public class OptionManagement extends Object
Modifier and Type | Field and Description |
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static String |
approximativeMode
Option name for the choice of approximative computation method.
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static String |
azobenzeneMethod
Option name for the choice of azobenzene computation method.
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static String |
CNGMethod
Option name for the choice of CNG repeats computation method.
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static String |
complementarySequence
Option name for the complementary sequence (3'5').
|
static String |
dataPathway
Option name for the default melting data files pathway.
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static String |
dataPathwayValue
String dataPathwayValue : default Melting data file pathway.
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static String |
DMSOCorrection
Option name for the choice of DMSO correction computation method.
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static String |
doubleDanglingEndMethod
Option name for the choice of double dangling end computation method.
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static String |
factor
Option name for the oligomer concentration correction factor.
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static String |
formamideCorrection
Option name for the choice of formamide correction computation method.
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static String |
globalMethod
Option name for the choice of computation method (approximative "-A" or nearest neighbor "-NN").
|
static String |
hybridization
Option name for the type of hybridization.
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static String |
hydroxyadenineMethod
Option name for the choice of hydroxyadenine computation method.
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static String |
inosineMethod
Option name for the choice of inosine computation method.
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static String |
internalLoopMethod
Option name for the choice of internal loop computation method.
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static String |
ionCorrection
Option name for the choice of ion correction method.
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static String |
legalInformation
Option name for the melting legal information.
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static String |
lockedAcidMethod
Option name for the choice of locked nucleic acid computation method.
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static String |
longBulgeLoopMethod
Option name for the choice of long bulge loop computation method.
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static String |
longDanglingEndMethod
Option name for the choice of long dangling end computation method.
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static String |
meltingHelp
Option name for the melting help documentation.
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static String |
meltingHelpAlt
Alternative option name for the melting help documentation.
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static String |
NaEquivalentMethod
Option name for the choice of sodium equivalence method.
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static String |
NN_Path
Option name for the data file pathway.
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static String |
NNMethod
Option name for the choice of nearest neighbor computation method.
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static String |
nucleotides
Option name for the oligomer concentration (mol/L).
|
static String |
outPutFile
Option name to print the melting results in an output file.
|
static String |
selfComplementarity
Option name to precise the self complementarity of the sequences.
|
static String |
sequence
Option name for the sequence (5'3').
|
static String |
singleBulgeLoopMethod
Option name for the choice of single bulge loop computation method.
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static String |
singleDanglingEndMethod
Option name for the choice of single dangling end computation method.
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static String |
singleMismatchMethod
Option name for the choice of single mismatch computation method.
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static String |
solutioncomposition
Option name for the different ion and agent concentrations (mol/L).
|
static String |
tandemMismatchMethod
Option name for the choice of tandem mismatches computation method.
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static String |
threshold
Option name for the threshold value.
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static String |
verboseMode
Option name to activate the verbose mode.
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static String |
versionNumber
Option name for the current melting version number.
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static String |
wobbleBaseMethod
Option name for the choice of GU base pairs computation method.
|
Constructor and Description |
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OptionManagement()
creates an OptionManagement object. initialises the default options, variables, etc.
|
Modifier and Type | Method and Description |
---|---|
Environment |
createEnvironment(String[] args)
collects the options entered by the user and creates an Environment from them.
|
HashMap<String,String> |
getDNADefaultOptions()
This method is called to get the DNADefaultOptions of OptionManagement.
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HashMap<String,String> |
getHybridDefaultOptions()
This method is called to get the hybridDefaultOptions of OptionManagement.
|
HashMap<String,String> |
getMRNADefaultOptions()
This method is called to get the mRNADefaultOptions of OptionManagement.
|
HashMap<String,String> |
getRNADefaultOptions()
This method is called to get the RNADefaultOptions of OptionManagement.
|
void |
initialiseLogger()
initialises the meltingLogger.
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boolean |
isMeltingInformationOption(String[] args)
to check if the user just wants to know some information about melting.
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static void |
logError(String errorText)
Logs an error to the melting logger.
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static void |
logError(String errorText,
Throwable throwable)
Logs an error message to the melting logger, along with the error itself.
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static void |
logFileName(String fileName)
Logs a file name to the melting logger.
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static void |
logInfo(String infoText)
Logs information to the melting logger.
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static void |
logMessage(String messageText)
Logs a message to the melting logger.
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static void |
logMethodName(String methodName)
Logs the name of a method to the melting logger.
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static void |
logTemperatureEquation(String temperatureEquation)
Logs a temperature equation to the melting logger.
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static void |
logWarning(String warningText)
Logs a warning to the melting logger.
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void |
readMeltingHelp()
displays Melting help documentation.
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void |
readOptions(String[] args)
if at least one of the options entered by the user is an option to display some information about Melting,
the requested information is displayed.
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public static final String meltingHelp
public static final String meltingHelpAlt
public static final String legalInformation
public static final String dataPathway
public static final String versionNumber
public static final String globalMethod
public static final String approximativeMode
public static final String NNMethod
public static final String singleMismatchMethod
public static final String wobbleBaseMethod
public static final String tandemMismatchMethod
public static final String internalLoopMethod
public static final String singleDanglingEndMethod
public static final String doubleDanglingEndMethod
public static final String longDanglingEndMethod
public static final String singleBulgeLoopMethod
public static final String longBulgeLoopMethod
public static final String CNGMethod
public static final String inosineMethod
public static final String hydroxyadenineMethod
public static final String azobenzeneMethod
public static final String lockedAcidMethod
public static final String sequence
public static final String complementarySequence
public static final String solutioncomposition
public static final String nucleotides
public static final String hybridization
public static final String ionCorrection
public static final String NaEquivalentMethod
public static final String DMSOCorrection
public static final String formamideCorrection
public static final String verboseMode
public static final String threshold
public static final String NN_Path
public static final String outPutFile
public static final String selfComplementarity
public static final String factor
public static String dataPathwayValue
public OptionManagement()
public void readMeltingHelp()
public void initialiseLogger()
public HashMap<String,String> getDNADefaultOptions()
public HashMap<String,String> getRNADefaultOptions()
public HashMap<String,String> getHybridDefaultOptions()
public HashMap<String,String> getMRNADefaultOptions()
public boolean isMeltingInformationOption(String[] args)
args
- : contains the options entered by the userpublic void readOptions(String[] args)
args
- : contains the option entered by the userpublic Environment createEnvironment(String[] args)
args
- : contains the options entered by the userpublic static void logError(String errorText)
errorText
- The text of the error.public static void logError(String errorText, Throwable throwable)
errorText
- The text of the error.throwable
- The error itself.public static void logWarning(String warningText)
warningText
- The text of the warning.public static void logInfo(String infoText)
infoText
- The information to log.public static void logMessage(String messageText)
messageText
- The text of the message.public static void logMethodName(String methodName)
methodName
- The method name.public static void logFileName(String fileName)
fileName
- The file name to log.public static void logTemperatureEquation(String temperatureEquation)
temperatureEquation
- The temperature equation to log.