IMPACT_S

Class CodemlOptions

java.lang.Object

IMPACT_S.CodemlOptions

public class CodemlOptions
extends java.lang.Object

Support class for the GUICodemlOptions for choosing (other) Codeml options.

Author:

Emanuel Maldonado

See Also:

GUICodemlOptions, GUI, CodemlTP

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	codemlCtrlflLocKey Location key for user codeml control file.
static java.lang.String	codemlDirLocKey Location key for base codeml directory: based on the codeml executable location.
static java.lang.String	msaflLocKey Location key for input MSA file.
static java.lang.String	outflLocKey Location key for output file.
static java.lang.String	tmpcodemlCtrlflLocKey Location key for system codeml control file.
static java.lang.String	tmpmsaflLocKey Location key for temporary input MSA file.
static java.lang.String	tmpoutflLocKey Location key for temporary output file.
static java.lang.String	tmptreeflLocKey Location key for temporary input Tree file.
static java.lang.String	treeflLocKey Location key for input Tree file.

Constructor Summary

Constructors

Constructor and Description
CodemlOptions() Initialize Codeml Options.

Method Summary

Modifier and Type	Method and Description
boolean	areLocationsEmpty() Tell if there are empty locations set.
java.lang.String	getCodemlCtlFileCtt() Get content for codeml control file to be viewed by user.
java.lang.String	getCOLocation(java.lang.String key) Get codeml location of files.
java.lang.String	getControlFilename() Get current codeml file name used.
int	getSelectedOption() Get selected PAML set of options index.
boolean	importInputFiles(boolean copy) Import input files to codeml directory.
boolean	isFileWritten() If codeml options file was written.
void	setCOLocation(java.lang.String key, java.lang.String value) Set codeml location of files.
void	setCtrlFlLocations(CodemlTP cdlres, java.lang.String codemldir) Set locations for user specified codeml control file mode.
void	setLocations(CodemlTP cdlres, java.lang.String codemldir) Set locations for files.
void	setOptionsKeys(java.lang.String[] optionsKeys) Set all keys for HashMap instantiation holding content for codeml control file. Performs initialization of HashMaps for parameters and values and copy of argument.
void	setOptionsM03(boolean wfinal) Instantiate set of DEFAULT options for Models 0 and 3.
void	setOptionsM12(boolean wfinal) Instantiate set of DEFAULT options for Models 1 and 2.
void	setOptionsM78(boolean wfinal) Instantiate set of DEFAULT options for Models 7 and 8.
void	setOptionsOther(boolean wfinal) Instantiate set of user selected options directly from GUI.
void	setOptionsParameters(java.lang.String[] optionsParam) Set all parameters for codeml control file.
void	setOptionsValues(java.lang.String[] optionsValues) Set all values for codeml parameters.
void	setValues(java.lang.String[] guivalues) Set gui values for codeml parameters.
void	writeCodemlCtlFile(boolean user) Write options to file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

msaflLocKey

public static final java.lang.String msaflLocKey

Location key for input MSA file.

See Also:

Constant Field Values

treeflLocKey

public static final java.lang.String treeflLocKey

Location key for input Tree file.

See Also:

Constant Field Values

outflLocKey

public static final java.lang.String outflLocKey

Location key for output file.

See Also:

Constant Field Values

codemlDirLocKey

public static final java.lang.String codemlDirLocKey

Location key for base codeml directory: based on the codeml executable location.

See Also:

Constant Field Values

tmpmsaflLocKey

public static final java.lang.String tmpmsaflLocKey

Location key for temporary input MSA file.

See Also:

Constant Field Values

tmptreeflLocKey

public static final java.lang.String tmptreeflLocKey

Location key for temporary input Tree file.

See Also:

Constant Field Values

tmpoutflLocKey

public static final java.lang.String tmpoutflLocKey

Location key for temporary output file.

See Also:

Constant Field Values

codemlCtrlflLocKey

public static final java.lang.String codemlCtrlflLocKey

Location key for user codeml control file.

See Also:

Constant Field Values

tmpcodemlCtrlflLocKey

public static final java.lang.String tmpcodemlCtrlflLocKey

Location key for system codeml control file.

See Also:

Constant Field Values

Constructor Detail

CodemlOptions

public CodemlOptions()

Initialize Codeml Options.

Method Detail

setLocations

public void setLocations(CodemlTP cdlres,
                         java.lang.String codemldir)

Set locations for files.

