X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fmetadata%2FRunnerConfig.html;h=71c68da0ebf3e66aca919bbcd354abf4333d15d9;hb=f1bdd8da517901fe1d7957d388ea579ad1fbaa3b;hp=7f59fd84318475df224d0ab8ebdfafb5061d7581;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/full_javadoc/compbio/metadata/RunnerConfig.html b/website/full_javadoc/compbio/metadata/RunnerConfig.html index 7f59fd8..71c68da 100644 --- a/website/full_javadoc/compbio/metadata/RunnerConfig.html +++ b/website/full_javadoc/compbio/metadata/RunnerConfig.html @@ -2,12 +2,12 @@
- +-java.lang.Object +java.lang.Objectcompbio.metadata.RunnerConfig<T>
@NotThreadSafe -public class RunnerConfig<T>
-The list of
Parameter
s and Option
s supported by executable.
+The list of Parameter
s and Option
s supported by executable.
+ The lists is defined in and loaded from
+
@@ -148,7 +149,7 @@ The list of addOption(Option<T> option)
-
+ Adds Option to the internal list of options
@@ -156,7 +157,7 @@ The list of addParameter(Parameter<T> param)
+ Adds parameter to the internal parameter list
-
@@ -169,7 +170,7 @@ The list of
- boolean
equals(java.lang.Object obj)
+
@@ -177,46 +178,47 @@ The list of
equals(Object obj)
- Option<T>
getArgument(java.lang.String name)
+
+ Returns the argument by its name if found, NULL otherwise.
getArgument(String name)
- Returns the argument by its name if found, NULL otherwise
- Option<T>
getArgumentByOptionName(java.lang.String optionName)
+getArgumentByOptionName(String optionName)
Returns the argument by option name, NULL if the argument is not found
-
+ java.util.List<Option<T>>
List<Option<T>>
+ Returns list of getArguments()
- Parameter
and Option
supported by current
+ runner
-
+ java.util.List<Option<T>>
List<Option<T>>
+ Returns the list of the Options supported by the executable of type T
getOptions()
-
-
+ java.util.List<Parameter<T>>
List<Parameter<T>>
+ Returns the list of parameters supported executable of type T.
getParameters()
-
-
+ java.lang.String
String
getPrmSeparator()
@@ -224,7 +226,7 @@ The list of
-
+ java.lang.String
String
getRunnerClassName()
@@ -233,7 +235,7 @@ The list of
- boolean
removeArgument(java.lang.String name)
+
@@ -241,46 +243,48 @@ The list of
removeArgument(String name)
Removes the argument Argument
if found.
- boolean
removeArgumentByOptionName(java.lang.String optionName)
+
+ Removes the argument which can be a Parameter or an Option instance by
+ the value in removeArgumentByOptionName(String optionName)
- Removes the argument
- void
setOptions(java.util.List<Option<T>> parameters)
+
+ Adds the list of options or parameters to the internal list of options
setOptions(List<Option<T>> parameters)
-
- void
setParameters(java.util.List<Parameter<T>> parameters)
+
+ Sets the list of parameters as internal list
setParameters(List<Parameter<T>> parameters)
-
- void
setPrmSeparator(java.lang.String prmSeparator)
+
+ Sets name value separator character
setPrmSeparator(String prmSeparator)
-
- void
setRunnerClassName(java.lang.String runnerClassName)
+
+ Set the name of a runner class
setRunnerClassName(String runnerClassName)
-
-
+ java.lang.String
String
+ Validate the value of the argument.
