From: westcott <westcott>
Date: Tue, 22 Mar 2011 11:38:42 +0000 (+0000)
Subject: fixed clearcut version bug, added group count output to get.groups and remove.groups
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=d0954e27635712cdbd8b86e3c4510670803a2665

fixed clearcut version bug, added group count output to get.groups and remove.groups
---

diff --git a/cmdargs.cpp b/cmdargs.cpp
index 4812442..929b4aa 100644
--- a/cmdargs.cpp
+++ b/cmdargs.cpp
@@ -259,12 +259,12 @@ NJ_handle_args(int argc,
   
   if(nj_args.version) {
     printf("Clearcut Version: %s\n", NJ_VERSION);
-    exit(0);
+   //exit(0);
   }
   
   if(nj_args.help) {
     NJ_usage();
-    exit(0);
+    //exit(0);
   }
   
   /* if stdin & explicit filename are specified for input */
diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index ac76d73..7d81aaa 100644
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -250,9 +250,11 @@ 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->mothurOutEndLine();	}
+		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut(" contains " + 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/helpcommand.cpp b/helpcommand.cpp
index aeb7efc..3c799b0 100644
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -58,12 +58,18 @@ HelpCommand::~HelpCommand(){}
 //**********************************************************************************************************************
 
 int HelpCommand::execute(){
-	validCommands->printCommands(cout);
-	m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine();
+	try {
+		validCommands->printCommands(cout);
+		m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine();
 	
-	m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n");
+		m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n");
 	
-	return 0;
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HelpCommand", "execute");
+		exit(1);
+	}
 }
 
 //**********************************************************************************************************************/
diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 34a072b..f70edb6 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -250,7 +250,7 @@ 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->mothurOutEndLine();	}
+		for (int i = 0; i < Groups.size(); i++) {	m->mothurOut(Groups[i]); m->mothurOut(" contains " + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine();	}
 		m->mothurOutEndLine();
 		
 		if (outputNames.size() != 0) {
diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 973e14f..2caad96 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -625,32 +625,36 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 	try {
 		
-		string time = name.substr(0, 6);
-		unsigned int timeNum = m->fromBase36(time);
-			
-		int q1 = timeNum / 60;
-		int sec = timeNum - 60 * q1;
-		int q2 = q1 / 60;
-		int minute = q1 - 60 * q2;
-		int q3 = q2 / 24;
-		int hr = q2 - 24 * q3;
-		int q4 = q3 / 32;
-		int day = q3 - 32 * q4;
-		int q5 = q4 / 13;
-		int mon = q4 - 13 * q5;
-		int year = 2000 + q5;
-		
-		timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
-		
-		region = name.substr(7, 2);
-		
-		string xyNum = name.substr(9);
-		unsigned int myXy = m->fromBase36(xyNum);
-		int x = myXy >> 12;
-		int y = myXy & 4095;
-		
-		xy = toString(x) + "_" + toString(y);
+		if (name.length() >= 6) {
+			string time = name.substr(0, 6);
+			unsigned int timeNum = m->fromBase36(time);
 			
+			int q1 = timeNum / 60;
+			int sec = timeNum - 60 * q1;
+			int q2 = q1 / 60;
+			int minute = q1 - 60 * q2;
+			int q3 = q2 / 24;
+			int hr = q2 - 24 * q3;
+			int q4 = q3 / 32;
+			int day = q3 - 32 * q4;
+			int q5 = q4 / 13;
+			int mon = q4 - 13 * q5;
+			int year = 2000 + q5;
+		
+			timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
+		}
+		
+		if (name.length() >= 9) {
+			region = name.substr(7, 2);
+		
+			string xyNum = name.substr(9);
+			unsigned int myXy = m->fromBase36(xyNum);
+			int x = myXy >> 12;
+			int y = myXy & 4095;
+		
+			xy = toString(x) + "_" + toString(y);
+		}
+		
 		return 0;
 	}
 	catch(exception& e) {