--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/align/AlignListUtils.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,53 @@
+import os
+import commons.core.coord.Align
+import commons.pyRepetUnit.align.AlignList
+from commons.core.utils.FileUtils import FileUtils
+
+class AlignListUtils:  
+  
+    ##read a file in align format and return a AlignList
+    #
+    # @param inFileName string name of file
+    # @return listAlignInstance list list of align instance
+    #
+    def read( inFileName ):
+        alignInstance = commons.core.coord.Align.Align() 
+        listAlignInstance = commons.pyRepetUnit.align.AlignList.AlignList()
+        f = open( inFileName , "r")
+        while alignInstance.read( f ):
+            listAlignInstance.append(alignInstance)
+            alignInstance = commons.core.coord.Align.Align()
+        f.close
+        return (listAlignInstance)
+    
+    read = staticmethod( read )
+    
+    ## write a file in align format from an AlignList
+    #
+    # @param alignListInstance list list of align instance object
+    # @param  inFileName string name of file
+    def write( alignListInstance, inFileName ):
+        f = open( inFileName , "w")
+        for alignInstance in alignListInstance.getList():
+            alignInstance.write( f )
+        f.close
+        
+    write = staticmethod( write )
+    
+    ## Filter an AlignList by removing all is <= minScore
+    #
+    # @param listAlignInstance list list of align instance object
+    # @param minScore integer minimum score to keep in result
+    # 
+    def filterOnAMinimalScore( listAlignInstance, minScore ):
+        listAlignInstanceOld = commons.pyRepetUnit.align.AlignList.AlignList() 
+        for alignInstance in listAlignInstance.getList():  
+            listAlignInstanceOld.append(alignInstance)
+        for alignInstance in listAlignInstanceOld.getList():
+            if alignInstance.score <= minScore:
+                listAlignInstance.remove(alignInstance)
+        
+    filterOnAMinimalScore = staticmethod( filterOnAMinimalScore )    
+    
+if __name__ == "__main__":                 
+    main()