toString()
@@ -292,16 +296,16 @@ The list of validate()
- Validate the arguments
@@ -348,11 +352,13 @@ public
-
Methods inherited from class java.lang.Object
+Methods inherited from class java.lang.Object
-
+getClass, hashCode, notify, notifyAll, wait, wait, wait
getClass, hashCode, notify, notifyAll, wait, wait, wait
getOptions
-public java.util.List<Option<T>> getOptions()
+public List<Option<T>> getOptions()
+
-
+Option
supported by type TOption
supported by type TOption
@@ -362,8 +368,10 @@ addParameter
public void addParameter(Parameter<T> param)
+
-
+param
- the Parameter
to addParameter
@@ -373,8 +381,10 @@ addOption
public void addOption(Option<T> option)
+
-
+option
- the Option
to add
@@ -382,8 +392,11 @@ public void addOption(
getArguments
-public java.util.List<Option<T>> getArguments()
+public List<Option<T>> getArguments()
+
Parameter
and Option
supported by current
+ runner
+
getPrmSeparator
-public java.lang.String getPrmSeparator()
+public String getPrmSeparator()
@@ -406,10 +419,12 @@ public java.lang.String getPrmSeparator()
setPrmSeparator
-public void setPrmSeparator(java.lang.String prmSeparator)
+public void setPrmSeparator(String prmSeparator)
+
-
+prmSeparator
- the separator char
@@ -417,10 +432,12 @@ public void setPrmSeparator(java.lang.String prmSeparator)
setOptions
-public void setOptions(java.util.List<Option<T>> parameters)
+public void setOptions(List<Option<T>> parameters)
+
-
+parameters
- the list of parameters to add
@@ -428,7 +445,7 @@ public void setOptions(java.util.List<
getRunnerClassName
-public java.lang.String getRunnerClassName()
+public String getRunnerClassName()
@@ -440,10 +457,12 @@ public java.lang.String getRunnerClassName()
setRunnerClassName
-public void setRunnerClassName(java.lang.String runnerClassName)
+public void setRunnerClassName(String runnerClassName)
+
-
+runnerClassName
- the name of the executable wrapping class
@@ -451,10 +470,12 @@ public void setRunnerClassName(java.lang.String runnerClassName)
setParameters
-public void setParameters(java.util.List<Parameter<T>> parameters)
+public void setParameters(List<Parameter<T>> parameters)
+
-
+parameters
- the list of parameters
@@ -462,8 +483,11 @@ public void setParameters(java.util.List<
getParameters
-public java.util.List<Parameter<T>> getParameters()
+public List<Parameter<T>> getParameters()
+
Parameter
is an Option
with value.
+
@@ -474,10 +498,10 @@ public java.util.List<Parameter
supported by type T.
toString
-public java.lang.String toString()
+public String toString()
@@ -488,10 +512,10 @@ public java.lang.String toString()
equals
-public boolean equals(java.lang.Object obj)
+public boolean equals(Object obj)
@@ -502,12 +526,33 @@ public boolean equals(java.lang.Object obj)
getArgument
-public Option<T> getArgument(java.lang.String name)
+public Option<T> getArgument(String name)
-
@@ -516,9 +561,10 @@ public Option
and Parameter
+ therefore this method can return either. If you need to retrieve the
+ Option by its optionNames use @link
+ getArgumentByOptionName(String)
method. The
+ difference between option name and optionName is explained by the
+ following example:
+
+
+
+
+ In the example, the "Sequence type" is a name whereas --amino, --nuc and
+ --auto are all optionNames. This dichotomy only manifests in
+ Option
never in Parameters
as the latter can
+ only have single
-
name
-
+name
- the Parameter of Option name
Argument
removeArgument
-public boolean removeArgument(java.lang.String name)
+public boolean removeArgument(String name)
-
Argument
if found.
+Argument
if found. Where Argument is either
+ Option
or Parameter
.
name
- of the argument
@@ -530,12 +576,28 @@ public boolean removeArgument(java.lang.String name)
getArgumentByOptionName
-public Option<T> getArgumentByOptionName(java.lang.String optionName)
+public Option<T> getArgumentByOptionName(String optionName)
@@ -544,14 +606,17 @@ public
-
optionName
- - the name of the option
+optionName
- - the optionName. This is not the same as an Option name.
+
+ For example:
+
+
+
+
+ The name of the option in the example is
+ "Output sequences order" whereas optionNames are
+ "--inputorder" and "--reorder". If you need to retrieve the
+ Option or Parameter by its names use
+ getArgument(String)
method
removeArgumentByOptionName
-public boolean removeArgumentByOptionName(java.lang.String optionName)
+public boolean removeArgumentByOptionName(String optionName)
-
-
+ otherwiseoptionName
-
+optionName
- the optionName of the option, do not confuse with the name!
for destinctions
+ between optionNames and the name of the Option
@@ -560,14 +625,15 @@ public boolean removeArgumentByOptionName(java.lang.String optionNam
validate
public void validate()
- throws javax.xml.bind.ValidationException
+ throws ValidationException
-
javax.xml.bind.ValidationException
- if any of the arguments found invalid which is when
+ValidationException
- if any of the arguments found invalid which is when
ValueConstrain
boundary