metastats in progress

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index 6f106187232335fbc39078cc478f60846b4319c5..3712302bee105cec37e6834dbc2b017584c9e2d5 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -22,8 +22,9 @@ struct seqPNode {
        Sequence seq;
        string names;
        bool active;
+       int diffs;
        seqPNode() {}
-       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) {}
+       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) { diffs = 0; }
        ~seqPNode() {}
 };
 /************************************************************/
@@ -72,10 +73,10 @@ private:
        //int readNamesFASTA();
        int calcMisMatches(string, string);
        void printData(string, string); //fasta filename, names file name
-       int process();
+       int process(string);
        int loadSeqs(map<string, string>&, vector<Sequence>&);
-       int driverGroups(SequenceParser*, string, string, int, int, vector<string> groups);
-       int createProcessesGroups(SequenceParser*, string, string, vector<string>);
+       int driverGroups(SequenceParser*, string, string, string, int, int, vector<string> groups);
+       int createProcessesGroups(SequenceParser*, string, string, string, vector<string>);
 };
 
 /**************************************************************************************************/
@@ -86,20 +87,22 @@ struct preClusterData {
        string fastafile; 
        string namefile; 
        string groupfile;
-       string newFName, newNName;
+       string newFName, newNName, newMName;
        MothurOut* m;
        int start;
        int end;
        int diffs, threadID;
        vector<string> groups;
+       vector<string> mapFileNames;
        
        preClusterData(){}
-       preClusterData(string f, string n, string g, string nff,  string nnf, vector<string> gr, MothurOut* mout, int st, int en, int d, int tid) {
+       preClusterData(string f, string n, string g, string nff,  string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int d, int tid) {
                fastafile = f;
                namefile = n;
                groupfile = g;
                newFName = nff;
                newNName = nnf;
+               newMName = nmf;
                m = mout;
                start = st;
                end = en;
@@ -193,6 +196,10 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                        ////////////////////////////////////////////////////
                        //int count = process(); - same function below
                        
+                       ofstream out;
+                       pDataArray->m->openOutputFile(pDataArray->newMName+pDataArray->groups[k]+".map", out);
+                       pDataArray->mapFileNames.push_back(pDataArray->newMName+pDataArray->groups[k]+".map");
+                       
                        //sort seqs by number of identical seqs
                        sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
                        
@@ -206,6 +213,8 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                                
                                if (alignSeqs[i].active) {  //this sequence has not been merged yet
                                        
+                                       string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
+
                                        //try to merge it with all smaller seqs
                                        for (int j = i+1; j < numSeqs; j++) {
                                                
@@ -229,18 +238,22 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                                                                
                                                                alignSeqs[j].active = 0;
                                                                alignSeqs[j].numIdentical = 0;
+                                                               alignSeqs[j].diffs = mismatch;
                                                                count++;
+                                                               chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
                                                        }
                                                }//end if j active
-                                       }//end if i != j
+                                       }//end for loop j
                                        
                                        //remove from active list 
                                        alignSeqs[i].active = 0;
                                        
+                                       out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;
+                                       
                                }//end if active i
                                if(i % 100 == 0)        { pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); }
                        }
-                       
+                       out.close();
                        if(numSeqs % 100 != 0)  { pDataArray->m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine();   }       
                        ////////////////////////////////////////////////////