3 * Copyright (C) 2016 EDIT
4 * European Distributed Institute of Taxonomy
5 * http://www.e-taxonomy.eu
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.
10 package eu
.etaxonomy
.taxeditor
.molecular
.io
;
13 import javax
.xml
.namespace
.QName
;
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.
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. //$NON-NLS-1$
25 public static final String PREDICATE_NAMESPACE_URI
= NAMESPACE_URI_PREFIX
+ "Predicates/"; //$NON-NLS-1$
26 public static final String PREDICATE_NAMESPACE_PREFIX
= "ra"; //$NON-NLS-1$
27 public static final String DATA_TYPE_NAMESPACE_URI
= NAMESPACE_URI_PREFIX
+ "DataTypes/"; //$NON-NLS-1$
28 public static final String DATA_TYPE_NAMESPACE_PREFIX
= "radt"; //$NON-NLS-1$
29 public static final String PHEROGRAM_ALIGNMENT_NAMESPACE_URI
= NAMESPACE_URI_PREFIX
+ "PherogramAlignment/"; //$NON-NLS-1$
30 public static final String PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX
= "pha"; //$NON-NLS-1$
32 public static final QName PREDICATE_IS_SINGLE_READ
= new QName(PREDICATE_NAMESPACE_URI
, "isSingleRead", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
33 public static final QName PREDICATE_IS_CONSENSUS_SEQUENCE
= new QName(PREDICATE_NAMESPACE_URI
, "isConsensus", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
34 public static final QName PREDICATE_IS_REVERSE_COMPLEMENTED
= new QName(PREDICATE_NAMESPACE_URI
, "isRCed", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
35 public static final QName PREDICATE_HAS_PHEROGRAM
= new QName(PREDICATE_NAMESPACE_URI
, "hasPherogram", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
36 public static final QName PREDICATE_HAS_PHEROGRAM_ALIGNMENT
= new QName(PREDICATE_NAMESPACE_URI
, "hasPherogramAlignment", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
37 public static final QName PREDICATE_HAS_LEFT_CUT_POSITION
= new QName(PREDICATE_NAMESPACE_URI
, "hasLeftCutPosition", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
38 public static final QName PREDICATE_HAS_RIGHT_CUT_POSITION
= new QName(PREDICATE_NAMESPACE_URI
, "hasRightCutPosition", PREDICATE_NAMESPACE_PREFIX
); //$NON-NLS-1$
40 public static final QName DATA_TYPE_PHERORAGM_ALIGNMENT
= new QName(DATA_TYPE_NAMESPACE_URI
, "pherogramAlignment", DATA_TYPE_NAMESPACE_PREFIX
); //$NON-NLS-1$
42 public static final QName TAG_SHIFTS
= new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI
, "shifts", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX
); //$NON-NLS-1$
43 public static final QName TAG_SHIFT
= new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI
, "shift", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX
); //$NON-NLS-1$
44 public static final QName ATTR_POSITION
= new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI
, "pos", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX
); //$NON-NLS-1$
45 public static final QName ATTR_SHIFT
= new QName(PHEROGRAM_ALIGNMENT_NAMESPACE_URI
, "shift", PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX
); //$NON-NLS-1$