pat's minor edits to distance calculations

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 57754667da593265618aa0d9e5c046e18b2b7203..36b072121b044490332a8926f0f3f287bf816fab 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -21,29 +21,32 @@ void FastaMap::readFastaFile(string inFileName) {
                string temp;
 
                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++;
-                       }       
-                       
+                       if (name != "") {
+                               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);
                }
                in.close();             
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "readFastaFile");
+               m->errorOut(e, "FastaMap", "readFastaFile");
                exit(1);
        }
 }
@@ -58,6 +61,8 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
        map<string,string> oldNameMap;
        string name, list;
        while(!oldNameFile.eof()){
+               if (m->control_pressed) { break; }
+               
                oldNameFile >> name >> list;
                oldNameMap[name] = list;
                gobble(oldNameFile);
@@ -68,23 +73,26 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
        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++;
-               }       
-               
+               if (name != "") {
+                       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);
        }
        
@@ -143,12 +151,13 @@ void FastaMap::printNamesFile(string outFileName){ //prints data
                
                // 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);
        }
 }
@@ -161,13 +170,14 @@ void FastaMap::printCondensedFasta(string outFileName){ //prints data
                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);
        }
 }