Merge remote-tracking branch 'mothur/master'

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index 082bff27e25209fc7db92404388ae40592d45bff..e63afa6c8af8ee442e267714fcfccd140d4f79dd 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -15,6 +15,7 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "sequenceparser.h"
+#include "sequencecountparser.h"
 
 /************************************************************/
 struct seqPNode {
@@ -28,7 +29,13 @@ struct seqPNode {
        ~seqPNode() {}
 };
 /************************************************************/
-inline bool comparePriority(seqPNode first, seqPNode second) {  return (first.numIdentical > second.numIdentical); }
+inline bool comparePriority(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 {
@@ -58,9 +65,13 @@ private:
                linePair(int i, int j) : start(i), end(j) {}
        };
        
+    SequenceParser* parser;
+    SequenceCountParser* cparser;
+    CountTable ct;
+    
        int diffs, length, processors;
        bool abort, bygroup;
-       string fastafile, namefile, outputDir, groupfile;
+       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
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
@@ -73,11 +84,12 @@ private:
        void readNameFile();
        //int readNamesFASTA();
        int calcMisMatches(string, string);
-       void printData(string, string); //fasta filename, names file name
+       void printData(string, string, string); //fasta filename, names file name
        int process(string);
-       int loadSeqs(map<string, string>&, vector<Sequence>&);
-       int driverGroups(SequenceParser*, string, string, string, int, int, vector<string> groups);
-       int createProcessesGroups(SequenceParser*, string, string, string, vector<string>);
+       int loadSeqs(map<string, string>&, vector<Sequence>&, string);
+       int driverGroups(string, string, string, int, int, vector<string> groups);
+       int createProcessesGroups(string, string, string, vector<string>);
+    int mergeGroupCounts(string, string, string);
 };
 
 /**************************************************************************************************/
@@ -87,7 +99,7 @@ private:
 struct preClusterData {
        string fastafile; 
        string namefile; 
-       string groupfile;
+       string groupfile, countfile;
        string newFName, newNName, newMName;
        MothurOut* m;
        int start;
@@ -97,7 +109,7 @@ struct preClusterData {
        vector<string> mapFileNames;
        
        preClusterData(){}
-       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) {
+       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) {
                fastafile = f;
                namefile = n;
                groupfile = g;
@@ -110,6 +122,7 @@ struct preClusterData {
                diffs = d;
                threadID = tid;
                groups = gr;
+        countfile = c;
        }
 };
 
@@ -124,10 +137,15 @@ static DWORD WINAPI MyPreclusterThreadFunction(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);                                            }
-               
-               int numSeqs = 0;
+        SequenceCountParser* cparser;
+        if (pDataArray->countfile != "") {
+            cparser = new SequenceCountParser(pDataArray->countfile, pDataArray->fastafile);
+        }else {
+            if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
+            else                               { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);                    }
+        }
+        
+               int numSeqs = 0;
                vector<seqPNode> alignSeqs;
                //clear out old files
                ofstream outF; pDataArray->m->openOutputFile(pDataArray->newFName, outF); outF.close();
@@ -143,8 +161,13 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                        pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Processing group " + pDataArray->groups[k] + ":"); pDataArray->m->mothurOutEndLine();
                        
                        map<string, string> thisNameMap;
-                       if (pDataArray->namefile != "") { thisNameMap = parser->getNameMap(pDataArray->groups[k]); }
-                       vector<Sequence> thisSeqs = parser->getSeqs(pDataArray->groups[k]);
+            vector<Sequence> thisSeqs;
+                       if (pDataArray->groupfile != "") { 
+                thisSeqs = parser->getSeqs(pDataArray->groups[k]);
+            }else if (pDataArray->countfile != "") {
+                thisSeqs = cparser->getSeqs(pDataArray->groups[k]);
+            }
+                       if (pDataArray->namefile != "") {  thisNameMap = parser->getNameMap(pDataArray->groups[k]); }
                        
                        //fill alignSeqs with this groups info.
                        ////////////////////////////////////////////////////
@@ -154,6 +177,9 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                        alignSeqs.clear();
                        map<string, string>::iterator it;
                        bool error = false;
+            map<string, int> thisCount;
+            if (pDataArray->countfile != "") { thisCount = cparser->getCountTable(pDataArray->groups[k]);  }
+
                        
                        for (int i = 0; i < thisSeqs.size(); i++) {
                                
@@ -176,8 +202,16 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                                                if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
                                        }       
                                }else { //no names file, you are identical to yourself 
-                                       seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
-                                       alignSeqs.push_back(tempNode);
+                                       int numRep = 1;
+                    if (pDataArray->countfile != "") { 
+                        map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
+                        
+                        //should never be true since parser checks for this
+                        if (it2 == thisCount.end()) { pDataArray->m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); error = true; }
+                        else { numRep = it2->second;  }
+                    }
+                    seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
+                    alignSeqs.push_back(tempNode);
                                        if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
                                }
                        }
@@ -274,7 +308,9 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                        for (int i = 0; i < alignSeqs.size(); i++) {
                                if (alignSeqs[i].numIdentical != 0) {
                                        alignSeqs[i].seq.printSequence(outFasta); 
-                                       outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
+                                       if (pDataArray->countfile != "") {  outNames << pDataArray->groups[k] << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; 
+                    }else {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;  }
+
                                }
                        }