added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 3c467936a38fbecc55034979a9211ee89c7241b6..537821134edebcf9dcad70f8c1f38be0da39b121 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -23,7 +23,7 @@ vector<string> ShhherCommand::setParameters(){
        try {
                CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow);
                CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile);
-               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plookup);
+               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
                CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
@@ -251,19 +251,19 @@ ShhherCommand::ShhherCommand(string option) {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
 
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.01";          }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){       temp = "0.000001";      }
-                       convert(temp, minDelta); 
+                       m->mothurConvert(temp, minDelta); 
 
                        temp = validParameter.validFile(parameters, "maxiter", false);  if (temp == "not found"){       temp = "1000";          }
-                       convert(temp, maxIters); 
+                       m->mothurConvert(temp, maxIters); 
 
                        temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
-                       convert(temp, sigma); 
+                       m->mothurConvert(temp, sigma); 
                        
                        flowOrder = validParameter.validFile(parameters, "order", false);
                        if (flowOrder == "not found"){ flowOrder = "TACG";              }
@@ -1501,9 +1501,8 @@ void ShhherCommand::getOTUData(string listFileName){
 
 void ShhherCommand::initPyroCluster(){                          
        try{
-               
                if (numOTUs < processors) { processors = 1; }
-               
+
                dist.assign(numSeqs * numOTUs, 0);
                change.assign(numOTUs, 1);
                centroids.assign(numOTUs, -1);
@@ -2151,7 +2150,9 @@ void ShhherCommand::setOTUs(){
 void ShhherCommand::writeQualities(vector<int> otuCounts){
        
        try {
-               string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.qual";
 
                ofstream qualityFile;
                m->openOutputFile(qualityFileName, qualityFile);
@@ -2256,8 +2257,9 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
-               
-               string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.fasta";
                ofstream fastaFile;
                m->openOutputFile(fastaFileName, fastaFile);
                
@@ -2303,7 +2305,9 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
 
 void ShhherCommand::writeNames(vector<int> otuCounts){
        try {
-               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.names";
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
                
@@ -2339,7 +2343,9 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
 
 void ShhherCommand::writeGroups(){
        try {
-               string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
                string groupFileName = fileRoot + ".shhh.groups";
                ofstream groupFile;
                m->openOutputFile(groupFileName, groupFile);
@@ -2362,7 +2368,9 @@ void ShhherCommand::writeGroups(){
 
 void ShhherCommand::writeClusters(vector<int> otuCounts){
        try {
-               string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.counts";
                ofstream otuCountsFile;
                m->openOutputFile(otuCountsFileName, otuCountsFile);