From 0bbebf27d045b1345bc042bdf24ef2e6808df251 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 7 Dec 2011 12:29:20 +0000 Subject: [PATCH] remove old project javadoc git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4790 e3abac25-378b-4346-85de-24260fe3988d --- website/full_javadoc/allclasses-frame.html | 429 ----- website/full_javadoc/allclasses-noframe.html | 429 ----- .../compbio/data/_structure/JnetAnnotation.html | 418 ----- .../compbio/data/_structure/JpredAnnotation.html | 418 ----- .../compbio/data/_structure/JpredResult.html | 260 ---- .../data/_structure/class-use/JnetAnnotation.html | 189 --- .../data/_structure/class-use/JpredAnnotation.html | 189 --- .../data/_structure/class-use/JpredResult.html | 144 -- .../compbio/data/_structure/package-frame.html | 45 - .../compbio/data/_structure/package-summary.html | 203 --- .../compbio/data/_structure/package-tree.html | 163 -- .../compbio/data/_structure/package-use.html | 176 --- 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- - - diff --git a/website/full_javadoc/allclasses-noframe.html b/website/full_javadoc/allclasses-noframe.html deleted file mode 100644 index 8aa2c88..0000000 --- a/website/full_javadoc/allclasses-noframe.html +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
AACon -
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-AnalizeResponse -
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-GetLimit -
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-GetLimitsResponse -
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-GetPresetsResponse -
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-GetSupportedServicesResponse -
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-
- - - diff --git a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html deleted file mode 100644 index 9693820..0000000 --- a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -JnetAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data._structure -
-Enum JnetAnnotation

-
-java.lang.Object
-  extended by java.lang.Enum<JnetAnnotation>
-      extended by compbio.data._structure.JnetAnnotation
-
-
-
All Implemented Interfaces:
Serializable, Comparable<JnetAnnotation>
-
-
-
-
public enum JnetAnnotation
extends Enum<JnetAnnotation>
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
JNETCONF - -
-           
JNETHMM - -
-           
jnetpred - -
-           
JNETPROPE - -
-           
JNETPROPH - -
-           
JNETSOL0 - -
-           
JNETSOL25 - -
-           
JNETSOL5 - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JnetAnnotationvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static JnetAnnotation[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-jnetpred

-
-public static final JnetAnnotation jnetpred
-
-
-
-
-
- -

-JNETCONF

-
-public static final JnetAnnotation JNETCONF
-
-
-
-
-
- -

-JNETSOL25

-
-public static final JnetAnnotation JNETSOL25
-
-
-
-
-
- -

-JNETSOL5

-
-public static final JnetAnnotation JNETSOL5
-
-
-
-
-
- -

-JNETSOL0

-
-public static final JnetAnnotation JNETSOL0
-
-
-
-
-
- -

-JNETHMM

-
-public static final JnetAnnotation JNETHMM
-
-
-
-
-
- -

-JNETPROPH

-
-public static final JnetAnnotation JNETPROPH
-
-
-
-
-
- -

-JNETPROPE

-
-public static final JnetAnnotation JNETPROPE
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static JnetAnnotation[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (JnetAnnotation c : JnetAnnotation.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static JnetAnnotation valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html deleted file mode 100644 index 5890499..0000000 --- a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -JpredAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data._structure -
-Enum JpredAnnotation

-
-java.lang.Object
-  extended by java.lang.Enum<JpredAnnotation>
-      extended by compbio.data._structure.JpredAnnotation
-
-
-
All Implemented Interfaces:
Serializable, Comparable<JpredAnnotation>
-
-
-
-
public enum JpredAnnotation
extends Enum<JpredAnnotation>
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
JNETCONF - -
-           
JNETHMM - -
-           
jnetpred - -
-           
JNETPROPE - -
-           
JNETPROPH - -
-           
JNETSOL0 - -
-           
JNETSOL25 - -
-           
JNETSOL5 - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JpredAnnotationvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static JpredAnnotation[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-jnetpred

-
-public static final JpredAnnotation jnetpred
-
-
-
-
-
- -

-JNETCONF

-
-public static final JpredAnnotation JNETCONF
-
-
-
-
-
- -

-JNETSOL25

-
-public static final JpredAnnotation JNETSOL25
-
-
-
-
-
- -

-JNETSOL5

-
-public static final JpredAnnotation JNETSOL5
-
-
-
-
-
- -

-JNETSOL0

-
-public static final JpredAnnotation JNETSOL0
-
-
-
-
-
- -

-JNETHMM

-
-public static final JpredAnnotation JNETHMM
-
-
-
-
-
- -

-JNETPROPH

-
-public static final JpredAnnotation JNETPROPH
-
-
-
-
-
- -

-JNETPROPE

-
-public static final JpredAnnotation JNETPROPE
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static JpredAnnotation[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (JpredAnnotation c : JpredAnnotation.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static JpredAnnotation valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/JpredResult.html b/website/full_javadoc/compbio/data/_structure/JpredResult.html deleted file mode 100644 index f61bce5..0000000 --- a/website/full_javadoc/compbio/data/_structure/JpredResult.html +++ /dev/null @@ -1,260 +0,0 @@ - - - - - - -JpredResult - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data._structure -
-Class JpredResult

-
-java.lang.Object
-  extended by compbio.data._structure.JpredResult
-
-
-
-
public class JpredResult
extends Object
- - -

-Jnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784, -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
JpredResult() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JpredResult

-
-public JpredResult()
-
-
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html deleted file mode 100644 index 0c855e8..0000000 --- a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Class compbio.data._structure.JnetAnnotation - - - - - - - - - - - - -
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-Uses of Class
compbio.data._structure.JnetAnnotation

-
- - - - - - - - - -
-Packages that use JnetAnnotation
compbio.data._structure  
-  -

- - - - - -
-Uses of JnetAnnotation in compbio.data._structure
-  -

- - - - - - - - - - - - - -
Methods in compbio.data._structure that return JnetAnnotation
-static JnetAnnotationJnetAnnotation.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static JnetAnnotation[]JnetAnnotation.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

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compbio.data._structure.JpredAnnotation

-
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-Packages that use JpredAnnotation
compbio.data._structure  
-  -

- - - - - -
-Uses of JpredAnnotation in compbio.data._structure
-  -

- - - - - - - - - - - - - -
Methods in compbio.data._structure that return JpredAnnotation
-static JpredAnnotationJpredAnnotation.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static JpredAnnotation[]JpredAnnotation.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

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-Classes  - -
-JpredResult
- - - - - - -
-Enums  - -
-JnetAnnotation -
-JpredAnnotation
- - - - diff --git a/website/full_javadoc/compbio/data/_structure/package-summary.html b/website/full_javadoc/compbio/data/_structure/package-summary.html deleted file mode 100644 index 1137dd0..0000000 --- a/website/full_javadoc/compbio/data/_structure/package-summary.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - -compbio.data._structure - - - - - - - - - - - - -
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-Package compbio.data._structure -

- - - - - - - - - -
-Class Summary
JpredResultJnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
-  - -

- - - - - - - - - - - - - -
-Enum Summary
JnetAnnotation 
JpredAnnotation 
-  - -

-

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-Hierarchy For Package compbio.data._structure -

-
-
-
Package Hierarchies:
All Packages
-
-

-Class Hierarchy -

- -

-Enum Hierarchy -

- -
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compbio.data._structure

-
- - - - - - - - - -
-Packages that use compbio.data._structure
compbio.data._structure  
-  -

- - - - - - - - - - - -
-Classes in compbio.data._structure used by compbio.data._structure
JnetAnnotation - -
-           
JpredAnnotation - -
-           
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/data/msa/JABAService.html b/website/full_javadoc/compbio/data/msa/JABAService.html deleted file mode 100644 index dfa85ee..0000000 --- a/website/full_javadoc/compbio/data/msa/JABAService.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - -JABAService - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface JABAService

-
-
All Known Subinterfaces:
MsaWS<T>, RegistryWS, SequenceAnnotation<T>
-
-
-
All Known Implementing Classes:
AAConWS, ClustalOWS, ClustalWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS, MafftWS, MuscleWS, ProbconsWS, RegistryWS, TcoffeeWS
-
-
-
-
public interface JABAService
- - -

-This is a marker interface, contains no methods -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - -
-Field Summary
-static StringSERVICE_NAMESPACE - -
-           
-static StringV2_SERVICE_NAMESPACE - -
-           
-  -

- - - - - - - - -
-Field Detail
- -

-SERVICE_NAMESPACE

-
-static final String SERVICE_NAMESPACE
-
-
-
See Also:
Constant Field Values
-
-
- -

-V2_SERVICE_NAMESPACE

-
-static final String V2_SERVICE_NAMESPACE
-
-
-
See Also:
Constant Field Values
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/JManagement.html b/website/full_javadoc/compbio/data/msa/JManagement.html deleted file mode 100644 index 5b67ec1..0000000 --- a/website/full_javadoc/compbio/data/msa/JManagement.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -JManagement - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface JManagement

-
-
All Known Subinterfaces:
MsaWS<T>, SequenceAnnotation<T>
-
-
-
All Known Implementing Classes:
AAConWS, ClustalOWS, ClustalWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
-
-
-
-
public interface JManagement
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(String jobId) - -
-          Stop running the job jobId but leave its output untouched
- JobStatusgetJobStatus(String jobId) - -
-          Return the status of the job.
- ChunkHolderpullExecStatistics(String jobId, - long position) - -
-          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
-  -

- - - - - - - - -
-Method Detail
- -

-cancelJob

-
-boolean cancelJob(String jobId)
-
-
Stop running the job jobId but leave its output untouched -

-

- -
Returns:
true if job was cancelled successfully, false otherwise -
Throws: -
InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in - invalid format
-
-
-
- -

-getJobStatus

-
-JobStatus getJobStatus(String jobId)
-
-
Return the status of the job. -

-

-
Parameters:
jobId - - unique job identifier -
Returns:
JobStatus - status of the job -
Throws: -
InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in - invalid format
See Also:
JobStatus
-
-
-
- -

-pullExecStatistics

-
-ChunkHolder pullExecStatistics(String jobId,
-                               long position)
-
-
Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

-

-
Parameters:
jobId - - unique job identifier
position - - next position within the file to read -
Returns:
ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read -
Throws: -
InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format and also if the position value is negative
See Also:
ChunkHolder
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/Metadata.html b/website/full_javadoc/compbio/data/msa/Metadata.html deleted file mode 100644 index d542da1..0000000 --- a/website/full_javadoc/compbio/data/msa/Metadata.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - -Metadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface Metadata<T>

-
-
All Known Subinterfaces:
MsaWS<T>, SequenceAnnotation<T>
-
-
-
All Known Implementing Classes:
AAConWS, ClustalOWS, ClustalWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
-
-
-
-
public interface Metadata<T>
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Limit<T>getLimit(String presetName) - -
-          Get a Limit for a preset.
- LimitsManager<T>getLimits() - -
-          List Limits supported by a web service.
- PresetManager<T>getPresets() - -
-          Get presets supported by a web service
- RunnerConfig<T>getRunnerOptions() - -
-          Get options supported by a web service
-  -

- - - - - - - - -
-Method Detail
- -

-getRunnerOptions

-
-RunnerConfig<T> getRunnerOptions()
-
-
Get options supported by a web service -

-

- -
Returns:
RunnerConfig the list of options and parameters supported by a - web service.
-
-
-
- -

-getPresets

-
-PresetManager<T> getPresets()
-
-
Get presets supported by a web service -

-

- -
Returns:
PresetManager the object contains information about presets - supported by a web service
-
-
-
- -

-getLimit

-
-Limit<T> getLimit(String presetName)
-
-
Get a Limit for a preset. -

-

-
Parameters:
presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
Returns:
Limit
-
-
-
- -

-getLimits

-
-LimitsManager<T> getLimits()
-
-
List Limits supported by a web service. -

-

- -
Returns:
LimitManager
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/MsaWS.html b/website/full_javadoc/compbio/data/msa/MsaWS.html deleted file mode 100644 index 7542acd..0000000 --- a/website/full_javadoc/compbio/data/msa/MsaWS.html +++ /dev/null @@ -1,436 +0,0 @@ - - - - - - -MsaWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface MsaWS<T>

-
-
Type Parameters:
T - executable type / web service type
-
-
All Superinterfaces:
JABAService, JManagement, Metadata<T>
-
-
-
All Known Implementing Classes:
ClustalOWS, ClustalWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
-
-
-
-
public interface MsaWS<T>
extends JABAService, JManagement, Metadata<T>
- - -

-Multiple Sequence Alignment (MSA) Web Services Interface -

- -

-

-
Author:
-
pvtroshin - - Date November 2010
-
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Stringalign(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- StringcustomAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- AlignmentgetResult(String jobId) - -
-          Return the result of the job.
- StringpresetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
-  -

- - - - - - - - -
-Method Detail
- -

-align

-
-String align(List<FastaSequence> sequences)
-             throws UnsupportedRuntimeException,
-                    LimitExceededException,
-                    JobSubmissionException
-
-
Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
InvalidParameterException - thrown if input list of FASTA sequences is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
-
-
-
- -

-customAlign

-
-String customAlign(List<FastaSequence> sequences,
-                   List<Option<T>> options)
-                   throws UnsupportedRuntimeException,
-                          LimitExceededException,
-                          JobSubmissionException,
-                          WrongParameterException
-
-
Align a list of sequences with options. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
options - A list of Options -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
InvalidParameterException - thrown if input list of FASTA sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
See Also:
Default Limit is used to decide whether the calculation will be - permitted or denied
-
-
-
- -

-presetAlign

-
-String presetAlign(List<FastaSequence> sequences,
-                   Preset<T> preset)
-                   throws UnsupportedRuntimeException,
-                          LimitExceededException,
-                          JobSubmissionException,
-                          WrongParameterException
-
-
Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
preset - A list of Options -
Returns:
String - jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
InvalidParameterException - thrown if input list of FASTA sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
See Also:
Preset
-
-
-
- -

-getResult

-
-Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
-
-
Return the result of the job. This method waits for the job - jobId to complete before return. -

-

-
-
-
-
Parameters:
jobId - a unique job identifier -
Returns:
Alignment -
Throws: -
ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid - format
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/RegistryWS.html b/website/full_javadoc/compbio/data/msa/RegistryWS.html deleted file mode 100644 index 249be0d..0000000 --- a/website/full_javadoc/compbio/data/msa/RegistryWS.html +++ /dev/null @@ -1,376 +0,0 @@ - - - - - - -RegistryWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa -
-Interface RegistryWS

-
-
All Superinterfaces:
JABAService
-
-
-
All Known Implementing Classes:
RegistryWS
-
-
-
-
public interface RegistryWS
extends JABAService
- - -

-JABAWS services registry -

- -

-

-
Version:
-
1.0 June 2011
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetLastTested(Services service) - -
-          Number of seconds since the last test.
- DategetLastTestedOn(Services service) - -
-          The date and time the service has been verified to work last time
- Set<Services>getSupportedServices() - -
-          List of services that are functioning on the server.
- booleanisOperating(Services service) - -
-          Check whether a particular web service is working on this server
- StringtestAllServices() - -
-          Test all JABAWS services on the server
- StringtestService(Services service) - -
-          Test a particular service
-  -

- - - - - - - - -
-Method Detail
- -

-getSupportedServices

-
-Set<Services> getSupportedServices()
-
-
List of services that are functioning on the server. This function - returns the results of testing performed some time ago by - testAllServices() or testService(Services) methods. The - time of last check can be obtained from - getLastTestedOn(Services) method -

-

-
-
-
- -
Returns:
the Set of Services which are functioning on the server
See Also:
testAllServices()
-
-
-
- -

-getLastTested

-
-int getLastTested(Services service)
-
-
Number of seconds since the last test. Returns 0 if the service was not - tested or tested less then a one second ago. -

-

-
-
-
-
Parameters:
service - -
Returns:
when last time tested
-
-
-
- -

-getLastTestedOn

-
-Date getLastTestedOn(Services service)
-
-
The date and time the service has been verified to work last time -

-

-
-
-
-
Parameters:
service - -
Returns:
the Date and time on which the service was last tested
-
-
-
- -

-testAllServices

-
-String testAllServices()
-
-
Test all JABAWS services on the server -

-

-
-
-
- -
Returns:
the test log
-
-
-
- -

-testService

-
-String testService(Services service)
-
-
Test a particular service -

-

-
-
-
-
Parameters:
service - -
Returns:
the testing log
-
-
-
- -

-isOperating

-
-boolean isOperating(Services service)
-
-
Check whether a particular web service is working on this server -

-

-
-
-
-
Parameters:
service - -
Returns:
true if the service was functioning in time of last testing.
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/SequenceAnnotation.html b/website/full_javadoc/compbio/data/msa/SequenceAnnotation.html deleted file mode 100644 index d9ca6b0..0000000 --- a/website/full_javadoc/compbio/data/msa/SequenceAnnotation.html +++ /dev/null @@ -1,448 +0,0 @@ - - - - - - -SequenceAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa -
-Interface SequenceAnnotation<T>

-
-
Type Parameters:
T - executable type / web service type
-
-
All Superinterfaces:
JABAService, JManagement, Metadata<T>
-
-
-
All Known Implementing Classes:
AAConWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS
-
-
-
-
public interface SequenceAnnotation<T>
extends JABAService, JManagement, Metadata<T>
- - -

-Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated -

- -

-

-
Version:
-
1.0 November 2010
-
Author:
-
Peter Troshin
-
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Stringanalize(List<FastaSequence> sequences) - -
-          Analyse the sequences.
- StringcustomAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Analyse the sequences according to custom settings defined in options - list.
- ScoreManagergetAnnotation(String jobId) - -
-          Return the result of the job.
- StringpresetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Analyse the sequences according to the preset settings.
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
-  -

- - - - - - - - -
-Method Detail
- -

-analize

-
-String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException
-
-
Analyse the sequences. The actual analysis algorithm is defined by the - type T. - - Any dataset containing a greater number of sequences or the average - length of the sequences are greater then defined in the default Limit - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
-
-
-
- -

-customAnalize

-
-String customAnalize(List<FastaSequence> sequences,
-                     List<Option<T>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
-
-
Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
options - A list of Options -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
See Also:
Option
-
-
-
- -

-presetAnalize

-
-String presetAnalize(List<FastaSequence> sequences,
-                     Preset<T> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
-
-
Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
preset - A list of Options -
Returns:
String - jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
-
-
-
- -

-getAnnotation

-
-ScoreManager getAnnotation(String jobId)
-                           throws ResultNotAvailableException
-
-
Return the result of the job. -

