--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniqprimer-0.5.0/primertools/primersequence.py	Mon Jan 03 09:56:55 2022 +0000
@@ -0,0 +1,110 @@
+'''
+Created on Jan 1, 2011
+
+@author: John L. Herndon
+@contact: herndon@cs.colostate.edu
+@organization: Colorado State University
+@group: Computer Science Department, Asa Ben-Hur's laboratory 
+'''
+
+import utils
+
+class PrimerSequence( object ):
+    """
+    record sequence data, and store matched parts of the sequence 
+    """
+    
+    def __init__( self, seqID, seqLength, sequence ):
+        #an unmatched sub-sequence that starts at 0 goes until the end of the the sequence, to start out with.
+        
+        self.seqID = seqID
+        self.seqLength = seqLength
+        self.matchedSubSequences = [ ] 
+        self.sequence = sequence
+        
+    def addMatch( self, match ):
+        """
+        Input: a utils.Match object
+        Removes the matched sequence from the list of valid sequence data
+        """
+        
+        self.matchedSubSequences.append( ( match.start, match.end ) )
+    
+    def findNonMatchedIndices( self ):
+        
+        utils.logMessage("PrimerSequence::findValidIndices( )", "getting unmatched sequence indices" )
+
+        sequence = set( range( self.seqLength ) )
+        
+        #find the indices that are NOT excluded
+        utils.logMessage( "PrimerSequence::findValidIndices( )", "there are {0} excluded sequences for {1}".format( len( self.matchedSubSequences ), self.seqID ) )
+        for exclude in self.matchedSubSequences:
+            excludedSequence = set( range( exclude[ 0 ], exclude[ 1 ] )  )
+            utils.logMessage("PrimerSequence::findValidIndices( )", "removing exclude sequence {0} - {1}".format( exclude[ 0 ], exclude[ 1 ] ) )
+            sequence = sequence - excludedSequence
+
+        utils.logMessage("PrimerSequence::findValidIndices( )", "{0} unique indices".format( len( sequence ) ) )
+            
+        return list( sequence )
+    
+    def findNonMatchedIndexSequences( self, indices ):
+        
+        utils.logMessage("PrimerSequence::findValidIndexSequences( )", "getting sequences from unique indices" )
+        
+        sequences = [ ]
+        curSeq = [ ]
+        for index in indices:
+            if len( curSeq ) == 0:
+                curSeq.append( index )
+            elif index == curSeq[ -1 ] + 1:
+                curSeq.append( index )
+            else:
+                sequences.append( curSeq )
+                curSeq = [ ]
+        sequences.append( curSeq )        
+        utils.logMessage("PrimerSequence::findValidIndexSequences( )", "{0} sequences found".format( len( sequences ) ) )        
+        
+        return sequences
+    
+    
+    def getNonMatchedSubSequences( self, minLength = 100 ):
+        """
+        Get all valid sub sequences after removing matches
+        """        
+
+        utils.logMessage("PrimerSequence::getNonMatchedSubSequences( )", "finding valid sub sequences for {0}".format( self.seqID ) )
+
+        indices = self.findNonMatchedIndices( ) 
+        indexSequences = self.findNonMatchedIndexSequences( indices )
+        
+        subSequences = [ ]
+        
+        for indexSequence in indexSequences:
+            subSequence = [ self.sequence[ i ] for i in indexSequence ]
+            
+            if len( subSequence ) >= minLength:
+                subSequences.append( subSequence )
+        
+        return subSequences
+    
+    def getMatchedSubSequences( self, minLength = 100 ):
+        utils.logMessage("PrimerSequence::getMatchedSubSequences( )", "finding valid sub sequences for {0}".format( self.seqID ) )
+        
+        returnValue = [ ]
+        for match in self.matchedSubSequences:
+            subSequence = self.sequence[ match[ 0 ]:match[ 1 ] ]
+            
+            if len( subSequence ) >= minLength :
+                returnValue.append( subSequence )
+            
+        return returnValue
+            
+                
+         
+        
+        
+        
+        
+        
+        
+    
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