fixed phylo.diversity

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index fe3ea097e64faf1b0418f22fa3b248b026ad4dd1..88a18ed452314c38c5d2cf6909ea44db465d61af 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -257,6 +257,8 @@ int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 /***********************************************************************/
 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
        try {
+               fileName = getFullPathName(fileName);
+               
                fileHandle.open(fileName.c_str(), ios::app);
                if(!fileHandle) {
                        mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
@@ -445,6 +447,9 @@ string MothurOut::getExtension(string longName){
 /***********************************************************************/
 bool MothurOut::isBlank(string fileName){
        try {
+               
+               fileName = getFullPathName(fileName);
+               
                ifstream fileHandle;
                fileHandle.open(fileName.c_str());
                if(!fileHandle) {
@@ -829,7 +834,8 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
 /**************************************************************************************************/
 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
        try {
-
+                       filename = getFullPathName(filename);
+                       
                        vector<unsigned long int> positions;
                        ifstream in;
                        openInputFile(filename, in);
@@ -851,7 +857,7 @@ vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& nu
                
                        FILE * pFile;
                        unsigned long int size;
-               
+                       
                        //get num bytes in file
                        pFile = fopen (filename.c_str(),"rb");
                        if (pFile==NULL) perror ("Error opening file");
@@ -881,6 +887,8 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                FILE * pFile;
                unsigned long int size;
                
+               filename = getFullPathName(filename);
+               
                //get num bytes in file
                pFile = fopen (filename.c_str(),"rb");
                if (pFile==NULL) perror ("Error opening file");
@@ -893,7 +901,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                //estimate file breaks
                unsigned long int chunkSize = 0;
                chunkSize = size / proc;
-               
+       
                //file to small to divide by processors
                if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
        
@@ -914,15 +922,16 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                        
                        //there was not another sequence before the end of the file
                        unsigned long int sanityPos = in.tellg();
-                       if (sanityPos = -1) {   break;  }
-                       else {   filePos.push_back(newSpot);  }
+
+                       if (sanityPos == -1) {  break;  }
+                       else {  filePos.push_back(newSpot);  }
                        
                        in.close();
                }
                
                //save end pos
                filePos.push_back(size);
-               
+
                //sanity check filePos
                for (int i = 0; i < (filePos.size()-1); i++) {
                        if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
@@ -1112,7 +1121,21 @@ void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbo
 //This function parses the estimator options and puts them in a vector
 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
        try {
-               string individual;
+               string individual = "";
+               int estimLength = estim.size();
+               for(int i=0;i<estimLength;i++){
+                       if(estim[i] == '-'){
+                               container.push_back(individual);
+                               individual = "";                                
+                       }
+                       else{
+                               individual += estim[i];
+                       }
+               }
+               container.push_back(individual);
+
+       
+       /*      string individual;
                
                while (estim.find_first_of('-') != -1) {
                        individual = estim.substr(0,estim.find_first_of('-'));
@@ -1122,7 +1145,7 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
                        }
                }
                //get last one
-               container.push_back(estim);
+               container.push_back(estim); */
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtDash");
@@ -1134,17 +1157,31 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
 //This function parses the label options and puts them in a set
 void MothurOut::splitAtDash(string& estim, set<string>& container) {
        try {
-               string individual;
-               
-               while (estim.find_first_of('-') != -1) {
-                       individual = estim.substr(0,estim.find_first_of('-'));
-                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+               string individual = "";
+               int estimLength = estim.size();
+               for(int i=0;i<estimLength;i++){
+                       if(estim[i] == '-'){
                                container.insert(individual);
+                               individual = "";                                
+                       }
+                       else{
+                               individual += estim[i];
                        }
                }
+               container.insert(individual);
+
+       //      string individual;
+               
+       //      while (estim.find_first_of('-') != -1) {
+       //              individual = estim.substr(0,estim.find_first_of('-'));
+       //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+       //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+       //                      container.insert(individual);
+       //              }
+       //      }
                //get last one
-               container.insert(estim);
+       //      container.insert(estim);
+       
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtDash");