added modify names parameter to set.dir

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index bc8523aa78b5d217fd5cfd12c8bade6bbb630721..e798ee14ac70837e795a7be3191a14f68788c234 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -15,7 +15,7 @@
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB() {}
+SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  length = 0; samelength = true; }
 /***********************************************************************/
 //the clear function free's the memory
 SequenceDB::~SequenceDB() { clear(); }
@@ -24,44 +24,35 @@ SequenceDB::~SequenceDB() { clear(); }
 
 SequenceDB::SequenceDB(int newSize) {
        data.resize(newSize, Sequence());
+       length = 0; samelength = true;
 }
 
 /***********************************************************************/
 
 SequenceDB::SequenceDB(ifstream& filehandle) {
        try{
-               string name, sequence, line;
-               sequence = "";
-               int c;
-               string temp;
-               
-               
+               length = 0; samelength = true;
+                               
                //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() != "") {   
+                               if (length == 0) { length = newSequence.getAligned().length(); }
+                               if (length != newSequence.getAligned().length()) { samelength = false; }
+                               data.push_back(newSequence);  
+                       }
                        
                        //takes care of white space
-                       gobble(filehandle);
+                       m->gobble(filehandle);
                }
 
                filehandle.close();
                
        }
        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";
+               m->errorOut(e, "SequenceDB", "SequenceDB");
                exit(1);
        }
 }
@@ -82,11 +73,7 @@ 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";
+               m->errorOut(e, "SequenceDB", "readName");
                exit(1);
        }
 }
@@ -111,15 +98,14 @@ string SequenceDB::readSequence(ifstream& in) {
                                break;
                        }else {  sequence += line;      }
                }
-                       
+               
+               if (length == 0) { length = sequence.length(); }
+               if (length != sequence.length()) { samelength = false; }
+               
                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";
+               m->errorOut(e, "SequenceDB", "readSequence");
                exit(1);
        }
 }
@@ -134,14 +120,13 @@ int SequenceDB::getNumSeqs() {
 
 void SequenceDB::set(int index, string newUnaligned) {
        try {
+               if (length == 0) { length = newUnaligned.length(); }
+               if (length != newUnaligned.length()) { samelength = false; }
+               
                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";
+               m->errorOut(e, "SequenceDB", "set");
                exit(1);
        }
 }
@@ -150,14 +135,13 @@ void SequenceDB::set(int index, string newUnaligned) {
 
 void SequenceDB::set(int index, Sequence newSeq) {
        try {
+               if (length == 0) { length = newSeq.getAligned().length(); }
+               if (length != newSeq.getAligned().length()) { samelength = false; }
+
                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";
+               m->errorOut(e, "SequenceDB", "set");
                exit(1);
        }
 }
@@ -175,11 +159,7 @@ 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";
+               m->errorOut(e, "SequenceDB", "resize");
                exit(1);
        }
 }
@@ -191,11 +171,7 @@ 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";
+               m->errorOut(e, "SequenceDB", "clear");
                exit(1);
        }
 }
@@ -215,11 +191,7 @@ 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";
+               m->errorOut(e, "SequenceDB", "print");
                exit(1);
        }
 }
@@ -228,14 +200,13 @@ void SequenceDB::print(ostream& out) {
 
 void SequenceDB::push_back(Sequence newSequence) {
        try {
+               if (length == 0) { length = newSequence.getAligned().length(); }
+               if (length != newSequence.getAligned().length()) { samelength = false; }
+
                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";
+               m->errorOut(e, "SequenceDB", "push_back");
                exit(1);
        }
 }