changing command name classify.shared to classifyrf.shared

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index ab8ca91a42b35a9a283a3f9c6f2ee4606a01f7a4..f5493eb7517db72c20048da57080a587ae675f7e 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -25,9 +25,11 @@ public:
        
        vector<string> setParameters();
        string getCommandName()                 { return "trim.flows";  }
-       string getCommandCategory()             { return "Hidden";              }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
        string getHelpString(); 
-       string getCitation() { return "no citation"; }
+    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;
        
@@ -58,7 +61,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-       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;
@@ -66,10 +69,11 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        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?
@@ -83,7 +87,7 @@ private:
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct trimFlowData {
+struct trimFlowData {
        string flowFileName; 
        string trimFlowFileName; 
        string scrapFlowFileName;
@@ -130,7 +134,7 @@ typedef 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;
@@ -220,7 +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;