added kruskal.wallis command. added worked on make.lefse. working of lefse command...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index fc16d204b142e5a6f55783f56bc52aafb8e6a4d1..1f1c96b6f203e4f1fa8b1dca2e018c735caa6b9f 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -796,6 +796,39 @@ bool MothurOut::dirCheck(string& dirName){
        }       
     
 }
+//**********************************************************************************************************************
+
+map<string, vector<string> > MothurOut::parseClasses(string classes){
+       try {
+        map<string, vector<string> > parts;
+        
+        //treatment<Early|Late>-age<young|old>
+        vector<string> pieces; splitAtDash(classes, pieces); // -> treatment<Early|Late>, age<young|old>
+        
+        for (int i = 0; i < pieces.size(); i++) {
+            string category = ""; string value = "";
+            bool foundOpen = false;
+            for (int j = 0; j < pieces[i].length(); j++) {
+                if (control_pressed) { return parts; }
+                
+                if (pieces[i][j] == '<')        { foundOpen = true;         }
+                else if (pieces[i][j] == '>')   { j += pieces[i].length();  }
+                else {
+                    if (!foundOpen) { category += pieces[i][j]; }
+                    else { value += pieces[i][j]; }
+                }
+            }
+            vector<string> values; splitAtChar(value, values, '|');
+            parts[category] = values;
+        }
+        
+        return parts;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "parseClasses");
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 string MothurOut::hasPath(string longName){
@@ -1360,6 +1393,67 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
                exit(1);
        }
 }
+//**********************************************************************************************************************
+vector<consTax> MothurOut::readConsTax(string inputfile){
+       try {
+               
+        vector<consTax> taxes;
+        
+        ifstream in;
+        openInputFile(inputfile, in);
+        
+        //read headers
+        getline(in);
+        
+        while (!in.eof()) {
+            
+            if (control_pressed) { break; }
+            
+            string otu = ""; string tax = "unknown";
+            int size = 0;
+            
+            in >> otu >> size >> tax; gobble(in);
+            consTax temp(otu, tax, size);
+            taxes.push_back(temp);
+        }
+        in.close();
+        
+        return taxes;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "readConsTax");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+int MothurOut::readConsTax(string inputfile, map<string, consTax2>& taxes){
+       try {
+        ifstream in;
+        openInputFile(inputfile, in);
+        
+        //read headers
+        getline(in);
+        
+        while (!in.eof()) {
+            
+            if (control_pressed) { break; }
+            
+            string otu = ""; string tax = "unknown";
+            int size = 0;
+            
+            in >> otu >> size >> tax; gobble(in);
+            consTax2 temp(tax, size);
+            taxes[otu] = temp;
+        }
+        in.close();
+        
+        return 0;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "readConsTax");
+               exit(1);
+       }
+}
 /**************************************************************************************************/
 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
        try {
@@ -2242,9 +2336,11 @@ map<string, int> MothurOut::readNames(string namefile, unsigned long int& numSeq
 /************************************************************/
 int MothurOut::checkName(string& name) {
     try {
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
-        }        
+        if (modifyNames) {
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
+            }
+        }
         return 0;
     }
        catch(exception& e) {
@@ -2346,7 +2442,9 @@ set<string> MothurOut::readAccnos(string accnosfile){
             in.read(buffer, 4096);
             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
             
-            for (int i = 0; i < pieces.size(); i++) {  checkName(pieces[i]); names.insert(pieces[i]);  }
+            for (int i = 0; i < pieces.size(); i++) {  checkName(pieces[i]);
+                names.insert(pieces[i]);
+            }
         }
                in.close();     
                
@@ -3270,6 +3368,26 @@ vector<double> MothurOut::getAverages(vector< vector<double> >& dists) {
                exit(1);
        }
 }
+/**************************************************************************************************/
+double MothurOut::getAverage(vector<double> dists) {
+       try{
+        double average = 0;
+        
+        for (int i = 0; i < dists.size(); i++) {
+            average += dists[i];
+        }
+       
+        //finds average.
+        average /= (double) dists.size(); 
+        
+        return average;
+    }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "getAverage");
+               exit(1);
+       }
+}
+
 /**************************************************************************************************/
 vector<double> MothurOut::getStandardDeviation(vector< vector<double> >& dists) {
        try{