some bug fixes

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 2404a84f08672c2178bd3e0a33946124348a72a7..1434482e9a9785485e0f898f88e352e6f7757659 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -54,6 +54,8 @@
 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
        #include <sys/wait.h>
+       #include <sys/time.h>
+       #include <sys/resource.h>
        #include <unistd.h>
        
        #ifdef USE_READLINE
@@ -64,6 +66,9 @@
 #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;
@@ -987,9 +992,9 @@ inline string sortFile(string distFile, string outputDir){
        }       
 }
 /**************************************************************************************************/
-inline vector<long> setFilePosFasta(string filename, int& num) {
+inline vector<unsigned long int> setFilePosFasta(string filename, int& num) {
 
-                       vector<long> positions;
+                       vector<unsigned long int> positions;
                        ifstream inFASTA;
                        openInputFile(filename, inFASTA);
                                
@@ -997,7 +1002,7 @@ inline vector<long> setFilePosFasta(string filename, int& num) {
                        while(!inFASTA.eof()){
                                input = getline(inFASTA); gobble(inFASTA);
                                if (input.length() != 0) {
-                                       if(input[0] == '>'){    long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);      }
+                                       if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
                                }
                        }
                        inFASTA.close();
@@ -1016,7 +1021,7 @@ inline vector<long> setFilePosFasta(string filename, int& num) {
                                fclose (pFile);
                        }*/
                        
-                       long size = positions[(positions.size()-1)];
+                       unsigned long int size = positions[(positions.size()-1)];
                        ifstream in;
                        openInputFile(filename, in);
                        
@@ -1033,18 +1038,18 @@ inline vector<long> setFilePosFasta(string filename, int& num) {
                        return positions;
 }
 /**************************************************************************************************/
-inline vector<long> setFilePosEachLine(string filename, int& num) {
+inline vector<unsigned long int> setFilePosEachLine(string filename, int& num) {
 
-                       vector<long> positions;
+                       vector<unsigned long int> positions;
                        ifstream in;
                        openInputFile(filename, in);
                                
                        string input;
                        while(!in.eof()){
-                               long lastpos = in.tellg();
+                               unsigned long int lastpos = in.tellg();
                                input = getline(in); gobble(in);
                                if (input.length() != 0) {
-                                       long pos = in.tellg(); 
+                                       unsigned long int pos = in.tellg(); 
                                        if (pos != -1) { positions.push_back(pos - input.length() - 1); }
                                        else {  positions.push_back(lastpos);  }
                                }
@@ -1054,7 +1059,7 @@ inline vector<long> setFilePosEachLine(string filename, int& num) {
                        num = positions.size();
                
                        FILE * pFile;
-                       long size;
+                       unsigned long int size;
                
                        //get num bytes in file
                        pFile = fopen (filename.c_str(),"rb");