--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/profilesDB/Profiles.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,91 @@
+import re
+
+#------------------------------------------------------------------------------
+
+class Profiles:
+    '''
+    Hmm profile Class
+    Attributes are name, desc, length, accNumber, GA_cut_off and retrieve
+    '''
+    
+    #--------------------------------------------------------------------------
+
+    def __init__( self, name="", desc="", length=0, accNumber = "", GA_cut_off = 0, retrieve = False ):
+        self.name = name
+        self.desc = desc
+        self.length = length
+        self.accNumber = accNumber
+        self.GA_cut_off = GA_cut_off
+        self.retrieve = retrieve
+        self.tab_profile = []
+        
+    #--------------------------------------------------------------------------
+
+    def _noProfileInFile(self):
+        self.name = None
+        self.desc = None
+        self.length = None
+        self.accNumber = None
+        self.GA_cut_off = None
+
+    #--------------------------------------------------------------------------
+
+    def _initialisation(self):
+        self.name = ""
+        self.desc = ""
+        self.length = 0
+        self.accNumber = ""
+        GA_cut_off = 0
+        self.tab_profile = []
+        
+    #--------------------------------------------------------------------------
+
+    def read( self, hmmFile ):
+        '''
+        Read a profile and characterize the object profile
+        attributes name, length, desc, accNumber and GA_cut_off are specified
+        '''
+        line = hmmFile.readline()
+        if line == "":
+            self._noProfileInFile()
+            return
+        self._initialisation()
+        if self.retrieve:
+            self.tab_profile.append(line)        
+        while not re.match("\/\/.*", line):            
+            line = hmmFile.readline()
+            if self.retrieve:
+                self.tab_profile.append(line)                  
+            name = re.match("NAME\s*(.*)", line)
+            if name:                    
+                self.name = name.group(1)
+            desc = re.match("DESC\s*(.*)", line)
+            if desc:                    
+                self.desc = desc.group(1)
+            length = re.match("LENG\s*(.*)", line)
+            if length:                    
+                self.length = int(length.group(1))
+            accNumber = re.match("ACC\s*(.*)", line)
+            if accNumber:                    
+                self.accNumber = accNumber.group(1)
+            GA_cut_off = re.match("GA\s*\d*\.\d*\s*(.*);", line)
+            if GA_cut_off:                    
+                self.GA_cut_off = float(GA_cut_off.group(1))
+            else : 
+                if (self.GA_cut_off == 0):
+                    self.GA_cut_off = "NA"
+        if self.retrieve:
+            return self.tab_profile
+        else:
+            return 1
+            
+    #--------------------------------------------------------------------------
+
+    def readAndRetrieve( self, hmmFile ):  
+        '''
+        Read a profile and characterize the object profile
+        attributes name, length, desc, accNumber and GA_cut_off are specified
+        And a list of each line of profile is returned
+        '''
+        self.retrieve = True
+        return self.read(hmmFile)