X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.cpp;h=8a3b6313072a158f611e1a69a84d0a9713add18c;hp=3e4db45bcc43990a18f7d8e51493388d28a6d850;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=196c22d0f93ba48e8ec54ab76608b6e3ba5e68cc

diff --git a/mothurout.cpp b/mothurout.cpp
index 3e4db45..8a3b631 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -23,6 +23,7 @@ set<string> MothurOut::getCurrentTypes()  {
         
         set<string> types;
         types.insert("fasta");
+        types.insert("summary");
         types.insert("accnos");
         types.insert("column");
         types.insert("design");
@@ -81,6 +82,7 @@ void MothurOut::printCurrentFiles()  {
         if (biomfile != "")			{  mothurOut("biom=" + biomfile); mothurOutEndLine();				}
         if (counttablefile != "")	{  mothurOut("count=" + counttablefile); mothurOutEndLine();	}
 		if (processors != "1")		{  mothurOut("processors=" + processors); mothurOutEndLine();		}
+        if (summaryfile != "")		{  mothurOut("summary=" + summaryfile); mothurOutEndLine();		}
 		
 	}
 	catch(exception& e) {
@@ -115,6 +117,7 @@ bool MothurOut::hasCurrentFiles()  {
 		if (flowfile != "")			{  return true;			}
         if (biomfile != "")			{  return true;			}
         if (counttablefile != "")	{  return true;			}
+        if (summaryfile != "")	{  return true;			}
 		if (processors != "1")		{  return true;			}
 		
 		return hasCurrent;
@@ -151,6 +154,7 @@ void MothurOut::clearCurrentFiles()  {
 		flowfile = "";
         biomfile = "";
         counttablefile = "";
+        summaryfile = "";
 		processors = "1";
 	}
 	catch(exception& e) {
@@ -344,6 +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
@@ -1292,15 +1317,15 @@ 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");
@@ -1309,9 +1334,9 @@ 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);
 			
@@ -1321,8 +1346,10 @@ 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;
 		
@@ -2215,9 +2242,11 @@ 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) {
@@ -3243,6 +3272,26 @@ 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{