added modify names parameter to set.dir

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index 585b3b3d8347272cb7b47afc9a923fb0af28eaa9..e798ee14ac70837e795a7be3191a14f68788c234 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -15,7 +15,7 @@
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  }
+SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  length = 0; samelength = true; }
 /***********************************************************************/
 //the clear function free's the memory
 SequenceDB::~SequenceDB() { clear(); }
@@ -24,19 +24,25 @@ SequenceDB::~SequenceDB() { clear(); }
 
 SequenceDB::SequenceDB(int newSize) {
        data.resize(newSize, Sequence());
+       length = 0; samelength = true;
 }
 
 /***********************************************************************/
 
 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() != "") {   data.push_back(newSequence);  }
+                       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);
@@ -92,7 +98,10 @@ 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) {
@@ -111,6 +120,9 @@ 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) {
@@ -123,6 +135,9 @@ 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) {
@@ -185,6 +200,9 @@ 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) {