try {
CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
try {
string helpString = "";
ValidCalculators validCalculator;
- helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc and label. shared or phylip or column and name are required unless valid current files exist.\n";
- helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
- helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
+ helpString += "The heatmap.sim command parameters are shared, phylip, column, name, count, groups, calc, fontsize and label. shared or phylip or column and name are required unless valid current files exist.\n";
+ helpString += "There are two ways to use the heatmap.sim command. The first is with a shared file, and you may use the groups, label and calc parameter. \n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n";
+ helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
exit(1);
}
}
+//**********************************************************************************************************************
+
+string HeatMapSimCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "svg") { outputFileName = "svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapSimCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
HeatMapSimCommand::HeatMapSimCommand(){
try {
outputTypes["svg"] = tempOutNames;
format = "";
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
-
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
//required parameters
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
//error checking on files
if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) {
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
- abort = true;
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a name or count file if you are going to use the column format."); m->mothurOutEndLine();
+ abort = true;
+ }
}
}
}
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
+ string temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ m->mothurConvert(temp, fontsize);
if (abort == false) {
ValidCalculators validCalculator;
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- heatmap = new HeatMapSim(outputDir, inputfile);
+ heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
if (format == "shared") {
runCommandShared();
delete heatmap;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
delete input;
in.close();
}else {
//read names file
- NameAssignment* nameMap = new NameAssignment(namefile);
- nameMap->readMap();
-
- //put names in order in vector
- for (int i = 0; i < nameMap->size(); i++) {
- names.push_back(nameMap->get(i));
- }
-
- //resize matrix
- matrix.resize(nameMap->size());
- for (int i = 0; i < nameMap->size(); i++) {
- matrix[i].resize(nameMap->size(), 0.0);
- }
-
+ NameAssignment* nameMap;
+ CountTable ct;
+ if (namefile != "") {
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+
+ //put names in order in vector
+ for (int i = 0; i < nameMap->size(); i++) {
+ names.push_back(nameMap->get(i));
+ }
+ }else if (countfile != "") {
+ nameMap = NULL;
+ ct.readTable(countfile);
+ names = ct.getNamesOfSeqs();
+ }
+
+ //resize matrix
+ matrix.resize(names.size());
+ for (int i = 0; i < names.size(); i++) {
+ matrix[i].resize(names.size(), 0.0);
+ }
+
//read column file
string first, second;
double dist;
if (m->control_pressed) { return 0; }
- map<string, int>::iterator itA = nameMap->find(first);
- map<string, int>::iterator itB = nameMap->find(second);
-
- if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); }
- if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); }
-
- //save distance
- matrix[itA->second][itB->second] = dist;
- matrix[itB->second][itA->second] = dist;
+ if (namefile != "") {
+ map<string, int>::iterator itA = nameMap->find(first);
+ map<string, int>::iterator itB = nameMap->find(second);
+
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); }
+
+ //save distance
+ matrix[itA->second][itB->second] = dist;
+ matrix[itB->second][itA->second] = dist;
+ }else if (countfile != "") {
+ int itA = ct.get(first);
+ int itB = ct.get(second);
+ matrix[itA][itB] = dist;
+ matrix[itB][itA] = dist;
+ }
}
in.close();
- delete nameMap;
+ if (namefile != "") { delete nameMap; }
}