X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=05c8b7d42a1ba7de160449f02707097800357bea;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=c0679155de1514a9ebb6845368b899140718b8d3;hpb=e0c50fc42e953dbe258feb9bc1d1d7dc10fafff0;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index c067915..05c8b7d 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -44,7 +44,7 @@ string PreClusterCommand::getHelpString(){
 		helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n";
         helpString += "The count parameter allows you to provide a count file so you can cluster by group. \n";
 		helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
-        helpString += "The topdown parameter allows you to specify whether to cluster from largest abundance to smallest or smallest to largest.  Default=T, meanging largest to smallest.\n";
+        helpString += "The topdown parameter allows you to specify whether to cluster from largest abundance to smallest or smallest to largest.  Default=T, meaning largest to smallest.\n";
 		helpString += "The pre.cluster command should be in the following format: \n";
 		helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
 		helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else if (countfile == "not open") { abort = true; countfile =  ""; }	
 			else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }
@@ -300,6 +300,7 @@ int PreClusterCommand::execute(){
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
 				
 		}else {
+            if (processors != 1) { m->mothurOut("When using running without group information mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 			if (namefile != "") { readNameFile(); }
 		
 			//reads fasta file and return number of seqs
@@ -368,13 +369,15 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
 		
 		//divide the groups between the processors
 		vector<linePair> lines;
-		int numGroupsPerProcessor = groups.size() / processors;
-		for (int i = 0; i < processors; i++) {
-			int startIndex =  i * numGroupsPerProcessor;
-			int endIndex = (i+1) * numGroupsPerProcessor;
-			if(i == (processors - 1)){	endIndex = groups.size(); 	}
-			lines.push_back(linePair(startIndex, endIndex));
-		}
+		int remainingPairs = groups.size();
+        int startIndex = 0;
+        for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
+            int numPairs = remainingPairs; //case for last processor
+            if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
+            lines.push_back(linePair(startIndex, (startIndex+numPairs))); //startIndex, endIndex
+            startIndex = startIndex + numPairs;
+            remainingPairs = remainingPairs - numPairs;
+        }
 		
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		
@@ -597,7 +600,7 @@ int PreClusterCommand::process(string newMapFile){
                     out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
                     
                 }//end if active i
-                if(i % 100 == 0)	{ m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();	}
+                if(i % 100 == 0)	{ m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); 	}
             }
         }else {
             map<int, string> mapFile;
@@ -632,7 +635,7 @@ int PreClusterCommand::process(string newMapFile){
                     }//end abundance check
                 }//end for loop j
                 
-                if(i % 100 == 0)	{ m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();	}
+                if(i % 100 == 0)	{ m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); 	}
             }
             
             for (int i = 0; i < numSeqs; i++) {
@@ -903,15 +906,9 @@ void PreClusterCommand::readNameFile(){
 		while (!in.eof()) {
 			in >> firstCol >> secondCol; m->gobble(in);
             
-            for (int i = 0; i < firstCol.length(); i++) {
-                if (firstCol[i] == ':') { firstCol[i] = '_'; m->changedSeqNames = true; }
-            }
-            
-            int size = 1;
-            for (int i = 0; i < secondCol.length(); i++) {
-                if (secondCol[i] == ':') { secondCol[i] = '_'; m->changedSeqNames = true; }
-                else if(secondCol[i] == ','){	size++;	}
-            }
+            m->checkName(firstCol);
+            m->checkName(secondCol);
+            int size = m->getNumNames(secondCol);
             
 			names[firstCol] = secondCol;
             sizes[firstCol] = size;