halapi
hierarchichalalignmentformatapi
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halAlignmentInstance.h
1 /*
2  * Copyright (C) 2012 by Glenn Hickey (hickey@soe.ucsc.edu)
3  *
4  * Released under the MIT license, see LICENSE.txt
5  */
6 
7 #ifndef _HALALIGNMENTINSTANCE_H
8 #define _HALALIGNMENTINSTANCE_H
9 
10 #include "halDefs.h"
11 #include "halAlignment.h"
12 #include "halCLParser.h"
13 
14 
15 // we don't include hdf5 from our interface headers.
16 namespace H5 {
17 class FileCreatPropList;
18 class FileAccPropList;
19 class DSetCreatPropList;
20 }
21 
23 namespace hal {
24 
27 AlignmentPtr hdf5AlignmentInstance();
28 
31 AlignmentConstPtr hdf5AlignmentInstanceReadOnly();
32 
40 AlignmentPtr
41 hdf5AlignmentInstance(const H5::FileCreatPropList& fileCreateProps,
42  const H5::FileAccPropList& fileAccessProps,
43  const H5::DSetCreatPropList& datasetCreateProps,
44  bool inMemory = false);
45 
53 AlignmentConstPtr
54 hdf5AlignmentInstanceReadOnly(const H5::FileCreatPropList& fileCreateProps,
55  const H5::FileAccPropList& fileAccessProps,
56  const H5::DSetCreatPropList& datasetCreateProps,
57  bool inMemory = false);
58 
64 AlignmentPtr openHalAlignment(const std::string& path,
65  CLParserConstPtr options);
66 
73 AlignmentConstPtr openHalAlignmentReadOnly(const std::string& path,
74  CLParserConstPtr options);
75 
76 }
77 
78 #endif
AlignmentPtr hdf5AlignmentInstance()
AlignmentPtr openHalAlignment(const std::string &path, CLParserConstPtr options)
AlignmentConstPtr hdf5AlignmentInstanceReadOnly()
AlignmentConstPtr openHalAlignmentReadOnly(const std::string &path, CLParserConstPtr options)