modifications to shhh.seqs

diff --git a/mothur b/mothur
index e36592e89bc100dea7c6fa4d156974d27838c63b..a425fb1254c4a3431571e1bde7e23bc48e8de236 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 224d3ce77cde444c07c0d1ebc393e270228fa620..f9b34298a6fc6eddb364f0148f8c44b3e6900aac 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -16,6 +16,7 @@
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsematrix.hpp"
+#include <cfloat>
 
 //**********************************************************************************************************************
 
@@ -183,7 +184,7 @@ ShhherCommand::ShhherCommand(string option) {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "lookup", true);
-                       if (temp == "not found")        {       lookupFileName = "LookUp_E123.pat";     }
+                       if (temp == "not found")        {       lookupFileName = "LookUp_Titanium.pat"; }
                        else if(temp == "not open")     {       abort = true;                   } 
                        else                                            {       lookupFileName = temp;  }
                        
@@ -259,7 +260,7 @@ int ShhherCommand::execute(){
                        cout << "\nGetting preliminary data..." << endl;
                        getSingleLookUp();
                        getJointLookUp();
-                                               
+                       
                        vector<string> flowFileVector;
                        if(flowFilesFileName != "not found"){
                                string fName;
@@ -655,8 +656,7 @@ int ShhherCommand::execute(){
                
                getSingleLookUp();
                getJointLookUp();
-               
-               
+                               
                vector<string> flowFileVector;
                if(flowFilesFileName != "not found"){
                        string fName;
@@ -1505,7 +1505,7 @@ double ShhherCommand::getLikelihood(){
        
        try{
                
-               vector<double> P(numSeqs, 0);
+               vector<long double> P(numSeqs, 0);
                int effNumOTUs = 0;
                
                for(int i=0;i<numOTUs;i++){
@@ -1514,6 +1514,7 @@ double ShhherCommand::getLikelihood(){
                        }
                }
                
+               string hold;
                for(int i=0;i<numOTUs;i++){
                        for(int j=0;j<nSeqsPerOTU[i];j++){
                                int index = cumNumSeqs[i] + j;
@@ -1523,14 +1524,15 @@ double ShhherCommand::getLikelihood(){
                                P[nI] += weight[i] * exp(-singleDist * sigma);
                        }
                }
-               
                double nLL = 0.00;
                for(int i=0;i<numSeqs;i++){
+                       if(P[i] == 0){  P[i] = DBL_EPSILON;     }
+
                        nLL += -log(P[i]);
                }
                
                nLL = nLL -(double)numSeqs * log(sigma);
-               
+
                return nLL; 
        }
        catch(exception& e) {