update to new version of Xcode

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index e63afa6c8af8ee442e267714fcfccd140d4f79dd..e0767826ecde2fcf8056bbdebfb8d1bd8ce435c4 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -29,13 +29,21 @@ struct seqPNode {
        ~seqPNode() {}
 };
 /************************************************************/
-inline bool comparePriority(seqPNode first, seqPNode second) {  
+inline bool comparePriorityTopDown(seqPNode first, seqPNode second) {  
     if (first.numIdentical > second.numIdentical) { return true;  }
     else if (first.numIdentical == second.numIdentical) { 
         if (first.seq.getName() > second.seq.getName()) { return true; }
     }
     return false; 
 }
+/************************************************************/
+inline bool comparePriorityDownTop(seqPNode first, seqPNode second) {  
+    if (first.numIdentical < second.numIdentical) { return true;  }
+    else if (first.numIdentical == second.numIdentical) { 
+        if (first.seq.getName() > second.seq.getName()) { return true; }
+    }
+    return false; 
+}
 //************************************************************/
 
 class PreClusterCommand : public Command {
@@ -48,8 +56,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "pre.cluster";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Pre.cluster"; }
        string getDescription()         { return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
 
@@ -70,7 +79,7 @@ private:
     CountTable ct;
     
        int diffs, length, processors;
-       bool abort, bygroup;
+       bool abort, bygroup, topdown;
        string fastafile, namefile, outputDir, groupfile, countfile;
        vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
        map<string, string> names; //represents the names file first column maps to second column
@@ -78,7 +87,6 @@ private:
        map<string, int>::iterator itSize; 
 //     map<string, bool> active; //maps sequence name to whether it has already been merged or not.
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();
@@ -103,13 +111,14 @@ struct preClusterData {
        string newFName, newNName, newMName;
        MothurOut* m;
        int start;
-       int end;
+       int end, count;
        int diffs, threadID;
        vector<string> groups;
        vector<string> mapFileNames;
+    bool topdown;
        
        preClusterData(){}
-       preClusterData(string f, string n, string g, string c, string nff,  string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int d, int tid) {
+       preClusterData(string f, string n, string g, string c, string nff,  string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int d, bool td, int tid) {
                fastafile = f;
                namefile = n;
                groupfile = g;
@@ -123,6 +132,8 @@ struct preClusterData {
                threadID = tid;
                groups = gr;
         countfile = c;
+        topdown = td;
+        count=0;
        }
 };
 
@@ -154,6 +165,8 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                //precluster each group
                for (int k = pDataArray->start; k < pDataArray->end; k++) {
                        
+            pDataArray->count++;
+            
                        int start = time(NULL);
                        
                        if (pDataArray->m->control_pressed) {  delete parser; return 0; }
@@ -235,9 +248,10 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                        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);
-                       
+            //sort seqs by number of identical seqs
+            if (pDataArray->topdown) { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityTopDown);  }
+            else {  sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityDownTop);  }
+            
                        int count = 0;
                        
                        //think about running through twice...