X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fmetadata%2FRunnerConfig.html;h=4a36a305cb9f16c213440cac3e94b84a1c0e9e7b;hb=6695d8f2418a044b900e9a23dfc3bd04e0f7c222;hp=f7fd597f8836f88ebb9544f2e3dd16a7f3d0f3b3;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html index f7fd597..4a36a30 100644 --- a/website/dm_javadoc/compbio/metadata/RunnerConfig.html +++ b/website/dm_javadoc/compbio/metadata/RunnerConfig.html @@ -2,12 +2,12 @@ - + RunnerConfig - + @@ -92,7 +92,7 @@ compbio.metadata
Class RunnerConfig<T> 
-java.lang.Object
+java.lang.Object
   extended by compbio.metadata.RunnerConfig<T>
@@ -100,19 +100,20 @@ java.lang.Object 
@NotThreadSafe
-public class RunnerConfig<T>
extends java.lang.Object
+public class RunnerConfig<T>
extends Object

-The list of Parameters and Options supported by executable. +The list of Parameters and Options supported by executable. + The lists is defined in and loaded from Parameters.xml file.

+
Version:
+
1.0 October 2009
Author:
-
pvtroshin - - Date October 2009
+
pvtroshin
@@ -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) +equals(Object obj)
            @@ -177,46 +178,47 @@ The list of  Option<T> -getArgument(java.lang.String name) +getArgument(String name)
-          Returns the argument by its name if found, NULL otherwise +          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>> getArguments()
-            +          Returns list of Parameter and Option supported by current + runner - java.util.List<Option<T>> + List<Option<T>> getOptions()
-            +          Returns the list of the Options supported by the executable of type T - java.util.List<Parameter<T>> + List<Parameter<T>> getParameters()
-            +          Returns the list of parameters supported executable of type T. - 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) +removeArgument(String name)
          Removes the argument Argument if found. @@ -241,46 +243,48 @@ The list of  boolean -removeArgumentByOptionName(java.lang.String optionName) +removeArgumentByOptionName(String optionName)
-          Removes the argument +          Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.  void -setOptions(java.util.List<Option<T>> parameters) +setOptions(List<Option<T>> parameters)
-            +          Adds the list of options or parameters to the internal list of options  void -setParameters(java.util.List<Parameter<T>> parameters) +setParameters(List<Parameter<T>> parameters)
-            +          Sets the list of parameters as internal list  void -setPrmSeparator(java.lang.String prmSeparator) +setPrmSeparator(String prmSeparator)
-            +          Sets name value separator character  void -setRunnerClassName(java.lang.String runnerClassName) +setRunnerClassName(String runnerClassName)
-            +          Set the name of a runner class - java.lang.String + String toString()
@@ -292,16 +296,16 @@ The list of validate()
-          Validate the arguments +          Validate the value of the argument.   - + - +
Methods inherited from class java.lang.ObjectMethods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, waitgetClass, hashCode, notify, notifyAll, wait, wait, wait
  @@ -348,11 +352,13 @@ public

getOptions

-public java.util.List<Option<T>> getOptions()
+public List<Option<T>> getOptions()
+
Returns the list of the Options supported by the executable of type T +

-
Returns:
list of Option supported by type T
+
Returns:
list of Option supported by type T
See Also:
Option
@@ -362,8 +368,10 @@ addParameter 
 public void addParameter(Parameter<T> param)
+
Adds parameter to the internal parameter list +

-
+
Parameters:
param - the Parameter to add
See Also:
Parameter
@@ -373,8 +381,10 @@ addOption 
 public void addOption(Option<T> option)
+
Adds Option to the internal list of options +

-
+
Parameters:
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()
+
Returns list of Parameter and Option supported by current + runner +

Returns:
list of Option and Parameter supported by type T
@@ -394,7 +407,7 @@ public java.util.List<

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)
+
Sets name value separator character +

-
+
Parameters:
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)
+
Adds the list of options or parameters to the internal list of options +

-
+
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)
+
Set the name of a runner class +

-
+
Parameters:
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)
+
Sets the list of parameters as internal list +

-
+
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()
+
Returns the list of parameters supported executable of type T. Where + Parameter is an Option with value. +

Returns:
List of Parameter supported by type T.
@@ -474,10 +498,10 @@ public java.util.List<

toString

-public java.lang.String toString()
+public String toString()
-
Overrides:
toString in class java.lang.Object
+
Overrides:
toString in class Object
@@ -488,10 +512,10 @@ public java.lang.String toString()

equals

-public boolean equals(java.lang.Object obj)
+public boolean equals(Object obj)
-
Overrides:
equals in class java.lang.Object
+
Overrides:
equals in class Object
@@ -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)
-
Returns the argument by its name if found, NULL otherwise +
Returns the argument by its name if found, NULL otherwise. Where the + Argument is a common interface for 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: + + 
+ Sequence type
+         
+         --nuc - Assume the sequences are nucleotide.
+         --amino - Assume the sequences are amino acid. 
+         --amino
+         --nuc
+         --auto
+
+ + 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 element

-
Parameters:
name - +
Parameters:
name - the Parameter of Option name
Returns:
Argument
@@ -516,9 +561,10 @@ public

removeArgument

-public boolean removeArgument(java.lang.String name)
+public boolean removeArgument(String name)
-
Removes the argument Argument if found. +
Removes the argument Argument if found. Where Argument is either + Option or Parameter.

Parameters:
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)
Returns the argument by option name, NULL if the argument is not found

-
Parameters:
optionName - - the name of the option +
Parameters:
optionName - - the optionName. This is not the same as an Option name. + + For example: + + 
+            Output sequences order
+                          --inputorder - Output order: same as input. 
+                           --reorder - Output order: aligned. Default: same as input
+                          --inputorder
+                          --reorder
+
+ + 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
Returns:
Option
@@ -544,14 +606,17 @@ public

removeArgumentByOptionName

-public boolean removeArgumentByOptionName(java.lang.String optionName)
+public boolean removeArgumentByOptionName(String optionName)
-
Removes the argument +
Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.

-
Parameters:
optionName - +
Parameters:
optionName - the optionName of the option, do not confuse with the name!
Returns:
true if argument with optionName exists and was removed, false - otherwise
+ otherwise
See Also:
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
-
Validate the arguments +
Validate the value of the argument. Checks whether the argument value is + in the valid values range.

Throws: -
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
  • Parameter value outside ValueConstrain boundary
  • Parameter name is not listed in possible values