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