changed random forest output filename

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 4d0a6112cb6e288600ae944e9340563f5973da47..53f04d37965d55c189447c7cbd1c702ac93dc5ac 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -261,7 +261,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                
         TrimOligos* trimOligos = NULL;
         int numBarcodes = pDataArray->barcodes.size();
-        if (pDataArray->pairedOligos)   {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes);   numBarcodes = pDataArray->pairedBarcodes.size(); }
+        if (pDataArray->pairedOligos)   {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes);   numBarcodes = pDataArray->pairedBarcodes.size(); pDataArray->numFPrimers = pDataArray->pairedPrimers.size(); }
         else                {   trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);  }
         
         TrimOligos* rtrimOligos = NULL;
@@ -283,7 +283,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
                                   
                        if (pDataArray->m->control_pressed) {
-                delete trimOligos;
+                delete trimOligos; if (pDataArray->reorient) { delete rtrimOligos; }
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
                                if ((pDataArray->createGroup) && (pDataArray->countfile == "")) {        outGroupsFile.close();   }
                 if(pDataArray->qFileName != "")        {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
@@ -299,11 +299,14 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                        int currentSeqsDiffs = 0;
             
                        Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);
+            Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
                        
-                       QualityScores currQual;
+                       QualityScores currQual; QualityScores savedQual;
                        if(pDataArray->qFileName != ""){
                                currQual = QualityScores(qFile);  pDataArray->m->gobble(qFile);
+                savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
                        }
+              
                        
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
@@ -353,13 +356,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                     int thisPrimerIndex = 0;
                     
                     if(numBarcodes != 0){
-                        thisSuccess = rtrimOligos->stripBarcode(currSeq, currQual, thisBarcodeIndex);
+                        thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
                         if(thisSuccess > pDataArray->bdiffs)           {       thisTrashCode += 'b';   }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
                     
                     if(pDataArray->numFPrimers != 0){
-                        thisSuccess = rtrimOligos->stripForward(currSeq, currQual, thisPrimerIndex, pDataArray->keepforward);
+                        thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, pDataArray->keepforward);
                         if(thisSuccess > pDataArray->pdiffs)           {       thisTrashCode += 'f';   }
                         else{ thisCurrentSeqsDiffs += thisSuccess;  }
                     }
@@ -372,7 +375,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                         currentSeqsDiffs = thisCurrentSeqsDiffs;
                         barcodeIndex = thisBarcodeIndex;
                         primerIndex = thisPrimerIndex;
-                    }
+                        savedSeq.reverseComplement();
+                        currSeq.setAligned(savedSeq.getAligned());
+                        if(pDataArray->qFileName != ""){
+                            savedQual.flipQScores();
+                            currQual.setScores(savedQual.getScores());
+                        }
+                    }else { trashCode += "(" + thisTrashCode + ")";  }
                 }
 
                 
@@ -567,12 +576,13 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                        }
                        
                        //report progress
-                       if((i) % 1000 == 0){    pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }
+                       if((pDataArray->count) % 1000 == 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
                        
                }
                //report progress
                if((pDataArray->count) % 1000 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
                
+        if (pDataArray->reorient) { delete rtrimOligos; }
                delete trimOligos;
                inFASTA.close();
                trimFASTAFile.close();