From: pschloss <pschloss>
Date: Fri, 11 Mar 2011 13:28:33 +0000 (+0000)
Subject: some changes to trim.flows
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=bbe1bea3cfef487d3c1657691480d4072fe0a07f

some changes to trim.flows
---

diff --git a/flowdata.cpp b/flowdata.cpp
index 39c1f83..d1769bb 100644
--- 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 612ed37..1007653 100644
--- 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 18b0b72..9a2851e 100644
--- 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 8184327..bb8d386 100644
--- 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 99103ba..7458dbe 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -65,7 +65,7 @@ private:
 	int numFlows;
 	float signal, noise;
 	bool fasta;
-	
+	string flowOrder;	
 	
 	string flowFileName, oligoFileName, outputDir;