added modify names parameter to set.dir

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index 657573e8b3d24ee40d5f7ac10270f72a792f69e0..e798ee14ac70837e795a7be3191a14f68788c234 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -15,17 +15,100 @@
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB() {}
+SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  length = 0; samelength = true; }
+/***********************************************************************/
+//the clear function free's the memory
+SequenceDB::~SequenceDB() { clear(); }
 
 /***********************************************************************/
 
 SequenceDB::SequenceDB(int newSize) {
-       data.resize(newSize);
+       data.resize(newSize, Sequence());
+       length = 0; samelength = true;
 }
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB(ifstream&) {}
+SequenceDB::SequenceDB(ifstream& filehandle) {
+       try{
+               length = 0; samelength = true;
+                               
+               //read through file
+               while (!filehandle.eof()) {
+                       //input sequence info into sequencedb
+                       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
+                       m->gobble(filehandle);
+               }
+
+               filehandle.close();
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "SequenceDB");
+               exit(1);
+       }
+}
+/*******************************************************************************/
+string SequenceDB::readName(ifstream& in) {
+       try{
+               string name = "";
+               int c;
+               string temp;
+               
+               while ((c = in.get()) != EOF) {
+                       //if c is not a line return
+                       if (c != 10) {
+                               name += c;
+                       }else { break;  }
+               }
+                       
+               return name;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "readName");
+               exit(1);
+       }
+}
+
+/*******************************************************************************/
+string SequenceDB::readSequence(ifstream& in) {
+       try{
+               string sequence = "";
+               string line;
+               int pos, c;
+               
+               while (!in.eof()) {
+                       //save position in file in case next line is a new name.
+                       pos = in.tellg();
+                       line = "";
+                       in >> line;                     
+                       //if you are at a new name
+                       if (line[0] == '>') {
+                               //put file pointer back since you are now at a new name
+                               in.seekg(pos, ios::beg);
+                               c = in.get();  //because you put it back to a newline char
+                               break;
+                       }else {  sequence += line;      }
+               }
+               
+               if (length == 0) { length = sequence.length(); }
+               if (length != sequence.length()) { samelength = false; }
+               
+               return sequence;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "readSequence");
+               exit(1);
+       }
+}
        
 /***********************************************************************/
 
@@ -36,14 +119,31 @@ int SequenceDB::getNumSeqs() {
 /***********************************************************************/
 
 void SequenceDB::set(int index, string newUnaligned) {
-       Sequence newSeq(data[index].getName(), newUnaligned);
-       data[index] = newSeq;
+       try {
+               if (length == 0) { length = newUnaligned.length(); }
+               if (length != newUnaligned.length()) { samelength = false; }
+               
+               data[index] = Sequence(data[index].getName(), newUnaligned);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "set");
+               exit(1);
+       }
 }
 
 /***********************************************************************/
 
 void SequenceDB::set(int index, Sequence newSeq) {
-       data[index] = newSeq;
+       try {
+               if (length == 0) { length = newSeq.getAligned().length(); }
+               if (length != newSeq.getAligned().length()) { samelength = false; }
+
+               data[index] = newSeq;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "set");
+               exit(1);
+       }
 }
 
 /***********************************************************************/
@@ -54,14 +154,26 @@ Sequence SequenceDB::get(int index) {
 
 /***********************************************************************/
 
-void SequenceDB::changeSize(int newSize) {
-       data.resize(newSize);
+void SequenceDB::resize(int newSize) {
+       try {
+               data.resize(newSize);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "resize");
+               exit(1);
+       }
 }
 
 /***********************************************************************/
 
 void SequenceDB::clear() {
-       data.clear();
+       try {
+               data.clear();
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "clear");
+               exit(1);
+       }
 }
 
 /***********************************************************************/
@@ -72,23 +184,32 @@ int SequenceDB::size() {
 
 /***********************************************************************/
 
-void SequenceDB::print(ofstream& out) {
-       for(int i = 0; i < data.size(); i++)
-               data[i].printSequence(out);
+void SequenceDB::print(ostream& out) {
+       try {
+               for(int i = 0; i < data.size(); i++) {
+                       data[i].printSequence(out);
+               }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceDB", "print");
+               exit(1);
+       }
 }
        
 /***********************************************************************/
 
-void SequenceDB::add(Sequence newSequence) {
+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 RAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SequenceDB", "push_back");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the RAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
\ No newline at end of file
+}
+
+/***********************************************************************/
+