changes while testing

[mothur.git] / chimeraperseuscommand.h

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index b3d6ccf56858deb00435ace345826450f7d4cd9e..b6d4fc9323f659abe52cd70a1e3598a84d9db936 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -64,8 +64,8 @@ private:
     vector<seqData> readFiles(string inputFile, CountTable* ct);
        vector<seqData> loadSequences(string);
        int deconvoluteResults(map<string, string>&, string, string);
-       int driverGroups(string, string, int, int, vector<string>);
-       int createProcessesGroups(string, string, vector<string>, string, string, string);
+       int driverGroups(string, string, string, int, int, vector<string>);
+       int createProcessesGroups(string, string, string, vector<string>, string, string, string);
     string removeNs(string);
 };
 
@@ -79,16 +79,17 @@ struct perseusData {
        string groupfile;
        string outputFName;
        string accnos;
+    string countlist;
        MothurOut* m;
        int start;
        int end;
-    bool hasName, hasCount;
+    bool hasName, hasCount, dups;
        int threadID, count, numChimeras;
        double alpha, beta, cutoff;
        vector<string> groups;
        
        perseusData(){}
-       perseusData(bool hn, bool hc, double a, double b, double c, string o,  string f, string n, string g, string ac, vector<string> gr, MothurOut* mout, int st, int en, int tid) {
+       perseusData(bool dps, bool hn, bool hc, double a, double b, double c, string o,  string f, string n, string g, string ac, string ctlist, vector<string> gr, MothurOut* mout, int st, int en, int tid) {
                alpha = a;
                beta = b;
                cutoff = c;
@@ -96,6 +97,7 @@ struct perseusData {
                namefile = n;
                groupfile = g;
                outputFName = o;
+        countlist = ctlist;
                accnos = ac;
                m = mout;
                start = st;
@@ -104,6 +106,7 @@ struct perseusData {
                groups = gr;
         hasName = hn;
         hasCount = hc;
+        dups = dps;
                count = 0;
                numChimeras = 0;
        }
@@ -127,7 +130,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
                if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile);
+            ct->readTable(pDataArray->namefile, true);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {
@@ -137,6 +140,9 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
     
                int totalSeqs = 0;
                int numChimeras = 0;
+        
+        ofstream outCountList;
+        if (pDataArray->hasCount && pDataArray->dups) { pDataArray->m->openOutputFile(pDataArray->countlist, outCountList); }
                
                for (int u = pDataArray->start; u < pDataArray->end; u++) {
                        
@@ -337,16 +343,49 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
                                        chimeraFile << j << '\t' << sequences[j].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
                                }
                                //report progress
-                               if((j+1) % 100 == 0){   pDataArray->m->mothurOut("Processing sequence: " + toString(j+1) + "\n");               }
+                               if((j+1) % 100 == 0){   pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(j+1) + "\n");           }
                        }
                        
-                       if((numSeqs) % 100 != 0){       pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");           }
+                       if((numSeqs) % 100 != 0){       pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n");               }
                        
                        chimeraFile.close();
                        accnosFile.close();
                        ////////////////////////////////////////////////////////////////////////////////////////
 
                        totalSeqs += numSeqs;
+            
+            if (pDataArray->dups) {
+                if (!pDataArray->m->isBlank(accnosFileName)) {
+                    ifstream in;
+                    pDataArray->m->openInputFile(accnosFileName, in);
+                    string name;
+                    if (pDataArray->hasCount) {
+                        while (!in.eof()) {
+                            in >> name; pDataArray->m->gobble(in);
+                            outCountList << name << '\t' << pDataArray->groups[u] << endl;
+                        }
+                        in.close();
+                    }else {
+                        map<string, string> thisnamemap = parser->getNameMap(pDataArray->groups[u]);
+                        map<string, string>::iterator itN;
+                        ofstream out;
+                        pDataArray->m->openOutputFile(accnosFileName+".temp", out);
+                        while (!in.eof()) {
+                            in >> name; pDataArray->m->gobble(in);
+                            itN = thisnamemap.find(name);
+                            if (itN != thisnamemap.end()) {
+                                vector<string> tempNames; pDataArray->m->splitAtComma(itN->second, tempNames);
+                                for (int j = 0; j < tempNames.size(); j++) { out << tempNames[j] << endl; }
+                                
+                            }else { pDataArray->m->mothurOut("[ERROR]: parsing cannot find " + name + ".\n"); pDataArray->m->control_pressed = true; }
+                        }
+                        out.close();
+                        in.close();
+                        pDataArray->m->renameFile(accnosFileName+".temp", accnosFileName);
+                    }
+                    
+                }
+            }
                        
                        //append files
                        pDataArray->m->appendFiles(chimeraFileName, pDataArray->outputFName); pDataArray->m->mothurRemove(chimeraFileName);
@@ -356,6 +395,8 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
                        if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
                }       
                
+        if (pDataArray->hasCount && pDataArray->dups) { outCountList.close(); }
+        
                pDataArray->count = totalSeqs;
                if (pDataArray->hasCount) { delete cparser; } { delete parser; }
                return totalSeqs;