added smart distance feature and optimized all commands using line by line processing

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 405e646a5276e9afa8acaa2b5d0dee776e35b94e..a8e88c52ffbd9d9fe9bb711d4be2cf0c361c9212 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -97,21 +97,22 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "gapopen")           { gapopen = value;              }
                                if (key == "gapextend" )        { gapextend = value;    }
                                
-                               if (key == "line") {//stores lines to be used in a set
+                               if (key == "line") {//stores lines to be used in a vector
                                        lines.clear();
                                        labels.clear();
                                        line = value;
                                        label = "";
-                                       splitAtDash(value, lines);
-                                       allLines = 0;
+                                       if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+                                       else { allLines = 1;  }
                                }
-                               if (key == "label") {//stores labels to be used in a set
+                       
+                               if (key == "label") {//stores lines to be used in a vector
                                        labels.clear();
                                        lines.clear();
                                        label = value;
                                        line = "";
-                                       splitAtDash(value, labels);
-                                       allLines = 0;
+                                       if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+                                       else { allLines = 1;  }
                                }
 
                                if (key == "groups") {//stores groups to be used in a vector