changing command name classify.shared to classifyrf.shared

[mothur.git] / sequenceparser.cpp

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index 08e5ae8b859280da965566ea9bf4d6dce3b202c7..37891eb44a0b42c2b9f0879dfd084da1893c289b 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -59,7 +59,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                in.close();
                                 
                if (error == 1) { m->control_pressed = true; }
-                                
+               
                //read name file
                ifstream inName;
                m->openInputFile(nameFile, inName);
@@ -148,6 +148,78 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
             }
                }
                inName.close();
+        
+        //in case file does not end in white space
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { //save one line
+                    if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
+                    vector<string> names;
+                    m->splitAtChar(secondCol, names, ',');
+                    
+                    //get aligned string for these seqs from the fasta file
+                    string alignedString = "";
+                    map<string, string>::iterator itAligned = seqName.find(names[0]);
+                    if (itAligned == seqName.end()) {
+                        error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
+                    }else {
+                        alignedString = itAligned->second;
+                    }
+                    
+                    //separate by group - parse one line in name file
+                    map<string, string> splitMap; //group -> name1,name2,...
+                    map<string, string>::iterator it;
+                    for (int i = 0; i < names.size(); i++) {
+                        
+                        string group = groupMap->getGroup(names[i]);
+                        if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
+                        else { 
+                            
+                            it = splitMap.find(group);
+                            if (it != splitMap.end()) { //adding seqs to this group
+                                (it->second) += "," + names[i];
+                                thisnames1.insert(names[i]);
+                                countName++;
+                            }else { //first sighting of this group
+                                splitMap[group] = names[i];
+                                countName++;
+                                thisnames1.insert(names[i]);
+                                
+                                //is this seq in the fasta file?
+                                if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
+                                    Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
+                                    seqs[group].push_back(tempSeq);
+                                }
+                            }
+                        }
+                        
+                        allSeqsMap[names[i]] = names[0];
+                    }
+                    
+                    
+                    //fill nameMapPerGroup - holds all lines in namefile separated by group
+                    for (it = splitMap.begin(); it != splitMap.end(); it++) {
+                        //grab first name
+                        string firstName = "";
+                        for(int i = 0; i < (it->second).length(); i++) {
+                            if (((it->second)[i]) != ',') {
+                                firstName += ((it->second)[i]);
+                            }else { break; }
+                        }
+                        
+                        //group1 -> seq1 -> seq1,seq2,seq3
+                        nameMapPerGroup[it->first][firstName] = it->second;
+                    }
+                    
+                    pairDone = false; 
+                }
+            }
+        }
                
                if (error == 1) { m->control_pressed = true; }
                        
@@ -238,8 +310,6 @@ vector<string> SequenceParser::getNamesOfGroups(){ return groupMap->getNamesOfGr
 /************************************************************/
 bool SequenceParser::isValidGroup(string g){ return groupMap->isValidGroup(g); }
 /************************************************************/
-string SequenceParser::getGroup(string g){ return groupMap->getGroup(g); }
-/************************************************************/
 int SequenceParser::getNumSeqs(string g){ 
        try {
                map<string, vector<Sequence> >::iterator it;
@@ -330,7 +400,7 @@ int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
                                        
                                        if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
                                        
-                                       out << ">" << nameVector[i].name  << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
+                                       out << ">" <<  nameVector[i].name << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl; //
                                }
                                
                        }else {