1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
#ifndef __SEQEUNCES_FILTER
#define __SEQEUNCES_FILTER
#include "definitions.h"
#include "sequenceContainer.h"
#include "codon.h"
#include "amino.h"
#include <string>
#include <fstream>
#include "fastaFormat.h"
using namespace std;
class seqeuncesFilter{
public:
static void removeSequencesWithStop(sequenceContainer & sc,codon & alpha);
static void removeSequencesWithMissingData(sequenceContainer & sc);
//applied only to coding nucleotide seqeunces: remove sequence that are not divisable by 3.
static void removeSequencesNotDivisableBy3(sequenceContainer & sc);
static void removeSequencesWithMissingDataAndStop(sequenceContainer & sc,codon & alpha);
static void removeSequencesNotStartWithATG(sequenceContainer & sc,codon & alpha);
static void removeSequencesNotStartWithInitiationCodons(sequenceContainer & sc,codon & alpha);
static void removeSequencesWithGapsAccordingRef(sequenceContainer & sc,int precent, string refName);
static void removeSequencesWithInserts(sequenceContainer & newSc, const sequenceContainer & sc, int percent, const string& refName = "", string outFileName = "");
//removes all sequences that are shorter than lowerBound and longer than upperBound
static void removeShortAndLongSequences(sequenceContainer & sc, int lowerBound, int upperBound);
virtual ~seqeuncesFilter();
};
#endif
|
