some changes to trim.flows

diff --git a/flowdata.cpp b/flowdata.cpp
index 39c1f8317a306c1a49488625725cbea7a4c6bd4e..d1769bbed46e34c12a1a8ad4a1f69bebaeca071d 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -19,14 +19,14 @@ FlowData::~FlowData(){      /*      do nothing      */      }
 
 //**********************************************************************************************************************
 
-FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP) : 
-                       numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP){
+FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string baseFlow) : 
+                       numFlows(numFlows), signalIntensity(signal), noiseIntensity(noise), maxHomoP(maxHomoP), baseFlow(baseFlow){
 
        try {
                m = MothurOut::getInstance();
 
                flowData.assign(numFlows, 0);
-               baseFlow = "TACG";
+//             baseFlow = "TACG";
                seqName = "";
                locationString = "";
        }
@@ -219,7 +219,7 @@ string FlowData::getName(){
                return seqName;
        }
        catch(exception& e) {
-               m->errorOut(e, "FlowData", "getSequence");
+               m->errorOut(e, "FlowData", "getName");
                exit(1);
        }
 }

diff --git a/flowdata.h b/flowdata.h
index 612ed37757ba942a6f4221660028ca819fdeac51..100765370ca5429e75b8688a6abc51d79f17edc5 100644 (file)
--- a/flowdata.h
+++ b/flowdata.h
@@ -18,7 +18,7 @@ class FlowData {
 
 public:
        FlowData();
-       FlowData(int, float, float, int);
+       FlowData(int, float, float, int, string);
        ~FlowData();
        bool getNext(ifstream&);
        string getName();

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 18b0b72f9ae536e01c889315d2d753b421ee6bb0..9a2851e343c2a151811770d32c1a71f75092c231 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -15,7 +15,7 @@
 //**********************************************************************************************************************
 vector<string> SeqErrorCommand::getValidParameters(){  
        try {
-               string Array[] =  {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
+               string Array[] =  {"query", "reference", "name", "qfile", "report", "threshold", "ignorechimeras", "inputdir", "outputdir"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 8184327e5bbfe33afa534cfc6515627d05403324..bb8d3863ea56b52dfea6c772dbf0beb397810849 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -16,7 +16,7 @@ vector<string> TrimFlowsCommand::getValidParameters(){
        try {
                string Array[] =  {"flow", "maxflows", "minflows",
                        "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise"
-                       "oligos", "pdiffs", "bdiffs", "tdiffs", 
+                       "oligos", "pdiffs", "bdiffs", "tdiffs",  "order",
                        "allfiles", "processors",
                        "outputdir","inputdir"
                
@@ -106,7 +106,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        //valid paramters for this command
                        string AlignArray[] =  {"flow", "maxflows", "minflows",
                                "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise",
-                               "oligos", "pdiffs", "bdiffs", "tdiffs", 
+                               "oligos", "pdiffs", "bdiffs", "tdiffs", "order",
                                "allfiles", "processors",
                
                                //                      "group",
@@ -226,7 +226,13 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){ temp = "1";           }
                        convert(temp, processors); 
-                       
+       
+                       flowOrder = validParameter.validFile(parameters, "order", false);
+                       if (flowOrder == "not found"){ flowOrder = "TACG";              }
+                       else if(flowOrder.length() != 4){
+                               m->mothurOut("The value of the order option must be four bases long\n");
+                       }
+
                        if(oligoFileName == ""){        allFiles = 0;           }
 
                        numFPrimers = 0;
@@ -367,7 +373,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                        }
                }
                
-               FlowData flowData(numFlows, signal, noise, maxHomoP);
+               FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
                
                ofstream fastaFile;
                if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 99103ba25af92565be2e0879c0904603aea5990c..7458dbe60b90f52c900e3ffd8fb645ccce0d0e86 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -65,7 +65,7 @@ private:
        int numFlows;
        float signal, noise;
        bool fasta;
-       
+       string flowOrder;       
        
        string flowFileName, oligoFileName, outputDir;