added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 240ba65adf628099e8234ed7c8c7a692913d71ee..8eaf536040a5703bbd7d9f4b93329f79cf6c6830 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -39,7 +39,7 @@ string ChimeraPerseusCommand::getHelpString(){
                helpString += "The chimera.perseus command reads a fastafile and namefile and outputs potentially chimeric sequences.\n";
                helpString += "The chimera.perseus command parameters are fasta, name, group, cutoff, processors, alpha and beta.\n";
                helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
-               helpString += "The name parameter allows you to provide a name file associated with your fasta file. If none is given unique.seqs will be run to generate one. \n";
+               helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
                helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
                helpString += "The group parameter allows you to provide a group file.  When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
                helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
@@ -345,16 +345,16 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.50";  }
-                       convert(temp, cutoff);
+                       m->mothurConvert(temp, cutoff);
                        
                        temp = validParameter.validFile(parameters, "alpha", false);    if (temp == "not found"){       temp = "-5.54"; }
-                       convert(temp, alpha);
+                       m->mothurConvert(temp, alpha);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.33";  }
-                       convert(temp, beta);
+                       m->mothurConvert(temp, beta);
                }
        }
        catch(exception& e) {
@@ -640,7 +640,6 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                vector<bool> chimeras(numSeqs, 0);
                
                for(int i=0;i<numSeqs;i++){     
-                       cout << sequences[i].seqName << endl << sequences[i].sequence << endl << sequences[i].frequency << endl;
                        if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
                        
                        vector<bool> restricted = chimeras;
@@ -657,7 +656,6 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                        vector<pwAlign> alignments(numSeqs);
                        
                        int comparisons = myPerseus.getAlignments(i, sequences, alignments, leftDiffs, leftMaps, rightDiffs, rightMaps, bestSingleIndex, bestSingleDiff, restricted);
-                       cout << "comparisons = " << comparisons << endl;
                        if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
                        int minMismatchToChimera, leftParentBi, rightParentBi, breakPointBi;
@@ -666,7 +664,6 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                        
                        if(comparisons >= 2){   
                                minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
-                               cout << "minMismatchToChimera = " << minMismatchToChimera << endl;
                                if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
                                int minMismatchToTrimera = numeric_limits<int>::max();
@@ -674,12 +671,11 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                                
                                if(minMismatchToChimera >= 3 && comparisons >= 3){
                                        minMismatchToTrimera = myPerseus.getTrimera(sequences, leftDiffs, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight, restricted);
-                                       cout << "minMismatchToTrimera = " << minMismatchToTrimera << endl;
                                        if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
                                }
                                
                                double singleDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, sequences[bestSingleIndex].sequence, dummyA, dummyB, correctModel);
-                               cout << "singleDist = " << singleDist << endl;
+                               
                                if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
                                string type;
@@ -693,16 +689,16 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                                        type = "chimera";
                                        chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, leftMaps, rightMaps);
                                }
-                               cout << "chimeraRefSeq = " << chimeraRefSeq << endl;
+                               ;
                                if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
                                
                                double chimeraDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq, dummyA, dummyB, correctModel);
-                               cout << "chimeraDist = " << chimeraDist << endl;
+                               
                                if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
                                double cIndex = chimeraDist;//modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq);
                                double loonIndex = myPerseus.calcLoonIndex(sequences[i].sequence, sequences[leftParentBi].sequence, sequences[rightParentBi].sequence, breakPointBi, binMatrix);                
-                               cout << "loonIndex = " << loonIndex << endl;
+                               
                                if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
                                chimeraFile << i << '\t' << sequences[i].seqName << '\t' << bestSingleDiff << '\t' << bestSingleIndex << '\t' << sequences[bestSingleIndex].seqName << '\t';
@@ -841,7 +837,7 @@ int ChimeraPerseusCommand::createProcessesGroups(SequenceParser& parser, string
                
                //Wait until all threads have terminated.
                WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
-               cout << "here" << endl; 
+                       
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;