added count file to chimera.uchime. found issue with uchime program that indicated...

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 5423a171d5698bda82c5869401e3509e1f059439..659d1ea39963f05a245cda03acf56f3b6e3d10e9 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -14,6 +14,8 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequenceparser.h"
+#include "counttable.h"
+#include "sequencecountparser.h"
 
 /***********************************************************/
 
@@ -45,11 +47,12 @@ private:
        int driver(string, string, string, string, int&);
        int createProcesses(string, string, string, string, int&);
                
-       bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract;
-       string fastafile, groupfile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, uchimeLocation;
+       bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName;
+       string fastafile, groupfile, templatefile, outputDir, namefile, countfile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, uchimeLocation;
        int processors;
        
-       
+       SequenceParser* sparser;
+    SequenceCountParser* cparser;
        vector<string> outputNames;
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
@@ -58,9 +61,9 @@ private:
        string getNamesFile(string&);
        int readFasta(string, map<string, string>&);
        int printFile(vector<seqPriorityNode>&, string);
-       int deconvoluteResults(SequenceParser&, string, string, string);
-       int driverGroups(SequenceParser&, string, string, string, string, int, int, vector<string>);
-       int createProcessesGroups(SequenceParser&, string, string, string, string, vector<string>, string, string, string);
+       int deconvoluteResults(map<string, string>&, string, string, string);
+       int driverGroups(string, string, string, string, int, int, vector<string>);
+       int createProcessesGroups(string, string, string, string, vector<string>, string, string, string);
 
 
 };
@@ -81,7 +84,7 @@ struct uchimeData {
        int end;
        int threadID, count, numChimeras;
        vector<string> groups;
-       bool useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract;
+       bool useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount;
        string abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
        
        uchimeData(){}
@@ -103,7 +106,7 @@ struct uchimeData {
                numChimeras = 0;
         uchimeLocation = uloc;
        }
-       void setBooleans(bool Abskew, bool calns, bool MinH, bool Mindiv, bool Xn, bool Dn, bool Xa, bool Chunks, bool Minchunk, bool Idsmoothwindow, bool Minsmoothid, bool Maxp, bool skipgap, bool skipgap2, bool Minlen, bool Maxlen, bool uc, bool Queryfract) {
+       void setBooleans(bool Abskew, bool calns, bool MinH, bool Mindiv, bool Xn, bool Dn, bool Xa, bool Chunks, bool Minchunk, bool Idsmoothwindow, bool Minsmoothid, bool Maxp, bool skipgap, bool skipgap2, bool Minlen, bool Maxlen, bool uc, bool Queryfract, bool hc) {
                useAbskew = Abskew;
                chimealns = calns;
                useMinH = MinH;
@@ -122,6 +125,7 @@ struct uchimeData {
                useMaxlen = Maxlen;
                ucl = uc;
                useQueryfract = Queryfract;
+        hasCount = hc;
        }
        
        void setVariables(string abske, string min, string mindi, string x, string d, string xa2, string chunk, string minchun, string idsmoothwindo, string minsmoothi, string max, string minle, string maxle, string queryfrac) {
@@ -163,16 +167,30 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                
                //parse fasta and name file by group
                SequenceParser* parser;
-               if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);      }
-               else                                                    { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);                                            }
+        SequenceCountParser* cparser;
+               if (pDataArray->hasCount) {
+            CountTable* ct = new CountTable();
+            ct->readTable(pDataArray->namefile);
+            cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+            delete ct;
+        }else {
+            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
+            else                                                       { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);                                            }
+        }
                
                int totalSeqs = 0;
                int numChimeras = 0;
                
                for (int i = pDataArray->start; i < pDataArray->end; i++) {
-                       int start = time(NULL);  if (pDataArray->m->control_pressed) {  delete parser; return 0; }
+                       int start = time(NULL);  if (pDataArray->m->control_pressed) {  if (pDataArray->hasCount) { delete cparser; } { delete parser; } return 0; }
                        
-                       int error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; }
+            
+                       int error;
+            if (pDataArray->hasCount) { 
+                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
+            }else {
+               error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
+            }
                        
                        //int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
                        ////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -410,7 +428,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                        filename = filename.substr(1, filename.length()-2);
                        alns = alns.substr(1, alns.length()-2);
                        
-                       if (pDataArray->m->control_pressed) { delete parser; return 0; }
+                       if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } return 0; }
                        
                        //create accnos file from uchime results
                        ifstream in; 
@@ -447,7 +465,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                        totalSeqs += num;
                        pDataArray->numChimeras += numChimeras;
                        
-                       if (pDataArray->m->control_pressed) { delete parser; return 0; }
+                       if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } return 0; }
                        
                        //remove file made for uchime
                        pDataArray->m->mothurRemove(filename);
@@ -462,7 +480,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                }       
                
                pDataArray->count = totalSeqs;
-               delete parser;
+               if (pDataArray->hasCount) { delete cparser; } { delete parser; }
                return totalSeqs;
                
        }