fineRADstructure/fsxml.cpp at master · millanek/fineRADstructure · GitHub

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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
#include "fsxml.h"
#include <fstream>
#include <sstream>
#include <cstdlib>

using namespace std;
namespace fines
{

FsXml::FsXml(std::string f)
{
	fname=f;
	iterfile.open(fname.data());
        if (!iterfile) {
            cerr << "Can't open input file " << f << endl;
            throw(std::string("Unable to open file"));
        }
}

FsXml::~FsXml()
{
	if(iterfile.is_open()) iterfile.close();
}

streampos FsXml::gotoLineContaining(std::string str,bool getlast){
	streampos pos =iterfile.tellg (),it=-1;
	string res;
	size_t found;
	int len=str.length();
	while(1){
		pos =iterfile.tellg ();
		res=getLine();
		found=res.find_first_of('<');
		if(found!=string::npos) if(res.length()>=len+found) if(res.substr(found,len).compare(str)==0) {it=pos;}
		if (iterfile.eof()||!iterfile.good()||(!getlast && it>=0)) break;
	}
	iterfile.clear();
	iterfile.seekg(it);
	return(it);
}

std::streampos FsXml::getLineContaining(std::string str,bool getlast){
	std::streampos p0=iterfile.tellg();
	std::streampos r=gotoLineContaining(str,getlast);
	iterfile.seekg(p0);
	return(r);
}

std::string FsXml::getParam(string tag, streampos itstart)
{
	string res;
	string stag=tag,etag=tag;
	stag.insert(0,"<");
	etag.insert(0,"</");
	stag.append(">");
	etag.append(">");
	if(itstart>=0) iterfile.seekg(itstart);
	else itstart=iterfile.tellg ();
	streampos p=gotoLineContaining(stag.c_str(),false);
	if(p<0){
		cout<<"Tag "<<stag<<" not found in "<<fname<<endl;
		iterfile.clear();
		iterfile.seekg(itstart);
		throw(string("Tag not found in file!"));
	}
    res=getLine();
	size_t found=res.find(stag.c_str());
	res.erase(found,stag.length());
	size_t found2=res.find(etag.c_str());
	res=res.substr(found,found2);
	iterfile.seekg(itstart);
	return(res);
}

std::string FsXml::getTree(streampos itstart)
{
	string res;
	size_t found;
	if(itstart>=0) iterfile.seekg(itstart);
	else itstart=iterfile.tellg ();
	getLineContaining("<Tree>",true);
	while((found=res.find_first_of('('))==string::npos) {
        res=getLine();
		if(iterfile.eof())throw(string("Error in readtree: <Tree> does not appear to contain a newick tree!"));
	}
	size_t found2=res.find("</Tree>");
	if(found2!=string::npos) found2-=6;
	res=res.substr(found,found2);
	iterfile.seekg(itstart);
	return(res);
}

void FsXml::rangeextract(long from, long to,std::ostream * out)
{
	clear();
	string res;
	size_t found;
	long iteron=0;
	if(from<0) from=0;
	if(to<0) to=0;
	bool putout=true;
	while(1){
		res=getLine();
		if((found=res.find("<Iteration>"))!=string::npos && (iteron<from || iteron>to))putout=false;
		if((found=res.find("<Iteration>"))!=string::npos && (iteron>=from && iteron<=to))putout=true;
		found=res.find("</Iteration>");
		size_t found2=res.find("</outputFile>");
		if(found2!=string::npos) putout=true;
		if(putout) *out<<res<<endl;
		if(found!=string::npos) iteron++;
		if (iterfile.eof()||!iterfile.good()) break;
	}
	iterfile.clear();
}

void FsXml::thin(long by,std::ostream * out)
{
	clear();
	string res;
	long iteron=0;
	if(by<=0) by=1;
	while(1){
		res=getLine();
		size_t found=res.find("</Iteration>");
		size_t found2=res.find("</outputFile>");
		if((iteron%by==0)||found2!=string::npos) *out<<res<<endl;
		if(found!=string::npos) iteron++;
		if (iterfile.eof()||!iterfile.good()) break;
	}
	iterfile.clear();

}

std::string FsXml::getLine(){
    std::string res;
    safeGetline(iterfile, res);
    return(res);
}

  /*
std::string FsXml::getLine(){
streampos tpos =iterfile.tellg ();
    std::string res;
    char c;
	while(1){
	    iterfile.get ( c );
        if (iterfile.eof()||!iterfile.good()) break;
	    if((c=='\n'||c=='\r') &&res.size()==0) continue;
        if(c=='\n'||c=='\r') break;
        res.push_back(c);
	}
	iterfile.seekg(tpos+(streampos)(res.size()+1));
	return(res);
}
*/

}//end namespace