chimeras

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index bc8523aa78b5d217fd5cfd12c8bade6bbb630721..b3da429fc57c9da7081640876ee9fbedda808e25 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -30,24 +30,13 @@ SequenceDB::SequenceDB(int newSize) {
 
 SequenceDB::SequenceDB(ifstream& filehandle) {
        try{
-               string name, sequence, line;
-               sequence = "";
-               int c;
-               string temp;
-               
-               
+                               
                //read through file
-               while ((c = filehandle.get()) != EOF) {
-                       name = ""; sequence = ""; 
-                       //is this a name
-                       if (c == '>') { 
-                               name = readName(filehandle); 
-                               sequence = readSequence(filehandle); 
-                       }else {  cout << "Error fasta in your file. Please correct." << endl; }
-
+               while (!filehandle.eof()) {
                        //input sequence info into sequencedb
-                       Sequence newSequence(name, sequence);
-                       data.push_back(newSequence);
+                       Sequence newSequence(filehandle);
+                       
+                       if (newSequence.getName() != "") {   data.push_back(newSequence);  }
                        
                        //takes care of white space
                        gobble(filehandle);
@@ -57,11 +46,7 @@ SequenceDB::SequenceDB(ifstream& filehandle) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function SequenceDB. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function SequenceDB. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "SequenceDB");
                exit(1);
        }
 }
@@ -82,11 +67,7 @@ string SequenceDB::readName(ifstream& in) {
                return name;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "readName");
                exit(1);
        }
 }
@@ -115,11 +96,7 @@ string SequenceDB::readSequence(ifstream& in) {
                return sequence;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "readSequence");
                exit(1);
        }
 }
@@ -137,11 +114,7 @@ void SequenceDB::set(int index, string newUnaligned) {
                data[index] = Sequence(data[index].getName(), newUnaligned);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "set");
                exit(1);
        }
 }
@@ -153,11 +126,7 @@ void SequenceDB::set(int index, Sequence newSeq) {
                data[index] = newSeq;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "set");
                exit(1);
        }
 }
@@ -175,11 +144,7 @@ void SequenceDB::resize(int newSize) {
                data.resize(newSize);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function resize. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function resize. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "resize");
                exit(1);
        }
 }
@@ -191,11 +156,7 @@ void SequenceDB::clear() {
                data.clear();
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "clear");
                exit(1);
        }
 }
@@ -215,11 +176,7 @@ void SequenceDB::print(ostream& out) {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "print");
                exit(1);
        }
 }
@@ -231,11 +188,7 @@ void SequenceDB::push_back(Sequence newSequence) {
                data.push_back(newSequence);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SequenceDB class function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SequenceDB", "push_back");
                exit(1);
        }
 }