From: westcott <westcott>
Date: Fri, 20 May 2011 10:48:01 +0000 (+0000)
Subject: finished adding the names option to trim.seqs
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=fc3a1319b64fd3638df074e4669a1fb0235d1b8d

finished adding the names option to trim.seqs
---

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index e38ac9b..37e5d40 100644
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -241,11 +241,9 @@ int GetGroupsCommand::execute(){
 		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 		
 		m->mothurOut("Selected " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
-		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine();	}
+		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine();	}
 		m->mothurOutEndLine();
 		
-		
-		
 		if (outputNames.size() != 0) {
 			m->mothurOutEndLine();
 			m->mothurOut("Output File names: "); m->mothurOutEndLine();
diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 5a70b27..7034941 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -243,7 +243,7 @@ int RemoveGroupsCommand::execute(){
 		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 		
 		m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
-		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i])) + " sequences."); m->mothurOutEndLine();	}
+		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine();	}
 		m->mothurOutEndLine();
 		
 		if (outputNames.size() != 0) {
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 2bb0e57..d06a5ad 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -22,6 +22,7 @@ vector<string> SeqErrorCommand::setParameters(){
 		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
 		CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
 		CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
@@ -200,6 +201,10 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "ignorechimeras", false);	if (temp == "not found") { temp = "1"; }
 			convert(temp, ignoreChimeras);  
+			
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
+			m->setProcessors(temp);
+			convert(temp, processors); 
 
 			substitutionMatrix.resize(6);
 			for(int i=0;i<6;i++){	substitutionMatrix[i].resize(6,0);	}
diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index a47f182..7e87ec6 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -70,7 +70,7 @@ private:
 	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
 	double threshold;
 	bool ignoreChimeras;
-	int numRefs;
+	int numRefs, processors;
 	int maxLength;
 	ofstream errorSummaryFile, errorSeqFile;
 	vector<string> outputNames;
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index ed84cc0..64522a5 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -432,8 +432,9 @@ int TrimSeqsCommand::execute(){
 		//output group counts
 		m->mothurOutEndLine();
 		int total = 0;
+		if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 		for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
-			 total += it->second; m->mothurOut("Group " + it->first + " contains " + toString(it->second) + " sequences."); m->mothurOutEndLine(); 
+			 total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine(); 
 		}
 		if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 		
@@ -650,6 +651,17 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 						
 						outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
 						
+						if (nameFile != "") {
+							map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+							if (itName != nameMap.end()) { 
+								vector<string> thisSeqsNames; 
+								m->splitAtChar(itName->second, thisSeqsNames, ',');
+								for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+									outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+								}
+							}else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }							
+						}
+						
 						map<string, int>::iterator it = groupCounts.find(thisGroup);
 						if (it == groupCounts.end()) {	groupCounts[thisGroup] = 1; }
 						else { groupCounts[it->first]++; }