X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2F_SkeletalCommandBuilder.html;h=92968231e891c9931edfdcb1d50d61d3e5fa4f80;hb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;hp=ff0efa877b7d68551cc9b240d2807fc767b99382;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html index ff0efa8..9296823 100644 --- a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html +++ b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html @@ -2,12 +2,12 @@ - + _SkeletalCommandBuilder - + @@ -92,18 +92,21 @@ compbio.runner
Class _SkeletalCommandBuilder 
-java.lang.Object
+java.lang.Object
   extended by compbio.runner._SkeletalCommandBuilder
All Implemented Interfaces:
Executable<_SkeletalCommandBuilder>
-
Direct Known Subclasses:
BlastAll, Disembl, Mcl, OB, PSIBlast, Ronn, RPSBlast
+
Direct Known Subclasses:
BlastAll, Mcl, OB, PSIBlast, Ronn, RPSBlast
+Deprecated. +

-
public abstract class _SkeletalCommandBuilder
extends java.lang.Object
implements Executable<_SkeletalCommandBuilder>
+
@Deprecated
+public abstract class _SkeletalCommandBuilder
extends Object
implements Executable<_SkeletalCommandBuilder>

@@ -142,7 +145,7 @@ java.lang.Object _SkeletalCommandBuilder()
-            +          Deprecated.     @@ -157,50 +160,58 @@ java.lang.Object  _SkeletalCommandBuilder -addParameter(java.lang.String parameter) +addParameter(String parameter)
-            +          Deprecated.    _SkeletalCommandBuilder -addParameters(java.util.List<java.lang.String> parameters) +addParameters(List<String> parameters)
-          Adds parameter to the list of parameters for a native executable +          Deprecated. Adds parameter to the list of parameters for a native executable  _SkeletalCommandBuilder -addParameters(java.lang.String[] parameters) +addParameters(String[] parameters) + +
+          Deprecated.   + + + + String +getClusterJobSettings()
-            +          Deprecated.   - java.lang.String + String getEmail()
-            +          Deprecated.   - java.lang.String + String getError()
-            +          Deprecated.    Limit<_SkeletalCommandBuilder> -getLimit(java.lang.String presetName) +getLimit(String presetName)
-            +          Deprecated.   @@ -208,23 +219,23 @@ java.lang.Object getLimits()
-            +          Deprecated.   - java.lang.String + String getName()
-            +          Deprecated.   - java.lang.String + String getOutput()
-            +          Deprecated.   @@ -232,7 +243,7 @@ java.lang.Object getParameters(Executable.ExecProvider provider)
-            +          Deprecated.   @@ -244,10 +255,10 @@ java.lang.Object -getResults(java.lang.String directory) +getResults(String directory)
-            +          Deprecated.   @@ -255,32 +266,32 @@ java.lang.Object loadRunConfiguration(RunConfiguration rconfig)
-            +          Deprecated.    _SkeletalCommandBuilder -setEmail(java.lang.String email) +setEmail(String email)
-            +          Deprecated.    _SkeletalCommandBuilder -setName(java.lang.String name) +setName(String name)
-            +          Deprecated.     - + - +
Methods inherited from class java.lang.ObjectMethods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitequals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  @@ -310,7 +321,7 @@ _SkeletalCommandBuilder 

 public _SkeletalCommandBuilder()
-
+
Deprecated.  @@ -325,9 +336,9 @@ public _SkeletalCommandBuilder()

setEmail

-public _SkeletalCommandBuilder setEmail(java.lang.String email)
+public _SkeletalCommandBuilder setEmail(String email)
-
+
Deprecated. 
@@ -339,9 +350,9 @@ public

setName

-public _SkeletalCommandBuilder setName(java.lang.String name)
+public _SkeletalCommandBuilder setName(String name)
-
+
Deprecated. 
@@ -353,9 +364,9 @@ public

getName

-public java.lang.String getName()
+public String getName()
-
+
Deprecated. 
@@ -367,9 +378,9 @@ public java.lang.String getName()

getEmail

-public java.lang.String getEmail()
+public String getEmail()
-
+
Deprecated. 
@@ -381,9 +392,9 @@ public java.lang.String getEmail()

addParameters

-public _SkeletalCommandBuilder addParameters(java.lang.String[] parameters)
+public _SkeletalCommandBuilder addParameters(String[] parameters)
-
+
Deprecated. 
@@ -395,9 +406,9 @@ public

addParameters

-public _SkeletalCommandBuilder addParameters(java.util.List<java.lang.String> parameters)
+public _SkeletalCommandBuilder addParameters(List<String> parameters)
-
Description copied from interface: Executable
+
Deprecated. 
Description copied from interface: Executable
Adds parameter to the list of parameters for a native executable

@@ -415,7 +426,7 @@ getParameters 
 public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)
-
+
Deprecated. 
Specified by:
getParameters in interface Executable<_SkeletalCommandBuilder>
@@ -427,9 +438,9 @@ public

addParameter

-public _SkeletalCommandBuilder addParameter(java.lang.String parameter)
+public _SkeletalCommandBuilder addParameter(String parameter)
-
+
Deprecated. 
@@ -441,9 +452,9 @@ public

getResults

-public <V> V getResults(java.lang.String directory)
+public <V> V getResults(String directory)
-
+
Deprecated. 
Specified by:
getResults in interface Executable<_SkeletalCommandBuilder>
@@ -457,7 +468,7 @@ loadRunConfiguration 
 public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
-
+
Deprecated. 
Specified by:
loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
@@ -469,9 +480,9 @@ public

getOutput

-public java.lang.String getOutput()
+public String getOutput()
-
+
Deprecated. 
Specified by:
getOutput in interface Executable<_SkeletalCommandBuilder>
@@ -483,9 +494,9 @@ public java.lang.String getOutput()

getError

-public java.lang.String getError()
+public String getError()
-
+
Deprecated. 
Specified by:
getError in interface Executable<_SkeletalCommandBuilder>
@@ -497,9 +508,9 @@ public java.lang.String getError()

getLimit

-public Limit<_SkeletalCommandBuilder> getLimit(java.lang.String presetName)
+public Limit<_SkeletalCommandBuilder> getLimit(String presetName)
-
+
Deprecated. 
Specified by:
getLimit in interface Executable<_SkeletalCommandBuilder>
@@ -513,13 +524,27 @@ getLimits 
 public LimitsManager<_SkeletalCommandBuilder> getLimits()
-
+
Deprecated. 
Specified by:
getLimits in interface Executable<_SkeletalCommandBuilder>
+
+ +

+getClusterJobSettings

+
+public String getClusterJobSettings()
+
+
Deprecated. 
+
Specified by:
getClusterJobSettings in interface Executable<_SkeletalCommandBuilder>
+
+
+
+
+