eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/SingleReadAlignmentRDFXMLConstants.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2016 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.taxeditor.molecular.io;
  11
  12
  13 import javax.xml.namespace.QName;
  14
  15
  16
  17 /**
  18  * Contains constants for <i>RDF</i> predicates used in the I/O of single read alignments e.g. from and to the <i>NeXML</i> format.
  19  *
  20  * @author Ben Stöver
  21  * @date 27.10.2016
  22  */
  23 public interface SingleReadAlignmentRDFXMLConstants {
  24     public static final String NAMESPACE_URI_PREFIX = "http://bioinfweb.info/xmlns/PhyDE/ReadAlignment/";  //TODO Possibly change this namespace, when according decision is made.
  25     public static final String PREDICATE_NAMESPACE_URI = NAMESPACE_URI_PREFIX + "Predicates/";
  26     public static final String PREDICATE_NAMESPACE_PREFIX = "ra";
  27     public static final String DATA_TYPE_NAMESPACE_URI = NAMESPACE_URI_PREFIX + "DataTypes/";
  28     public static final String DATA_TYPE_NAMESPACE_PREFIX = "radt";
  29     public static final String PHEROGRAM_ALIGNMENT_NAMESPACE_URI = NAMESPACE_URI_PREFIX + "PherogramAlignment/";
  30     public static final String PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX = "pha";
  31
  32     public static final QName PREDICATE_IS_SINGLE_READ = new QName(PREDICATE_NAMESPACE_URI, "isSingleRead", PREDICATE_NAMESPACE_PREFIX);
  33     public static final QName PREDICATE_IS_CONSENSUS_SEQUENCE = new QName(PREDICATE_NAMESPACE_URI, "isConsensus", PREDICATE_NAMESPACE_PREFIX);
  34     public static final QName PREDICATE_IS_REVERSE_COMPLEMENTED = new QName(PREDICATE_NAMESPACE_URI, "isRCed", PREDICATE_NAMESPACE_PREFIX);
  35     public static final QName PREDICATE_HAS_PHEROGRAM = new QName(PREDICATE_NAMESPACE_URI, "hasPherogram", PREDICATE_NAMESPACE_PREFIX);
  36     public static final QName PREDICATE_HAS_PHEROGRAM_ALIGNMENT = new QName(PREDICATE_NAMESPACE_URI, "hasPherogramAlignment", PREDICATE_NAMESPACE_PREFIX);
  37     public static final QName PREDICATE_HAS_LEFT_CUT_POSITION = new QName(PREDICATE_NAMESPACE_URI, "hasLeftCutPosition", PREDICATE_NAMESPACE_PREFIX);
  38     public static final QName PREDICATE_HAS_RIGHT_CUT_POSITION = new QName(PREDICATE_NAMESPACE_URI, "hasRightCutPosition", PREDICATE_NAMESPACE_PREFIX);
  39
  40     public static final QName DATA_TYPE_PHERORAGM_ALIGNMENT = new QName(DATA_TYPE_NAMESPACE_URI, "pherogramAlignment", DATA_TYPE_NAMESPACE_PREFIX);
  41
  42     public static final QName TAG_SHIFTS = new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI, "shifts", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX);
  43     public static final QName TAG_SHIFT = new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI, "shift", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX);
  44     public static final QName ATTR_POSITION = new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI, "pos", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX);
  45     public static final QName ATTR_SHIFT = new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI, "shift", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX);
  46 }