bpp-seq-omics  2.4.1
WindowSplitMafIterator.h
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1 //
2 // File: WindowSplitMafIterator.h
3 // Authors: Julien Dutheil
4 // Created: Tue Sep 07 2010
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (2010)
9 
10 This software is a computer program whose purpose is to provide classes
11 for sequences analysis.
12 
13 This software is governed by the CeCILL license under French law and
14 abiding by the rules of distribution of free software. You can use,
15 modify and/ or redistribute the software under the terms of the CeCILL
16 license as circulated by CEA, CNRS and INRIA at the following URL
17 "http://www.cecill.info".
18 
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21 with a limited warranty and the software's author, the holder of the
22 economic rights, and the successive licensors have only limited
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24 
25 In this respect, the user's attention is drawn to the risks associated
26 with loading, using, modifying and/or developing or reproducing the
27 software by the user in light of its specific status of free software,
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38 */
39 
40 #ifndef _WINDOWSPLITMAFITERATOR_H_
41 #define _WINDOWSPLITMAFITERATOR_H_
42 
43 #include "MafIterator.h"
44 
45 //From the STL:
46 #include <iostream>
47 #include <string>
48 #include <deque>
49 
50 namespace bpp {
51 
57 {
58  private:
59  size_t windowSize_;
60  size_t windowStep_;
61  short align_;
62  std::deque<MafBlock*> blockBuffer_;
64 
65  public:
66  static const short RAGGED_LEFT;
67  static const short RAGGED_RIGHT;
68  static const short CENTER;
69  static const short ADJUST;
70 
71  public:
72  WindowSplitMafIterator(MafIterator* iterator, size_t windowSize, size_t windowStep, short splitOption = CENTER, bool keepSmallBlocks = false):
73  AbstractFilterMafIterator(iterator),
74  windowSize_(windowSize), windowStep_(windowStep),
75  align_(splitOption), blockBuffer_(), keepSmallBlocks_(keepSmallBlocks)
76  {
77  if (splitOption != RAGGED_LEFT && splitOption != RAGGED_RIGHT
78  && splitOption != CENTER && splitOption != ADJUST)
79  throw Exception("WindowSplitMafIterator: unvalid split option: " + TextTools::toString(splitOption));
80  if (splitOption != RAGGED_LEFT && windowStep != windowSize)
81  throw Exception("WindowSplitMafIterator: overlapping windows are only supported together with the RAGGED_LEFT option.");
82  }
83 
84  private:
86 
87 };
88 
89 } // end of namespace bpp.
90 
91 #endif //_WINDOWSPLITMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
Interface to loop over maf alignment blocks.
Definition: MafIterator.h:59
Splits block into windows of given sizes.
std::deque< MafBlock * > blockBuffer_
WindowSplitMafIterator(MafIterator *iterator, size_t windowSize, size_t windowStep, short splitOption=CENTER, bool keepSmallBlocks=false)
std::string toString(T t)