public class CodemlOptions
extends java.lang.Object
GUICodemlOptions,
GUI,
CodemlTP| 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 and Description |
|---|
CodemlOptions()
Initialize Codeml Options.
|
| 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.
|
public static final java.lang.String msaflLocKey
public static final java.lang.String treeflLocKey
public static final java.lang.String outflLocKey
public static final java.lang.String codemlDirLocKey
public static final java.lang.String tmpmsaflLocKey
public static final java.lang.String tmptreeflLocKey
public static final java.lang.String tmpoutflLocKey
public static final java.lang.String codemlCtrlflLocKey
public static final java.lang.String tmpcodemlCtrlflLocKey
public void setLocations(CodemlTP cdlres, java.lang.String codemldir)
cdlres - the object containing locations for files.codemldir - directory of codeml executable.public void setCtrlFlLocations(CodemlTP cdlres, java.lang.String codemldir)
cdlres - the object containing locations for files.codemldir - directory of codeml executable.public boolean areLocationsEmpty()
public java.lang.String getControlFilename()
public java.lang.String getCOLocation(java.lang.String key)
key - key for selecting location.public void setCOLocation(java.lang.String key,
java.lang.String value)
key - key for selecting location.value - value associated to key.public void setOptionsKeys(java.lang.String[] optionsKeys)
optionsKeys - keys in specific order (from GUI) which will guide order of parameters in file.public void setOptionsValues(java.lang.String[] optionsValues)
optionsValues - array containing all values for codeml parameters.setOptionsParameters(java.lang.String[]),
setOptionsKeys(java.lang.String[])public void setOptionsParameters(java.lang.String[] optionsParam)
optionsParam - set the parameters to write in control file.setOptionsValues(java.lang.String[]),
setOptionsKeys(java.lang.String[])public void setValues(java.lang.String[] guivalues)
guivalues - gui values for codeml parameters.public int getSelectedOption()
public void setOptionsOther(boolean wfinal)
wfinal - allows to set final options regarding input files.setValues(java.lang.String[])public void setOptionsM78(boolean wfinal)
wfinal - allows to set final options regarding input files.setOptionsM12(boolean),
setOptionsM03(boolean)public void setOptionsM12(boolean wfinal)
wfinal - allows to set final options regarding input files.setOptionsM78(boolean),
setOptionsM03(boolean)public void setOptionsM03(boolean wfinal)
wfinal - allows to set final options regarding input files.setOptionsM78(boolean),
setOptionsM12(boolean)public boolean isFileWritten()
public boolean importInputFiles(boolean copy)
copy - if true, makes a copy of input files to codeml directory,public void writeCodemlCtlFile(boolean user)
user - if true write user selected file.public java.lang.String getCodemlCtlFileCtt()