Update version number to 1.3

ghuls · ghuls · commit 96d0b44ab9d7 · 2016-09-23T18:39:48.000+02:00
Update version number to 1.3

Signed-off-by: Gert Hulselmans &lt;gert.hulselmans@kuleuven.be&gt;
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# STAMP v.1.2.
+# STAMP v.1.3.
 
 [STAMP](http://www.benoslab.pitt.edu/stamp/) is a tool for characterizing similarities between transcription factor binding motifs. 
 
@@ -121,6 +121,17 @@ the **formatMotifs.pl** script.
 
 ## Version history:
 
+ * **v.1.3:** 2016-09-23:
+    * Make parsing of STAMP specific TRANSFAC file more robust.
+      Before this change STAMP only processes TRANSFAC files
+      correctly when they looked exactly like this:
+        - motif starts with tag "DE  motif_name".
+        - "DE" tag is directly followed by matrix lines
+          (no "P0" or "PO" tag allowed).
+        - matrix lines are directly followed by a "XX" tag line.
+        - if other tags are present between "DE" and matrix lines or between matrix
+          lines and "XX", STAMP adds for each of those lines "0.0  0.0  0.0  0.0"
+          to the matrix (which was wrong).
  * **v.1.2:** 2015-05-27:
     * This version includes bug fixes and updated compilation instructons
       that [Gert Hulselmans (KU Leuven)](https://github.com/ghuls/) performed
@@ -130,9 +141,9 @@ the **formatMotifs.pl** script.
       comparisons to a single strand (e.g. for comparing RNA-binding motifs). 
 
  * **v.1.1 and earlier:** 2006 - 2008:
-	* STAMP was written by [Shaun Mahony](http://mahonylab.org/) during
-	  his time as a postdoc in
-	  [Takis Benos' lab at the University of Pittsburgh](http://www.benoslab.pitt.edu). 
+    * STAMP was written by [Shaun Mahony](http://mahonylab.org/) during
+      his time as a postdoc in
+      [Takis Benos' lab at the University of Pittsburgh](http://www.benoslab.pitt.edu). 
 
 
 ## Citations:
diff --git a/src/Alignment.cpp b/src/Alignment.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/Alignment.h b/src/Alignment.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/ColumnComp.cpp b/src/ColumnComp.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/ColumnComp.h b/src/ColumnComp.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/Motif.cpp b/src/Motif.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/Motif.h b/src/Motif.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/MultipleAlignment.cpp b/src/MultipleAlignment.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/NeuralTree.cpp b/src/NeuralTree.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/NeuralTree.h b/src/NeuralTree.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/PSSM.cpp b/src/PSSM.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/PSSM.h b/src/PSSM.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/PlatformSupport.cpp b/src/PlatformSupport.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/PlatformSupport.h b/src/PlatformSupport.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/PlatformTesting.cpp b/src/PlatformTesting.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/PlatformTesting.h b/src/PlatformTesting.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/ProteinDomains.cpp b/src/ProteinDomains.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/ProteinDomains.h b/src/ProteinDomains.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/RandPSSMGen.cpp b/src/RandPSSMGen.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/RandPSSMGen.h b/src/RandPSSMGen.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/globals.h b/src/globals.h
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 //
diff --git a/src/main.cpp b/src/main.cpp
@@ -1,6 +1,6 @@
 //////////////////////////////////////////////////////////////////////////////////
 //
-// STAMP version 1.2
+// STAMP version 1.3
 //
 // Written By: Shaun Mahony
 // Bug fixes by: Gert Hulselmans
@@ -93,7 +93,7 @@ int main (int argc, char *argv[])
 	}
 
 	//Welcome message
-	if(!silent && !htmlOutput){printf("\n\tSTAMP\n\tSimilarity, Tree-building, & Alignment of Motifs and Profiles\n\n\tShaun Mahony\n\tDepartment of Biochemistry & Molecular Biology\n\tPenn State University\n\tVersion 1.2 (May 2015)\n\n");}
+	if(!silent && !htmlOutput){printf("\n\tSTAMP\n\tSimilarity, Tree-building, & Alignment of Motifs and Profiles\n\n\tShaun Mahony\n\tDepartment of Biochemistry & Molecular Biology\n\tPenn State University\n\tVersion 1.3 (September 2016)\n\n");}
 
 	if(argc ==1) //First and Foremost, the help option
 	{	DisplayHelp();
