Fixes bug where matrix format could be confused if sequence names wer…

…e all numeric OptiCluster
mothur · 4ec2078e79a9429ef8133d16dd65ab1794477c0e · mothur-westcott committed Sep 28, 2016 · Sep 28, 2016 · 4ec2078
1 parent bdac507
commit 4ec2078e79a9429ef8133d16dd65ab1794477c0e
Unified Split

Showing with 15 additions and 20 deletions.

+6 −6 Mothur.xcodeproj/project.pbxproj

+1 −1 source/commands/clustercommand.cpp

+1 −1 source/commands/clustersplitcommand.cpp

+4 −9 source/datastructures/optimatrix.cpp

+3 −3 source/datastructures/optimatrix.h
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
@@ -3386,7 +3386,7 @@
 				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
 				PRODUCT_NAME = mothur;
-				SDKROOT = macosx10.11;
+				SDKROOT = macosx;
 				SKIP_INSTALL = NO;
 			};
 			name = Debug;
@@ -3420,7 +3420,7 @@
 				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
 				PRODUCT_NAME = mothur;
-				SDKROOT = macosx10.11;
+				SDKROOT = macosx;
 				SKIP_INSTALL = NO;
 				"VALID_ARCHS[sdk=*]" = "i386 x86_64";
 			};
@@ -3471,7 +3471,7 @@
 					"-lboost_iostreams",
 					"-lz",
 				);
-				SDKROOT = macosx10.11;
+				SDKROOT = macosx;
 				SKIP_INSTALL = NO;
 				USER_HEADER_SEARCH_PATHS = /usr/local/include/;
 			};
@@ -3525,7 +3525,7 @@
 					"-lboost_iostreams",
 					"-lz",
 				);
-				SDKROOT = macosx10.11;
+				SDKROOT = macosx;
 				SKIP_INSTALL = NO;
 				USER_HEADER_SEARCH_PATHS = /usr/local/include/;
 			};
@@ -3565,7 +3565,7 @@
 				MTL_ENABLE_DEBUG_INFO = YES;
 				ONLY_ACTIVE_ARCH = YES;
 				PRODUCT_NAME = "$(TARGET_NAME)";
-				SDKROOT = macosx10.9;
+				SDKROOT = macosx;
 			};
 			name = Debug;
 		};
@@ -3602,7 +3602,7 @@
 				MTL_ENABLE_DEBUG_INFO = NO;
 				ONLY_ACTIVE_ARCH = YES;
 				PRODUCT_NAME = "$(TARGET_NAME)";
-				SDKROOT = macosx10.9;
+				SDKROOT = macosx;
 			};
 			name = Release;
 		};
diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
@@ -856,7 +856,7 @@ int ClusterCommand::runOptiCluster(){
         string distfile = columnfile;
         if (format == "phylip") { distfile = phylipfile; }
         
-        OptiMatrix matrix(distfile, thisNamefile, nameOrCount, cutoff, false);
+        OptiMatrix matrix(distfile, thisNamefile, nameOrCount, format, cutoff, false);
         
         OptiCluster cluster(&matrix, metric, 0);
         tag = cluster.getTag();
diff --git a/source/commands/clustersplitcommand.cpp b/source/commands/clustersplitcommand.cpp
@@ -1393,7 +1393,7 @@ string ClusterSplitCommand::runOptiCluster(string thisDistFile, string thisNamef
         string nameOrCount = "count";
         if (namefile != "") { nameOrCount = "name"; }
         
-        OptiMatrix matrix(thisDistFile, thisNamefile, nameOrCount, cutoff, false);
+        OptiMatrix matrix(thisDistFile, thisNamefile, nameOrCount, "column", cutoff, false);
         
         OptiCluster cluster(&matrix, metric, numSingletons);
         tag = cluster.getTag();
diff --git a/source/datastructures/optimatrix.cpp b/source/datastructures/optimatrix.cpp
@@ -12,37 +12,32 @@
 
 /***********************************************************************/
 
-OptiMatrix::OptiMatrix(string d, double c, bool s) : distFile(d), cutoff(c), sim(s) {
+OptiMatrix::OptiMatrix(string d, string df, double c, bool s) : distFile(d), distFormat(df), cutoff(c), sim(s) {
     m = MothurOut::getInstance();
     countfile = ""; namefile = "";
-    distFormat = findDistFormat(distFile);
     
     if (distFormat == "phylip") { readPhylip(); }
     else { readColumn();  }
 }
 /***********************************************************************/
-OptiMatrix::OptiMatrix(string d, string nc, string f, double c, bool s) : distFile(d), format(f), cutoff(c), sim(s) {
+OptiMatrix::OptiMatrix(string d, string nc, string f, string df, double c, bool s) : distFile(d), distFormat(df), format(f), cutoff(c), sim(s) {
     m = MothurOut::getInstance();
     
     if (format == "name") { namefile = nc; countfile = ""; }
     else if (format == "count") { countfile = nc; namefile = ""; }
     else { countfile = ""; namefile = ""; }
     
-    distFormat = findDistFormat(distFile);
-    
     if (distFormat == "phylip") { readPhylip(); }
     else { readColumn();  }
 }
 /***********************************************************************/
-int OptiMatrix::readFile(string d, string nc, string f, double c, bool s)  {
-    distFile = d; format = f; cutoff = c; sim = s;
+int OptiMatrix::readFile(string d, string nc, string f, string df, double c, bool s)  {
+    distFile = d; format = f; cutoff = c; sim = s; distFormat = df;
     
     if (format == "name") { namefile = nc; countfile = ""; }
     else if (format == "count") { countfile = nc; namefile = ""; }
     else { countfile = ""; namefile = ""; }
     
-    distFormat = findDistFormat(distFile);
-    
     if (distFormat == "phylip") { readPhylip(); }
     else { readColumn();  }
     
diff --git a/source/datastructures/optimatrix.h b/source/datastructures/optimatrix.h
@@ -21,8 +21,8 @@ class OptiMatrix {
     
 public:
     OptiMatrix() { m = MothurOut::getInstance(); }
-    OptiMatrix(string, double, bool); //distfile, cutoff, sim
-    OptiMatrix(string, string, string, double, bool); //distfile, name or count, format, cutoff, sim
+    OptiMatrix(string, string, double, bool); //distfile, distformat, cutoff, sim
+    OptiMatrix(string, string, string, string, double, bool); //distfile, name or count, format, distformat, cutoff, sim
     ~OptiMatrix(){ }
     
     vector<int> getCloseSeqs(int i) { return closeness[i]; }
@@ -35,7 +35,7 @@ class OptiMatrix {
     string getName(int); //name from nameMap index
     ListVector* getListSingle();
     long int print(ostream&);
-    int readFile(string, string, string, double, bool); //distfile, name or count, format, cutoff, sim
+    int readFile(string, string, string, string, double, bool); //distfile, name or count, format, distformat, cutoff, sim
     
 private: