#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#include <sys/wait.h>
+ #include <sys/time.h>
+ #include <sys/resource.h>
#include <unistd.h>
#ifdef USE_READLINE
#else
#include <conio.h> //allows unbuffered screen capture from stdin
#include <direct.h> //get cwd
+ #include <windows.h>
+ #include <psapi.h>
+
#endif
using namespace std;
return int(dist * precision + 0.5)/float(precision);
+}
+/***********************************************************************/
+
+inline float ceilDist(float dist, int precision){
+
+ return int(ceil(dist * precision))/float(precision);
+
}
/***********************************************************************/
string path = "";
size_t found;
- found=longName.find_last_of("/\\");
+ found=longName.find_last_of("~/\\");
if(found != longName.npos){
path = longName.substr(0, found+1);
string cwd;
//get current working directory
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if (path.rfind("./") == -1) { return fileName; } //already complete name
- else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
- char* cwdpath = new char[1024];
+ if (path.find("~") != -1) { //go to home directory
+ string homeDir = getenv ("HOME");
+ newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+ return newFileName;
+ }else { //find path
+ if (path.rfind("./") == -1) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
+
+ char* cwdpath = new char[1024];
- size_t size;
- cwdpath=getcwd(cwdpath,size);
-
- cwd = cwdpath;
+ size_t size;
+ cwdpath=getcwd(cwdpath,size);
- //rip off first '/'
- string simpleCWD;
- if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
-
- //break apart the current working directory
- vector<string> dirs;
- while (simpleCWD.find_first_of('/') != -1) {
- string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
- simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
- dirs.push_back(dir);
- }
- //get last one // ex. ../../../filename = /user/work/desktop/filename
- dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+ cwd = cwdpath;
+
+ //rip off first '/'
+ string simpleCWD;
+ if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
+
+ //break apart the current working directory
+ vector<string> dirs;
+ while (simpleCWD.find_first_of('/') != -1) {
+ string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
+ simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
+ dirs.push_back(dir);
+ }
+ //get last one // ex. ../../../filename = /user/work/desktop/filename
+ dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+
+ int index = dirs.size()-1;
- int index = dirs.size()-1;
-
- while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
- if (pos == 0) { break; //you are at the end
- }else if (path[(pos-1)] == '.') { //you want your parent directory ../
- path = path.substr(0, pos-1);
- index--;
- if (index == 0) { break; }
- }else if (path[(pos-1)] == '/') { //you want the current working dir ./
- path = path.substr(0, pos);
- }else if (pos == 1) { break; //you are at the end
- }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
- }
-
- for (int i = index; i >= 0; i--) {
- newFileName = dirs[i] + "/" + newFileName;
- }
+ while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+ if (pos == 0) { break; //you are at the end
+ }else if (path[(pos-1)] == '.') { //you want your parent directory ../
+ path = path.substr(0, pos-1);
+ index--;
+ if (index == 0) { break; }
+ }else if (path[(pos-1)] == '/') { //you want the current working dir ./
+ path = path.substr(0, pos);
+ }else if (pos == 1) { break; //you are at the end
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
+ }
- newFileName = "/" + newFileName;
- return newFileName;
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "/" + newFileName;
+ }
+ newFileName = "/" + newFileName;
+ return newFileName;
+ }
#else
- if (path.rfind(".\\") == -1) { return fileName; } //already complete name
- else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
-
- char *cwdpath = NULL;
- cwdpath = getcwd(NULL, 0); // or _getcwd
- if ( cwdpath != NULL) { cwd = cwdpath; }
- else { cwd = ""; }
-
- //break apart the current working directory
- vector<string> dirs;
- while (cwd.find_first_of('\\') != -1) {
- string dir = cwd.substr(0,cwd.find_first_of('\\'));
- cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
- dirs.push_back(dir);
-
- }
- //get last one
- dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
-
- int index = dirs.size()-1;
+ if (path.find("~") != -1) { //go to home directory
+ string homeDir = getenv ("HOMEPATH");
+ newFileName = homeDir + fileName.substr(fileName.find("~")+1);
+ return newFileName;
+ }else { //find path
+ if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
+
+ char *cwdpath = NULL;
+ cwdpath = getcwd(NULL, 0); // or _getcwd
+ if ( cwdpath != NULL) { cwd = cwdpath; }
+ else { cwd = ""; }
- while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
- if (pos == 0) { break; //you are at the end
- }else if (path[(pos-1)] == '.') { //you want your parent directory ../
- path = path.substr(0, pos-1);
- index--;
- if (index == 0) { break; }
- }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
- path = path.substr(0, pos);
- }else if (pos == 1) { break; //you are at the end
- }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
- }
+ //break apart the current working directory
+ vector<string> dirs;
+ while (cwd.find_first_of('\\') != -1) {
+ string dir = cwd.substr(0,cwd.find_first_of('\\'));
+ cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
+ dirs.push_back(dir);
- for (int i = index; i >= 0; i--) {
- newFileName = dirs[i] + "\\" + newFileName;
- }
+ }
+ //get last one
+ dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+
+ int index = dirs.size()-1;
+
+ while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+ if (pos == 0) { break; //you are at the end
+ }else if (path[(pos-1)] == '.') { //you want your parent directory ../
+ path = path.substr(0, pos-1);
+ index--;
+ if (index == 0) { break; }
+ }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
+ path = path.substr(0, pos);
+ }else if (pos == 1) { break; //you are at the end
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
+ }
- return newFileName;
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "\\" + newFileName;
+ }
+
+ return newFileName;
+ }
#endif
}
else {
//check for blank file
gobble(fileHandle);
- if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; return 1; }
+ if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; }
return 0;
}
return numSeqs;
}
+/***********************************************************************/
+inline void getNumSeqs(ifstream& file, int& numSeqs){
+
+ string input;
+ numSeqs = 0;
+ while(!file.eof()){
+ input = getline(file);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ numSeqs++; }
+ }
+ }
+}
+
/***********************************************************************/
inline bool inVector(string member, vector<string> group){
//unique is the smallest line
if (label == "unique") { return false; }
- else { convert(label, labelFloat); }
+ else {
+ if (convertTestFloat(label, labelFloat)) {
+ convert(label, labelFloat);
+ }else { //cant convert
+ return false;
+ }
+ }
//go through users set and make them floats
for(it = userLabels.begin(); it != userLabels.end(); ++it) {