-

-
-
-
-
Parameters:
jobId - a unique job identifier -
Returns:
the Map with the sequence names, sequence group names or the word - 'Alignment' in case of alignments and values the represented by a - Set of Score objects. The alignment can be represented in as - little as one key->value pair in this map, the list of sequences - will be represented by multiple key->value mappings. If multiple - annotations were calculated, then they are represented as a Set - of Scores. -
Throws: -
ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/JABAService.html b/website/full_javadoc/compbio/data/msa/class-use/JABAService.html deleted file mode 100644 index 597f1b9..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/JABAService.html +++ /dev/null @@ -1,347 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.JABAService - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.JABAService

-
- - - - - - - - - - - - - - - - - -
-Packages that use JABAService
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - -
-Uses of JABAService in compbio.data.msa
-  -

- - - - - - - - - - - - - - - - - -
Subinterfaces of JABAService in compbio.data.msa
- interfaceMsaWS<T> - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
- interfaceRegistryWS - -
-          JABAWS services registry
- interfaceSequenceAnnotation<T> - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

- - - - - -
-Uses of JABAService in compbio.ws.client
-  -

- - - - - - - - - -
Methods in compbio.ws.client that return JABAService
-static JABAServiceJws2Client.connect(String host, - Services service) - -
-          Connects to a web service by the host and the service name web service - type
-  -

- - - - - -
-Uses of JABAService in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.ws.server that implement JABAService
- classAAConWS - -
-           
- classClustalOWS - -
-           
- classClustalWS - -
-           
- classDisemblWS - -
-           
- classGlobPlotWS - -
-           
- classIUPredWS - -
-           
- classJronnWS - -
-           
- classMafftWS - -
-           
- classMuscleWS - -
-           
- classProbconsWS - -
-           
- classRegistryWS - -
-          JABAWS services registry
- classTcoffeeWS - -
-           
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/JManagement.html b/website/full_javadoc/compbio/data/msa/class-use/JManagement.html deleted file mode 100644 index 1410b3a..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/JManagement.html +++ /dev/null @@ -1,299 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.JManagement - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.JManagement

-
- - - - - - - - - - - - - -
-Packages that use JManagement
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - -
-Uses of JManagement in compbio.data.msa
-  -

- - - - - - - - - - - - - -
Subinterfaces of JManagement in compbio.data.msa
- interfaceMsaWS<T> - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
- interfaceSequenceAnnotation<T> - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

- - - - - -
-Uses of JManagement in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.ws.server that implement JManagement
- classAAConWS - -
-           
- classClustalOWS - -
-           
- classClustalWS - -
-           
- classDisemblWS - -
-           
- classGlobPlotWS - -
-           
- classIUPredWS - -
-           
- classJronnWS - -
-           
- classMafftWS - -
-           
- classMuscleWS - -
-           
- classProbconsWS - -
-           
- classTcoffeeWS - -
-           
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/Metadata.html b/website/full_javadoc/compbio/data/msa/class-use/Metadata.html deleted file mode 100644 index 8faf993..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/Metadata.html +++ /dev/null @@ -1,299 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.Metadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Interface
compbio.data.msa.Metadata

-
- - - - - - - - - - - - - -
-Packages that use Metadata
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - -
-Uses of Metadata in compbio.data.msa
-  -

- - - - - - - - - - - - - -
Subinterfaces of Metadata in compbio.data.msa
- interfaceMsaWS<T> - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
- interfaceSequenceAnnotation<T> - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

- - - - - -
-Uses of Metadata in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.ws.server that implement Metadata
- classAAConWS - -
-           
- classClustalOWS - -
-           
- classClustalWS - -
-           
- classDisemblWS - -
-           
- classGlobPlotWS - -
-           
- classIUPredWS - -
-           
- classJronnWS - -
-           
- classMafftWS - -
-           
- classMuscleWS - -
-           
- classProbconsWS - -
-           
- classTcoffeeWS - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html deleted file mode 100644 index 5cea9e4..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.MsaWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Interface
compbio.data.msa.MsaWS

-
- - - - - - - - - -
-Packages that use MsaWS
compbio.ws.server  
-  -

- - - - - -
-Uses of MsaWS in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.ws.server that implement MsaWS
- classClustalOWS - -
-           
- classClustalWS - -
-           
- classMafftWS - -
-           
- classMuscleWS - -
-           
- classProbconsWS - -
-           
- classTcoffeeWS - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/RegistryWS.html b/website/full_javadoc/compbio/data/msa/class-use/RegistryWS.html deleted file mode 100644 index 4a8ba3b..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/RegistryWS.html +++ /dev/null @@ -1,210 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.RegistryWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Interface
compbio.data.msa.RegistryWS

-
- - - - - - - - - - - - - -
-Packages that use RegistryWS
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - -
-Uses of RegistryWS in compbio.ws.client
-  -

- - - - - - - - - -
Methods in compbio.ws.client that return RegistryWS
-static RegistryWSJws2Client.connectToRegistry(String host) - -
-          Get a connection of JABAWS registry
-  -

- - - - - -
-Uses of RegistryWS in compbio.ws.server
-  -

- - - - - - - - - -
Classes in compbio.ws.server that implement RegistryWS
- classRegistryWS - -
-          JABAWS services registry
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html b/website/full_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html deleted file mode 100644 index d244623..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html +++ /dev/null @@ -1,242 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.SequenceAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Interface
compbio.data.msa.SequenceAnnotation

-
- - - - - - - - - - - - - -
-Packages that use SequenceAnnotation
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - -
-Uses of SequenceAnnotation in compbio.ws.client
-  -

- - - - - - - - - -
Methods in compbio.ws.client that return SequenceAnnotation
-static SequenceAnnotation<AAConWS>AAConClient.connect() - -
-          Connects to a AACon web service by the host and the service name
-  -

- - - - - -
-Uses of SequenceAnnotation in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.ws.server that implement SequenceAnnotation
- classAAConWS - -
-           
- classDisemblWS - -
-           
- classGlobPlotWS - -
-           
- classIUPredWS - -
-           
- classJronnWS - -
-           
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/Align.html deleted file mode 100644 index 277fb00..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/Align.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Align - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class Align

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.Align
-
-
-
-
public class Align
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Align() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- List<FastaSequence>getFastaSequences() - -
-           
- voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Align

-
-public Align()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html deleted file mode 100644 index ed54261..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -AlignResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class AlignResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.AlignResponse
-
-
-
-
public class AlignResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
AlignResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-AlignResponse

-
-public AlignResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Analize.html b/website/full_javadoc/compbio/data/msa/jaxws/Analize.html deleted file mode 100644 index f1e4316..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/Analize.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Analize - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa.jaxws -
-Class Analize

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.Analize
-
-
-
-
public class Analize
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Analize() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- List<FastaSequence>getFastaSequences() - -
-           
- voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Analize

-
-public Analize()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html deleted file mode 100644 index ef28a3a..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -AnalizeResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class AnalizeResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.AnalizeResponse
-
-
-
-
public class AnalizeResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
AnalizeResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-AnalizeResponse

-
-public AnalizeResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html deleted file mode 100644 index ba21fa1..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJob - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa.jaxws -
-Class CancelJob

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CancelJob
-
-
-
-
public class CancelJob
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CancelJob() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetJobId() - -
-           
- voidsetJobId(String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CancelJob

-
-public CancelJob()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html deleted file mode 100644 index 89ecebb..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJobResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class CancelJobResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CancelJobResponse
-
-
-
-
public class CancelJobResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CancelJobResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- booleanisReturn() - -
-           
- voidsetReturn(boolean _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CancelJobResponse

-
-public CancelJobResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-isReturn

-
-public boolean isReturn()
-
-
- -
Returns:
returns boolean
-
-
-
- -

-setReturn

-
-public void setReturn(boolean _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html deleted file mode 100644 index a7a77de..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -CustomAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class CustomAlign

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAlign
-
-
-
-
public class CustomAlign
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAlign() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- List<FastaSequence>getFastaSequences() - -
-           
- List<Option>getOptions() - -
-           
- voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidsetOptions(List<Option> options) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAlign

-
-public CustomAlign()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getOptions

-
-public List<Option> getOptions()
-
-
- -
Returns:
returns List
-
-
-
- -

-setOptions

-
-public void setOptions(List<Option> options)
-
-
-
Parameters:
options - the value for the options property
-
-
- -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class CustomAlignResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAlignResponse
-
-
-
-
public class CustomAlignResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAlignResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAlignResponse

-
-public CustomAlignResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class CustomAnalize

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAnalize
-
-
-
-
public class CustomAnalize
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAnalize() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- List<FastaSequence>getFastaSequences() - -
-           
- List<Option>getOptions() - -
-           
- voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidsetOptions(List<Option> options) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAnalize

-
-public CustomAnalize()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getOptions

-
-public List<Option> getOptions()
-
-
- -
Returns:
returns List
-
-
-
- -

-setOptions

-
-public void setOptions(List<Option> options)
-
-
-
Parameters:
options - the value for the options property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class CustomAnalizeResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAnalizeResponse
-
-
-
-
public class CustomAnalizeResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAnalizeResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAnalizeResponse

-
-public CustomAnalizeResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html b/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html deleted file mode 100644 index 179905d..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetAnnotation - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetAnnotation

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotation
-
-
-
-
public class GetAnnotation
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetAnnotation() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetJobId() - -
-           
- voidsetJobId(String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetAnnotation

-
-public GetAnnotation()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html deleted file mode 100644 index 20f3f33..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetAnnotationResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetAnnotationResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotationResponse
-
-
-
-
public class GetAnnotationResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetAnnotationResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ScoreManagergetReturn() - -
-           
- voidsetReturn(ScoreManager _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetAnnotationResponse

-
-public GetAnnotationResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public ScoreManager getReturn()
-
-
- -
Returns:
returns ScoreManager
-
-
-
- -

-setReturn

-
-public void setReturn(ScoreManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html deleted file mode 100644 index bccd65e..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetJobStatus - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetJobStatus

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetJobStatus
-
-
-
-
public class GetJobStatus
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetJobStatus() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetJobId() - -
-           
- voidsetJobId(String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetJobStatus

-
-public GetJobStatus()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetJobStatusResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetJobStatusResponse
-
-
-
-
public class GetJobStatusResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetJobStatusResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- JobStatusgetReturn() - -
-           
- voidsetReturn(JobStatus _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetJobStatusResponse

-
-public GetJobStatusResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public JobStatus getReturn()
-
-
- -
Returns:
returns JobStatus
-
-
-
- -

-setReturn

-
-public void setReturn(JobStatus _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLastTested.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLastTested.html deleted file mode 100644 index 96ccad2..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLastTested.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLastTested - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLastTested

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTested
-
-
-
-
public class GetLastTested
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTested() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLastTested

-
-public GetLastTested()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLastTestedOn

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedOn
-
-
-
-
public class GetLastTestedOn
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTestedOn() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLastTestedOn

-
-public GetLastTestedOn()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html deleted file mode 100644 index 55fc241..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLastTestedOnResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLastTestedOnResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedOnResponse
-
-
-
-
public class GetLastTestedOnResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTestedOnResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- DategetReturn() - -
-           
- voidsetReturn(Date _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLastTestedOnResponse

-
-public GetLastTestedOnResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public Date getReturn()
-
-
- -
Returns:
returns Date
-
-
-
- -

-setReturn

-
-public void setReturn(Date _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLastTestedResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedResponse
-
-
-
-
public class GetLastTestedResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTestedResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- intgetReturn() - -
-           
- voidsetReturn(int _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLastTestedResponse

-
-public GetLastTestedResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public int getReturn()
-
-
- -
Returns:
returns int
-
-
-
- -

-setReturn

-
-public void setReturn(int _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html deleted file mode 100644 index cb00128..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimit - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLimit

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimit
-
-
-
-
public class GetLimit
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimit() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetPresetName() - -
-           
- voidsetPresetName(String presetName) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimit

-
-public GetLimit()
-
-
- - - - - - - - -
-Method Detail
- -

-getPresetName

-
-public String getPresetName()
-
-
- -
Returns:
returns String
-
-
-
- -

-setPresetName

-
-public void setPresetName(String presetName)
-
-
-
Parameters:
presetName - the value for the presetName property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html deleted file mode 100644 index b20cf2a..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLimitResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimitResponse
-
-
-
-
public class GetLimitResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimitResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- LimitgetReturn() - -
-           
- voidsetReturn(Limit _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimitResponse

-
-public GetLimitResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public Limit getReturn()
-
-
- -
Returns:
returns Limit
-
-
-
- -

-setReturn

-
-public void setReturn(Limit _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html deleted file mode 100644 index 9de31c3..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetLimits - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLimits

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimits
-
-
-
-
public class GetLimits
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimits() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimits

-
-public GetLimits()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html deleted file mode 100644 index 3a97854..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLimitsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimitsResponse
-
-
-
-
public class GetLimitsResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimitsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- LimitsManagergetReturn() - -
-           
- voidsetReturn(LimitsManager _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimitsResponse

-
-public GetLimitsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public LimitsManager getReturn()
-
-
- -
Returns:
returns LimitsManager
-
-
-
- -

-setReturn

-
-public void setReturn(LimitsManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html deleted file mode 100644 index 3b42f6d..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetPresets - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetPresets

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetPresets
-
-
-
-
public class GetPresets
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetPresets() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetPresets

-
-public GetPresets()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html deleted file mode 100644 index cc8cfb9..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetPresetsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa.jaxws -
-Class GetPresetsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetPresetsResponse
-
-
-
-
public class GetPresetsResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetPresetsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- PresetManagergetReturn() - -
-           
- voidsetReturn(PresetManager _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetPresetsResponse

-
-public GetPresetsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public PresetManager getReturn()
-
-
- -
Returns:
returns PresetManager
-
-
-
- -

-setReturn

-
-public void setReturn(PresetManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html deleted file mode 100644 index b6f96a3..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetResult - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetResult

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetResult
-
-
-
-
public class GetResult
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetResult() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetJobId() - -
-           
- voidsetJobId(String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetResult

-
-public GetResult()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html deleted file mode 100644 index 1626da9..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetResultResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa.jaxws -
-Class GetResultResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetResultResponse
-
-
-
-
public class GetResultResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetResultResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- AlignmentgetReturn() - -
-           
- voidsetReturn(Alignment _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetResultResponse

-
-public GetResultResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public Alignment getReturn()
-
-
- -
Returns:
returns Alignment
-
-
-
- -

-setReturn

-
-public void setReturn(Alignment _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetRunnerOptions

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetRunnerOptions
-
-
-
-
public class GetRunnerOptions
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetRunnerOptions() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetRunnerOptions

-
-public GetRunnerOptions()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetRunnerOptionsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetRunnerOptionsResponse
-
-
-
-
public class GetRunnerOptionsResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetRunnerOptionsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- RunnerConfiggetReturn() - -
-           
- voidsetReturn(RunnerConfig _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetRunnerOptionsResponse

-
-public GetRunnerOptionsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public RunnerConfig getReturn()
-
-
- -
Returns:
returns RunnerConfig
-
-
-
- -

-setReturn

-
-public void setReturn(RunnerConfig _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html b/website/full_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html deleted file mode 100644 index 0a4cd5c..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetSupportedServices - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetSupportedServices

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetSupportedServices
-
-
-
-
public class GetSupportedServices
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetSupportedServices() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetSupportedServices

-
-public GetSupportedServices()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html deleted file mode 100644 index 8051c14..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetSupportedServicesResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetSupportedServicesResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetSupportedServicesResponse
-
-
-
-
public class GetSupportedServicesResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetSupportedServicesResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- Set<Services>getReturn() - -
-           
- voidsetReturn(Set<Services> _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetSupportedServicesResponse

-
-public GetSupportedServicesResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public Set<Services> getReturn()
-
-
- -
Returns:
returns Set
-
-
-
- -

-setReturn

-
-public void setReturn(Set<Services> _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/IsOperating.html b/website/full_javadoc/compbio/data/msa/jaxws/IsOperating.html deleted file mode 100644 index 98e5cb4..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/IsOperating.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -IsOperating - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class IsOperating

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.IsOperating
-
-
-
-
public class IsOperating
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
IsOperating() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-IsOperating

-
-public IsOperating()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class IsOperatingResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.IsOperatingResponse
-
-
-
-
public class IsOperatingResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
IsOperatingResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- booleanisReturn() - -
-           
- voidsetReturn(boolean _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-IsOperatingResponse

-
-public IsOperatingResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-isReturn

-
-public boolean isReturn()
-
-
- -
Returns:
returns boolean
-
-
-
- -

-setReturn

-
-public void setReturn(boolean _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html deleted file mode 100644 index 24388e1..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -JobSubmissionExceptionBean - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class JobSubmissionExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.JobSubmissionExceptionBean
-
-
-
-
public class JobSubmissionExceptionBean
extends Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
JobSubmissionExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetMessage() - -
-           
- voidsetMessage(String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobSubmissionExceptionBean

-
-public JobSubmissionExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class LimitExceededExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.LimitExceededExceptionBean
-
-
-
-
public class LimitExceededExceptionBean
extends Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
LimitExceededExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetActualNumberofSequences() - -
-           
- StringgetMessage() - -
-           
- intgetNumberOfSequencesAllowed() - -
-           
- intgetSequenceLenghtActual() - -
-           
- intgetSequenceLenghtAllowed() - -
-           
- voidsetActualNumberofSequences(int actualNumberofSequences) - -
-           
- voidsetMessage(String message) - -
-           
- voidsetNumberOfSequencesAllowed(int numberOfSequencesAllowed) - -
-           
- voidsetSequenceLenghtActual(int sequenceLenghtActual) - -
-           
- voidsetSequenceLenghtAllowed(int sequenceLenghtAllowed) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LimitExceededExceptionBean

-
-public LimitExceededExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getActualNumberofSequences

-
-public int getActualNumberofSequences()
-
-
- -
Returns:
returns int
-
-
-
- -

-setActualNumberofSequences

-
-public void setActualNumberofSequences(int actualNumberofSequences)
-
-
-
Parameters:
actualNumberofSequences - the value for the actualNumberofSequences property
-
-
-
- -

-getMessage

-
-public String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(String message)
-
-
-
Parameters:
message - the value for the message property
-
-
-
- -

-getNumberOfSequencesAllowed

-
-public int getNumberOfSequencesAllowed()
-
-
- -
Returns:
returns int
-
-
-
- -

-setNumberOfSequencesAllowed

-
-public void setNumberOfSequencesAllowed(int numberOfSequencesAllowed)
-
-
-
Parameters:
numberOfSequencesAllowed - the value for the numberOfSequencesAllowed property
-
-
-
- -

-getSequenceLenghtActual

-
-public int getSequenceLenghtActual()
-
-
- -
Returns:
returns int
-
-
-
- -

-setSequenceLenghtActual

-
-public void setSequenceLenghtActual(int sequenceLenghtActual)
-
-
-
Parameters:
sequenceLenghtActual - the value for the sequenceLenghtActual property
-
-
-
- -

-getSequenceLenghtAllowed

-
-public int getSequenceLenghtAllowed()
-
-
- -
Returns:
returns int
-
-
-
- -

-setSequenceLenghtAllowed

-
-public void setSequenceLenghtAllowed(int sequenceLenghtAllowed)
-
-
-
Parameters:
sequenceLenghtAllowed - the value for the sequenceLenghtAllowed property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html deleted file mode 100644 index 2576fe3..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PresetAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class PresetAlign

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAlign
-
-
-
-
public class PresetAlign
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PresetAlign() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- List<FastaSequence>getFastaSequences() - -
-           
- PresetgetPreset() - -
-           
- voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidsetPreset(Preset preset) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PresetAlign

-
-public PresetAlign()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getPreset

-
-public Preset getPreset()
-
-
- -
Returns:
returns Preset
-
-
-
- -

-setPreset

-
-public void setPreset(Preset preset)
-
-
-
Parameters:
preset - the value for the preset property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class PresetAlignResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAlignResponse
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public class PresetAlignResponse
extends Object
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-

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- - - - - - - - - - - -
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PresetAlignResponse() - -
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-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
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- voidsetReturn(String _return) - -
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-PresetAlignResponse

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-public PresetAlignResponse()
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-getReturn

-
-public String getReturn()
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-
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Returns:
returns String
-
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-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
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- -compbio.data.msa.jaxws -
-Class PresetAnalize

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAnalize
-
-
-
-
public class PresetAnalize
extends Object
- - -

-

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- - - - - - - - - - - -
-Constructor Summary
PresetAnalize() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- List<FastaSequence>getFastaSequences() - -
-           
- PresetgetPreset() - -
-           
- voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidsetPreset(Preset preset) - -
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Methods inherited from class java.lang.Object
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-Constructor Detail
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-PresetAnalize

-
-public PresetAnalize()
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-
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-Method Detail
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-getFastaSequences

-
-public List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
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-
- -

-setFastaSequences

-
-public void setFastaSequences(List<FastaSequence> fastaSequences)
-
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-
Parameters:
fastaSequences - the value for the fastaSequences property
-
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-
- -

-getPreset

-
-public Preset getPreset()
-
-
- -
Returns:
returns Preset
-
-
-
- -

-setPreset

-
-public void setPreset(Preset preset)
-
-
-
Parameters:
preset - the value for the preset property
-
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- -compbio.data.msa.jaxws -
-Class PresetAnalizeResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAnalizeResponse
-
-
-
-
public class PresetAnalizeResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PresetAnalizeResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
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-Constructor Detail
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-PresetAnalizeResponse

-
-public PresetAnalizeResponse()
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-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
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- -compbio.data.msa.jaxws -
-Class PullExecStatistics

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PullExecStatistics
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-
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-
public class PullExecStatistics
extends Object
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-

- -

- - - - - - - - - - - -
-Constructor Summary
PullExecStatistics() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- StringgetJobId() - -
-           
- longgetPosition() - -
-           
- voidsetJobId(String jobId) - -
-           
- voidsetPosition(long position) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-PullExecStatistics

-
-public PullExecStatistics()
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-Method Detail
- -

-getJobId

-
-public String getJobId()
-
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- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
-
- -

-getPosition

-
-public long getPosition()
-
-
- -
Returns:
returns long
-
-
-
- -

-setPosition

-
-public void setPosition(long position)
-
-
-
Parameters:
position - the value for the position property
-
-
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- -compbio.data.msa.jaxws -
-Class PullExecStatisticsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PullExecStatisticsResponse
-
-
-
-
public class PullExecStatisticsResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PullExecStatisticsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ChunkHoldergetReturn() - -
-           
- voidsetReturn(ChunkHolder _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PullExecStatisticsResponse

-
-public PullExecStatisticsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public ChunkHolder getReturn()
-
-
- -
Returns:
returns ChunkHolder
-
-
-
- -

-setReturn

-
-public void setReturn(ChunkHolder _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
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- -compbio.data.msa.jaxws -
-Class ResultNotAvailableExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
-
-
-
-
public class ResultNotAvailableExceptionBean
extends Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
ResultNotAvailableExceptionBean() - -
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- StringgetMessage() - -
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- voidsetMessage(String message) - -
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-ResultNotAvailableExceptionBean

-
-public ResultNotAvailableExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(String message)
-
-
-
Parameters:
message - the value for the message property
-
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- -compbio.data.msa.jaxws -
-Class TestAllServices

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestAllServices
-
-
-
-
public class TestAllServices
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestAllServices() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
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-TestAllServices

-
-public TestAllServices()
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- -compbio.data.msa.jaxws -
-Class TestAllServicesResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestAllServicesResponse
-
-
-
-
public class TestAllServicesResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestAllServicesResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-TestAllServicesResponse

-
-public TestAllServicesResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
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- -compbio.data.msa.jaxws -
-Class TestService

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestService
-
-
-
-
public class TestService
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestService() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
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-TestService

-
-public TestService()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
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- -compbio.data.msa.jaxws -
-Class TestServiceResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestServiceResponse
-
-
-
-
public class TestServiceResponse
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestServiceResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-TestServiceResponse

-
-public TestServiceResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(String _return)
-
-
-
Parameters:
_return - the value for the _return property
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- -

- -compbio.data.msa.jaxws -
-Class UnsupportedRuntimeExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
-
-
-
-
public class UnsupportedRuntimeExceptionBean
extends Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
UnsupportedRuntimeExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetMessage() - -
-           
- voidsetMessage(String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-UnsupportedRuntimeExceptionBean

-
-public UnsupportedRuntimeExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(String message)
-
-
-
Parameters:
message - the value for the message property
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- -

- -compbio.data.msa.jaxws -
-Class WrongParameterExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.WrongParameterExceptionBean
-
-
-
-
public class WrongParameterExceptionBean
extends Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
WrongParameterExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetMessage() - -
-           
- voidsetMessage(String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-WrongParameterExceptionBean

-
-public WrongParameterExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(String message)
-
-
-
Parameters:
message - the value for the message property
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compbio.data.msa.jaxws.Align

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-

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compbio.data.msa.jaxws.AlignResponse

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-No usage of compbio.data.msa.jaxws.AlignResponse -

-

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compbio.data.msa.jaxws.Analize

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-

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-Uses of Class
compbio.data.msa.jaxws.AnalizeResponse

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-No usage of compbio.data.msa.jaxws.AnalizeResponse -

-

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compbio.data.msa.jaxws.CancelJob

-
-No usage of compbio.data.msa.jaxws.CancelJob -

-

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compbio.data.msa.jaxws.CancelJobResponse

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-No usage of compbio.data.msa.jaxws.CancelJobResponse -

-

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compbio.data.msa.jaxws.CustomAlign

-
-No usage of compbio.data.msa.jaxws.CustomAlign -

-

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Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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compbio.data.msa.jaxws.CustomAlignResponse

-
-No usage of compbio.data.msa.jaxws.CustomAlignResponse -

-

- - - - - - - - - - - - - - - -
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compbio.data.msa.jaxws.CustomAnalize

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-No usage of compbio.data.msa.jaxws.CustomAnalize -

-

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compbio.data.msa.jaxws.CustomAnalizeResponse

-
-No usage of compbio.data.msa.jaxws.CustomAnalizeResponse -

-

- - - - - - - - - - - - - - - -
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compbio.data.msa.jaxws.GetAnnotation

-
-No usage of compbio.data.msa.jaxws.GetAnnotation -

-

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compbio.data.msa.jaxws.GetAnnotationResponse

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-No usage of compbio.data.msa.jaxws.GetAnnotationResponse -

-

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compbio.data.msa.jaxws.GetJobStatus

-
-No usage of compbio.data.msa.jaxws.GetJobStatus -

-

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compbio.data.msa.jaxws.GetJobStatusResponse

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-No usage of compbio.data.msa.jaxws.GetJobStatusResponse -

-

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compbio.data.msa.jaxws.GetLastTested

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-No usage of compbio.data.msa.jaxws.GetLastTested -

-

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compbio.data.msa.jaxws.GetLastTestedOnResponse

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compbio.data.msa.jaxws.GetLastTestedResponse

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compbio.data.msa.jaxws.GetLimit

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compbio.data.msa.jaxws.GetLimitResponse

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compbio.data.msa.jaxws.GetLimits

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compbio.data.msa.jaxws.GetLimitsResponse

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compbio.data.msa.jaxws.GetPresets

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compbio.data.msa.jaxws.GetPresetsResponse

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compbio.data.msa.jaxws.GetResult

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compbio.data.msa.jaxws.GetResultResponse

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compbio.data.msa.jaxws.GetRunnerOptions

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compbio.data.msa.jaxws.GetRunnerOptionsResponse

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compbio.data.msa.jaxws.GetSupportedServices

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compbio.data.msa.jaxws.GetSupportedServicesResponse

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compbio.data.msa.jaxws.IsOperating

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compbio.data.msa.jaxws.IsOperatingResponse

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compbio.data.msa.jaxws.JobSubmissionExceptionBean

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compbio.data.msa.jaxws.LimitExceededExceptionBean

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compbio.data.msa.jaxws.PresetAlign

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-Classes  - -
-Align -
-AlignResponse -
-Analize -
-AnalizeResponse -
-CancelJob -
-CancelJobResponse -
-CustomAlign -
-CustomAlignResponse -
-CustomAnalize -
-CustomAnalizeResponse -
-GetAnnotation -
-GetAnnotationResponse -
-GetJobStatus -
-GetJobStatusResponse -
-GetLastTested -
-GetLastTestedOn -
-GetLastTestedOnResponse -
-GetLastTestedResponse -
-GetLimit -
-GetLimitResponse -
-GetLimits -
-GetLimitsResponse -
-GetPresets -
-GetPresetsResponse -
-GetResult -
-GetResultResponse -
-GetRunnerOptions -
-GetRunnerOptionsResponse -
-GetSupportedServices -
-GetSupportedServicesResponse -
-IsOperating -
-IsOperatingResponse -
-JobSubmissionExceptionBean -
-LimitExceededExceptionBean -
-PresetAlign -
-PresetAlignResponse -
-PresetAnalize -
-PresetAnalizeResponse -
-PullExecStatistics -
-PullExecStatisticsResponse -
-ResultNotAvailableExceptionBean -
-TestAllServices -
-TestAllServicesResponse -
-TestService -
-TestServiceResponse -
-UnsupportedRuntimeExceptionBean -
-WrongParameterExceptionBean
- - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html b/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html deleted file mode 100644 index 134c774..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -compbio.data.msa.jaxws - - - - - - - - - - - - -
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-Class Summary
Align 
AlignResponse 
Analize 
AnalizeResponse 
CancelJob 
CancelJobResponse 
CustomAlign 
CustomAlignResponse 
CustomAnalize 
CustomAnalizeResponse 
GetAnnotation 
GetAnnotationResponse 
GetJobStatus 
GetJobStatusResponse 
GetLastTested 
GetLastTestedOn 
GetLastTestedOnResponse 
GetLastTestedResponse 
GetLimit 
GetLimitResponse 
GetLimits 
GetLimitsResponse 
GetPresets 
GetPresetsResponse 
GetResult 
GetResultResponse 
GetRunnerOptions 
GetRunnerOptionsResponse 
GetSupportedServices 
GetSupportedServicesResponse 
IsOperating 
IsOperatingResponse 
JobSubmissionExceptionBeanThis class was generated by the JAX-WS RI.
LimitExceededExceptionBeanThis class was generated by the JAX-WS RI.
PresetAlign 
PresetAlignResponse 
PresetAnalize 
PresetAnalizeResponse 
PullExecStatistics 
PullExecStatisticsResponse 
ResultNotAvailableExceptionBeanThis class was generated by the JAX-WS RI.
TestAllServices 
TestAllServicesResponse 
TestService 
TestServiceResponse 
UnsupportedRuntimeExceptionBeanThis class was generated by the JAX-WS RI.
WrongParameterExceptionBeanThis class was generated by the JAX-WS RI.
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-Interfaces  - -
-JABAService -
-JManagement -
-Metadata -
-MsaWS -
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-SequenceAnnotation
- - - - diff --git a/website/full_javadoc/compbio/data/msa/package-summary.html b/website/full_javadoc/compbio/data/msa/package-summary.html deleted file mode 100644 index 3c6978e..0000000 --- a/website/full_javadoc/compbio/data/msa/package-summary.html +++ /dev/null @@ -1,198 +0,0 @@ - - - - - - -compbio.data.msa - - - - - - - - - - - - -
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-Package compbio.data.msa -

-Web Service interfaces for JAva Bioinformatics Analysis Web Services. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Interface Summary
JABAServiceThis is a marker interface, contains no methods
JManagement 
Metadata<T> 
MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
RegistryWSJABAWS services registry
SequenceAnnotation<T>Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  - -

-

-Package compbio.data.msa Description -

- -

-Web Service interfaces for JAva Bioinformatics Analysis Web Services. -

- -

-

-
Version:
-
1.0 April 2010
-
Author:
-
Peter Troshin
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-Uses of Package
compbio.data.msa

-
- - - - - - - - - - - - - - - - - -
-Packages that use compbio.data.msa
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.msa used by compbio.data.msa
JABAService - -
-          This is a marker interface, contains no methods
JManagement - -
-           
Metadata - -
-           
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.msa used by compbio.ws.client
JABAService - -
-          This is a marker interface, contains no methods
RegistryWS - -
-          JABAWS services registry
SequenceAnnotation - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

- - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.data.msa used by compbio.ws.server
JABAService - -
-          This is a marker interface, contains no methods
JManagement - -
-           
Metadata - -
-           
MsaWS - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
RegistryWS - -
-          JABAWS services registry
SequenceAnnotation - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/sequence/Alignment.html b/website/full_javadoc/compbio/data/sequence/Alignment.html deleted file mode 100644 index ce29939..0000000 --- a/website/full_javadoc/compbio/data/sequence/Alignment.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - -Alignment - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class Alignment

-
-java.lang.Object
-  extended by compbio.data.sequence.Alignment
-
-
-
-
@Immutable
-public final class Alignment
extends Object
- - -

-Multiple sequence alignment. - - Does not give any guarantees on the content of individual FastaSequece - records. It does not guarantee neither the uniqueness of the names of - sequences nor it guarantees the uniqueness of the sequences. -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
pvtroshin
-
See Also:
FastaSequence, -AlignmentMetadata
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-           
Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-          Please note that this implementation does not take the order of sequences - into account!
- AlignmentMetadatagetMetadata() - -
-           
- List<FastaSequence>getSequences() - -
-           
- intgetSize() - -
-           
- inthashCode() - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Alignment

-
-public Alignment(List<FastaSequence> sequences,
-                 Program program,
-                 char gapchar)
-
-
-
Parameters:
sequences -
program -
gapchar -
-
-
- -

-Alignment

-
-public Alignment(List<FastaSequence> sequences,
-                 AlignmentMetadata metadata)
-
-
-
Parameters:
sequences -
metadata -
-
- - - - - - - - -
-Method Detail
- -

-getSequences

-
-public List<FastaSequence> getSequences()
-
-
- -
Returns:
list of FastaSequence records
-
-
-
- -

-getSize

-
-public int getSize()
-
-
- -
Returns:
a number of sequence in the alignment
-
-
-
- -

-getMetadata

-
-public AlignmentMetadata getMetadata()
-
-
- -
Returns:
AlignmentMetadata object
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
Please note that this implementation does not take the order of sequences - into account! -

-

-
Overrides:
equals in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html deleted file mode 100644 index cf21ebf..0000000 --- a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -AlignmentMetadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class AlignmentMetadata

-
-java.lang.Object
-  extended by compbio.data.sequence.AlignmentMetadata
-
-
-
-
@Immutable
-public class AlignmentMetadata
extends Object
- - -

-Alignment metadata e.g. method/program being used to generate the alignment - and its parameters -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
AlignmentMetadata(Program program, - char gapchar) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- chargetGapchar() - -
-           
- ProgramgetProgram() - -
-           
- inthashCode() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-AlignmentMetadata

-
-public AlignmentMetadata(Program program,
-                         char gapchar)
-
-
- - - - - - - - -
-Method Detail
- -

-getProgram

-
-public Program getProgram()
-
-
-
-
-
-
- -

-getGapchar

-
-public char getGapchar()
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index 1df3a86..0000000 --- a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html +++ /dev/null @@ -1,387 +0,0 @@ - - - - - - -ClustalAlignmentUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class ClustalAlignmentUtil

-
-java.lang.Object
-  extended by compbio.data.sequence.ClustalAlignmentUtil
-
-
-
-
public final class ClustalAlignmentUtil
extends Object
- - -

-Tools to read and write clustal formated files -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
Petr Troshin based on jimp class
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static chargapchar - -
-          Dash char to be used as gap char in the alignments
-  - - - - - - - - - - -
-Constructor Summary
ClustalAlignmentUtil() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleanisValidClustalFile(InputStream input) - -
-          Please note this method closes the input stream provided as a parameter
-static AlignmentreadClustalFile(File file) - -
-           
-static AlignmentreadClustalFile(InputStream instream) - -
-          Read Clustal formatted alignment.
-static voidwriteClustalAlignment(Writer out, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-gapchar

-
-public static final char gapchar
-
-
Dash char to be used as gap char in the alignments -

-

-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-ClustalAlignmentUtil

-
-public ClustalAlignmentUtil()
-
-
- - - - - - - - -
-Method Detail
- -

-readClustalFile

-
-public static Alignment readClustalFile(InputStream instream)
-                                 throws IOException,
-                                        UnknownFileFormatException
-
-
Read Clustal formatted alignment. Limitations: Does not read consensus - - Sequence names as well as the sequences are not guaranteed to be unique! -

-

- -
Throws: -
{@link - IOException} -
{@link - UnknownFileFormatException} -
IOException -
UnknownFileFormatException
-
-
-
- -

-isValidClustalFile

-
-public static boolean isValidClustalFile(InputStream input)
-
-
Please note this method closes the input stream provided as a parameter -

-

-
Parameters:
input - -
Returns:
true if the file is recognised as Clustal formatted alignment, - false otherwise
-
-
-
- -

-writeClustalAlignment

-
-public static void writeClustalAlignment(Writer out,
-                                         Alignment alignment)
-                                  throws IOException
-
-
Write Clustal formatted alignment Limitations: does not record the - consensus. Potential bug - records 60 chars length alignment where - Clustal would have recorded 50 chars. -

