1 /*==========================================================================
2 SeqAn - The Library for Sequence Analysis
4 ============================================================================
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.
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.
17 ============================================================================
18 $Id: sequence_shortcuts.h,v 1.1 2008/08/25 16:20:04 langmead Exp $
19 ==========================================================================*/
21 #ifndef SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
22 #define SEQAN_HEADER_SEQUENCE_SHORTCUTS_H
24 namespace SEQAN_NAMESPACE_MAIN
27 //////////////////////////////////////////////////////////////////////////////
31 ..summary:A string of $char$.
32 ..signature:CharString
33 ..shortcutfor:Spec.Alloc String
34 ...signature:String<char, Alloc<> >
37 typedef String<char, Alloc<void> > CharString;
39 //____________________________________________________________________________
42 .Shortcut.CharIterator:
44 ..summary:Iterator for @Shortcut.CharString@.
45 ..signature:CharIterator
46 ..shortcutfor:Concept.Rooted Iterator
47 ...signature:Iterator<CharString, Rooted>::Type
48 ..see:Shortcut.CharString
51 typedef Iterator<CharString, Rooted>::Type CharIterator;
53 //////////////////////////////////////////////////////////////////////////////
55 .Shortcut.UnicodeString:
57 ..summary:A string of $wchar_t$.
58 ..signature:UnicodeString
59 ..shortcutfor:Spec.Alloc String
60 ...signature:String<wchar_t, Alloc<> >
63 typedef String<wchar_t, Alloc<void> > UnicodeString;
65 //____________________________________________________________________________
68 .Shortcut.UnicodeIterator:
70 ..summary:Iterator for @Shortcut.UnicodeString@.
71 ..signature:UnicodeIterator
72 ..shortcutfor:Concept.Rooted Iterator
73 ...signature:Iterator<UnicodeString, Rooted>::Type
74 ..see:Shortcut.UnicodeString
77 typedef Iterator<UnicodeString, Rooted>::Type UnicodeIterator;
79 //////////////////////////////////////////////////////////////////////////////
83 ..summary:A string of @Spec.Dna@.
85 ..shortcutfor:Spec.Alloc String
86 ...signature:String<Dna, Alloc<> >
90 typedef String<Dna, Alloc<void> > DnaString;
92 //____________________________________________________________________________
95 .Shortcut.DnaIterator:
97 ..summary:Iterator for @Shortcut.DnaString@.
98 ..signature:DnaIterator
99 ..shortcutfor:Concept.Rooted Iterator
100 ...signature:Iterator<DnaString, Rooted>::Type
102 ..see:Shortcut.DnaString
105 typedef Iterator<DnaString, Rooted>::Type DnaIterator;
107 //////////////////////////////////////////////////////////////////////////////
109 .Shortcut.Dna5String:
111 ..summary:A string of @Spec.Dna5@.
112 ..signature:Dna5String
113 ..shortcutfor:Spec.Alloc String
114 ...signature:String<Dna5, Alloc<> >
116 ..see:Shortcut.DnaString
119 typedef String<Dna5, Alloc<void> > Dna5String;
121 //____________________________________________________________________________
124 .Shortcut.Dna5Iterator:
126 ..summary:Iterator for @Shortcut.Dna5String@.
127 ..signature:Dna5Iterator
128 ..shortcutfor:Concept.Rooted Iterator
129 ...signature:Iterator<Dna5String, Rooted>::Type
131 ..see:Shortcut.Dna5String
132 ..see:Shortcut.DnaIterator
135 typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
137 //////////////////////////////////////////////////////////////////////////////
139 .Shortcut.IupacString:
141 ..summary:A string of @Spec.Iupac@.
142 ..signature:IupacString
143 ..shortcutfor:Spec.Alloc String
144 ...signature:String<Iupac, Alloc<> >
148 typedef String<Iupac, Alloc<void> > IupacString;
150 //____________________________________________________________________________
153 .Shortcut.IupacIterator:
155 ..summary:Iterator for @Shortcut.IupacString@.
156 ..signature:IupacIterator
157 ..shortcutfor:Concept.Rooted Iterator
158 ...signature:Iterator<IupacString, Rooted>::Type
160 ..see:Shortcut.IupacString
163 typedef Iterator<IupacString, Rooted>::Type IupacIterator;
165 //////////////////////////////////////////////////////////////////////////////
169 ..summary:A string of @Spec.AminoAcid@.
170 ..signature:IupacString
171 ..shortcutfor:Spec.Alloc String
172 ...signature:String<AminoAcid, Alloc<> >
176 typedef String<AminoAcid, Alloc<void> > Peptide;
178 //____________________________________________________________________________
181 .Shortcut.PeptideIterator:
183 ..summary:Iterator for @Shortcut.Peptide@.
184 ..signature:PeptideIterator
185 ..shortcutfor:Concept.Rooted Iterator
186 ...signature:Iterator<Peptide, Rooted>::Type
188 ..see:Shortcut.Peptide
191 typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
193 //////////////////////////////////////////////////////////////////////////////
195 } //namespace SEQAN_NAMESPACE_MAIN
197 #endif //#ifndef SEQAN_HEADER_...