X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2FUtil.html;h=8db9c58c38d9e78c381f9bb6c2dc41c175604769;hb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;hp=d09afc73680aff08602545759f13fe6f2b315cf3;hpb=b413eee53fa3cc22a6bd4e03c9ac64bf26b7c834;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/Util.html b/website/full_javadoc/compbio/runner/Util.html index d09afc7..8db9c58 100644 --- a/website/full_javadoc/compbio/runner/Util.html +++ b/website/full_javadoc/compbio/runner/Util.html @@ -2,12 +2,12 @@ - + Util - + @@ -92,12 +92,12 @@ compbio.runner
Class Util 
-java.lang.Object
+java.lang.Object
   extended by compbio.runner.Util
-
public final class Util
extends java.lang.Object
+
public final class Util
extends Object

@@ -114,7 +114,15 @@ java.lang.Object -static java.lang.String +static org.apache.log4j.Logger +log + +
+            + + + +static String SPACE
@@ -152,15 +160,14 @@ java.lang.Object +<T> PresetManager<T>
-<T> LimitsManager<T>
-getLimits(java.lang.Class<? extends Executable<T>> clazz) +getPresets(Class<? extends Executable<T>> clazz)
-          For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then +            @@ -168,35 +175,29 @@ java.lang.Object +<T> RunnerConfig<T>
-<T> PresetManager<T>
-getPresets(java.lang.Class<? extends Executable<T>> clazz) +getSupportedOptions(Class<? extends Executable<T>> clazz)
            -static - - - - -
-<T> RunnerConfig<T>
- -getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) +static Alignment +readClustalFile(String workDirectory, + String clustFile)
            -static Alignment -readClustalFile(java.lang.String workDirectory, - java.lang.String clustFile) +static Map<String,Score> +readJronnFile(String workDirectory, + String clustFile)
            @@ -204,7 +205,7 @@ java.lang.Object static void -writeInput(java.util.List<FastaSequence> sequences, +writeInput(List<FastaSequence> sequences, ConfiguredExecutable<?> exec)
@@ -214,10 +215,10 @@ java.lang.Object   - + - +
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
  @@ -233,10 +234,20 @@ java.lang.Object +

+log

+
+public static org.apache.log4j.Logger log
+
+
+
+
+
+

SPACE

-public static final java.lang.String SPACE
+public static final String SPACE
See Also:
Constant Field Values
@@ -269,31 +280,10 @@ public Util() -

-getLimits

-
-public static <T> LimitsManager<T> getLimits(java.lang.Class<? extends Executable<T>> clazz)
-
-
For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then -

-

-
Parameters:
rconfig - -
Returns:
public static List toOptionString(RunnerConfig - rconfig) { String option = ""; List options = new - ArrayList(); for (Parameter par : - rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) - { option = par.getOptionName(); } else { option = - par.getOptionName() + "=" + par.getPossibleValues().get(0); } // - separate options options.add(option); } return options; }
-
-
-
-

getSupportedOptions

-public static <T> RunnerConfig<T> getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
+public static <T> RunnerConfig<T> getSupportedOptions(Class<? extends Executable<T>> clazz)
@@ -304,7 +294,7 @@ public static <T>

getPresets

-public static <T> PresetManager<T> getPresets(java.lang.Class<? extends Executable<T>> clazz)
+public static <T> PresetManager<T> getPresets(Class<? extends Executable<T>> clazz)
@@ -315,20 +305,41 @@ public static <T>

readClustalFile

-public static final Alignment readClustalFile(java.lang.String workDirectory,
-                                              java.lang.String clustFile)
+public static final Alignment readClustalFile(String workDirectory,
+                                              String clustFile)
                                        throws UnknownFileFormatException,
-                                              java.io.IOException,
-                                              java.io.FileNotFoundException,
-                                              java.lang.NullPointerException
+ IOException, + FileNotFoundException, + NullPointerException +
+
+ +
Throws: +
UnknownFileFormatException +
IOException +
FileNotFoundException +
NullPointerException
+
+
+
+ +

+readJronnFile

+
+public static final Map<String,Score> readJronnFile(String workDirectory,
+                                                    String clustFile)
+                                             throws UnknownFileFormatException,
+                                                    IOException,
+                                                    FileNotFoundException,
+                                                    NullPointerException
Throws:
UnknownFileFormatException -
java.io.IOException -
java.io.FileNotFoundException -
java.lang.NullPointerException
+
IOException +
FileNotFoundException +
NullPointerException
@@ -336,11 +347,14 @@ public static final

writeInput

-public static void writeInput(java.util.List<FastaSequence> sequences,
-                              ConfiguredExecutable<?> exec)
+public static void writeInput(List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + throws JobSubmissionException
-
+ +
Throws: +
JobSubmissionException