-

-
Parameters:
out -
alignment - -
Throws: -
IOException
-
-
-
- -

-readClustalFile

-
-public static Alignment readClustalFile(File file)
-                                 throws UnknownFileFormatException,
-                                        IOException
-
-
- -
Throws: -
UnknownFileFormatException -
IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/ConservationMethod.html b/website/full_javadoc/compbio/data/sequence/ConservationMethod.html deleted file mode 100644 index dc88967..0000000 --- a/website/full_javadoc/compbio/data/sequence/ConservationMethod.html +++ /dev/null @@ -1,605 +0,0 @@ - - - - - - -ConservationMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum ConservationMethod

-
-java.lang.Object
-  extended by java.lang.Enum<ConservationMethod>
-      extended by compbio.data.sequence.ConservationMethod
-
-
-
All Implemented Interfaces:
Serializable, Comparable<ConservationMethod>
-
-
-
-
public enum ConservationMethod
extends Enum<ConservationMethod>
- - -

-Enumeration listing of all the supported methods. -

- -

-

-
Author:
-
Agnieszka Golicz & Peter Troshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
ARMON - -
-           
GERSTEIN - -
-           
JORES - -
-           
KABAT - -
-           
KARLIN - -
-           
LANDGRAF - -
-           
MIRNY - -
-           
NOT_LANCET - -
-           
SANDER - -
-           
SCHNEIDER - -
-           
SHENKIN - -
-           
SMERFS - -
-           
TAYLOR_GAPS - -
-           
TAYLOR_NO_GAPS - -
-           
THOMPSON - -
-           
VALDAR - -
-           
WILLIAMSON - -
-           
ZVELIBIL - -
-           
-  - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static ConservationMethodgetMethod(String meth) - -
-           
-static ConservationMethodvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static ConservationMethod[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-KABAT

-
-public static final ConservationMethod KABAT
-
-
-
-
-
- -

-JORES

-
-public static final ConservationMethod JORES
-
-
-
-
-
- -

-SCHNEIDER

-
-public static final ConservationMethod SCHNEIDER
-
-
-
-
-
- -

-SHENKIN

-
-public static final ConservationMethod SHENKIN
-
-
-
-
-
- -

-GERSTEIN

-
-public static final ConservationMethod GERSTEIN
-
-
-
-
-
- -

-TAYLOR_GAPS

-
-public static final ConservationMethod TAYLOR_GAPS
-
-
-
-
-
- -

-TAYLOR_NO_GAPS

-
-public static final ConservationMethod TAYLOR_NO_GAPS
-
-
-
-
-
- -

-ZVELIBIL

-
-public static final ConservationMethod ZVELIBIL
-
-
-
-
-
- -

-KARLIN

-
-public static final ConservationMethod KARLIN
-
-
-
-
-
- -

-ARMON

-
-public static final ConservationMethod ARMON
-
-
-
-
-
- -

-THOMPSON

-
-public static final ConservationMethod THOMPSON
-
-
-
-
-
- -

-NOT_LANCET

-
-public static final ConservationMethod NOT_LANCET
-
-
-
-
-
- -

-MIRNY

-
-public static final ConservationMethod MIRNY
-
-
-
-
-
- -

-WILLIAMSON

-
-public static final ConservationMethod WILLIAMSON
-
-
-
-
-
- -

-LANDGRAF

-
-public static final ConservationMethod LANDGRAF
-
-
-
-
-
- -

-SANDER

-
-public static final ConservationMethod SANDER
-
-
-
-
-
- -

-VALDAR

-
-public static final ConservationMethod VALDAR
-
-
-
-
-
- -

-SMERFS

-
-public static final ConservationMethod SMERFS
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static ConservationMethod[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (ConservationMethod c : ConservationMethod.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static ConservationMethod valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
-
- -

-getMethod

-
-public static ConservationMethod getMethod(String meth)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/DisorderMethod.html b/website/full_javadoc/compbio/data/sequence/DisorderMethod.html deleted file mode 100644 index 49a1d9f..0000000 --- a/website/full_javadoc/compbio/data/sequence/DisorderMethod.html +++ /dev/null @@ -1,322 +0,0 @@ - - - - - - -DisorderMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum DisorderMethod

-
-java.lang.Object
-  extended by java.lang.Enum<DisorderMethod>
-      extended by compbio.data.sequence.DisorderMethod
-
-
-
All Implemented Interfaces:
Serializable, Comparable<DisorderMethod>
-
-
-
-
public enum DisorderMethod
extends Enum<DisorderMethod>
- - -

-

- -

- - - - - - - - - - - - - -
-Enum Constant Summary
Disembl - -
-           
JRonn - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static DisorderMethodvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static DisorderMethod[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-JRonn

-
-public static final DisorderMethod JRonn
-
-
-
-
-
- -

-Disembl

-
-public static final DisorderMethod Disembl
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static DisorderMethod[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (DisorderMethod c : DisorderMethod.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static DisorderMethod valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/FastaReader.html b/website/full_javadoc/compbio/data/sequence/FastaReader.html deleted file mode 100644 index 868b43e..0000000 --- a/website/full_javadoc/compbio/data/sequence/FastaReader.html +++ /dev/null @@ -1,415 +0,0 @@ - - - - - - -FastaReader - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.sequence -
-Class FastaReader

-
-java.lang.Object
-  extended by compbio.data.sequence.FastaReader
-
-
-
All Implemented Interfaces:
Iterator<FastaSequence>
-
-
-
-
public class FastaReader
extends Object
implements Iterator<FastaSequence>
- - -

-Reads files with FASTA formatted sequences. All the information in the FASTA - header is preserved including trailing white spaces. All the white spaces are - removed from the sequence. - - Examples of the correct input: - - 

- 
- >zedpshvyzg
- GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
- 
- >xovkactesa
- CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
- FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
- FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
- DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
- 
- >ntazzewyvv
- CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
- EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      
- EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW 
-   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
-   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
-   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
- 
-    > 12 d t y wi               k       jbke    
-   KLSHHDCD
-    N
-     H
-     HSKCTEPHCGNSHQMLHRDP
-     CCDQCQSWEAENWCASMRKAILF
- 
-
-

- -

-

-
Version:
-
1.0 April 2011
-
Author:
-
Peter Troshin
-
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
FastaReader(InputStream inputStream) - -
-          This class will not close the incoming stream! So the client should do - so.
FastaReader(String inputFile) - -
-          Header data can contain non-ASCII symbols and read in UTF8
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidclose() - -
-          Call this method to close the connection to the input file if you want to - free up the resources.
- booleanhasNext() - -
-          
- FastaSequencenext() - -
-          Reads the next FastaSequence from the input
- voidremove() - -
-          Not implemented
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-FastaReader

-
-public FastaReader(String inputFile)
-            throws FileNotFoundException
-
-
Header data can contain non-ASCII symbols and read in UTF8 -

-

-
Parameters:
inputFile - the file containing the list of FASTA formatted sequences to - read from -
Throws: -
FileNotFoundException - if the input file is not found -
IllegalStateException - if the close method was called on this instance
-
-
- -

-FastaReader

-
-public FastaReader(InputStream inputStream)
-            throws FileNotFoundException
-
-
This class will not close the incoming stream! So the client should do - so. -

-

-
Parameters:
inputStream - -
Throws: -
FileNotFoundException
-
- - - - - - - - -
-Method Detail
- -

-hasNext

-
-public boolean hasNext()
-
-
-

-

-
Specified by:
hasNext in interface Iterator<FastaSequence>
-
-
- -
Throws: -
IllegalStateException - if the close method was called on this instance
-
-
-
- -

-next

-
-public FastaSequence next()
-
-
Reads the next FastaSequence from the input -

-

-
Specified by:
next in interface Iterator<FastaSequence>
-
-
- -
Throws: -
AssertionError - if the header or the sequence is missing -
IllegalStateException - if the close method was called on this instance
-
-
-
- -

-remove

-
-public void remove()
-
-
Not implemented -

-

-
Specified by:
remove in interface Iterator<FastaSequence>
-
-
-
-
-
-
- -

-close

-
-public void close()
-
-
Call this method to close the connection to the input file if you want to - free up the resources. The connection will be closed on the JVM shutdown - if this method was not called explicitly. No further reading on this - instance of the FastaReader will be possible after calling this method. -

-

-
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index 364a74a..0000000 --- a/website/full_javadoc/compbio/data/sequence/FastaSequence.html +++ /dev/null @@ -1,471 +0,0 @@ - - - - - - -FastaSequence - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.sequence -
-Class FastaSequence

-
-java.lang.Object
-  extended by compbio.data.sequence.FastaSequence
-
-
-
-
@Immutable
-public class FastaSequence
extends Object
- - -

-A FASTA formatted sequence. Please note that this class does not make any - assumptions as to what sequence it stores e.g. it could be nucleotide, - protein or even gapped alignment sequence! The only guarantee it makes is - that the sequence does not contain white space characters e.g. spaces, new - lines etc -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
FastaSequence(String id, - String sequence) - -
-          Upon construction the any whitespace characters are removed from the - sequence
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static intcountMatchesInSequence(String theString, - String theRegExp) - -
-           
- booleanequals(Object obj) - -
-           
- StringgetFormatedSequence(int width) - -
-          Format sequence per width letter in one string.
- StringgetFormattedFasta() - -
-           
- StringgetId() - -
-          Gets the value of id
- intgetLength() - -
-           
- StringgetOnelineFasta() - -
-           
- StringgetSequence() - -
-          Gets the value of sequence
- inthashCode() - -
-           
- StringtoString() - -
-          Same as oneLineFasta
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-FastaSequence

-
-public FastaSequence(String id,
-                     String sequence)
-
-
Upon construction the any whitespace characters are removed from the - sequence -

-

-
Parameters:
id -
sequence -
-
- - - - - - - - -
-Method Detail
- -

-getId

-
-public String getId()
-
-
Gets the value of id -

-

- -
Returns:
the value of id
-
-
-
- -

-getSequence

-
-public String getSequence()
-
-
Gets the value of sequence -

-

- -
Returns:
the value of sequence
-
-
-
- -

-countMatchesInSequence

-
-public static int countMatchesInSequence(String theString,
-                                         String theRegExp)
-
-
-
-
-
-
- -

-getFormattedFasta

-
-public String getFormattedFasta()
-
-
-
-
-
-
- -

-getOnelineFasta

-
-public String getOnelineFasta()
-
-
- -
Returns:
one line name, next line sequence, no matter what the sequence - length is
-
-
-
- -

-getFormatedSequence

-
-public String getFormatedSequence(int width)
-
-
Format sequence per width letter in one string. Without spaces. -

-

- -
Returns:
multiple line formated sequence, one line width letters length
-
-
-
- -

-getLength

-
-public int getLength()
-
-
- -
Returns:
sequence length
-
-
-
- -

-toString

-
-public String toString()
-
-
Same as oneLineFasta -

-

-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/Program.html b/website/full_javadoc/compbio/data/sequence/Program.html deleted file mode 100644 index 92ec97d..0000000 --- a/website/full_javadoc/compbio/data/sequence/Program.html +++ /dev/null @@ -1,388 +0,0 @@ - - - - - - -Program - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum Program

-
-java.lang.Object
-  extended by java.lang.Enum<Program>
-      extended by compbio.data.sequence.Program
-
-
-
All Implemented Interfaces:
Serializable, Comparable<Program>
-
-
-
-
public enum Program
extends Enum<Program>
- - -

-The list of programmes that can produce alignments -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CLUSTAL - -
-          ClustalW
MAFFT - -
-          Mafft
MUSCLE - -
-          Muscle
Probcons - -
-          Probcons
Tcoffee - -
-          Tcoffee
-  - - - - - - - - - - - - - - - -
-Method Summary
-static ProgramvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static Program[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-CLUSTAL

-
-public static final Program CLUSTAL
-
-
ClustalW -

-

-
-
-
- -

-MAFFT

-
-public static final Program MAFFT
-
-
Mafft -

-

-
-
-
- -

-MUSCLE

-
-public static final Program MUSCLE
-
-
Muscle -

-

-
-
-
- -

-Tcoffee

-
-public static final Program Tcoffee
-
-
Tcoffee -

-

-
-
-
- -

-Probcons

-
-public static final Program Probcons
-
-
Probcons -

-

-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static Program[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (Program c : Program.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static Program valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/Range.html b/website/full_javadoc/compbio/data/sequence/Range.html deleted file mode 100644 index 7f10689..0000000 --- a/website/full_javadoc/compbio/data/sequence/Range.html +++ /dev/null @@ -1,394 +0,0 @@ - - - - - - -Range - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.sequence -
-Class Range

-
-java.lang.Object
-  extended by compbio.data.sequence.Range
-
-
-
All Implemented Interfaces:
Comparable<Range>
-
-
-
-
public class Range
extends Object
implements Comparable<Range>
- - -

-

- -

- - - - - - - - - - - - - - - -
-Field Summary
- intfrom - -
-           
- intto - -
-           
-  - - - - - - - - - - - - - -
-Constructor Summary
Range(int from, - int to) - -
-           
Range(String[] twoElementAr) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(Range o) - -
-           
- booleanequals(Object obj) - -
-           
- inthashCode() - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-from

-
-public final int from
-
-
-
-
-
- -

-to

-
-public final int to
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-Range

-
-public Range(int from,
-             int to)
-
-
-
- -

-Range

-
-public Range(String[] twoElementAr)
-
-
- - - - - - - - -
-Method Detail
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-compareTo

-
-public int compareTo(Range o)
-
-
-
Specified by:
compareTo in interface Comparable<Range>
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html deleted file mode 100644 index a47cf0e..0000000 --- a/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - -SMERFSConstraints - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum SMERFSConstraints

-
-java.lang.Object
-  extended by java.lang.Enum<SMERFSConstraints>
-      extended by compbio.data.sequence.SMERFSConstraints
-
-
-
All Implemented Interfaces:
Serializable, Comparable<SMERFSConstraints>
-
-
-
-
public enum SMERFSConstraints
extends Enum<SMERFSConstraints>
- - -

-Enumeration defining two constraints for SMERFS columns score calculation. - MAX_SCORE gives the highest core of all the windows the column belongs to. - MID_SCORE gives the window score to the column in the middle. -

- -

-

-
Author:
-
Agnieszka Golicz & Peter Troshin
-
-
- -

- - - - - - - - - - - - - -
-Enum Constant Summary
MAX_SCORE - -
-           
MID_SCORE - -
-           
-  - - - - - - - - - - - - - - - - - - -
-Field Summary
-static SMERFSConstraintsDEFAULT_COLUMN_SCORE - -
-          Default column scoring schema
-static doubleDEFAULT_GAP_THRESHOLD - -
-          Default gap threshold value for SMERFS algorithm
-static intDEFAULT_WINDOW_SIZE - -
-          Default window size value for SMERFS algorithm
-  - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static SMERFSConstraintsgetSMERFSColumnScore(String score) - -
-           
-static SMERFSConstraintsvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static SMERFSConstraints[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-MAX_SCORE

-
-public static final SMERFSConstraints MAX_SCORE
-
-
-
-
-
- -

-MID_SCORE

-
-public static final SMERFSConstraints MID_SCORE
-
-
-
-
- - - - - - - - -
-Field Detail
- -

-DEFAULT_COLUMN_SCORE

-
-public static final SMERFSConstraints DEFAULT_COLUMN_SCORE
-
-
Default column scoring schema -

-

-
-
-
- -

-DEFAULT_WINDOW_SIZE

-
-public static final int DEFAULT_WINDOW_SIZE
-
-
Default window size value for SMERFS algorithm -

-

-
See Also:
Constant Field Values
-
-
- -

-DEFAULT_GAP_THRESHOLD

-
-public static final double DEFAULT_GAP_THRESHOLD
-
-
Default gap threshold value for SMERFS algorithm -

-

-
See Also:
Constant Field Values
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static SMERFSConstraints[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (SMERFSConstraints c : SMERFSConstraints.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static SMERFSConstraints valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
-
- -

-getSMERFSColumnScore

-
-public static SMERFSConstraints getSMERFSColumnScore(String score)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/Score.html b/website/full_javadoc/compbio/data/sequence/Score.html deleted file mode 100644 index cb0ea67..0000000 --- a/website/full_javadoc/compbio/data/sequence/Score.html +++ /dev/null @@ -1,537 +0,0 @@ - - - - - - -Score - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
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- - - -
- -

- -compbio.data.sequence -
-Class Score

-
-java.lang.Object
-  extended by compbio.data.sequence.Score
-
-
-
All Implemented Interfaces:
Comparable<Score>
-
-
-
-
@Immutable
-public class Score
extends Object
implements Comparable<Score>
- - -

-A value class for AACon annotation results storage. The objects of this type - are immutable -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - -
-Constructor Summary
Score(Enum<?> method, - ArrayList<Float> scores) - -
-          Instantiate the Score
Score(Enum<?> method, - ArrayList<Float> scores, - TreeSet<Range> ranges) - -
-           
Score(Enum<?> method, - float[] scores) - -
-           
Score(Enum<?> method, - TreeSet<Range> ranges) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(Score o) - -
-           
- booleanequals(Object obj) - -
-           
- StringgetMethod() - -
-          Returns the ConservationMethod
- TreeSet<Range>getRanges() - -
-          Return Ranges if any Collections.EMPTY_SET otherwise
- ArrayList<Float>getScores() - -
-          The column scores for the alignment
- inthashCode() - -
-           
- voidsetRanges(TreeSet<Range> ranges) - -
-           
- StringtoString() - -
-           
-static voidwrite(TreeSet<Score> scores, - Writer writer) - -
-          Outputs the List of Score objects into the Output stream.
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Score

-
-public Score(Enum<?> method,
-             ArrayList<Float> scores)
-
-
Instantiate the Score -

-

-
Parameters:
method - the ConservationMethod with which scores were - calculated
scores - the actual conservation values for each column of the - alignment
-
-
- -

-Score

-
-public Score(Enum<?> method,
-             ArrayList<Float> scores,
-             TreeSet<Range> ranges)
-
-
-
Parameters:
method - the ConservationMethod with which scores were - calculated
scores - the actual conservation values for each column of the - alignment
ranges - The set of ranges i.e. parts of the sequence with specific - function, usually can be calculated based on scores
-
-
- -

-Score

-
-public Score(Enum<?> method,
-             TreeSet<Range> ranges)
-
-
-
- -

-Score

-
-public Score(Enum<?> method,
-             float[] scores)
-
-
- - - - - - - - -
-Method Detail
- -

