String ALIGNMENT = "Alignment";
public static final String ALIGNMENT_SCORING = "AlignmentScoring";
public static final String QUERY = "Query";
public static final String SUBJECT = "Subject";
public static final String KA_SET_TAG = "KaSet";
public static final String PKA_TAG = "pKa";
public static final String N_TERM_PKA_TAG = "NTerm_pKa";
public static final String C_TERM_PKA_TAG = "CTerm_pKa";
public static final String C_TERM_AA_PKA_TAG = "CTermAA_pKa";
public static final String PROTEIN_ANALYSIS_MODE_TAG = "ProteinAnalysisMode";
public static final String INTRON_TAG = "Intron";
public static final String DNA_TAG = "DNA";
public static final String AA_ATT = "aa";
public static final String ASSEMBLY_ATT = "assembly";
public static final String BUILD_ATT = "build";
public static final String C_TERM_ATT = "cTerm";
public static final String CHROMOSOME_ATT = "chromosome";
public static final String CLASS_ATT = "class";
public static final String CONTIG_ATT = "contig";
public static final String CONTIG_LENGTH_ATT = "contigLength";
public static final String ID_ATT = "id";
public static final String NAME_ATT = "name";
public static final String MONO_MASS_ATT = "monoMass";
public static final String AVG_MASS_ATT = "avgMass";
public static final String SHORT_NAME_ATT = "shortName";
public static final String DEFAULT_ANALYSIS_MODE_ATT = "defaultAnalysisMode";
public static final String DISULFIDE_CNT_ATT = "disulfideBonds";
public static final String LOCKED_ATT = "locked";
public static final String MAPPING_ATT = "mapping";
public static final String N_TERM_ATT = "nTerm";
public static final String THREE_LTR_CODE_ATT = "threeLtrCode";
public static final String ONE_LTR_CODE_ATT = "oneLtrCode";
public static final String IS_APPROX_ATT = "isApprox";
public static final String IS_NULL_ATT = "isNull";
public static final String CHAIN_ID_ATT = "chainId";
public static final String RESIDUE_ATT = "residue";
public static final String RESIDUE_NUM_ATT = "residueNum";
public static final String SCORE_ATT = "score";
public static final String SEQ_LENGTH_ATT = "seqLength";
public static final String START_ATT = "start";
public static final String STRAND_ATT = "strand";
public static final String COMPARISON_LENGTH_ATT = "comparisionLength";
public static final String NUM_IDENTITIES_ATT = "numIdentitites";
public static final String PROTONATED_FORM_ATT = "protonatedForm";
public static final String TAXON_ATT = "taxon";
public static final String VALUE_ATT = "value";
public static final String MONOSACCHARIDE_ATT = "monosaccharide";
public static final String DONOR_SITE_ATT = "donorSite";
public static final String ACCEPTOR_SITE_ATT = "acceptorSite";
}