added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 905076b7dcd56b62102a3dbdbcef5de9024d0fef..1864f7473b0e21ff06d84ce76968f81374189954 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -42,7 +42,7 @@ string IndicatorCommand::getHelpString(){
                helpString += "The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. \n";
                helpString += "The new tree contains labels at each internal node.  The label is the node number so you can relate the tree to the summary file.\n";
                helpString += "The summary file lists the indicator value for each OTU for each node.\n";
-               helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n";
+               helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. \n";
                helpString += "The design parameter allows you to relate the tree to the shared or relabund file, if your tree contains the grouping names, or if no tree is provided to group your groups into groupings.\n";                  
                helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file.  The groups may be entered separated by dashes.\n";
                helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
@@ -96,8 +96,8 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        }
                        
                        m->runParse = true;
-                       m->Groups.clear();
-                       m->namesOfGroups.clear();
+                       m->clearGroups();
+                       m->clearAllGroups();
                        m->Treenames.clear();
                        m->names.clear();
                        
@@ -169,17 +169,17 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "";  Groups.push_back("all"); }
                        else { m->splitAtDash(groups, Groups);  }                       
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }  
                        
                        string temp = validParameter.validFile(parameters, "iters", false);             if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        if ((relabundfile == "") && (sharedfile == "")) { 
                                //is there are current file available for either of these?
@@ -237,11 +237,14 @@ int IndicatorCommand::execute(){
                        
                        //fill Groups - checks for "all" and for any typo groups
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, designMap->namesOfGroups);
+                       vector<string> nameGroups = designMap->getNamesOfGroups();
+                       util->setGroups(Groups, nameGroups);
+                       designMap->setNamesOfGroups(nameGroups);
                        delete util;
                        
                        //loop through the Groups and fill Globaldata's Groups with the design file info
-                       m->Groups = designMap->getNamesSeqs(Groups);
+                       vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
+                       m->setGroups(namesSeqs);
                }
        
                /***************************************************/
@@ -258,7 +261,7 @@ int IndicatorCommand::execute(){
                }
                
                //reset groups if needed
-               if (designfile != "") { m->Groups = Groups; }
+               if (designfile != "") { m->setGroups(Groups); }
                        
                /***************************************************/
                //    reading tree info                                                    //
@@ -273,7 +276,7 @@ int IndicatorCommand::execute(){
                        for (int i = 0; i < m->Treenames.size(); i++) { 
                                //sanity check - is this a group that is not in the sharedfile?
                                if (designfile == "") {
-                                       if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
+                                       if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
                                                m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
                                                mismatch = true;
                                        }
@@ -283,7 +286,7 @@ int IndicatorCommand::execute(){
                                        vector<string> myNames = designMap->getNamesSeqs(myGroups);
                                        
                                        for(int k = 0; k < myNames.size(); k++) {
-                                               if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
+                                               if (!(m->inUsersGroups(myNames[k], m->getAllGroups()))) {
                                                        m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
                                                        mismatch = true;
                                                }
@@ -323,9 +326,9 @@ int IndicatorCommand::execute(){
                        /***************************************************/
                        //    create ouptut tree - respecting pickedGroups //
                        /***************************************************/
-                       Tree* outputTree = new Tree(m->Groups.size(), treeMap); 
+                       Tree* outputTree = new Tree(m->getNumGroups(), treeMap); 
                        
-                       outputTree->getSubTree(T[0], m->Groups);
+                       outputTree->getSubTree(T[0], m->getGroups());
                        outputTree->assembleTree();
                                
                        //no longer need original tree, we have output tree to use and label
@@ -413,11 +416,11 @@ int IndicatorCommand::GetIndicatorSpecies(){
                        vector<SharedRAbundVector*> subset;
                        
                        //for each grouping
-                       for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
+                       for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
                                
                                for (int k = 0; k < lookup.size(); k++) {
                                        //are you from this grouping?
-                                       if (designMap->getGroup(lookup[k]->getGroup()) == designMap->namesOfGroups[i]) {
+                                       if (designMap->getGroup(lookup[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
                                                subset.push_back(lookup[k]);
                                                groupsAlreadyAdded.insert(lookup[k]->getGroup());
                                        }
@@ -437,10 +440,10 @@ int IndicatorCommand::GetIndicatorSpecies(){
                        vector<SharedRAbundFloatVector*> subset;
                        
                        //for each grouping
-                       for (int i = 0; i < designMap->namesOfGroups.size(); i++) {
+                       for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
                                for (int k = 0; k < lookupFloat.size(); k++) {
                                        //are you from this grouping?
-                                       if (designMap->getGroup(lookupFloat[k]->getGroup()) == designMap->namesOfGroups[i]) {
+                                       if (designMap->getGroup(lookupFloat[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
                                                subset.push_back(lookupFloat[k]);
                                                groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
                                        }