--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_NWalignProgramLauncher.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,78 @@
+import unittest
+from commons.launcher.NWalignProgramLauncher import NWalignProgramLauncher
+
+
+class Test_NWalignProgramLauncher( unittest.TestCase ):
+    
+    def setUp( self ):
+        self._i = NWalignProgramLauncher()
+        
+        
+    def tearDown( self ):
+        self._i = None
+        
+        
+    def test_getSpecificHelpAsString( self ):
+        exp = ""
+        exp += "\nspecific options:"
+        exp += "\n     -s: name of the subject file (format='fasta')"
+        exp += "\n     -p: parameters for 'NWalign'"
+        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
+        obs = self._i.getSpecificHelpAsString()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setASpecificAttributeFromCmdLine( self ):
+        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
+        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
+        
+        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
+        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
+        
+        
+    def test_setWrapperCommandLine( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        self._i.setSubjectFile( "dummySubjectFile.fa" )
+        exp = "NWalignProgramLauncher.py"
+        exp += " -i %s" % ( "dummyInFile.fa" )
+        exp += " -s %s" % ( "dummySubjectFile.fa" )
+        exp += " -o %s.align" % ( "dummyInFile.fa" )
+        exp += " -v 0"
+        self._i.setWrapperCommandLine()
+        obs = self._i.getWrapperCommandLine()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setProgramCommandLine( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        self._i.setSubjectFile( "dummySubjectFile.fa" )
+        self._i.setProgramParameters( "-m 2" )
+        exp = "NWalign -m 2 -o dummyInFile.fa.afa -v 0 dummySubjectFile.fa dummyInFile.fa"
+        self._i.setProgramCommandLine()
+        obs = self._i.getProgramCommandLine()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setListFilesToKeep( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        lExp = [ "dummyInFile.fa.afa" ]
+        self._i.setListFilesToKeep()
+        lObs = self._i.getListFilesToKeep()
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_setSummary( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        self._i.setSubjectFile( "dummySubjectFile.fa" )
+        exp = "input file: %s" % ( self._i.getInputFile() )
+        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
+        exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
+        exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
+        self._i.setSummary()
+        obs = self._i.getSummary()
+        self.assertEqual( exp, obs )
+        
+if __name__ == "__main__":
+        unittest.main()
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