fixed multiple bugs for 1.4 release

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 8b80580a26faf27b8504f55039e494952a9f1be9..e4c1877907e272c89a0be023ec21ad6bf2947f50 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -236,7 +236,7 @@ bool ErrorCheck::checkInput(string input) {
                
                //check for valid method
                if(commandName == "get.group") {
-                       if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
+                       if ((globaldata->getSharedFile() == "")) { cout << "You must read a groupfile or a sharedfile before you can use the get.group command." << endl; return false; }
                }
                if (commandName == "get.label" || commandName == "get.line") {
                        if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; }
@@ -250,13 +250,22 @@ bool ErrorCheck::checkInput(string input) {
                        if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
                }
                
-               if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){ 
+               if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){ 
                        if (globaldata->getSharedFile() == "") {
                                if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; }
                                else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; }
                        }
                }
                
+               if  (commandName == "tree.shared")  {
+                       //given no files                        
+                       if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; return false; }
+                       //you want to do single commands
+                       else if ((globaldata->getSharedFile() == "") && ((phylipfile != "") || (columnfile != ""))) {
+                               validateReadDist();
+                       }
+               }
+               
                if ((commandName == "heatmap") || (commandName == "venn")) { 
                        if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
                                 cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap or venn commands." << endl; return false; 
@@ -354,6 +363,12 @@ void ErrorCheck::validateReadFiles() {
                        //unable to open
                        if (ableToOpen == 1) {  errorFree = false; }
                        else { globaldata->inputFileName = sharedfile; }
+               }else if (groupfile != "") {
+                       ableToOpen = openInputFile(groupfile, filehandle);
+                       filehandle.close();
+                       if (ableToOpen == 1) { //unable to open
+                               errorFree = false;
+                       }
                }else{ //no file given
                        errorFree = false;
                }
@@ -385,8 +400,8 @@ void ErrorCheck::validateReadDist() {
                        if (ableToOpen == 1) {  errorFree = false; }
                }
                
-               if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
-               else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
+               if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter a phylip or a column." << endl; errorFree = false; }
+               else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
                
                if (columnfile != "") {
                        if (namefile == "") {
@@ -435,7 +450,7 @@ void ErrorCheck::validateParseFiles() {
                                ableToOpen = openInputFile(groupfile, filehandle);
                                filehandle.close();
                                if (ableToOpen == 1) { //unable to open
-                                       errorFree = false;;
+                                       errorFree = false;
                                }
                        }
                }