removed unused copy constructors and comments within comments that where causing...

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 582da493e4dc5cdf5267d65606181d1594f56a87..8e4f3274a490679c85f992f8584605c877c84850 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -514,7 +514,7 @@ int PreClusterCommand::readFASTA(){
                m->openInputFile(fastafile, inFasta);
                
                //string firstCol, secondCol, nameString;
-               length = 0;
+               set<int> lengths;
                
                while (!inFasta.eof()) {
                        
@@ -540,17 +540,20 @@ int PreClusterCommand::readFASTA(){
                                        else{
                                                seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
                                                alignSeqs.push_back(tempNode);
-                                               if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
+                                               lengths.insert(seq.getAligned().length());
                                        }       
                                }else { //no names file, you are identical to yourself 
                                        seqPNode tempNode(1, seq, seq.getName());
                                        alignSeqs.push_back(tempNode);
-                                       if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
+                                       lengths.insert(seq.getAligned().length());
                                }
                        }
                }
                inFasta.close();
                //inNames.close();
+        
+        if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        
                return alignSeqs.size();
        }
        
@@ -562,7 +565,7 @@ int PreClusterCommand::readFASTA(){
 /**************************************************************************************************/
 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
        try {
-               length = 0;
+               set<int> lengths;
                alignSeqs.clear();
                map<string, string>::iterator it;
                bool error = false;
@@ -585,15 +588,17 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
                                        
                                        seqPNode tempNode(numReps, thisSeqs[i], it->second);
                                        alignSeqs.push_back(tempNode);
-                                       if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
+                    lengths.insert(thisSeqs[i].getAligned().length());
                                }       
                        }else { //no names file, you are identical to yourself 
                                seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
                                alignSeqs.push_back(tempNode);
-                               if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
+                               lengths.insert(thisSeqs[i].getAligned().length());
                        }
                }
                
+        if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        
                //sanity check
                if (error) { m->control_pressed = true; }