From df82ee669d7eb9ae9a1a334339dfab7961cb16c6 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 8 Jun 2009 16:22:46 +0000
Subject: [PATCH] added help for heatmap.sim

---
 helpcommand.cpp     | 12 ++++++++++++
 validcalculator.cpp |  4 ++++
 2 files changed, 16 insertions(+)

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 00cd8dd..acc5353 100644
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -241,6 +241,18 @@ int HelpCommand::execute(){
 		cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
 		cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n";
 		cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+	}else if (globaldata->helpRequest == "heatmap.sim") { 
+		cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n";
+		cout << "The heatmap.sim command parameters are groups, calc, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
+		cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
+		cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
+		cout << "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n";
+		cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n";
+		cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
+		validCalcs->printCalc("heat", cout);
+		cout << "The default value for calc is jclass-thetayc." << "\n";
+		cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "venn") { 
 		cout << "The venn command can only be executed after a successful read.otu command." << "\n";
 		cout << "The venn command parameters are groups, calc, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
diff --git a/validcalculator.cpp b/validcalculator.cpp
index c0e5eed..3e698bf 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -591,6 +591,10 @@ void ValidCalculators::printCalc(string parameter, ostream& out) {
 			for (it = matrix.begin(); it != matrix.end(); it++) {
 				out << it->first << ", ";
 			}
+		}else if (parameter == "heat") {
+			for (it = heat.begin(); it != heat.end(); it++) {
+				out << it->first << ", ";
+			}
 		}else if (parameter == "boot") {
 			for (it = boot.begin(); it != boot.end(); it++) {
 				out << it->first << ", ";
-- 
2.39.2