-getMethod

-
-public String getMethod()
-
-
Returns the ConservationMethod -

-

-
-
-
- -
Returns:
the ConservationMethod
-
-
-
- -

-getScores

-
-public ArrayList<Float> getScores()
-
-
The column scores for the alignment -

-

-
-
-
- -
Returns:
the column scores for the alignment
-
-
-
- -

-getRanges

-
-public TreeSet<Range> getRanges()
-
-
Return Ranges if any Collections.EMPTY_SET otherwise -

-

-
-
-
- -
Returns:
ordered set of Range
-
-
-
- -

-setRanges

-
-public void setRanges(TreeSet<Range> ranges)
-
-
-
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-write

-
-public static void write(TreeSet<Score> scores,
-                         Writer writer)
-                  throws IOException
-
-
Outputs the List of Score objects into the Output stream. The output - format is as follows: - - 
- #MethodName <space separated list of values>
- 	  
- For example:
- 	 
- #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
- #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
- 
-
- - The maximum precision for values is 3 digits, but can be less. -

-

-
-
-
-
Parameters:
scores - the list of scores to output
writer - -
Throws: -
IOException - if the OutputStream cannot be written into -
NullPointerException - if the output stream is null
-
-
-
- -

-compareTo

-
-public int compareTo(Score o)
-
-
-
Specified by:
compareTo in interface Comparable<Score>
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html b/website/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html deleted file mode 100644 index 7ca1a2e..0000000 --- a/website/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html +++ /dev/null @@ -1,380 +0,0 @@ - - - - - - -ScoreManager.ScoreHolder - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.sequence -
-Class ScoreManager.ScoreHolder

-
-java.lang.Object
-  extended by compbio.data.sequence.ScoreManager.ScoreHolder
-
-
-
Enclosing class:
ScoreManager
-
-
-
-
public static class ScoreManager.ScoreHolder
extends Object
- - -

-

- -

- - - - - - - - - - - - - - - -
-Field Summary
- Stringid - -
-           
- TreeSet<Score>scores - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- intgetNumberOfScores() - -
-           
- ScoregetScoreByMethod(Enum<?> method) - -
-           
- ScoregetScoreByMethod(String method) - -
-           
- inthashCode() - -
-           
- voidwriteOut(Writer writer) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-id

-
-public String id
-
-
-
-
-
- -

-scores

-
-public TreeSet<Score> scores
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-writeOut

-
-public void writeOut(Writer writer)
-              throws IOException
-
-
- -
Throws: -
IOException
-
-
-
- -

-getScoreByMethod

-
-public Score getScoreByMethod(Enum<?> method)
-
-
-
-
-
-
- -

-getScoreByMethod

-
-public Score getScoreByMethod(String method)
-
-
-
-
-
-
- -

-getNumberOfScores

-
-public int getNumberOfScores()
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/ScoreManager.html b/website/full_javadoc/compbio/data/sequence/ScoreManager.html deleted file mode 100644 index 4612dc7..0000000 --- a/website/full_javadoc/compbio/data/sequence/ScoreManager.html +++ /dev/null @@ -1,452 +0,0 @@ - - - - - - -ScoreManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.sequence -
-Class ScoreManager

-
-java.lang.Object
-  extended by compbio.data.sequence.ScoreManager
-
-
-
-
public class ScoreManager
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Nested Class Summary
-static classScoreManager.ScoreHolder - -
-           
-  - - - - - - - - - - -
-Field Summary
-static StringSINGLE_ENTRY_KEY - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Map<String,TreeSet<Score>>asMap() - -
-           
- Set<Score>asSet() - -
-           
- booleanequals(Object obj) - -
-           
- ScoreManager.ScoreHoldergetAnnotationForSequence(String seqId) - -
-           
- intgetNumberOfSeq() - -
-           
- inthashCode() - -
-           
-static ScoreManagernewInstance(Map<String,Set<Score>> data) - -
-           
-static ScoreManagernewInstanceSingleScore(Map<String,Score> seqScoresMap) - -
-           
-static ScoreManagernewInstanceSingleSequence(Set<Score> data) - -
-           
- voidwriteOut(Writer outStream) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-SINGLE_ENTRY_KEY

-
-public static final String SINGLE_ENTRY_KEY
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Method Detail
- -

-newInstance

-
-public static ScoreManager newInstance(Map<String,Set<Score>> data)
-
-
-
-
-
-
- -

-newInstanceSingleScore

-
-public static ScoreManager newInstanceSingleScore(Map<String,Score> seqScoresMap)
-
-
-
-
-
-
- -

-newInstanceSingleSequence

-
-public static ScoreManager newInstanceSingleSequence(Set<Score> data)
-
-
-
-
-
-
- -

-asMap

-
-public Map<String,TreeSet<Score>> asMap()
-
-
-
-
-
-
- -

-asSet

-
-public Set<Score> asSet()
-
-
-
-
-
-
- -

-getNumberOfSeq

-
-public int getNumberOfSeq()
-
-
-
-
-
-
- -

-getAnnotationForSequence

-
-public ScoreManager.ScoreHolder getAnnotationForSequence(String seqId)
-
-
-
-
-
-
- -

-writeOut

-
-public void writeOut(Writer outStream)
-              throws IOException
-
-
- -
Throws: -
IOException
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index c65f680..0000000 --- a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html +++ /dev/null @@ -1,946 +0,0 @@ - - - - - - -SequenceUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.sequence -
-Class SequenceUtil

-
-java.lang.Object
-  extended by compbio.data.sequence.SequenceUtil
-
-
-
-
public final class SequenceUtil
extends Object
- - -

-Utility class for operations on sequences -

- -

-

-
Since:
-
1.0
-
Version:
-
2.0 June 2011
-
Author:
-
Peter Troshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static PatternAA - -
-          Valid Amino acids
-static PatternAMBIGUOUS_AA - -
-          Same as AA pattern but with two additional letters - XU
-static PatternAMBIGUOUS_NUCLEOTIDE - -
-          Ambiguous nucleotide
-static PatternDIGIT - -
-          A digit
-static PatternNON_AA - -
-          inversion of AA pattern
-static PatternNON_NUCLEOTIDE - -
-          Non nucleotide
-static PatternNONWORD - -
-          Non word
-static PatternNUCLEOTIDE - -
-          Nucleotides a, t, g, c, u
-static PatternWHITE_SPACE - -
-          A whitespace character: [\t\n\x0B\f\r]
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static StringcleanProteinSequence(String sequence) - -
-          Remove all non AA chars from the sequence
-static StringcleanSequence(String sequence) - -
-          Removes all whitespace chars in the sequence string
-static voidcloseSilently(Logger log, - Closeable stream) - -
-          Closes the Closable and logs the exception if any
-static StringdeepCleanSequence(String sequence) - -
-          Removes all special characters and digits as well as whitespace chars - from the sequence
-static booleanisAmbiguosProtein(String sequence) - -
-          Check whether the sequence confirms to amboguous protein sequence
-static booleanisNonAmbNucleotideSequence(String sequence) - -
-          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char
-static booleanisNucleotideSequence(FastaSequence s) - -
-           
-static booleanisProteinSequence(String sequence) - -
-           
-static List<FastaSequence>openInputStream(String inFilePath) - -
-          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
-static HashSet<Score>readAAConResults(InputStream results) - -
-          Read AACon result with no alignment files.
-static HashMap<String,Set<Score>>readDisembl(InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static List<FastaSequence>readFasta(InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-static HashMap<String,Set<Score>>readGlobPlot(InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static Map<String,Score>readIUPred(File result) - -
-          Read IUPred output
-static Map<String,Score>readJRonn(File result) - -
-           
-static Map<String,Score>readJRonn(InputStream inStream) - -
-          Reader for JRonn horizontal file format
-static voidwriteFasta(OutputStream os, - List<FastaSequence> sequences) - -
-          Writes FastaSequence in the file, each sequence will take one line only
-static voidwriteFasta(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
-          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-static voidwriteFastaKeepTheStream(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-WHITE_SPACE

-
-public static final Pattern WHITE_SPACE
-
-
A whitespace character: [\t\n\x0B\f\r] -

-

-
-
-
- -

-DIGIT

-
-public static final Pattern DIGIT
-
-
A digit -

-

-
-
-
- -

-NONWORD

-
-public static final Pattern NONWORD
-
-
Non word -

-

-
-
-
- -

-AA

-
-public static final Pattern AA
-
-
Valid Amino acids -

-

-
-
-
- -

-NON_AA

-
-public static final Pattern NON_AA
-
-
inversion of AA pattern -

-

-
-
-
- -

-AMBIGUOUS_AA

-
-public static final Pattern AMBIGUOUS_AA
-
-
Same as AA pattern but with two additional letters - XU -

-

-
-
-
- -

-NUCLEOTIDE

-
-public static final Pattern NUCLEOTIDE
-
-
Nucleotides a, t, g, c, u -

-

-
-
-
- -

-AMBIGUOUS_NUCLEOTIDE

-
-public static final Pattern AMBIGUOUS_NUCLEOTIDE
-
-
Ambiguous nucleotide -

-

-
-
-
- -

-NON_NUCLEOTIDE

-
-public static final Pattern NON_NUCLEOTIDE
-
-
Non nucleotide -

-

-
-
- - - - - - - - -
-Method Detail
- -

-isNucleotideSequence

-
-public static boolean isNucleotideSequence(FastaSequence s)
-
-
- -
Returns:
true is the sequence contains only letters a,c, t, g, u
-
-
-
- -

-isNonAmbNucleotideSequence

-
-public static boolean isNonAmbNucleotideSequence(String sequence)
-
-
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -

-

-
-
-
-
- -

-cleanSequence

-
-public static String cleanSequence(String sequence)
-
-
Removes all whitespace chars in the sequence string -

-

-
Parameters:
sequence - -
Returns:
cleaned up sequence
-
-
-
- -

-deepCleanSequence

-
-public static String deepCleanSequence(String sequence)
-
-
Removes all special characters and digits as well as whitespace chars - from the sequence -

-

-
Parameters:
sequence - -
Returns:
cleaned up sequence
-
-
-
- -

-cleanProteinSequence

-
-public static String cleanProteinSequence(String sequence)
-
-
Remove all non AA chars from the sequence -

-

-
Parameters:
sequence - the sequence to clean -
Returns:
cleaned sequence
-
-
-
- -

-isProteinSequence

-
-public static boolean isProteinSequence(String sequence)
-
-
-
Parameters:
sequence - -
Returns:
true is the sequence is a protein sequence, false overwise
-
-
-
- -

-isAmbiguosProtein

-
-public static boolean isAmbiguosProtein(String sequence)
-
-
Check whether the sequence confirms to amboguous protein sequence -

-

-
Parameters:
sequence - -
Returns:
return true only if the sequence if ambiguous protein sequence - Return false otherwise. e.g. if the sequence is non-ambiguous - protein or DNA
-
-
-
- -

-writeFasta

-
-public static void writeFasta(OutputStream outstream,
-                              List<FastaSequence> sequences,
-                              int width)
-                       throws IOException
-
-
Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -

-

-
Parameters:
outstream -
sequences -
width - - the maximum number of characters to write in one line -
Throws: -
IOException
-
-
-
- -

-writeFastaKeepTheStream

-
-public static void writeFastaKeepTheStream(OutputStream outstream,
-                                           List<FastaSequence> sequences,
-                                           int width)
-                                    throws IOException
-
-
- -
Throws: -
IOException
-
-
-
- -

-readFasta

-
-public static List<FastaSequence> readFasta(InputStream inStream)
-                                     throws IOException
-
-
Reads fasta sequences from inStream into the list of FastaSequence - objects -

-

-
Parameters:
inStream - from -
Returns:
list of FastaSequence objects -
Throws: -
IOException
-
-
-
- -

-writeFasta

-
-public static void writeFasta(OutputStream os,
-                              List<FastaSequence> sequences)
-                       throws IOException
-
-
Writes FastaSequence in the file, each sequence will take one line only -

-

-
Parameters:
os -
sequences - -
Throws: -
IOException
-
-
-
- -

-readIUPred

-
-public static Map<String,Score> readIUPred(File result)
-                                    throws IOException,
-                                           UnknownFileFormatException
-
-
Read IUPred output -

-

-
Parameters:
result - -
Returns:
Map key->sequence name, value->Score -
Throws: -
IOException -
UnknownFileFormatException
-
-
-
- -

-readJRonn

-
-public static Map<String,Score> readJRonn(File result)
-                                   throws IOException,
-                                          UnknownFileFormatException
-
-
- -
Throws: -
IOException -
UnknownFileFormatException
-
-
-
- -

-readJRonn

-
-public static Map<String,Score> readJRonn(InputStream inStream)
-                                   throws IOException,
-                                          UnknownFileFormatException
-
-
Reader for JRonn horizontal file format - - 
- >Foobar M G D T T A G 0.48 0.42
- 0.42 0.48 0.52 0.53 0.54
- 
- 
- Where all values are tab delimited
-

-

-
Parameters:
inStream - the InputStream connected to the JRonn output file
-
Returns:
Map key=sequence name value=Score
-
Throws:
-
IOException - is thrown if the inStream has problems accessing the data
-
UnknownFileFormatException - is thrown if the inStream represents an unknown source of
- data, i.e. not a JRonn output

-

-
-
- -

-closeSilently

-
-public static final void closeSilently(Logger log,
-                                       Closeable stream)
-
-
Closes the Closable and logs the exception if any -

-

-
Parameters:
log -
stream -
-
-
-
- -

-readDisembl

-
-public static HashMap<String,Set<Score>> readDisembl(InputStream input)
-                                              throws IOException,
-                                                     UnknownFileFormatException
-
-
> Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -

-

-
Parameters:
input - the InputStream -
Returns:
Map key=sequence name, value=set of score -
Throws: -
IOException -
UnknownFileFormatException
-
-
-
- -

-readGlobPlot

-
-public static HashMap<String,Set<Score>> readGlobPlot(InputStream input)
-                                               throws IOException,
-                                                      UnknownFileFormatException
-
-
> Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -

-

-
Parameters:
input - -
Returns:
Map key=sequence name, value=set of score -
Throws: -
IOException -
UnknownFileFormatException
-
-
-
- -

-readAAConResults

-
-public static HashSet<Score> readAAConResults(InputStream results)
-
-
Read AACon result with no alignment files. This method leaves incoming - InputStream open! -

-

-
Parameters:
results - output file of AAConservation -
Returns:
Map with keys ConservationMethod -> float[]
-
-
-
- -

-openInputStream

-
-public static List<FastaSequence> openInputStream(String inFilePath)
-                                           throws IOException,
-                                                  UnknownFileFormatException
-
-
Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects -

-

-
Parameters:
inFilePath - the path to the input file -
Returns:
the List of FastaSequence objects -
Throws: -
IOException - if the file denoted by inFilePath cannot be read -
UnknownFileFormatException - if the inFilePath points to the file which format cannot be - recognised
-
-
- -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html deleted file mode 100644 index 5c7fc70..0000000 --- a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - -UnknownFileFormatException - - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.sequence -
-Class UnknownFileFormatException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.data.sequence.UnknownFileFormatException
-
-
-
All Implemented Interfaces:
Serializable
-
-
-
-
public class UnknownFileFormatException
extends Exception
- - -

-

-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - - - - - - - -
-Constructor Summary
UnknownFileFormatException() - -
-           
UnknownFileFormatException(File file, - Throwable cause) - -
-           
UnknownFileFormatException(String message) - -
-           
UnknownFileFormatException(String message, - Throwable cause) - -
-           
UnknownFileFormatException(Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException()
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(File file,
-                                  Throwable cause)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(String message,
-                                  Throwable cause)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(String message)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(Throwable cause)
-
-
- -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html deleted file mode 100644 index ac64d26..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html +++ /dev/null @@ -1,457 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Alignment - - - - - - - - - - - - -
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-
-

-Uses of Class
compbio.data.sequence.Alignment

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use Alignment
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.server  
-  -

- - - - - -
-Uses of Alignment in compbio.data.msa
-  -

- - - - - - - - - -
Methods in compbio.data.msa that return Alignment
- AlignmentMsaWS.getResult(String jobId) - -
-          Return the result of the job.
-  -

- - - - - -
-Uses of Alignment in compbio.data.msa.jaxws
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws that return Alignment
- AlignmentGetResultResponse.getReturn() - -
-           
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws with parameters of type Alignment
- voidGetResultResponse.setReturn(Alignment _return) - -
-           
-  -

- - - - - -
-Uses of Alignment in compbio.data.sequence
-  -

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return Alignment
-static AlignmentClustalAlignmentUtil.readClustalFile(File file) - -
-           
-static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) - -
-          Read Clustal formatted alignment.
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type Alignment
-static voidClustalAlignmentUtil.writeClustalAlignment(Writer out, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  -

- - - - - -
-Uses of Alignment in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return Alignment
-static AlignmentUtil.readClustalFile(String workDirectory, - String clustFile) - -
-           
-  -

- - - - - -
-Uses of Alignment in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.runner.msa that return Alignment
- AlignmentMafft.getResults(String workDirectory) - -
-           
- AlignmentClustalW.getResults(String workDirectory) - -
-           
- AlignmentTcoffee.getResults(String workDirectory) - -
-           
- AlignmentMuscle.getResults(String workDirectory) - -
-           
- AlignmentClustalO.getResults(String workDirectory) - -
-           
- AlignmentProbcons.getResults(String workDirectory) - -
-           
-  -

- - - - - -
-Uses of Alignment in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.ws.server that return Alignment
- AlignmentClustalWS.getResult(String jobId) - -
-           
- Alignment_MsaService.getResult(String jobId) - -
-           
- AlignmentMuscleWS.getResult(String jobId) - -
-           
- AlignmentMafftWS.getResult(String jobId) - -
-           
- AlignmentTcoffeeWS.getResult(String jobId) - -
-           
- AlignmentProbconsWS.getResult(String jobId) - -
-           
- AlignmentClustalOWS.getResult(String jobId) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html deleted file mode 100644 index b4e4319..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.AlignmentMetadata - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.AlignmentMetadata

-
- - - - - - - - - -
-Packages that use AlignmentMetadata
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of AlignmentMetadata in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return AlignmentMetadata
- AlignmentMetadataAlignment.getMetadata() - -
-           
-  -

- - - - - - - - -
Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-           
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html deleted file mode 100644 index 81189c9..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ClustalAlignmentUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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-Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

-
-No usage of compbio.data.sequence.ClustalAlignmentUtil -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ConservationMethod.html b/website/full_javadoc/compbio/data/sequence/class-use/ConservationMethod.html deleted file mode 100644 index fc170e6..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/ConservationMethod.html +++ /dev/null @@ -1,198 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ConservationMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.ConservationMethod

-
- - - - - - - - - -
-Packages that use ConservationMethod
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of ConservationMethod in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return ConservationMethod
-static ConservationMethodConservationMethod.getMethod(String meth) - -
-           
-static ConservationMethodConservationMethod.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static ConservationMethod[]ConservationMethod.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

- - - - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.DisorderMethod

-
- - - - - - - - - -
-Packages that use DisorderMethod
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of DisorderMethod in compbio.data.sequence
-  -

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return DisorderMethod
-static DisorderMethodDisorderMethod.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static DisorderMethod[]DisorderMethod.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaReader.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaReader.html deleted file mode 100644 index 4548283..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/FastaReader.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.FastaReader - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.FastaReader

-
-No usage of compbio.data.sequence.FastaReader -

-

- - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.FastaSequence

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use FastaSequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.engine  
compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.pipeline._jpred  
compbio.runnerUtilities commonly used by all runners. 
compbio.ws.server  
-  -

- - - - - -
-Uses of FastaSequence in compbio.data.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.msa with type arguments of type FastaSequence
- StringMsaWS.align(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
-          Analyse the sequences.
- StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Analyse the sequences according to custom settings defined in options - list.
- StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
- StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Analyse the sequences according to the preset settings.
-  -

- - - - - -
-Uses of FastaSequence in compbio.data.msa.jaxws
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
- List<FastaSequence>PresetAnalize.getFastaSequences() - -
-           
- List<FastaSequence>PresetAlign.getFastaSequences() - -
-           
- List<FastaSequence>CustomAnalize.getFastaSequences() - -
-           
- List<FastaSequence>CustomAlign.getFastaSequences() - -
-           
- List<FastaSequence>Analize.getFastaSequences() - -
-           
- List<FastaSequence>Align.getFastaSequences() - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
- voidPresetAnalize.setFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidPresetAlign.setFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidCustomAnalize.setFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidCustomAlign.setFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidAnalize.setFastaSequences(List<FastaSequence> fastaSequences) - -
-           
- voidAlign.setFastaSequences(List<FastaSequence> fastaSequences) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return FastaSequence
- FastaSequenceFastaReader.next() - -
-          Reads the next FastaSequence from the input
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
- List<FastaSequence>Alignment.getSequences() - -
-           
-static List<FastaSequence>SequenceUtil.openInputStream(String inFilePath) - -
-          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
-static List<FastaSequence>SequenceUtil.readFasta(InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type FastaSequence
-static booleanSequenceUtil.isNucleotideSequence(FastaSequence s) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.sequence with type arguments of type FastaSequence
-static voidSequenceUtil.writeFasta(OutputStream os, - List<FastaSequence> sequences) - -
-          Writes FastaSequence in the file, each sequence will take one line only
-static voidSequenceUtil.writeFasta(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
-          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-static voidSequenceUtil.writeFastaKeepTheStream(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
-           
-  -

- - - - - - - - - - - -
Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-           
Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.engine
-  -

- - - - - - - - - - - - - -
Method parameters in compbio.engine with type arguments of type FastaSequence
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		LoadBalancer.getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.metadata
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.metadata with type arguments of type FastaSequence
-static intLimit.getAvgSequenceLength(List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- booleanLimit.isExceeded(List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
-static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.pipeline._jpred
-  -

- - - - - - - - -
Constructor parameters in compbio.pipeline._jpred with type arguments of type FastaSequence
Pairwise(List<FastaSequence> sequences) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.runner
-  -

- - - - - - - - - -
Method parameters in compbio.runner with type arguments of type FastaSequence
-static voidUtil.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.ws.server with type arguments of type FastaSequence
- StringClustalWS.align(List<FastaSequence> sequences) - -
-           
- String_MsaService.align(List<FastaSequence> sequences) - -
-           
- StringMuscleWS.align(List<FastaSequence> sequences) - -
-           
- StringMafftWS.align(List<FastaSequence> sequences) - -
-           
- StringTcoffeeWS.align(List<FastaSequence> sequences) - -
-           
- StringProbconsWS.align(List<FastaSequence> sequences) - -
-           
- StringClustalOWS.align(List<FastaSequence> sequences) - -
-           
-static - - - - -
-<T> String
-		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
-           
- StringAAConWS.analize(List<FastaSequence> sequences) - -
-           
- StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
-           
-static - - - - -
-<T> String
-		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
-           
- StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
-           
- StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
-           
- StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
-           
- StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
-           
- StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
-           
- String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-           
- StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
-           
- StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
-           
- StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
-           
- StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
-           
- StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
-           
- StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
-           
- StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
-           
- StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
-           
- StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
-           
- String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-           
- StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
-           
- StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
-           
- StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
-           
- StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
-           
- StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
-           
-static voidWSUtil.validateAAConInput(List<FastaSequence> sequences) - -
-           
-static voidWSUtil.validateFastaInput(List<FastaSequence> sequences) - -
-           
-  -

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-Uses of Class
compbio.data.sequence.Program

-
- - - - - - - - - -
-Packages that use Program
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of Program in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return Program
- ProgramAlignmentMetadata.getProgram() - -
-           
-static ProgramProgram.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static Program[]Program.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

- - - - - - - - - - - -
Constructors in compbio.data.sequence with parameters of type Program
Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
-           
AlignmentMetadata(Program program, - char gapchar) - -
-           
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Range.html b/website/full_javadoc/compbio/data/sequence/class-use/Range.html deleted file mode 100644 index 80cf87f..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Range.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Range - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.Range

-
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-Packages that use Range
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of Range in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type Range
- TreeSet<Range>Score.getRanges() - -
-          Return Ranges if any Collections.EMPTY_SET otherwise
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type Range
- intRange.compareTo(Range o) - -
-           
-  -

- - - - - - - - - -
Method parameters in compbio.data.sequence with type arguments of type Range
- voidScore.setRanges(TreeSet<Range> ranges) - -
-           
-  -

- - - - - - - - - - - -
Constructor parameters in compbio.data.sequence with type arguments of type Range
Score(Enum<?> method, - ArrayList<Float> scores, - TreeSet<Range> ranges) - -
-           
Score(Enum<?> method, - TreeSet<Range> ranges) - -
-           
-  -

-

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-Uses of Class
compbio.data.sequence.SMERFSConstraints

-
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-Packages that use SMERFSConstraints
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of SMERFSConstraints in compbio.data.sequence
-  -

- - - - - - - - - -
Fields in compbio.data.sequence declared as SMERFSConstraints
-static SMERFSConstraintsSMERFSConstraints.DEFAULT_COLUMN_SCORE - -
-          Default column scoring schema
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return SMERFSConstraints
-static SMERFSConstraintsSMERFSConstraints.getSMERFSColumnScore(String score) - -
-           
-static SMERFSConstraintsSMERFSConstraints.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static SMERFSConstraints[]SMERFSConstraints.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Score.html b/website/full_javadoc/compbio/data/sequence/class-use/Score.html deleted file mode 100644 index aecd763..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Score.html +++ /dev/null @@ -1,392 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Score - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.Score

-
- - - - - - - - - - - - - -
-Packages that use Score
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.runnerUtilities commonly used by all runners. 
-  -

- - - - - -
-Uses of Score in compbio.data.sequence
-  -

- - - - - - - - - -
Fields in compbio.data.sequence with type parameters of type Score
- TreeSet<Score>ScoreManager.ScoreHolder.scores - -
-           
-  -

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return Score
- ScoreScoreManager.ScoreHolder.getScoreByMethod(Enum<?> method) - -
-           
- ScoreScoreManager.ScoreHolder.getScoreByMethod(String method) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type Score
- Map<String,TreeSet<Score>>ScoreManager.asMap() - -
-           
- Set<Score>ScoreManager.asSet() - -
-           
-static HashSet<Score>SequenceUtil.readAAConResults(InputStream results) - -
-          Read AACon result with no alignment files.
-static HashMap<String,Set<Score>>SequenceUtil.readDisembl(InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static HashMap<String,Set<Score>>SequenceUtil.readGlobPlot(InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static Map<String,Score>SequenceUtil.readIUPred(File result) - -
-          Read IUPred output
-static Map<String,Score>SequenceUtil.readJRonn(File result) - -
-           
-static Map<String,Score>SequenceUtil.readJRonn(InputStream inStream) - -
-          Reader for JRonn horizontal file format
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type Score
- intScore.compareTo(Score o) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.sequence with type arguments of type Score
-static ScoreManagerScoreManager.newInstance(Map<String,Set<Score>> data) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleScore(Map<String,Score> seqScoresMap) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleSequence(Set<Score> data) - -
-           
-static voidScore.write(TreeSet<Score> scores, - Writer writer) - -
-          Outputs the List of Score objects into the Output stream.
-  -

- - - - - -
-Uses of Score in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return types with arguments of type Score
-static Map<String,Score>Util.readJronnFile(String workDirectory, - String clustFile) - -
-           
-  -

-

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-Uses of Class
compbio.data.sequence.ScoreManager.ScoreHolder

-
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-Packages that use ScoreManager.ScoreHolder
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of ScoreManager.ScoreHolder in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return ScoreManager.ScoreHolder
- ScoreManager.ScoreHolderScoreManager.getAnnotationForSequence(String seqId) - -
-           
-  -

-

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-Uses of Class
compbio.data.sequence.ScoreManager

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use ScoreManager
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.runner.conservation  
compbio.runner.disorder  
compbio.ws.server  
-  -

- - - - - -
-Uses of ScoreManager in compbio.data.msa
-  -

- - - - - - - - - -
Methods in compbio.data.msa that return ScoreManager
- ScoreManagerSequenceAnnotation.getAnnotation(String jobId) - -
-          Return the result of the job.
-  -

- - - - - -
-Uses of ScoreManager in compbio.data.msa.jaxws
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws that return ScoreManager
- ScoreManagerGetAnnotationResponse.getReturn() - -
-           
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws with parameters of type ScoreManager
- voidGetAnnotationResponse.setReturn(ScoreManager _return) - -
-           
-  -

- - - - - -
-Uses of ScoreManager in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return ScoreManager
-static ScoreManagerScoreManager.newInstance(Map<String,Set<Score>> data) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleScore(Map<String,Score> seqScoresMap) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleSequence(Set<Score> data) - -
-           
-  -

- - - - - -
-Uses of ScoreManager in compbio.runner.conservation
-  -

- - - - - - - - - -
Methods in compbio.runner.conservation that return ScoreManager
- ScoreManagerAACon.getResults(String workDirectory) - -
-           
-  -

- - - - - -
-Uses of ScoreManager in compbio.runner.disorder
-  -

- - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.runner.disorder that return ScoreManager
- ScoreManagerJronn.getResults(String workDirectory) - -
-           
- ScoreManagerIUPred.getResults(String workDirectory) - -
-           
- ScoreManagerGlobPlot.getResults(String workDirectory) - -
-           
- ScoreManagerDisembl.getResults(String workDirectory) - -
-           
-  -

- - - - - -
-Uses of ScoreManager in compbio.ws.server
-  -

- - - - - - - - - - - - - -
Methods in compbio.ws.server that return ScoreManager
- ScoreManagerSequenceAnnotationService.getAnnotation(String jobId) - -
-           
-static - - - - -
-<T> ScoreManager
-		WSUtil.getAnnotation(String jobId, - org.apache.log4j.Logger log) - -
-           
-  -

-

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compbio.data.sequence.SequenceUtil

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-
- - - - - - - - - - - - - -
-Packages that use UnknownFileFormatException
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.runnerUtilities commonly used by all runners. 
-  -

- - - - - -
-Uses of UnknownFileFormatException in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that throw UnknownFileFormatException
-static List<FastaSequence>SequenceUtil.openInputStream(String inFilePath) - -
-          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
-static AlignmentClustalAlignmentUtil.readClustalFile(File file) - -
-           
-static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) - -
-          Read Clustal formatted alignment.
-static HashMap<String,Set<Score>>SequenceUtil.readDisembl(InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static HashMap<String,Set<Score>>SequenceUtil.readGlobPlot(InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static Map<String,Score>SequenceUtil.readIUPred(File result) - -
-          Read IUPred output
-static Map<String,Score>SequenceUtil.readJRonn(File result) - -
-           
-static Map<String,Score>SequenceUtil.readJRonn(InputStream inStream) - -
-          Reader for JRonn horizontal file format
-  -

- - - - - -
-Uses of UnknownFileFormatException in compbio.runner
-  -

- - - - - - - - - - - - - -
Methods in compbio.runner that throw UnknownFileFormatException
-static AlignmentUtil.readClustalFile(String workDirectory, - String clustFile) - -
-           
-static Map<String,Score>Util.readJronnFile(String workDirectory, - String clustFile) - -
-           
-  -

-

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-Classes  - -
-Alignment -
-AlignmentMetadata -
-ClustalAlignmentUtil -
-FastaReader -
-FastaSequence -
-Range -
-Score -
-ScoreManager -
-ScoreManager.ScoreHolder -
-SequenceUtil
- - - - - - -
-Enums  - -
-ConservationMethod -
-DisorderMethod -
-Program -
-SMERFSConstraints
- - - - - - -
-Exceptions  - -
-UnknownFileFormatException
- - - - diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html deleted file mode 100644 index bd7d97a..0000000 --- a/website/full_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,256 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -
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-Package compbio.data.sequence -

-A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
AlignmentMultiple sequence alignment.
AlignmentMetadataAlignment metadata e.g.
ClustalAlignmentUtilTools to read and write clustal formated files
FastaReaderReads files with FASTA formatted sequences.
FastaSequenceA FASTA formatted sequence.
Range 
ScoreA value class for AACon annotation results storage.
ScoreManager 
ScoreManager.ScoreHolder 
SequenceUtilUtility class for operations on sequences
-  - -

- - - - - - - - - - - - - - - - - - - - - -
-Enum Summary
ConservationMethodEnumeration listing of all the supported methods.
DisorderMethod 
ProgramThe list of programmes that can produce alignments
SMERFSConstraintsEnumeration defining two constraints for SMERFS columns score calculation.
-  - -

- - - - - - - - - -
-Exception Summary
UnknownFileFormatException 
-  - -

-

-Package compbio.data.sequence Description -

- -

-A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services. -

- -

-

-
Version:
-
1.0 January 2010
-
Author:
-
Petr Troshin
-
-
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-Hierarchy For Package compbio.data.sequence -

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Package Hierarchies:
All Packages
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-Class Hierarchy -

- -

-Enum Hierarchy -

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compbio.data.sequence

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-Packages that use compbio.data.sequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.engine  
compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.pipeline._jpred  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.server  
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.msa
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
ScoreManager - -
-           
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.msa.jaxws
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
ScoreManager - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.sequence
Alignment - -
-          Multiple sequence alignment.
AlignmentMetadata - -
-          Alignment metadata e.g.
ConservationMethod - -
-          Enumeration listing of all the supported methods.
DisorderMethod - -
-           
FastaSequence - -
-          A FASTA formatted sequence.
Program - -
-          The list of programmes that can produce alignments
Range - -
-           
Score - -
-          A value class for AACon annotation results storage.
ScoreManager - -
-           
ScoreManager.ScoreHolder - -
-           
SMERFSConstraints - -
-          Enumeration defining two constraints for SMERFS columns score calculation.
UnknownFileFormatException - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.engine
FastaSequence - -
-          A FASTA formatted sequence.
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.metadata
FastaSequence - -
-          A FASTA formatted sequence.
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.pipeline._jpred
FastaSequence - -
-          A FASTA formatted sequence.
-  -

- - - - - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.runner
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
Score - -
-          A value class for AACon annotation results storage.
UnknownFileFormatException - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.runner.conservation
ScoreManager - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.runner.disorder
ScoreManager - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.runner.msa
Alignment - -
-          Multiple sequence alignment.
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.ws.server
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
ScoreManager - -
-           
-  -

-

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- - - -
- -

- -compbio.engine -
-Interface AsyncExecutor

-
-
All Known Implementing Classes:
AsyncJobRunner, AsyncLocalRunner
-
-
-
-
public interface AsyncExecutor
- - -

-An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface. - Implementation agnostic. Executables can be run either locally to the JVM or on the cluster. -

- -

-

-
Author:
-
pvtroshin - Date October 2009
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(String jobId) - -
-          Stop running job.
- booleancleanup(String jobId) - -
-          Remove all files and a job directory for a jobid.
- JobStatusgetJobStatus(String jobId) - -
-          Query the status of the job
- ConfiguredExecutable<?>getResults(String jobId) - -
-          Retrieve the results of the job.
- StringgetWorkDirectory(String jobId) - -
-           
- StringsubmitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  -

- - - - - - - - -
-Method Detail
- -

-submitJob

-
-String submitJob(ConfiguredExecutable<?> executable)
-                 throws JobSubmissionException
-
-
Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

-

- -
Returns:
unique job identifier -
Throws: -
JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
-
-
-
- -

-getResults

-
-ConfiguredExecutable<?> getResults(String jobId)
-                                   throws ResultNotAvailableException
-
-
Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

-

-
Parameters:
jobId - job identifier obtained at the job submission -
Returns:
ConfiguredExecutable object from which result can be obtained -
Throws: -
ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
-
-
-
- -

-getWorkDirectory

-
-String getWorkDirectory(String jobId)
-
-
-
Parameters:
jobId - unique job identifier -
Returns:
task working directory
-
-
-
- -

-cleanup

-
-boolean cleanup(String jobId)
-
-
Remove all files and a job directory for a jobid. -

-

-
Parameters:
jobId - -
Returns:
true if job directory was successfully removed, false otherwise.
-
-
-
- -

-cancelJob

-
-boolean cancelJob(String jobId)
-
-
Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

-

- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-JobStatus getJobStatus(String jobId)
-
-
Query the status of the job -

-

-
Parameters:
String - jobId - unique job identifier -
Returns:
The JobStatus object representing the status of the job
See Also:
JobStatus
-
-
- -
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- - - -
- -

- -compbio.engine -
-Class Cleaner

-
-java.lang.Object
-  extended by compbio.engine.Cleaner
-
-
-Deprecated. -

-

-
@Deprecated
-public class Cleaner
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Cleaner() - -
-          Deprecated.  
-  - - - - - - - - - - - - - - - -
-Method Summary
-static booleandeleteAllFiles(String directory) - -
-          Deprecated.  
-static booleandeleteFiles(ConfiguredExecutable<?> exec) - -
-          Deprecated. This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty)
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Cleaner

-
-public Cleaner()
-
-
Deprecated. 
- - - - - - - - -
-Method Detail
- -

-deleteFiles

-
-public static boolean deleteFiles(ConfiguredExecutable<?> exec)
-
-
Deprecated. 
This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty) -

-

-
Parameters:
workDirectory -
files - -
Returns:
This method returns true if all files specified by List files - were successfully removed, false otherwise
-
-
-
- -

