sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 57754667da593265618aa0d9e5c046e18b2b7203..bf55493faece21cbd6c0043ac89149826c83c166 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -15,35 +15,43 @@
 void FastaMap::readFastaFile(string inFileName) {
        try {
                ifstream in;
-               openInputFile(inFileName, in);
+               m->openInputFile(inFileName, in);
                string name, sequence, line;
                sequence = "";
                string temp;
-
+               map<string, string>::iterator itName;
+               
+               
                while(!in.eof()){
+                       if (m->control_pressed) { break; }
+                       
                        Sequence currSeq(in);
                        name = currSeq.getName();
                        
-                       if(currSeq.getIsAligned())      {       sequence = currSeq.getAligned();        }
-                       else                                            {       sequence = currSeq.getUnaligned();      }
-                       
-                       seqmap[name] = sequence;  
-                       map<string,group>::iterator it = data.find(sequence);
-                       if (it == data.end()) {         //it's unique.
-                               data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-//                             data[sequence].groupnumber = 1;
-                               data[sequence].names = name;
-                       }else { // its a duplicate.
-                               data[sequence].names += "," + name;
-//                             data[sequence].groupnumber++;
-                       }       
-                       
-                       gobble(in);
+                       if (name != "") {
+                               if(currSeq.getIsAligned())      {       sequence = currSeq.getAligned();        }
+                               else                                            {       sequence = currSeq.getUnaligned();      }
+                               
+                               itName = seqmap.find(name);
+                               if (itName == seqmap.end()) { seqmap[name] = sequence;  }
+                               else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+                               
+                               map<string,group>::iterator it = data.find(sequence);
+                               if (it == data.end()) {         //it's unique.
+                                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+                                       //                              data[sequence].groupnumber = 1;
+                                       data[sequence].names = name;
+                               }else { // its a duplicate.
+                                       data[sequence].names += "," + name;
+                                       //                              data[sequence].groupnumber++;
+                               }       
+                       }
+                       m->gobble(in);
                }
                in.close();             
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "readFastaFile");
+               m->errorOut(e, "FastaMap", "readFastaFile");
                exit(1);
        }
 }
@@ -53,39 +61,50 @@ void FastaMap::readFastaFile(string inFileName) {
 void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
        
        ifstream oldNameFile;
-       openInputFile(oldNameFileName, oldNameFile);
+       m->openInputFile(oldNameFileName, oldNameFile);
        
        map<string,string> oldNameMap;
+       map<string, string>::iterator itName;
        string name, list;
        while(!oldNameFile.eof()){
-               oldNameFile >> name >> list;
+               if (m->control_pressed) { break; }
+               
+               oldNameFile >> name; m->gobble(oldNameFile);
+               oldNameFile >> list;
                oldNameMap[name] = list;
-               gobble(oldNameFile);
+               m->gobble(oldNameFile);
        }
        oldNameFile.close();
        
        ifstream inFASTA;
-       openInputFile(inFastaFile, inFASTA);
+       m->openInputFile(inFastaFile, inFASTA);
        string sequence;
        while(!inFASTA.eof()){
+               if (m->control_pressed) { break; }
+               
                Sequence currSeq(inFASTA);
                name = currSeq.getName();
                
-               if(currSeq.getIsAligned())      {       sequence = currSeq.getAligned();        }
-               else                                            {       sequence = currSeq.getUnaligned();      }
-               
-               seqmap[name] = sequence;  
-               map<string,group>::iterator it = data.find(sequence);
-               if (it == data.end()) {         //it's unique.
-                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-//                     data[sequence].groupnumber = 1;
-                       data[sequence].names = oldNameMap[name];
-               }else { // its a duplicate.
-                       data[sequence].names += "," + oldNameMap[name];
-//                     data[sequence].groupnumber++;
-               }       
-               
-               gobble(inFASTA);
+               if (name != "") {
+                       if(currSeq.getIsAligned())      {       sequence = currSeq.getAligned();        }
+                       else                                            {       sequence = currSeq.getUnaligned();      }
+                       
+                       itName = seqmap.find(name);
+                       if (itName == seqmap.end()) { seqmap[name] = sequence;  }
+                       else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+                       
+                       seqmap[name] = sequence;  
+                       map<string,group>::iterator it = data.find(sequence);
+                       if (it == data.end()) {         //it's unique.
+                               data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+                               //                      data[sequence].groupnumber = 1;
+                               data[sequence].names = oldNameMap[name];
+                       }else { // its a duplicate.
+                               data[sequence].names += "," + oldNameMap[name];
+                               //                      data[sequence].groupnumber++;
+                       }       
+               }
+               m->gobble(inFASTA);
        }
        
        
@@ -139,16 +158,17 @@ int FastaMap::sizeUnique(){ //returns datas size which is the number of unique s
 void FastaMap::printNamesFile(string outFileName){ //prints data
        try {
                ofstream outFile;
-               openOutputFile(outFileName, outFile);
+               m->openOutputFile(outFileName, outFile);
                
                // two column file created with groupname and them list of identical sequence names
                for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+                       if (m->control_pressed) { break; }
                        outFile << it->second.groupname << '\t' << it->second.names << endl;
                }
                outFile.close();
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "printNamesFile");
+               m->errorOut(e, "FastaMap", "printNamesFile");
                exit(1);
        }
 }
@@ -158,16 +178,17 @@ void FastaMap::printNamesFile(string outFileName){ //prints data
 void FastaMap::printCondensedFasta(string outFileName){ //prints data
        try {
                ofstream out;
-               openOutputFile(outFileName, out);
+               m->openOutputFile(outFileName, out);
                //creates a fasta file
                for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+                       if (m->control_pressed) { break; }
                        out << ">" << it->second.groupname << endl;
                        out << it->first << endl;
                }
                out.close();
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "printCondensedFasta");
+               m->errorOut(e, "FastaMap", "printCondensedFasta");
                exit(1);
        }
 }