Parameters:

cdlres - the object containing locations for files.

codemldir - directory of codeml executable.

setCtrlFlLocations

public void setCtrlFlLocations(CodemlTP cdlres,
                               java.lang.String codemldir)

Set locations for user specified codeml control file mode. These are based on the given file names in the GUI fields and which are expected to be the same as in the control file.

Parameters:

cdlres - the object containing locations for files.

codemldir - directory of codeml executable.

areLocationsEmpty

public boolean areLocationsEmpty()

Tell if there are empty locations set.

Returns:

true if any is empty; false, otherwise.

getControlFilename

public java.lang.String getControlFilename()

Get current codeml file name used.

Returns:

codeml control file name.

getCOLocation

public java.lang.String getCOLocation(java.lang.String key)

Get codeml location of files.

Parameters:

key - key for selecting location.

Returns:

location value matching key.

setCOLocation

public void setCOLocation(java.lang.String key,
                          java.lang.String value)

Set codeml location of files.

Parameters:

key - key for selecting location.

value - value associated to key.

setOptionsKeys

public void setOptionsKeys(java.lang.String[] optionsKeys)

Set all keys for HashMap instantiation holding content for codeml control file.
Performs initialization of HashMaps for parameters and values and copy of argument.

Parameters:

optionsKeys - keys in specific order (from GUI) which will guide order of parameters in file.

setOptionsValues

public void setOptionsValues(java.lang.String[] optionsValues)

Set all values for codeml parameters.

Parameters:

optionsValues - array containing all values for codeml parameters.

See Also:

setOptionsParameters(java.lang.String[]), setOptionsKeys(java.lang.String[])

setOptionsParameters

public void setOptionsParameters(java.lang.String[] optionsParam)

Set all parameters for codeml control file.

Parameters:

optionsParam - set the parameters to write in control file.

See Also:

setOptionsValues(java.lang.String[]), setOptionsKeys(java.lang.String[])

setValues

public void setValues(java.lang.String[] guivalues)

Set gui values for codeml parameters.

Parameters:

guivalues - gui values for codeml parameters.

getSelectedOption

public int getSelectedOption()

Get selected PAML set of options index.

Returns:

selected option: Options(M7,M8) = 1 Options(M1,M2) = 2 Options(M0,M3) = 3 OptionsFile = 4 OptionsOther = 5

setOptionsOther

public void setOptionsOther(boolean wfinal)

Instantiate set of user selected options directly from GUI.

Parameters:

wfinal - allows to set final options regarding input files.

See Also:

setValues(java.lang.String[])

setOptionsM78

public void setOptionsM78(boolean wfinal)

Instantiate set of DEFAULT options for Models 7 and 8.

Parameters:

wfinal - allows to set final options regarding input files.

See Also:

setOptionsM12(boolean), setOptionsM03(boolean)

setOptionsM12

public void setOptionsM12(boolean wfinal)

Instantiate set of DEFAULT options for Models 1 and 2.

Parameters:

wfinal - allows to set final options regarding input files.

See Also:

setOptionsM78(boolean), setOptionsM03(boolean)

setOptionsM03

public void setOptionsM03(boolean wfinal)

Instantiate set of DEFAULT options for Models 0 and 3.

Parameters:

wfinal - allows to set final options regarding input files.

See Also:

setOptionsM78(boolean), setOptionsM12(boolean)

isFileWritten

public boolean isFileWritten()

If codeml options file was written.

Returns:

true if was written (Accept button); or false, otherwise (Canceled/Closed)

importInputFiles

public boolean importInputFiles(boolean copy)

Import input files to codeml directory. The user may specify any location for his files in the GUI. These are always copied/renamed to/in the codeml directory, creating temporary
files that are to be deleted after execution finishes. User specified files must exist, otherwise nothing is done, thus returning false. It is assumed that files browsed by user are all absolute paths.

Parameters:

copy - if true, makes a copy of input files to codeml directory,
otherwise content is put in temporary files.

Returns:

true if files were successfully imported; false otherwise.

writeCodemlCtlFile

public void writeCodemlCtlFile(boolean user)

Write options to file.

Parameters:

user - if true write user selected file.

getCodemlCtlFileCtt

public java.lang.String getCodemlCtlFileCtt()

Get content for codeml control file to be viewed by user. This simulates reading the file.

Returns:

array of pairs key = value, selected options for codeml.