X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.cpp;h=1f1c96b6f203e4f1fa8b1dca2e018c735caa6b9f;hp=8892febb384cbb07233858f2c6b608f8153ca09f;hb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7;hpb=a54ba6143022dc7294f4fdc468fc10b627c64b0e

diff --git a/mothurout.cpp b/mothurout.cpp
index 8892feb..1f1c96b 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -348,6 +348,27 @@ void MothurOut::mothurOut(string output) {
 	}
 }
 /*********************************************************************************************/
+void MothurOut::mothurOutJustToScreen(string output) {
+	try {
+		
+#ifdef USE_MPI
+        int pid;
+        MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+        
+        if (pid == 0) { //only one process should output to screen
+#endif
+            logger() << output;
+            
+#ifdef USE_MPI
+        }
+#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutEndLine() {
 	try {
 		#ifdef USE_MPI
@@ -775,6 +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){
@@ -1296,15 +1350,15 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
 				char c = inFASTA.get(); count++;
 				if (c == '>') {
 					positions.push_back(count-1);
-					//cout << count << endl;
+					if (debug) { mothurOut("[DEBUG]: numSeqs = " + toString(positions.size()) +  " count = " + toString(count) + ".\n"); }
 				}
 			}
 			inFASTA.close();
 		
 			num = positions.size();
-		
-			/*FILE * pFile;
-			long size;
+            if (debug) { mothurOut("[DEBUG]: num = " + toString(num) + ".\n"); }
+			FILE * pFile;
+			unsigned long long size;
 		
 			//get num bytes in file
 			pFile = fopen (filename.c_str(),"rb");
@@ -1313,9 +1367,9 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
 				fseek (pFile, 0, SEEK_END);
 				size=ftell (pFile);
 				fclose (pFile);
-			}*/
+			}
 			
-			unsigned long long size = positions[(positions.size()-1)];
+			/*unsigned long long size = positions[(positions.size()-1)];
 			ifstream in;
 			openInputFile(filename, in);
 			
@@ -1325,8 +1379,10 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
 				if(in.eof())		{	break;	}
 				else				{	size++;	}
 			}
-			in.close();
-		
+			in.close();*/
+        
+            if (debug) { mothurOut("[DEBUG]: size = " + toString(size) + ".\n"); }
+        
 			positions.push_back(size);
 			positions[0] = 0;
 		
@@ -1337,6 +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 {
@@ -2219,9 +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) {
@@ -2323,7 +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();	
 		
@@ -3247,6 +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{