changes while testing

[mothur.git] / summaryqualcommand.cpp

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 5a073677804ae2e3176f08a3d4ff1e26a1bc5c03..e1e626ea273a650840dd849442e43762e9a100cf 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -13,12 +13,12 @@
 //**********************************************************************************************************************
 vector<string> SummaryQualCommand::setParameters(){    
        try {
-               CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
-               CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pqual);
+               CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -48,24 +48,19 @@ string SummaryQualCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string SummaryQualCommand::getOutputFileNameTag(string type, string inputName=""){     
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string SummaryQualCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "summary")            {   outputFileName =  "qual.summary";   }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SummaryQualCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "summary") {  pattern = "[filename],qual.summary"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SummaryQualCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 SummaryQualCommand::SummaryQualCommand(){      
@@ -201,7 +196,7 @@ int SummaryQualCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
                else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
         
@@ -233,7 +228,9 @@ int SummaryQualCommand::execute(){
                if (m->control_pressed) {  return 0; }
                
                //print summary file
-               string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile));
+               string summaryFile = getOutputFileName("summary",variables);
                printQual(summaryFile, position, averageQ, scores);
                
                if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
@@ -251,7 +248,7 @@ int SummaryQualCommand::execute(){
                m->mothurOutEndLine();
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
                m->mothurOutEndLine();
                
@@ -444,7 +441,10 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
                
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
-                       numSeqs += pDataArray[i]->count;
+                       numSeqs += pDataArray[i]->numSeqs;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             int tempNum = pDataArray[i]->position.size();
             if (position.size() < tempNum) { position.resize(tempNum, 0); }
                        if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }