X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2FUtil.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2FUtil.html;h=5372c7366afd31812905b369d00decc94fd79d28;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/Util.html b/website/full_javadoc/compbio/runner/Util.html new file mode 100644 index 0000000..5372c73 --- /dev/null +++ b/website/full_javadoc/compbio/runner/Util.html @@ -0,0 +1,423 @@ + + + + + + +Util + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.runner +
+Class Util

+
+java.lang.Object
+  extended by compbio.runner.Util
+
+
+
+
public final class Util
extends Object
+ + +

+

+ +

+ + + + + + + + + + + + + + + +
+Field Summary
+static org.apache.log4j.Loggerlog + +
+           
+static StringSPACE + +
+           
+  + + + + + + + + + + +
+Constructor Summary
Util() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static + + + + +
+<T> PresetManager<T>
+		getPresets(Class<? extends Executable<T>> clazz) + +
+           
+static + + + + +
+<T> RunnerConfig<T>
+		getSupportedOptions(Class<? extends Executable<T>> clazz) + +
+           
+static AlignmentreadClustalFile(String workDirectory, + String clustFile) + +
+           
+static Map<String,Score>readJronnFile(String workDirectory, + String clustFile) + +
+           
+static voidwriteInput(List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+log

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

+SPACE

+
+public static final String SPACE
+
+
+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Constructor Detail
+ +

+Util

+
+public Util()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getSupportedOptions

+
+public static <T> RunnerConfig<T> getSupportedOptions(Class<? extends Executable<T>> clazz)
+
+
+
+
+
+
+ +

+getPresets

+
+public static <T> PresetManager<T> getPresets(Class<? extends Executable<T>> clazz)
+
+
+
+
+
+
+ +

+readClustalFile

+
+public static final Alignment readClustalFile(String workDirectory,
+                                              String clustFile)
+                                       throws UnknownFileFormatException,
+                                              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 +
IOException +
FileNotFoundException +
NullPointerException
+
+
+
+ +

+writeInput

+
+public static void writeInput(List<FastaSequence> sequences,
+                              ConfiguredExecutable<?> exec)
+                       throws JobSubmissionException
+
+
+ +
Throws: +
JobSubmissionException
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + +