Removes alphasort in precluster

#220

source/commands/preclustercommand.cpp

@@ -800,6 +800,8 @@ int PreClusterCommand::readFASTA(){
         
         length = *(lengths.begin());
         
+        random_shuffle(alignSeqs.begin(), alignSeqs.end());
+        
 		return alignSeqs.size();
 	}
 	
@@ -862,6 +864,8 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
 		if (error) { m->control_pressed = true; }
 		
 		thisSeqs.clear();
+        
+        random_shuffle(alignSeqs.begin(), alignSeqs.end());
 		
 		return alignSeqs.size();
 	}

source/commands/preclustercommand.h

@@ -37,17 +37,11 @@ struct seqPNode {
 /************************************************************/
 inline bool comparePriorityTopDown(seqPNode first, seqPNode second) {  
     if (first.numIdentical > second.numIdentical) { return true;  }
-    else if (first.numIdentical == second.numIdentical) { 
-        if (first.seq.getName() > second.seq.getName()) { return true; }
-    }
     return false; 
 }
 /************************************************************/
 inline bool comparePriorityDownTop(seqPNode first, seqPNode second) {  
     if (first.numIdentical < second.numIdentical) { return true;  }
-    else if (first.numIdentical == second.numIdentical) { 
-        if (first.seq.getName() > second.seq.getName()) { return true; }
-    }
     return false; 
 }
 //************************************************************/
@@ -86,12 +80,10 @@ class PreClusterCommand : public Command {
 	map<string, string> names; //represents the names file first column maps to second column
 	map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
 	map<string, int>::iterator itSize; 
-//	map<string, bool> active; //maps sequence name to whether it has already been merged or not.
 	vector<string> outputNames;
 	
 	int readFASTA();
 	void readNameFile();
-	//int readNamesFASTA();
 	int calcMisMatches(string, string);
 	void printData(string, string, string); //fasta filename, names file name
 	int process(string);