X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fdisorder%2FGlobPlot.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fdisorder%2FGlobPlot.html;h=6243d243b7f92bb0cfd964eed4d6a01f37c02a26;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/disorder/GlobPlot.html b/website/full_javadoc/compbio/runner/disorder/GlobPlot.html new file mode 100644 index 0000000..6243d24 --- /dev/null +++ b/website/full_javadoc/compbio/runner/disorder/GlobPlot.html @@ -0,0 +1,405 @@ + + + + + + +GlobPlot + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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.disorder +
+Class GlobPlot

+
+java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<GlobPlot>
+      extended by compbio.runner.disorder.GlobPlot
+
+
+
All Implemented Interfaces:
Executable<GlobPlot>, PipedExecutable<GlobPlot>
+
+
+
+
public class GlobPlot
extends SkeletalExecutable<GlobPlot>
implements PipedExecutable<GlobPlot>
+ + +

+./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5. + + Changing these values are not recommended by developers, apart from smoothing + window. However, the binary, GlobPlot depends on - Tisean which is not happy + with arbitrary changes to these values, so changing them can lead to + problems. May be we can offer preset? + + This is not a standard GlobPlot! The script has been modified! +

+ +

+

+ +

+ + + + + + + +
+Nested Class Summary
+  + + + + + + + +
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
+  + + + + + + + + + + + +
+Field Summary
+static StringKEY_VALUE_SEPARATOR + +
+           
+  + + + + + + + +
Fields inherited from class compbio.engine.client.SkeletalExecutable
ERROR, INPUT, OUTPUT
+  + + + + + + + + + + +
+Constructor Summary
GlobPlot() + +
+           
+  + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ ScoreManagergetResults(String workDirectory) + +
+           
+ Class<GlobPlot>getType() + +
+           
+ GlobPlotsetInput(String inFile) + +
+           
+  + + + + + + + +
Methods inherited from class compbio.engine.client.SkeletalExecutable
addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  + + + + + + + +
Methods inherited from interface compbio.engine.client.Executable
addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
+  +

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

+KEY_VALUE_SEPARATOR

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

+GlobPlot

+
+public GlobPlot()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getResults

+
+public ScoreManager getResults(String workDirectory)
+                        throws ResultNotAvailableException
+
+
+
Specified by:
getResults in interface Executable<GlobPlot>
+
+
+ +
Throws: +
ResultNotAvailableException
+
+
+
+ +

+setInput

+
+public GlobPlot setInput(String inFile)
+
+
+
Overrides:
setInput in class SkeletalExecutable<GlobPlot>
+
+
+
+
+
+
+ +

+getType

+
+public Class<GlobPlot> getType()
+
+
+
Specified by:
getType in class SkeletalExecutable<GlobPlot>
+
+
+ +
Returns:
subclasses must return their type
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + +