public class IO
extends java.lang.Object
Constructor and Description |
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IO() |
Modifier and Type | Method and Description |
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static void |
fatalErrorMessAndShutdown(java.lang.String message)
fatalErrorMess gives information for the user on the console and performs logging along with the shutdown of ProLiC.
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static BiomoleculeList |
readProLiCformatedProteinFile(java.io.File file_,
java.lang.String delimiter_,
java.lang.String origin_,
boolean considerProteinNames,
boolean considerGeneNames,
org.apache.logging.log4j.Logger log4j,
java.lang.Boolean inconsistenciesExist)
Reads protein data (including the related peptide information) from a file in the ProLiC format and builds the protein instances.
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static java.util.Map<java.lang.String,java.lang.String> |
readSectionFromIni(java.lang.String iniFile,
java.lang.String sectionName,
java.lang.Boolean success,
java.lang.String mess,
boolean doShutdown)
Reading the settings for ProLiC from a specific section of the configuration file.
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static java.lang.String |
writeBGIdentifier(BiomoleculeGroup aBG_,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write information concerning the identifier of the biomolecule group
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static java.lang.String |
writeBMIdentifier(Biomolecule aBM,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write the identifier of the biomolecule
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static java.lang.String |
writeBMOrigin(Biomolecule aBM,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write the origin of the biomolecule (i.e. the list where the biomolecule originate from)
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static java.lang.String |
writeBMSequence(Biomolecule aBM,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write the sequence of the biomolecule (either amino acid or nucleotide sequences)
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static java.lang.String |
writeGeneName(Biomolecule aB_,
java.lang.String outStringData_,
java.lang.String columnDelim_,
java.lang.String BiomoleculeType_)
Auxiliary method used to ensure correct output format of the ProLiC result file even in case of wrong user settings, i.e. enabling writing
of gene name information in case of missing availability of such information.
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static java.lang.String |
writePeptideInformations(Biomolecule aB_,
java.lang.String outStringData_,
java.lang.String columnDelim_,
java.lang.String BiomoleculeType_)
Auxiliary method used to ensure correct output format of the ProLiC result file even in case of wrong user settings, i.e. enabling writing
of peptide information in case of missing availability of such information.
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static java.lang.String |
writeProteinName(Biomolecule aB_,
java.lang.String outStringData_,
java.lang.String columnDelim_,
java.lang.String BiomoleculeType_)
Auxiliary method used to ensure correct output format of the ProLiC result file even in case of wrong user settings, i.e. enabling writing
of protein name information in case of missing information.
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static java.lang.String |
writeRepresentative(Biomolecule bgRepr,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write group representative information
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static void |
writeResults(java.util.TreeSet<BiomoleculeGroupList> resultLists,
java.lang.String filename,
java.lang.String extension,
java.lang.String output_dir,
java.lang.String columnDelim,
boolean writeProteinNames,
boolean writeGeneNames,
boolean writePeptideSeq,
int maxNumbPeptides,
org.apache.logging.log4j.Logger log4j,
java.lang.Boolean inconsistenciesExist,
java.lang.String encoding)
Writing the results of the comparison to a file.
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public static java.util.Map<java.lang.String,java.lang.String> readSectionFromIni(java.lang.String iniFile, java.lang.String sectionName, java.lang.Boolean success, java.lang.String mess, boolean doShutdown)
iniFile
- sectionName
- success
- public static BiomoleculeList readProLiCformatedProteinFile(java.io.File file_, java.lang.String delimiter_, java.lang.String origin_, boolean considerProteinNames, boolean considerGeneNames, org.apache.logging.log4j.Logger log4j, java.lang.Boolean inconsistenciesExist)
file_
- delimiter_
- origin_
- considerProteinNames
- considerGeneNames
- log4j
- inconsistenciesExist
- public static void writeResults(java.util.TreeSet<BiomoleculeGroupList> resultLists, java.lang.String filename, java.lang.String extension, java.lang.String output_dir, java.lang.String columnDelim, boolean writeProteinNames, boolean writeGeneNames, boolean writePeptideSeq, int maxNumbPeptides, org.apache.logging.log4j.Logger log4j, java.lang.Boolean inconsistenciesExist, java.lang.String encoding)
resultLists
- filename
- extension
- output_dir
- columnDelim
- writeProteinNames
- writeGeneNames
- writePeptideSeq
- maxNumbPeptides
- public static java.lang.String writeProteinName(Biomolecule aB_, java.lang.String outStringData_, java.lang.String columnDelim_, java.lang.String BiomoleculeType_)
aB_
- outStringData_
- columnDelim_
- BiomoleculeType_
- public static java.lang.String writeGeneName(Biomolecule aB_, java.lang.String outStringData_, java.lang.String columnDelim_, java.lang.String BiomoleculeType_) throws MissingMemberException
aB_
- outStringData_
- columnDelim_
- BiomoleculeType_
- MissingMemberException
public static java.lang.String writeBGIdentifier(BiomoleculeGroup aBG_, java.lang.String outStringData_, java.lang.String columnDelim_)
aBG_
- outStringData_
- columnDelim_
- public static java.lang.String writeRepresentative(Biomolecule bgRepr, java.lang.String outStringData_, java.lang.String columnDelim_)
bgRepr
- outStringData_
- columnDelim_
- public static java.lang.String writeBMIdentifier(Biomolecule aBM, java.lang.String outStringData_, java.lang.String columnDelim_)
aBM
- outStringData_
- columnDelim_
- public static java.lang.String writeBMSequence(Biomolecule aBM, java.lang.String outStringData_, java.lang.String columnDelim_)
aBM
- outStringData_
- columnDelim_
- public static java.lang.String writeBMOrigin(Biomolecule aBM, java.lang.String outStringData_, java.lang.String columnDelim_)
aBM
- outStringData_
- columnDelim_
- public static java.lang.String writePeptideInformations(Biomolecule aB_, java.lang.String outStringData_, java.lang.String columnDelim_, java.lang.String BiomoleculeType_) throws MissingMemberException
aB_
- outStringData_
- columnDelim_
- BiomoleculeType_
- MissingMemberException
public static void fatalErrorMessAndShutdown(java.lang.String message)