--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_MafftProgramLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,105 @@
+import unittest
+from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
+
+class Test_MafftProgramLauncher( unittest.TestCase ):
+    
+    
+    def setUp( self ):
+        self._i = MafftProgramLauncher()
+        
+        
+    def tearDown( self ):
+        self._i = None
+        
+        
+    def test_getSpecificHelpAsString( self ):
+        exp = ""
+        exp += "\nspecific options:"
+        exp += "\n     -p: parameters for '%s' (default='--auto')" % ( "mafft" )
+        exp += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
+        obs = self._i.getSpecificHelpAsString()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setASpecificAttributeFromCmdLine( self ):
+        self._i.setASpecificAttributeFromCmdLine( "-p", "'--auto --maxiterate 500'" )
+        self.assertEqual( "'--auto --maxiterate 500'", self._i.getProgramParameters() )
+        
+        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
+        self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
+        
+        
+    def test_setWrapperCommandLine( self ):
+        inFile = "dummyInFile.fa"
+        self._i.setInputFile( inFile )
+        exp = "MafftProgramLauncher.py"
+        exp += " -i %s" % ( inFile )
+        exp += " -p '%s'" % ( "--auto" )
+        exp += " -o %s.fa_aln" % ( inFile )
+        exp += " -v 0"
+        self._i.setWrapperCommandLine()
+        obs = self._i.getWrapperCommandLine()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setProgramCommandLine( self ):
+        inFile = "dummyInFile.fa"
+        self._i.setInputFile( inFile )
+        exp = self._i.getProgramName()
+        exp += " %s" % ( "--auto" )
+        exp += " --quiet"
+        exp += " %s.shortH" % ( inFile )
+        exp += " > %s.shortH.fa_aln" % ( inFile )
+        exp += " 2> /dev/null"
+        self._i.setProgramCommandLine()
+        obs = self._i.getProgramCommandLine()
+        self.assertEqual( exp, obs )
+        
+        
+    def test_setListFilesToKeep( self ):
+        inFile = "dummyInFile.fa"
+        self._i.setInputFile( inFile )
+        self._i.setListFilesToKeep()
+        lExp = [ "dummyInFile.fa.fa_aln" ]
+        lObs = self._i.getListFilesToKeep()
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        self._i._lFilesToKeep = []
+        
+        outFile = "dummyOutFile.fa_aln"
+        self._i.setOutputFile( outFile )
+        self._i.setListFilesToKeep()
+        lExp = [ outFile ]
+        lObs = self._i.getListFilesToKeep()
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_setListFilesToRemove( self ):
+        inFile = "dummyInFile.fa"
+        self._i.setInputFile( inFile )
+        self._i.setListFilesToRemove()
+        lExp = [ "dummyInFile.fa.shortH", \
+                 "dummyInFile.fa.shortH.fa_aln", \
+                 "dummyInFile.fa.shortHlink" ]
+        lObs = self._i.getListFilesToRemove()
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_setSummary( self ):
+        self._i.setInputFile( "dummyInFile.fa" )
+        exp = "input file: %s" % ( "dummyInFile.fa" )
+        exp += "\nparameters: %s" % ( "--auto" )
+        exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
+        self._i.setSummary()
+        obs = self._i.getSummary()
+        self.assertEqual( exp, obs )
+        
+        
+if __name__ == "__main__":
+        unittest.main()
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