Removed some weird characteres from setup.prop

Author: Salvador Martinez-Bartolome

ProtClusterQuant/setup.properties

@@ -145,14 +145,14 @@ minConsecutiveIdenticalAlignment = NUMERIC_VALUE
 ############################################################################
 # PARAMETERS TO PROPERLY READ IN THE DATABASE AND ASSIGN PEPTIDES TO PROTEINS:
 ############################################################################
-# In case the input files doesn\u2019t contains all the peptide-to-protein connections (because the software who generated them remove some of the subset proteins or performed a protein inference heuristic),
+# In case the input files doesn't contains all the peptide-to-protein connections (because the software who generated them remove some of the subset proteins or performed a protein inference heuristic),
 # you can use a protein sequence database in order to map all the possible peptide-to-protein connections without losing any isoform for example. 
 # Note: These parameters should be set according to the initial parameters used to search the database for identified peptide hits as well as how the search results were filtered.
 
 enzymeArray =  TEXT, TEXT, ...
 #	This parameter specify the aminoacids where protease cleaves. Note: amino acids that are recognized as cleavage site are provided as comma-separated (',') values.
-o	Trypsin cleaves at K and R, so 'K,R' should set here.
-o	LysC cleaves at K only, so 'K' should be set here.
+#	Trypsin cleaves at K and R, so 'K,R' should set here.
+#	LysC cleaves at K only, so 'K' should be set here.
 #	Default value if not provided: K,R
 #	Example: enzymeArray = K,R 
 
@@ -187,11 +187,11 @@ fastaFile = FILEPATH
 
 inputFilePath = FILEPATH
 #	Full path of the folder in which all the input files are located.
-#	Default value if not provided: the system user\u2019s home folder.
+#	Default value if not provided: the system user's home folder.
 #	Example: inputFilePath = C:\\Users\\Salva\\Desktop\\data\\PINT projects\\Fibulin\\LacZ
 
 inputFiles = EXP_NAME[FILE_NAME1, FILE_NAME2, ...] | EXP2_NAME[FILE_NAME4, FILE_NAME5, ...]
-#	This parameter specifies the quantification input files to be used and groups them into groups, in order to be treated properly. EXP_NAME is an internal tag for the group of files provided subsequently between brackets. Several groups are separated by '|'. Several file names are separated by ','. File names don\u2019t include path names, because they are expected to be found in the folder specified by the inputFilePath parameter.
+#	This parameter specifies the quantification input files to be used and groups them into groups, in order to be treated properly. EXP_NAME is an internal tag for the group of files provided subsequently between brackets. Several groups are separated by '|'. Several file names are separated by ','. File names don't include path names, because they are expected to be found in the folder specified by the inputFilePath parameter.
 #	This parameter is required.
 #	Examples:
 #		DmDv[DmDv_rep1.xml, DmDv_rep2.xml, DmDv_rep3.xml] | DvDm[DvDm_rep1.xml, DvDm_rep2.xml, DvDm_rep3.xml]
@@ -201,7 +201,7 @@ inputFiles = EXP_NAME[FILE_NAME1, FILE_NAME2, ...] | EXP2_NAME[FILE_NAME4, FILE_
 #		Fibulin_LacZ[Fibulin_LacZ_rep1.txt, Fibulin_LacZ_rep2.txt, Fibulin_LacZ_rep3.txt]
 
 inputIDFiles = EXP_NAME[FILE_NAME1, FILE_NAME2, ...] | EXP2_NAME[FILE_NAME4, FILE_NAME5, ...]
-#	This parameter specifies the identification input files to be used and groups them into groups, in order to be treated properly. EXP_NAME is an internal tag for the group of files provided subsequently between brackets. Several groups are separated by '|'. Several file names are separated by ','. File names don\u2019t include path names, because they are expected to be found in the folder specified by the inputFilePath parameter.
+#	This parameter specifies the identification input files to be used and groups them into groups, in order to be treated properly. EXP_NAME is an internal tag for the group of files provided subsequently between brackets. Several groups are separated by '|'. Several file names are separated by ','. File names don't include path names, because they are expected to be found in the folder specified by the inputFilePath parameter.
 #	This parameter is required.
 #	Examples:
 #		DmDv[DmDv_rep1.xml, DmDv_rep2.xml, DmDv_rep3.xml] | DvDm[DvDm_rep1.xml, DvDm_rep2.xml, DvDm_rep3.xml]
@@ -213,7 +213,7 @@ inputIDFiles = EXP_NAME[FILE_NAME1, FILE_NAME2, ...] | EXP2_NAME[FILE_NAME4, FIL
 uniprotReleasesFolder = FILEPATH
 #	This parameter points to the folder where the UniProt annotations are going to be automatically stored in the machine were PCQ runs. UniProt annotations are retrieved from the latest version of UniProtKB in order to associate gene names, taxonomies, etc... that may not be available in the protein description line provided in the input files.
 #	This process may take some time and some disk space, depending on the dataset size. However, once the annotations are locally stored, PCQ will retrieve the annotations from the local resource, taking just a few seconds.
-#	Default value if not provided: the system user\u2019s home directory.
+#	Default value if not provided: the system user's home directory.
 #	Example: uniprotReleasesFolder = C:\\Users\\Salva\\Desktop\\tmp\\uniprotKB
 
 uniprotVersion = FORMATED_DATE
@@ -223,7 +223,7 @@ uniprotVersion = FORMATED_DATE
 
 outputFilePath = FILEPATH
 #	This parameter points to the folder in which all output files will be generated on computer.
-#	Default value if not provided: system user\u2019s home folder.
+#	Default value if not provided: system user's home folder.
 #	Example: outputFilePath = C:\\Users\\Salva\\Desktop\\data\\Fibulin\\LacZ\\quant
 
 outputPrefix = TEXT