X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2FClustalW.html;h=69d8c79ded547565dadbecb4da5fa6c5e6442f15;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=e2cbdb5af7cbe33c633cbf190c52ff3233577a26;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html index e2cbdb5..69d8c79 100644 --- a/website/full_javadoc/compbio/runner/msa/ClustalW.html +++ b/website/full_javadoc/compbio/runner/msa/ClustalW.html @@ -2,12 +2,12 @@ - + ClustalW - + @@ -55,7 +55,7 @@ function windowTitle() - PREV CLASS  + PREV CLASS   NEXT CLASS FRAMES   @@ -92,7 +92,7 @@ compbio.runner.msa
Class ClustalW 
-java.lang.Object
+java.lang.Object
   extended by compbio.engine.client.SkeletalExecutable<ClustalW>
       extended by compbio.runner.msa.ClustalW
@@ -137,13 +137,22 @@ java.lang.Object -static java.lang.String +static String KEY_VALUE_SEPARATOR
            +  + + + + + + + +
Fields inherited from class compbio.engine.client.SkeletalExecutable
ERROR, INPUT, OUTPUT
  @@ -171,7 +180,7 @@ java.lang.Object - java.util.List<java.lang.String> + List<String> getCreatedFiles()
@@ -180,31 +189,15 @@ java.lang.Object - Limit<ClustalW> -getLimit(java.lang.String presetName) - -
-            - - - - LimitsManager<ClustalW> -getLimits() - -
-            - - -  Alignment -getResults(java.lang.String workDirectory) +getResults(String workDirectory)
            -static java.lang.String +static String getStatFile()
@@ -212,7 +205,7 @@ java.lang.Object - java.lang.Class<? extends Executable<?>> + Class<ClustalW> getType()
@@ -221,7 +214,7 @@ java.lang.Object  ClustalW -setInput(java.lang.String inFile) +setInput(String inFile)
            @@ -229,7 +222,7 @@ java.lang.Object  ClustalW -setOutput(java.lang.String outFile) +setOutput(String outFile)
            @@ -241,16 +234,16 @@ java.lang.Object Methods inherited from class compbio.engine.client.SkeletalExecutable -addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString +addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString   - + - +
Methods inherited from class java.lang.ObjectMethods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, waitgetClass, notify, notifyAll, wait, wait, wait
  @@ -269,7 +262,7 @@ java.lang.Object

KEY_VALUE_SEPARATOR

-public static final java.lang.String KEY_VALUE_SEPARATOR
+public static final String KEY_VALUE_SEPARATOR
See Also:
Constant Field Values
@@ -305,7 +298,7 @@ public ClustalW()

setOutput

-public ClustalW setOutput(java.lang.String outFile)
+public ClustalW setOutput(String outFile)
Overrides:
setOutput in class SkeletalExecutable<ClustalW>
@@ -319,7 +312,7 @@ public

setInput

-public ClustalW setInput(java.lang.String inFile)
+public ClustalW setInput(String inFile)
Overrides:
setInput in class SkeletalExecutable<ClustalW>
@@ -333,7 +326,7 @@ public

getResults

-public Alignment getResults(java.lang.String workDirectory)
+public Alignment getResults(String workDirectory)
                      throws ResultNotAvailableException
@@ -347,7 +340,7 @@ public

getCreatedFiles

-public java.util.List<java.lang.String> getCreatedFiles()
+public List<String> getCreatedFiles()
Description copied from class: SkeletalExecutable
This method cannot really tell whether the files has actually been @@ -365,29 +358,7 @@ public java.util.List<java.lang.String> getCreatedFiles()

getStatFile

-public static java.lang.String getStatFile()
-
-
-
-
-
-
- -

-getLimit

-
-public Limit<ClustalW> getLimit(java.lang.String presetName)
-
-
-
-
-
-
- -

-getLimits

-
-public LimitsManager<ClustalW> getLimits()
+public static String getStatFile()
@@ -398,13 +369,14 @@ public

getType

-public java.lang.Class<? extends Executable<?>> getType()
+public Class<ClustalW> getType()
Specified by:
getType in class SkeletalExecutable<ClustalW>
-
+ +
Returns:
subclasses must return their type
@@ -438,7 +410,7 @@ public java.lang.Class<? extends - PREV CLASS  + PREV CLASS   NEXT CLASS FRAMES