--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/align/hmmOutputParsing/HmmpfamOutput2align.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,32 @@
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
+
+##data processor : read an output from hmmpfam and transform it into .align file
+#    
+class HmmpfamOutput2align( object ):
+
+    ## constructor
+    #
+    def __init__(self):
+        self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
+        self._inputFile = "" 
+        self._outputFile =  ""    
+    
+    ## set input file
+    #
+    # @param input file input file
+    #    
+    def setInputFile(self, input):
+        self._inputFile = input
+    
+    ## set output file
+    #
+    # @param output file output file
+    #         
+    def setOutputFile(self, output):
+        self._outputFile = output   
+    
+    
+    ##read a hmmpfam output file, parse it and, write the corresponding .align file
+    #
+    def run( self ):
+        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )