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
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
#ifndef NASTREPORT_HPP
#define NASTREPORT_HPP
/*
* nastreport.hpp
*
*
* Created by Pat Schloss on 12/19/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "report.hpp"
#include "nast.hpp"
#include "alignment.hpp"
/******************************************************************************************************************/
class AlignReport : public Report {
public:
AlignReport();
~AlignReport() = default;
//io functions, note - printHeaders / readHeaders / getHeaders in Report parent class
void read(ifstream&); //read line in report file
void print(ofstream&); //print line in report file
string getSeqReport(); //return string containing line from report file
//set values from objects
void setCandidate(Sequence*); //sets query name and length
void setTemplate(Sequence*); //sets template name and length
void setSearchParameters(string, float); //sets searchMethod, searchScore
void setAlignmentParameters(string, Alignment*); //sets queryStart, queryEnd, templateStart, templateEnd, gapsInQuery, gapsInTemplate, alignmentMethod, pairwiseAlignmentLength
void setNastParameters(Nast); //sets longestInsert and simBtwnQueryAndTemplate
//set values
void setQueryName(string n) { queryName = n; }
void setTemplateName(string n) { templateName = n; }
void setSearchMethod(string n) { searchMethod = n; }
void setAlignmentMethod(string n) { alignmentMethod = n; }
void setQueryLength(int n) { queryLength = n; }
void setTemplateLength(int n) { templateLength = n; }
void setQueryStart(int n) { queryStart = n; }
void setQueryEnd(int n) { queryEnd = n; }
void setTemplateStart(int n) { templateStart = n; }
void setTemplateEnd(int n) { templateEnd = n; }
void setPairwiseAlignmentLength(int n) { pairwiseAlignmentLength = n; }
void setGapsInQuery(int n) { gapsInQuery = n; }
void setGapsInTemplate(int n) { gapsInTemplate = n; }
void setLongestInsert(int i) { longestInsert = i; }
void setSearchScore(float i) { searchScore = i; }
void setSimBtwnQueryAndTemplate(float i) { simBtwnQueryAndTemplate = i; }
//get values
string getQueryName() { return queryName; }
string getTemplateName() { return templateName; }
string getSearchMethod() { return searchMethod; }
string getAlignmentMethod() { return alignmentMethod; }
int getQueryLength() { return queryLength; }
int getTemplateLength() { return templateLength; }
int getQueryStart() { return queryStart; }
int getQueryEnd() { return queryEnd; }
int getTemplateStart() { return templateStart; }
int getTemplateEnd() { return templateEnd; }
int getPairwiseAlignmentLength() { return pairwiseAlignmentLength; }
int getGapsInQuery() { return gapsInQuery; }
int getGapsInTemplate() { return gapsInTemplate; }
int getLongestInsert() { return longestInsert; }
float getSearchScore() { return searchScore; }
float getSimBtwnQueryAndTemplate() { return simBtwnQueryAndTemplate; }
private:
void fillHeaders();
string queryName, templateName, searchMethod, alignmentMethod, dummySearchScore;
int queryLength, templateLength, queryStart, queryEnd, templateStart, templateEnd, pairwiseAlignmentLength, gapsInQuery, gapsInTemplate, longestInsert;
float searchScore, simBtwnQueryAndTemplate;
};
/******************************************************************************************************************/
#endif
|
