From: westcott <westcott>
Date: Mon, 8 Nov 2010 13:55:38 +0000 (+0000)
Subject: fixed cluster.split bug
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=cdf9083dc32543cc640e72e9ca3aee0323cbad45

fixed cluster.split bug
---

diff --git a/distancecommand.cpp b/distancecommand.cpp
index edb6314..70c0a78 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -540,7 +540,7 @@ void DistanceCommand::createProcesses(string filename) {
 			int pid = fork();
 			
 			if (pid > 0) {
-				processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
+				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
 				if (output != "square") {  driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
@@ -548,7 +548,8 @@ void DistanceCommand::createProcesses(string filename) {
 				exit(0);
 			}else { 
 				m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine(); 
-				for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { int temp = it->second; kill (temp, SIGINT); }
+				perror(" : ");
+				for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
 				exit(0);
 			}
 		}
@@ -559,15 +560,15 @@ void DistanceCommand::createProcesses(string filename) {
 		
 		
 		//force parent to wait until all the processes are done
-		for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { 
-			int temp = it->second;
+		for (int i=0;i<processIDS.size();i++) { 
+			int temp = processIDS[i];
 			wait(&temp);
 		}
 		
 		//append and remove temp files
-		for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
-			m->appendFiles((filename + toString(it->second) + ".temp"), filename);
-			remove((filename + toString(it->second) + ".temp").c_str());
+		for (int i=0;i<processIDS.size();i++) { 
+			m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+			remove((filename + toString(processIDS[i]) + ".temp").c_str());
 		}
 #endif
 	}
diff --git a/distancecommand.h b/distancecommand.h
index 3b2d345..3e3dc70 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -43,7 +43,7 @@ private:
 
 	int processors, numNewFasta;
 	float cutoff;
-	map<int, int> processIDS;   //end line, processid
+	vector<int> processIDS;   //end line, processid
 	vector<linePair*> lines;
 	
 	bool abort;
diff --git a/mothur b/mothur
index 5b2897b..607932c 100755
Binary files a/mothur and b/mothur differ
diff --git a/mothurout.cpp b/mothurout.cpp
index de6da8c..9ec847c 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -658,6 +658,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 
 			fileHandle.open(completeFileName.c_str());
 			if(!fileHandle) {
+				mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 				return 1;
 			}else {
 				//check for blank file
@@ -801,6 +802,7 @@ void MothurOut::appendFiles(string temp, string filename) {
 		//open output file in append mode
 		openOutputFileAppend(filename, output);
 		int ableToOpen = openInputFile(temp, input, "no error");
+		//int ableToOpen = openInputFile(temp, input);
 		
 		if (ableToOpen == 0) { //you opened it
 			while(char c = input.get()){
@@ -1038,7 +1040,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 
 		//sanity check filePos
 		for (int i = 0; i < (filePos.size()-1); i++) {
-			if (filePos[(i+1)] <= filePos[i]) {  cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
+			if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 		}
 
 		proc = (filePos.size() - 1);
diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 13b4bd4..1f23ec3 100644
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -10,6 +10,7 @@
 #include "splitmatrix.h"
 #include "phylotree.h"
 #include "distancecommand.h"
+#include "seqsummarycommand.h"
 
 /***********************************************************************/
 
@@ -185,6 +186,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
 			string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
 			
 			Command* command = new DistanceCommand(options);
+			
 			command->execute();
 			delete command;
 			
@@ -193,7 +195,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
 			//remove old names files just in case
 			remove((namefile + "." + toString(i) + ".temp").c_str());
 		}
-		
+			
 		singleton = namefile + ".extra.temp";
 		ofstream remainingNames;
 		m->openOutputFile(singleton, remainingNames);