added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / readcolumn.cpp

diff --git a/readcolumn.cpp b/readcolumn.cpp
index f29f70b11fd66d8b8d9a87fdb5502ed289c7d657..53a8c4263dddc4687acc5a64cf7c5b1d27aac647 100644 (file)
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -14,9 +14,17 @@
 
 ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
        
-       successOpen = openInputFile(distFile, fileHandle);
+       successOpen = m->openInputFile(distFile, fileHandle);
+       sim = false;
        
 }
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df, bool s) : distFile(df){
+       
+       successOpen = m->openInputFile(distFile, fileHandle);
+       sim = s;
+}
 
 /***********************************************************************/
 
@@ -47,16 +55,11 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                        map<string,int>::iterator itA = nameMap->find(firstName);
                        map<string,int>::iterator itB = nameMap->find(secondName);
                                
-                       if(itA == nameMap->end()){
-                               cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
-                       }
-                       if(itB == nameMap->end()){
-                               cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
-                       }
-//if (((itA->second == 8) && (itB->second == 1588)) || ((itA->second == 1588) && (itB->second == 8))) { cout << "found it" << endl; }
+                       if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+                       if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 
                        if (distance == -1) { distance = 1000000; }
-                       else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                       else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                        
                        if(distance < cutoff && itA != itB){
                                if(itA->second > itB->second){
@@ -91,7 +94,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                                }
                                reading->update(itA->second * nseqs);
                        }
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
 
                if(lt == 0){  // oops, it was square
@@ -99,7 +102,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                        fileHandle.close();  //let's start over
                        D->clear();  //let's start over
                   
-                       openInputFile(distFile, fileHandle);  //let's start over
+                       m->openInputFile(distFile, fileHandle);  //let's start over
 
                        while(fileHandle){
                                fileHandle >> firstName >> secondName >> distance;
@@ -109,15 +112,11 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                                map<string,int>::iterator itA = nameMap->find(firstName);
                                map<string,int>::iterator itB = nameMap->find(secondName);
                                
-                               if(itA == nameMap->end()){
-                                       cerr << "BError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
-                               }
-                               if(itB == nameMap->end()){
-                                       cerr << "BError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
-                               }
+                               if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+                               if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
                                
                                if (distance == -1) { distance = 1000000; }
-                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                
                                if(distance < cutoff && itA->second > itB->second){
                                        PCell value(itA->second, itB->second, distance);
@@ -125,7 +124,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                                        reading->update(itA->second * nseqs);
                                }
                
-                               gobble(fileHandle);
+                               m->gobble(fileHandle);
                        }
                }