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com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
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 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 AA_ATT              = "aa";
   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 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";
}