added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / summaryqualcommand.cpp

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 5d7971349656d4400e5d41a24c15e576ccdf57f7..5a073677804ae2e3176f08a3d4ff1e26a1bc5c03 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -8,13 +8,14 @@
  */
 
 #include "summaryqualcommand.h"
-
+#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> SummaryQualCommand::setParameters(){    
        try {
                CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               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);
@@ -32,9 +33,10 @@ vector<string> SummaryQualCommand::setParameters(){
 string SummaryQualCommand::getHelpString(){    
        try {
                string helpString = "";
-               helpString += "The summary.qual command reads a quality file and an optional name file, and summarizes the quality information.\n";
-               helpString += "The summary.tax command parameters are qfile, name and processors. qfile is required, unless you have a valid current quality file.\n";
+               helpString += "The summary.qual command reads a quality file and an optional name or count file, and summarizes the quality information.\n";
+               helpString += "The summary.tax command parameters are qfile, name, count and processors. qfile is required, unless you have a valid current quality file.\n";
                helpString += "The name parameter allows you to enter a name file associated with your quality file. \n";
+        helpString += "The count parameter allows you to enter a count file associated with your quality file. \n";
                helpString += "The summary.qual command should be in the following format: \n";
                helpString += "summary.qual(qfile=yourQualityFile) \n";
                helpString += "Note: No spaces between parameter labels (i.e. qfile), '=' and parameters (i.e.yourQualityFile).\n";     
@@ -122,6 +124,14 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
+                
+                it = parameters.find("count");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["count"] = inputDir + it->second;            }
+                               }
                        }
                        
                        //initialize outputTypes
@@ -141,6 +151,13 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = "";  }   
                        else { m->setNameFile(namefile); }
+            
+            countfile = validParameter.validFile(parameters, "count", true);
+                       if (countfile == "not open") { abort = true; countfile = ""; }  
+                       else if (countfile == "not found") { countfile = ""; }
+                       else { m->setCountTableFile(countfile); }
+                       
+            if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -152,10 +169,13 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);     
                        
-                       if (namefile == "") {
-                               vector<string> files; files.push_back(qualfile);
-                               parser.getNameFile(files);
-                       }
+            
+                       if (countfile == "") {
+                if (namefile == "") {
+                    vector<string> files; files.push_back(qualfile);
+                    parser.getNameFile(files);
+                }
+            }
                }
        }
        catch(exception& e) {
@@ -179,7 +199,12 @@ int SummaryQualCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                if (namefile != "") { nameMap = m->readNames(namefile); }
-               
+               else if (countfile != "") {
+            CountTable ct;
+            ct.readTable(countfile);
+            nameMap = ct.getNameMap();
+        }
+        
                vector<unsigned long long> positions; 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                positions = m->divideFile(qualfile, processors);
@@ -257,7 +282,7 @@ int SummaryQualCommand::driverCreateSummary(vector<int>& position, vector<int>&
                        if (current.getName() != "") {
                                
                                int num = 1;
-                               if (namefile != "") {
+                               if ((namefile != "") || (countfile != "")) {
                                        //make sure this sequence is in the namefile, else error 
                                        map<string, int>::iterator it = nameMap.find(current.getName());
                                        
@@ -400,11 +425,14 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
                DWORD   dwThreadIdArray[processors];
                HANDLE  hThreadArray[processors]; 
                
+        bool hasNameMap = false;
+        if ((namefile !="") || (countfile != "")) { hasNameMap = true; }
+        
                //Create processor worker threads.
                for( int i=0; i<processors; i++ ){
                        
                        // Allocate memory for thread data.
-                       seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+                       seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, hasNameMap, nameMap);
                        pDataArray.push_back(tempSum);
                        processIDS.push_back(i);
         
@@ -457,7 +485,7 @@ int SummaryQualCommand::printQual(string sumFile, vector<int>& position, vector<
                        
                        if (m->control_pressed) { out.close(); return 0; }
                        
-                       float average = averageQ[i] / (float) position[i];
+                       double average = averageQ[i] / (float) position[i];
                        out << i << '\t' << position[i] << '\t' << average << '\t';
                        
                        for (int j = 0; j < 41; j++) {