-deleteAllFiles

-
-public static boolean deleteAllFiles(String directory)
-
-
Deprecated. 
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/ClusterJobId.html b/website/full_javadoc/compbio/engine/ClusterJobId.html deleted file mode 100644 index e5aba10..0000000 --- a/website/full_javadoc/compbio/engine/ClusterJobId.html +++ /dev/null @@ -1,297 +0,0 @@ - - - - - - -ClusterJobId - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine -
-Class ClusterJobId

-
-java.lang.Object
-  extended by compbio.engine.ClusterJobId
-
-
-
-
@Immutable
-public class ClusterJobId
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
ClusterJobId(String jobId) - -
-           
-  - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- StringgetJobId() - -
-           
- inthashCode() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-ClusterJobId

-
-public ClusterJobId(String jobId)
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public String getJobId()
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/Configurator.html b/website/full_javadoc/compbio/engine/Configurator.html deleted file mode 100644 index 2c4ae6c..0000000 --- a/website/full_javadoc/compbio/engine/Configurator.html +++ /dev/null @@ -1,538 +0,0 @@ - - - - - - -Configurator - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.engine -
-Class Configurator

-
-java.lang.Object
-  extended by compbio.engine.Configurator
-
-
-
-
public class Configurator
extends Object
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static StringCLUSTER_WORK_DIRECTORY - -
-           
-static booleanIS_CLUSTER_ENGINE_ENABLED - -
-           
-static booleanIS_LOCAL_ENGINE_ENABLED - -
-           
-static StringLOCAL_WORK_DIRECTORY - -
-           
-  - - - - - - - - - - -
-Constructor Summary
Configurator() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static - - - - -
-<T> ConfiguredExecutable<T>
-		configureExecutable(Executable<T> executable) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
-           
-static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static AsyncExecutorgetAsyncEngine(String taskId) - -
-           
-static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static StringgetWorkDirectory(String taskId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-IS_LOCAL_ENGINE_ENABLED

-
-public static final boolean IS_LOCAL_ENGINE_ENABLED
-
-
-
-
-
- -

-IS_CLUSTER_ENGINE_ENABLED

-
-public static final boolean IS_CLUSTER_ENGINE_ENABLED
-
-
-
-
-
- -

-LOCAL_WORK_DIRECTORY

-
-public static final String LOCAL_WORK_DIRECTORY
-
-
-
-
-
- -

-CLUSTER_WORK_DIRECTORY

-
-public static final String CLUSTER_WORK_DIRECTORY
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-Configurator

-
-public Configurator()
-
-
- - - - - - - - -
-Method Detail
- -

-configureExecutable

-
-public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable)
-                                                   throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-configureExecutable

-
-public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
-                                                              List<FastaSequence> dataSet)
-                                                   throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-configureExecutable

-
-public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
-                                                              Executable.ExecProvider provider)
-                                                   throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getAsyncEngine

-
-public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable,
-                                           Executable.ExecProvider provider)
-
-
-
-
-
-
- -

-getSyncEngine

-
-public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable,
-                                         Executable.ExecProvider provider)
-                                  throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getAsyncEngine

-
-public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable)
-
-
-
-
-
-
- -

-getAsyncEngine

-
-public static AsyncExecutor getAsyncEngine(String taskId)
-
-
-
-
-
-
- -

-getSyncEngine

-
-public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable)
-                                  throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getWorkDirectory

-
-public static String getWorkDirectory(String taskId)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/FilePuller.html b/website/full_javadoc/compbio/engine/FilePuller.html deleted file mode 100644 index 305cca8..0000000 --- a/website/full_javadoc/compbio/engine/FilePuller.html +++ /dev/null @@ -1,551 +0,0 @@ - - - - - - -FilePuller - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine -
-Class FilePuller

-
-java.lang.Object
-  extended by compbio.engine.FilePuller
-
-
-
All Implemented Interfaces:
Comparable<Delayed>, Delayed
-
-
-
-
public class FilePuller
extends Object
implements Delayed
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(Delayed o) - -
-           
- voiddisconnect() - -
-           
- booleanequals(Object obj) - -
-           
- longgetDelay(TimeUnit unit) - -
-           
- StringgetFile() - -
-           
- bytegetProgress() - -
-           
- inthashCode() - -
-           
- booleanhasMoreData() - -
-           
- voidinitPull() - -
-           
- booleanisFileCreated() - -
-           
-static FilePullernewFilePuller(String file, - int chunkSize) - -
-           
-static FilePullernewProgressPuller(String file) - -
-          Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more.
- ChunkHolderpull(long position) - -
-           
- StringtoString() - -
-           
- voidwaitForFile(long maxWaitSeconds) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Method Detail
- -

-newFilePuller

-
-public static FilePuller newFilePuller(String file,
-                                       int chunkSize)
-
-
-
-
-
-
-
-
-
- -

-newProgressPuller

-
-public static FilePuller newProgressPuller(String file)
-
-
Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more. Intended to be used in conjunction with a tool - which output progress as a percent value from 0 to 100. In any cases - progress could not be more than the largest byte value 255. -

-

-
-
-
-
Parameters:
file - -
Returns:
instance
-
-
-
- -

-pull

-
-public ChunkHolder pull(long position)
-                 throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
-
- -

-initPull

-
-public void initPull()
-
-
-
-
-
-
-
-
-
- -

-getFile

-
-public String getFile()
-
-
-
-
-
-
-
-
-
- -

-isFileCreated

-
-public boolean isFileCreated()
-
-
-
-
-
-
-
-
-
- -

-waitForFile

-
-public void waitForFile(long maxWaitSeconds)
-
-
-
-
-
-
-
-
-
- -

-hasMoreData

-
-public boolean hasMoreData()
-                    throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
-
- -

-compareTo

-
-public int compareTo(Delayed o)
-
-
-
Specified by:
compareTo in interface Comparable<Delayed>
-
-
-
-
-
-
- -

-getDelay

-
-public long getDelay(TimeUnit unit)
-
-
-
Specified by:
getDelay in interface Delayed
-
-
-
-
-
-
- -

-disconnect

-
-public void disconnect()
-
-
-
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-getProgress

-
-public byte getProgress()
-                 throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/Job.html b/website/full_javadoc/compbio/engine/Job.html deleted file mode 100644 index 5f1099f..0000000 --- a/website/full_javadoc/compbio/engine/Job.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - -Job - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine -
-Class Job

-
-java.lang.Object
-  extended by compbio.engine.Job
-
-
-
-
@Immutable
-public final class Job
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Job(String taskId, - String jobId, - ConfiguredExecutable<?> cexecutable) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
-static JobgetByJobId(String jobId, - List<Job> jobs) - -
-           
-static JobgetByTaskId(String taskId, - List<Job> jobs) - -
-           
- ConfiguredExecutable<?>getConfExecutable() - -
-           
- ClusterJobIdgetJobId() - -
-           
- StringgetTaskId() - -
-           
- inthashCode() - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Job

-
-public Job(String taskId,
-           String jobId,
-           ConfiguredExecutable<?> cexecutable)
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public ClusterJobId getJobId()
-
-
-
-
-
-
- -

-getTaskId

-
-public String getTaskId()
-
-
-
-
-
-
- -

-getConfExecutable

-
-public ConfiguredExecutable<?> getConfExecutable()
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-getByTaskId

-
-public static Job getByTaskId(String taskId,
-                              List<Job> jobs)
-
-
-
-
-
-
- -

-getByJobId

-
-public static Job getByJobId(String jobId,
-                             List<Job> jobs)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/LoadBalancer.html b/website/full_javadoc/compbio/engine/LoadBalancer.html deleted file mode 100644 index 769d68f..0000000 --- a/website/full_javadoc/compbio/engine/LoadBalancer.html +++ /dev/null @@ -1,259 +0,0 @@ - - - - - - -LoadBalancer - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine -
-Class LoadBalancer

-
-java.lang.Object
-  extended by compbio.engine.LoadBalancer
-
-
-
-
public class LoadBalancer
extends Object
- - -

-This class decides where to execute the job. If the local engine is enabled - in the configuration file and it has free threads and the size of the tasks - permits the local execution, then the local execution will be favoured. -

- -

-

-
Version:
-
1.0 March 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - -
-Method Summary
-static Executable.ExecProvidergetEngine(Executable<?> executable) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Method Detail
- -

-getEngine

-
-public static Executable.ExecProvider getEngine(Executable<?> executable)
-
-
-
-
-
-
- -

-getEngine

-
-public static <T,V> Executable.ExecProvider getEngine(Executable<V> executable,
-                                                      List<FastaSequence> dataSet)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/ProgressGetter.html b/website/full_javadoc/compbio/engine/ProgressGetter.html deleted file mode 100644 index 878037e..0000000 --- a/website/full_javadoc/compbio/engine/ProgressGetter.html +++ /dev/null @@ -1,273 +0,0 @@ - - - - - - -ProgressGetter - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine -
-Class ProgressGetter

-
-java.lang.Object
-  extended by compbio.engine.ProgressGetter
-
-
-
-
public class ProgressGetter
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
ProgressGetter() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static bytegetProgress(String progressFile) - -
-           
-static ChunkHolderpull(String file, - long position) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-ProgressGetter

-
-public ProgressGetter()
-
-
- - - - - - - - -
-Method Detail
- -

-pull

-
-public static final ChunkHolder pull(String file,
-                                     long position)
-
-
-
-
-
-
- -

-getProgress

-
-public static final byte getProgress(String progressFile)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/PulledFileCache.html b/website/full_javadoc/compbio/engine/PulledFileCache.html deleted file mode 100644 index 24e6bfa..0000000 --- a/website/full_javadoc/compbio/engine/PulledFileCache.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -PulledFileCache - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine -
-Class PulledFileCache

-
-java.lang.Object
-  extended by compbio.engine.PulledFileCache
-
-
-
-
public final class PulledFileCache
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PulledFileCache() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static FilePullerget(String fileName) - -
-           
-static booleanput(FilePuller fpuller) - -
-          This method allows duplicates to be added.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PulledFileCache

-
-public PulledFileCache()
-
-
- - - - - - - - -
-Method Detail
- -

-get

-
-public static FilePuller get(String fileName)
-
-
-
-
-
-
- -

-put

-
-public static boolean put(FilePuller fpuller)
-
-
This method allows duplicates to be added. This is a responsibility of - the called to ensure this will not happen! -

-

-
Parameters:
fpuller - -
Returns:
true if the same filepooler is already in cache
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/SubmissionManager.html b/website/full_javadoc/compbio/engine/SubmissionManager.html deleted file mode 100644 index cb4a27c..0000000 --- a/website/full_javadoc/compbio/engine/SubmissionManager.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -SubmissionManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine -
-Class SubmissionManager

-
-java.lang.Object
-  extended by compbio.engine.SubmissionManager
-
-
-
-
public class SubmissionManager
extends Object
- - -

-Submit jobs for execution -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static voidaddTask(ConfiguredExecutable<?> executable, - Future<ConfiguredExecutable<?>> future) - -
-           
-static Future<ConfiguredExecutable<?>>getTask(String taskId) - -
-           
-static voidremoveTask(ConfiguredExecutable<?> executable) - -
-           
-static voidremoveTask(String key) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Method Detail
- -

-addTask

-
-public static void addTask(ConfiguredExecutable<?> executable,
-                           Future<ConfiguredExecutable<?>> future)
-
-
-
-
-
-
- -

-getTask

-
-public static Future<ConfiguredExecutable<?>> getTask(String taskId)
-
-
-
-
-
-
- -

-removeTask

-
-public static void removeTask(ConfiguredExecutable<?> executable)
-
-
-
-
-
-
- -

-removeTask

-
-public static void removeTask(String key)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/SyncExecutor.html b/website/full_javadoc/compbio/engine/SyncExecutor.html deleted file mode 100644 index b96838f..0000000 --- a/website/full_javadoc/compbio/engine/SyncExecutor.html +++ /dev/null @@ -1,337 +0,0 @@ - - - - - - -SyncExecutor - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine -
-Interface SyncExecutor

-
-
All Known Implementing Classes:
JobRunner, LocalRunner
-
-
-
-
public interface SyncExecutor
- - -

-Synchronous executor, is an engine to run the Executable synchronously. -

- -

-

-
Author:
-
pvtroshin - Date October 2009
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob() - -
-          Stops running job.
- booleancleanup() - -
-          Clean up after the job
- voidexecuteJob() - -
-          Execute the job
- JobStatusgetJobStatus() - -
-          Query the status of the job by its id.
- StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  -

- - - - - - - - -
-Method Detail
- -

-executeJob

-
-void executeJob()
-                throws JobSubmissionException
-
-
Execute the job -

-

- -
Throws: -
JobSubmissionException - if submission fails
-
-
-
- -

-cleanup

-
-boolean cleanup()
-
-
Clean up after the job -

-

- -
Returns:
true if all the files created by this job have been removed successfully, false otherwise
-
-
-
- -

-waitForResult

-
-ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
-
-
Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

-

- -
Returns:
object from wich the result can be obtained -
Throws: -
JobExecutionException
-
-
-
- -

-getWorkDirectory

-
-String getWorkDirectory()
-
-
- -
Returns:
working directory if the task
-
-
-
- -

-cancelJob

-
-boolean cancelJob()
-
-
Stops running job. - Clean up is not performed. -

-

- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-JobStatus getJobStatus()
-
-
Query the status of the job by its id. -

-

- -
Returns:
- JobStatus
-
-
- -
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-Uses of Interface
compbio.engine.AsyncExecutor

-
- - - - - - - - - - - - - - - - - - - - - -
-Packages that use AsyncExecutor
compbio.engine  
compbio.engine.cluster.drmaa  
compbio.engine.local  
compbio.ws.server  
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.engine
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine that return AsyncExecutor
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(String taskId) - -
-           
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Classes in compbio.engine.cluster.drmaa that implement AsyncExecutor
- classAsyncJobRunner - -
-          Single cluster job runner class
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.engine.local
-  -

- - - - - - - - - -
Classes in compbio.engine.local that implement AsyncExecutor
- classAsyncLocalRunner - -
-           
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.ws.server
-  -

- - - - - - - - - -
Methods in compbio.ws.server that return AsyncExecutor
-static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) - -
-           
-  -

-

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compbio.engine.ClusterJobId

-
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-Packages that use ClusterJobId
compbio.engine  
compbio.engine.cluster.drmaa  
-  -

- - - - - -
-Uses of ClusterJobId in compbio.engine
-  -

- - - - - - - - - -
Methods in compbio.engine that return ClusterJobId
- ClusterJobIdJob.getJobId() - -
-           
-  -

- - - - - -
-Uses of ClusterJobId in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return ClusterJobId
-static ClusterJobIdClusterSession.getClusterJobId(String taskId) - -
-           
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa with parameters of type ClusterJobId
- intClusterSession.getJobStatus(ClusterJobId jobId) - -
-          Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed.
-  -

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compbio.engine.Configurator

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-Uses of Class
compbio.engine.FilePuller

-
- - - - - - - - - -
-Packages that use FilePuller
compbio.engine  
-  -

- - - - - -
-Uses of FilePuller in compbio.engine
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine that return FilePuller
-static FilePullerPulledFileCache.get(String fileName) - -
-           
-static FilePullerFilePuller.newFilePuller(String file, - int chunkSize) - -
-           
-static FilePullerFilePuller.newProgressPuller(String file) - -
-          Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more.
-  -

- - - - - - - - - -
Methods in compbio.engine with parameters of type FilePuller
-static booleanPulledFileCache.put(FilePuller fpuller) - -
-          This method allows duplicates to be added.
-  -

-

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compbio.engine.Job

-
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-Packages that use Job
compbio.engine  
-  -

- - - - - -
-Uses of Job in compbio.engine
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine that return Job
-static JobJob.getByJobId(String jobId, - List<Job> jobs) - -
-           
-static JobJob.getByTaskId(String taskId, - List<Job> jobs) - -
-           
-  -

- - - - - - - - - - - - - -
Method parameters in compbio.engine with type arguments of type Job
-static JobJob.getByJobId(String jobId, - List<Job> jobs) - -
-           
-static JobJob.getByTaskId(String taskId, - List<Job> jobs) - -
-           
-  -

-

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compbio.engine.ProgressGetter

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compbio.engine.PulledFileCache

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-

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compbio.engine.SubmissionManager

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-Uses of Interface
compbio.engine.SyncExecutor

-
- - - - - - - - - - - - - - - - - -
-Packages that use SyncExecutor
compbio.engine  
compbio.engine.cluster.drmaa  
compbio.engine.local  
-  -

- - - - - -
-Uses of SyncExecutor in compbio.engine
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine that return SyncExecutor
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of SyncExecutor in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Classes in compbio.engine.cluster.drmaa that implement SyncExecutor
- classJobRunner - -
-          Single cluster job runner class
-  -

- - - - - -
-Uses of SyncExecutor in compbio.engine.local
-  -

- - - - - - - - - -
Classes in compbio.engine.local that implement SyncExecutor
- classLocalRunner - -
-           
-  -

-

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- -

- -compbio.engine.client -
-Class CommandBuilder<T>

-
-java.lang.Object
-  extended by compbio.engine.client.CommandBuilder<T>
-
-
-
-
public class CommandBuilder<T>
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CommandBuilder(String nameValueSeparator) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidaddParams(List<String> params) - -
-           
- booleanequals(Object obj) - -
-           
- List<String>getCommands() - -
-           
- StringgetCommandString() - -
-           
- StringgetParamValue(String paramName) - -
-           
- inthashCode() - -
-           
- booleanhasParam(String paramName) - -
-           
-static - - - - -
-<T> CommandBuilder<T>
-		newCommandBuilder(List<? extends Option<T>> arguments, - String nameValueSeparator) - -
-          This produces the same result as getCommands method.
- booleanremoveParam(String paramName) - -
-           
- booleansetFirst(String param) - -
-           
- booleansetLast(String paramName) - -
-           
- booleansetLast(String paramName, - String paramValue) - -
-           
- booleansetParam(String param) - -
-           
- booleansetParam(String paramName, - String paramValue) - -
-           
- voidsetParams(List<String> params) - -
-           
- intsize() - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CommandBuilder

-
-public CommandBuilder(String nameValueSeparator)
-
-
- - - - - - - - -
-Method Detail
- -

-addParams

-
-public void addParams(List<String> params)
-
-
-
-
-
-
- -

-setParams

-
-public void setParams(List<String> params)
-
-
-
-
-
-
- -

-hasParam

-
-public boolean hasParam(String paramName)
-
-
-
-
-
-
- -

-setFirst

-
-public boolean setFirst(String param)
-
-
-
-
-
-
- -

-setParam

-
-public boolean setParam(String param)
-
-
-
-
-
-
- -

-setLast

-
-public boolean setLast(String paramName)
-
-
-
-
-
-
- -

-setLast

-
-public boolean setLast(String paramName,
-                       String paramValue)
-
-
-
-
-
-
- -

