SeqAn-1.1/seqan/sequence/sequence_shortcuts.h

   1  /*==========================================================================
   2                 SeqAn - The Library for Sequence Analysis
   3                           http://www.seqan.de
   4  ============================================================================
   5   Copyright (C) 2007
   6
   7   This library is free software; you can redistribute it and/or
   8   modify it under the terms of the GNU Lesser General Public
   9   License as published by the Free Software Foundation; either
  10   version 3 of the License, or (at your option) any later version.
  11
  12   This library is distributed in the hope that it will be useful,
  13   but WITHOUT ANY WARRANTY; without even the implied warranty of
  14   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  15   Lesser General Public License for more details.
  16
  17  ============================================================================
  18   $Id: sequence_shortcuts.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
  19  ==========================================================================*/
  20
  21 #ifndef SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
  22 #define SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
  23
  24 namespace SEQAN_NAMESPACE_MAIN
  25 {
  26
  27 //////////////////////////////////////////////////////////////////////////////
  28 /**
  29 .Shortcut.CharString:
  30 ..cat:Strings
  31 ..summary:A string of $char$.
  32 ..signature:CharString
  33 ..shortcutfor:Spec.Alloc String
  34 ...signature:String<char, Alloc<> >
  35 */
  36
  37 typedef String<char, Alloc<void> > CharString;
  38
  39 //____________________________________________________________________________
  40
  41 /**
  42 .Shortcut.CharIterator:
  43 ..cat:Iterators
  44 ..summary:Iterator for @Shortcut.CharString@.
  45 ..signature:CharIterator
  46 ..shortcutfor:Concept.Rooted Iterator
  47 ...signature:Iterator<CharString, Rooted>::Type
  48 ..see:Shortcut.CharString
  49 */
  50
  51 typedef Iterator<CharString, Rooted>::Type CharIterator;
  52
  53 //////////////////////////////////////////////////////////////////////////////
  54 /**
  55 .Shortcut.UnicodeString:
  56 ..cat:Strings
  57 ..summary:A string of $wchar_t$.
  58 ..signature:UnicodeString
  59 ..shortcutfor:Spec.Alloc String
  60 ...signature:String<wchar_t, Alloc<> >
  61 */
  62
  63 typedef String<wchar_t, Alloc<void> > UnicodeString;
  64
  65 //____________________________________________________________________________
  66
  67 /**
  68 .Shortcut.UnicodeIterator:
  69 ..cat:Iterators
  70 ..summary:Iterator for @Shortcut.UnicodeString@.
  71 ..signature:UnicodeIterator
  72 ..shortcutfor:Concept.Rooted Iterator
  73 ...signature:Iterator<UnicodeString, Rooted>::Type
  74 ..see:Shortcut.UnicodeString
  75 */
  76
  77 typedef Iterator<UnicodeString, Rooted>::Type UnicodeIterator;
  78
  79 //////////////////////////////////////////////////////////////////////////////
  80 /**
  81 .Shortcut.DnaString:
  82 ..cat:Strings
  83 ..summary:A string of @Spec.Dna@.
  84 ..signature:DnaString
  85 ..shortcutfor:Spec.Alloc String
  86 ...signature:String<Dna, Alloc<> >
  87 ..see:Spec.Dna
  88 */
  89
  90 typedef String<Dna, Alloc<void> > DnaString;
  91
  92 //____________________________________________________________________________
  93
  94 /**
  95 .Shortcut.DnaIterator:
  96 ..cat:Iterators
  97 ..summary:Iterator for @Shortcut.DnaString@.
  98 ..signature:DnaIterator
  99 ..shortcutfor:Concept.Rooted Iterator
 100 ...signature:Iterator<DnaString, Rooted>::Type
 101 ..see:Spec.Dna
 102 ..see:Shortcut.DnaString
 103 */
 104
 105 typedef Iterator<DnaString, Rooted>::Type DnaIterator;
 106
 107 //////////////////////////////////////////////////////////////////////////////
 108 /**
 109 .Shortcut.Dna5String:
 110 ..cat:Strings
 111 ..summary:A string of @Spec.Dna5@.
 112 ..signature:Dna5String
 113 ..shortcutfor:Spec.Alloc String
 114 ...signature:String<Dna5, Alloc<> >
 115 ..see:Spec.Dna5
 116 ..see:Shortcut.DnaString
 117 */
 118
 119 typedef String<Dna5, Alloc<void> > Dna5String;
 120
 121 //____________________________________________________________________________
 122
 123 /**
 124 .Shortcut.Dna5Iterator:
 125 ..cat:Iterators
 126 ..summary:Iterator for @Shortcut.Dna5String@.
 127 ..signature:Dna5Iterator
 128 ..shortcutfor:Concept.Rooted Iterator
 129 ...signature:Iterator<Dna5String, Rooted>::Type
 130 ..see:Spec.Dna5
 131 ..see:Shortcut.Dna5String
 132 ..see:Shortcut.DnaIterator
 133 */
 134
 135 typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
 136
 137 //////////////////////////////////////////////////////////////////////////////
 138 /**
 139 .Shortcut.IupacString:
 140 ..cat:Strings
 141 ..summary:A string of @Spec.Iupac@.
 142 ..signature:IupacString
 143 ..shortcutfor:Spec.Alloc String
 144 ...signature:String<Iupac, Alloc<> >
 145 ..see:Spec.Iupac
 146 */
 147
 148 typedef String<Iupac, Alloc<void> > IupacString;
 149
 150 //____________________________________________________________________________
 151
 152 /**
 153 .Shortcut.IupacIterator:
 154 ..cat:Iterators
 155 ..summary:Iterator for @Shortcut.IupacString@.
 156 ..signature:IupacIterator
 157 ..shortcutfor:Concept.Rooted Iterator
 158 ...signature:Iterator<IupacString, Rooted>::Type
 159 ..see:Spec.Iupac
 160 ..see:Shortcut.IupacString
 161 */
 162
 163 typedef Iterator<IupacString, Rooted>::Type IupacIterator;
 164
 165 //////////////////////////////////////////////////////////////////////////////
 166 /**
 167 .Shortcut.Peptide:
 168 ..cat:Strings
 169 ..summary:A string of @Spec.AminoAcid@.
 170 ..signature:IupacString
 171 ..shortcutfor:Spec.Alloc String
 172 ...signature:String<AminoAcid, Alloc<> >
 173 ..see:Spec.AminoAcid
 174 */
 175
 176 typedef String<AminoAcid, Alloc<void> > Peptide;
 177
 178 //____________________________________________________________________________
 179
 180 /**
 181 .Shortcut.PeptideIterator:
 182 ..cat:Iterators
 183 ..summary:Iterator for @Shortcut.Peptide@.
 184 ..signature:PeptideIterator
 185 ..shortcutfor:Concept.Rooted Iterator
 186 ...signature:Iterator<Peptide, Rooted>::Type
 187 ..see:Spec.AminoAcid
 188 ..see:Shortcut.Peptide
 189 */
 190
 191 typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
 192
 193 //////////////////////////////////////////////////////////////////////////////
 194
 195 } //namespace SEQAN_NAMESPACE_MAIN
 196
 197 #endif //#ifndef SEQAN_HEADER_...