changing command name classify.shared to classifyrf.shared

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 8656fd0b5b314084c6fd08cf614288aca2bbc763..f5493eb7517db72c20048da57080a587ae675f7e 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,7 +26,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
        string getCommandCategory()             { return "Sequence Processing";         }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
        string getDescription()         { return "trim.flows"; }
 
@@ -49,7 +51,8 @@ private:
        vector<unsigned long long> getFlowFileBreaks();
        int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
        int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+    string reverseOligo(string);
+    
        vector<string> outputNames;
        set<string> filesToRemove;
        
@@ -58,9 +61,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
        int numFlows;
        float signal, noise;
        bool fasta;
@@ -71,6 +72,8 @@ private:
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;
+    vector<string> linker;
+    vector<string> spacer;
 
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?
@@ -131,7 +134,7 @@ struct trimFlowData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){ 
        trimFlowData* pDataArray;
@@ -221,7 +224,7 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
                                
                                flowData.printFlows(trimFlowFile);
                                
-                               if(pDataArray->fasta)   {       currSeq.printSequence(fastaFile);       }
+                               if(pDataArray->fasta)   {       currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);   }
                                
                                if(pDataArray->allFiles){
                                        ofstream output;