-getParamValue

-
-public String getParamValue(String paramName)
-
-
-
-
-
-
- -

-removeParam

-
-public boolean removeParam(String paramName)
-
-
-
-
-
-
- -

-setParam

-
-public boolean setParam(String paramName,
-                        String paramValue)
-
-
-
-
-
-
- -

-getCommands

-
-public List<String> getCommands()
-
-
-
-
-
-
- -

-getCommandString

-
-public String getCommandString()
-
-
-
-
-
-
- -

-newCommandBuilder

-
-public static <T> CommandBuilder<T> newCommandBuilder(List<? extends Option<T>> arguments,
-                                                      String nameValueSeparator)
-
-
This produces the same result as getCommands method. The only difference - is that it accepts a List of Options as an input -

-

-
Parameters:
arguments - -
Returns:
the instance of the CommandBuilder
-
-
-
- -

-size

-
-public int size()
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/ConfExecutable.html deleted file mode 100644 index d7efbf2..0000000 --- a/website/full_javadoc/compbio/engine/client/ConfExecutable.html +++ /dev/null @@ -1,1022 +0,0 @@ - - - - - - -ConfExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Class ConfExecutable<T>

-
-java.lang.Object
-  extended by compbio.engine.client.ConfExecutable<T>
-
-
-
All Implemented Interfaces:
ConfiguredExecutable<T>, Executable<T>, PipedExecutable<T>
-
-
-
-
public class ConfExecutable<T>
extends Object
implements ConfiguredExecutable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - -
-Field Summary
-static StringCLUSTER_TASK_ID_PREFIX - -
-           
-  - - - - - - - - - - -
-Constructor Summary
ConfExecutable(Executable<T> executable, - String taskDirectory) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(List<String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- StringgetClusterJobSettings() - -
-           
- StringgetCommand(Executable.ExecProvider provider) - -
-           
- List<String>getCreatedFiles() - -
-           
- Map<String,String>getEnvironment() - -
-           
- StringgetError() - -
-           
- Executable.ExecProvidergetExecProvider() - -
-           
- Executable<T>getExecutable() - -
-           
- StringgetInput() - -
-          Not all input paths are relative! Input path could be absolute!
- Limit<T>getLimit(String presetName) - -
-           
- LimitsManager<T>getLimits() - -
-           
- StringgetOutput() - -
-           
- CommandBuilder<T>getParameters() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
- - - - - -
-<V> V
-		getResults() - -
-           
- - - - - -
-<V> V
-		getResults(String directory) - -
-           
- RunConfigurationgetRunConfiguration() - -
-           
-static - - - - -
-<V> LimitsManager<V>
-		getRunnerLimits(Class<V> clazz) - -
-          This method should be executed once and result of its execution reused.
-static - - - - -
-<V> RunnerConfig<V>
-		getRunnerOptions(Class<? extends Executable<V>> clazz) - -
-           
-static - - - - -
-<V> PresetManager<V>
-		getRunnerPresets(Class<? extends Executable<V>> clazz) - -
-           
- Executable.ExecProvidergetSupportedRuntimes() - -
-           
- StringgetTaskId() - -
-           
- StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>loadRunConfiguration(InputStream input) - -
-           
- ConfiguredExecutable<?>loadRunConfiguration(RunConfiguration rconf) - -
-           
-static ConfiguredExecutable<?>newConfExecutable(RunConfiguration rconf) - -
-           
- booleansaveRunConfiguration() - -
-           
- voidsetExecProvider(Executable.ExecProvider provider) - -
-           
- voidsetWorkDirectory(String workDirectory) - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-CLUSTER_TASK_ID_PREFIX

-
-public static final String CLUSTER_TASK_ID_PREFIX
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-ConfExecutable

-
-public ConfExecutable(Executable<T> executable,
-                      String taskDirectory)
-
-
- - - - - - - - -
-Method Detail
- -

-getExecProvider

-
-public Executable.ExecProvider getExecProvider()
-
-
-
Specified by:
getExecProvider in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-setExecProvider

-
-public void setExecProvider(Executable.ExecProvider provider)
-
-
-
-
-
-
-
-
-
- -

-getCommand

-
-public String getCommand(Executable.ExecProvider provider)
-                  throws UnsupportedRuntimeException
-
-
-
Specified by:
getCommand in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
UnsupportedRuntimeException
-
-
-
- -

-getSupportedRuntimes

-
-public Executable.ExecProvider getSupportedRuntimes()
-
-
-
Specified by:
getSupportedRuntimes in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getLimit

-
-public Limit<T> getLimit(String presetName)
-
-
-
Specified by:
getLimit in interface Executable<T>
-
-
-
-
-
-
- -

-getLimits

-
-public LimitsManager<T> getLimits()
-
-
-
Specified by:
getLimits in interface Executable<T>
-
-
-
-
-
-
- -

-getTaskId

-
-public String getTaskId()
-
-
-
Specified by:
getTaskId in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-setWorkDirectory

-
-public void setWorkDirectory(String workDirectory)
-
-
-
Specified by:
setWorkDirectory in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getWorkDirectory

-
-public String getWorkDirectory()
-
-
-
Specified by:
getWorkDirectory in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-addParameters

-
-public Executable<T> addParameters(List<String> parameters)
-
-
Description copied from interface: Executable
-
Adds parameter to the list of parameters for a native executable -

-

-
Specified by:
addParameters in interface Executable<T>
-
-
- -
Returns:
this Executable
-
-
-
- -

-getOutput

-
-public String getOutput()
-
-
-
Specified by:
getOutput in interface Executable<T>
-
-
-
-
-
-
- -

-getError

-
-public String getError()
-
-
-
Specified by:
getError in interface Executable<T>
-
-
-
-
-
-
- -

-getCreatedFiles

-
-public List<String> getCreatedFiles()
-
-
-
Specified by:
getCreatedFiles in interface Executable<T>
-
-
-
-
-
-
- -

-getInput

-
-public String getInput()
-
-
Not all input paths are relative! Input path could be absolute! -

-

-
Specified by:
getInput in interface Executable<T>
-
-
-
See Also:
compbio.engine.client.Executable#getInputFiles()
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters()
-
-
-
Specified by:
getParameters in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
Specified by:
getParameters in interface Executable<T>
-
-
-
-
-
-
- -

-getExecutable

-
-public Executable<T> getExecutable()
-
-
-
Specified by:
getExecutable in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getResults

-
-public <V> V getResults()
-             throws ResultNotAvailableException
-
-
-
Specified by:
getResults in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getResults

-
-public <V> V getResults(String directory)
-             throws ResultNotAvailableException
-
-
-
Specified by:
getResults in interface Executable<T>
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getRunnerOptions

-
-public static <V> RunnerConfig<V> getRunnerOptions(Class<? extends Executable<V>> clazz)
-                                        throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
-
- -

-getRunnerPresets

-
-public static <V> PresetManager<V> getRunnerPresets(Class<? extends Executable<V>> clazz)
-                                         throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
-
- -

-getRunnerLimits

-
-public static <V> LimitsManager<V> getRunnerLimits(Class<V> clazz)
-                                        throws IOException
-
-
This method should be executed once and result of its execution reused. - If not used carefully it could slow down the system! -

-

-
-
-
-
Type Parameters:
V -
Parameters:
clazz - -
Returns:
LimitsManager instance -
Throws: -
IOException
-
-
-
- -

-getEnvironment

-
-public Map<String,String> getEnvironment()
-
-
-
Specified by:
getEnvironment in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-loadRunConfiguration

-
-public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf)
-
-
-
Specified by:
loadRunConfiguration in interface Executable<T>
-
-
-
-
-
-
- -

-newConfExecutable

-
-public static ConfiguredExecutable<?> newConfExecutable(RunConfiguration rconf)
-
-
-
-
-
-
-
-
-
- -

-saveRunConfiguration

-
-public boolean saveRunConfiguration()
-                             throws IOException
-
-
-
Specified by:
saveRunConfiguration in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
IOException
-
-
-
- -

-getRunConfiguration

-
-public RunConfiguration getRunConfiguration()
-
-
-
-
-
-
-
-
-
- -

-loadRunConfiguration

-
-public ConfiguredExecutable<?> loadRunConfiguration(InputStream input)
-                                             throws IOException
-
-
-
Specified by:
loadRunConfiguration in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
IOException
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-getClusterJobSettings

-
-public String getClusterJobSettings()
-
-
-
Specified by:
getClusterJobSettings in interface Executable<T>
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html deleted file mode 100644 index 285dd58..0000000 --- a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html +++ /dev/null @@ -1,504 +0,0 @@ - - - - - - -ConfiguredExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Interface ConfiguredExecutable<T>

-
-
All Superinterfaces:
Executable<T>, PipedExecutable<T>
-
-
-
All Known Implementing Classes:
ConfExecutable
-
-
-
-
public interface ConfiguredExecutable<T>
extends Executable<T>, PipedExecutable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- StringgetCommand(Executable.ExecProvider provider) - -
-           
- Map<String,String>getEnvironment() - -
-           
- Executable.ExecProvidergetExecProvider() - -
-           
- Executable<T>getExecutable() - -
-           
- CommandBuilder<T>getParameters() - -
-           
- - - - - -
-<V> V
-		getResults() - -
-           
- Executable.ExecProvidergetSupportedRuntimes() - -
-           
- StringgetTaskId() - -
-           
- StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>loadRunConfiguration(InputStream input) - -
-           
- booleansaveRunConfiguration() - -
-           
- voidsetWorkDirectory(String workDirectory) - -
-           
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
-  -

- - - - - - - - -
-Method Detail
- -

-getEnvironment

-
-Map<String,String> getEnvironment()
-
-
-
-
-
-
-
-
-
- -

-getTaskId

-
-String getTaskId()
-
-
-
-
-
-
-
-
-
- -

-getCommand

-
-String getCommand(Executable.ExecProvider provider)
-                  throws JobSubmissionException
-
-
-
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getSupportedRuntimes

-
-Executable.ExecProvider getSupportedRuntimes()
-
-
-
-
-
-
-
-
-
- -

-getWorkDirectory

-
-String getWorkDirectory()
-
-
-
-
-
-
-
-
-
- -

-setWorkDirectory

-
-void setWorkDirectory(String workDirectory)
-
-
-
-
-
-
-
-
-
- -

-getResults

-
-<V> V getResults()
-             throws ResultNotAvailableException
-
-
-
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getExecutable

-
-Executable<T> getExecutable()
-
-
-
-
-
-
-
-
-
- -

-getParameters

-
-CommandBuilder<T> getParameters()
-
-
-
-
-
-
-
-
-
- -

-saveRunConfiguration

-
-boolean saveRunConfiguration()
-                             throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
-
- -

-loadRunConfiguration

-
-ConfiguredExecutable<?> loadRunConfiguration(InputStream input)
-                                             throws IOException
-
-
-
-
-
- -
Throws: -
IOException
-
-
-
- -

-getExecProvider

-
-Executable.ExecProvider getExecProvider()
-
-
-
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html deleted file mode 100644 index 2287844..0000000 --- a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -EnvVariableProcessor - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Class EnvVariableProcessor

-
-java.lang.Object
-  extended by compbio.engine.client.EnvVariableProcessor
-
-
-
-
public class EnvVariableProcessor
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static StringPATH - -
-          Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable
-  - - - - - - - - - - -
-Constructor Summary
EnvVariableProcessor() - -
-           
-  - - - - - - - - - - - -
-Method Summary
-static Map<String,String>getEnvVariables(String property, - Class<?> clazz) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-PATH

-
-public static final String PATH
-
-
Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable -

-

-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-EnvVariableProcessor

-
-public EnvVariableProcessor()
-
-
- - - - - - - - -
-Method Detail
- -

-getEnvVariables

-
-public static Map<String,String> getEnvVariables(String property,
-                                                 Class<?> clazz)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html deleted file mode 100644 index ec1b755..0000000 --- a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -Executable.ExecProvider - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.engine.client -
-Enum Executable.ExecProvider

-
-java.lang.Object
-  extended by java.lang.Enum<Executable.ExecProvider>
-      extended by compbio.engine.client.Executable.ExecProvider
-
-
-
All Implemented Interfaces:
Serializable, Comparable<Executable.ExecProvider>
-
-
-
Enclosing interface:
Executable<T>
-
-
-
-
public static enum Executable.ExecProvider
extends Enum<Executable.ExecProvider>
- - -

-

- -

- - - - - - - - - - - - - - - - -
-Enum Constant Summary
Any - -
-           
Cluster - -
-           
Local - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static Executable.ExecProvidervalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static Executable.ExecProvider[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-Local

-
-public static final Executable.ExecProvider Local
-
-
-
-
-
- -

-Cluster

-
-public static final Executable.ExecProvider Cluster
-
-
-
-
-
- -

-Any

-
-public static final Executable.ExecProvider Any
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static Executable.ExecProvider[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (Executable.ExecProvider c : Executable.ExecProvider.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static Executable.ExecProvider valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/Executable.html b/website/full_javadoc/compbio/engine/client/Executable.html deleted file mode 100644 index e59a18f..0000000 --- a/website/full_javadoc/compbio/engine/client/Executable.html +++ /dev/null @@ -1,445 +0,0 @@ - - - - - - -Executable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Interface Executable<T>

-
-
Type Parameters:
T -
-
-
All Known Subinterfaces:
ConfiguredExecutable<T>, PipedExecutable<T>
-
-
-
All Known Implementing Classes:
_SkeletalCommandBuilder, AACon, BlastAll, ClustalO, ClustalW, ConfExecutable, Disembl, GlobPlot, IUPred, Jronn, Mafft, Mcl, Muscle, NetNglyc, OB, Probcons, PSIBlast, Ronn, RPSBlast, SkeletalExecutable, Tcoffee
-
-
-
-
public interface Executable<T>
- - -

-Interface to a native executable. -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Nested Class Summary
-static classExecutable.ExecProvider - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(List<String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- StringgetClusterJobSettings() - -
-           
- List<String>getCreatedFiles() - -
-          Deprecated. 
- StringgetError() - -
-           
- StringgetInput() - -
-           
- Limit<T>getLimit(String presetName) - -
-           
- LimitsManager<T>getLimits() - -
-           
- StringgetOutput() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
- - - - - -
-<V> V
-		getResults(String directory) - -
-           
- Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

- - - - - - - - -
-Method Detail
- -

-addParameters

-
-Executable<T> addParameters(List<String> parameters)
-
-
Adds parameter to the list of parameters for a native executable -

-

-
Parameters:
parameters - -
Returns:
this Executable
-
-
-
- -

-getCreatedFiles

-
-@Deprecated
-List<String> getCreatedFiles()
-
-
Deprecated.  -

-

-
-
-
-
- -

-getInput

-
-String getInput()
-
-
-
-
-
-
- -

-getOutput

-
-String getOutput()
-
-
-
-
-
-
- -

-getError

-
-String getError()
-
-
-
-
-
-
- -

-getParameters

-
-CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
-
-
-
- -

-getResults

-
-<V> V getResults(String directory)
-             throws ResultNotAvailableException
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-loadRunConfiguration

-
-Executable<?> loadRunConfiguration(RunConfiguration rconfig)
-
-
-
-
-
-
- -

-getLimit

-
-Limit<T> getLimit(String presetName)
-
-
-
-
-
-
- -

-getLimits

-
-LimitsManager<T> getLimits()
-
-
-
-
-
-
- -

-getClusterJobSettings

-
-String getClusterJobSettings()
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/PathValidator.html b/website/full_javadoc/compbio/engine/client/PathValidator.html deleted file mode 100644 index fd02d1a..0000000 --- a/website/full_javadoc/compbio/engine/client/PathValidator.html +++ /dev/null @@ -1,362 +0,0 @@ - - - - - - -PathValidator - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Class PathValidator

-
-java.lang.Object
-  extended by compbio.engine.client.PathValidator
-
-
-
-
public final class PathValidator
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PathValidator() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleanisAbsolutePath(String path) - -
-          Whether a certain path is absolute or not is operation system dependent!
-static booleanisValidDirectory(String directory) - -
-           
-static booleanisValidExecutable(String command) - -
-           
-static voidvalidateDirectory(String workDirectory) - -
-           
-static voidvalidateExecutable(String command) - -
-           
-static voidvalidatePathNames(List<String> filenames, - String type) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PathValidator

-
-public PathValidator()
-
-
- - - - - - - - -
-Method Detail
- -

-isValidExecutable

-
-public static boolean isValidExecutable(String command)
-
-
-
-
-
-
- -

-validateExecutable

-
-public static void validateExecutable(String command)
-                               throws IllegalArgumentException
-
-
- -
Throws: -
IllegalArgumentException
-
-
-
- -

-isValidDirectory

-
-public static boolean isValidDirectory(String directory)
-
-
-
-
-
-
- -

-validatePathNames

-
-public static void validatePathNames(List<String> filenames,
-                                     String type)
-                              throws IllegalArgumentException
-
-
-
Parameters:
filenames -
type - - merely a string to be added to error message to explain what - type of files are lacking -
Throws: -
IllegalArgumentException
-
-
-
- -

-isAbsolutePath

-
-public static boolean isAbsolutePath(String path)
-
-
Whether a certain path is absolute or not is operation system dependent! -

-

-
Parameters:
path - -
Returns:
true is the path is absolute, false otherwise
-
-
-
- -

-validateDirectory

-
-public static void validateDirectory(String workDirectory)
-                              throws IllegalArgumentException
-
-
- -
Throws: -
IllegalArgumentException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/PipedExecutable.html deleted file mode 100644 index 1994dbc..0000000 --- a/website/full_javadoc/compbio/engine/client/PipedExecutable.html +++ /dev/null @@ -1,230 +0,0 @@ - - - - - - -PipedExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Interface PipedExecutable<T>

-
-
Type Parameters:
T -
-
-
All Superinterfaces:
Executable<T>
-
-
-
All Known Subinterfaces:
ConfiguredExecutable<T>
-
-
-
All Known Implementing Classes:
ConfExecutable, Disembl, GlobPlot, Mafft, Probcons, Tcoffee
-
-
-
-
public interface PipedExecutable<T>
extends Executable<T>
- - -

-This is a marker interface to indicate that the output of the process must be - captured. It is in generally better for the process to manage its own - streams, but some executables are not capable of this thus require different - handling -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
-  -

- -

- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/RunConfiguration.html deleted file mode 100644 index 79c9837..0000000 --- a/website/full_javadoc/compbio/engine/client/RunConfiguration.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -RunConfiguration - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Class RunConfiguration

-
-java.lang.Object
-  extended by compbio.engine.client.RunConfiguration
-
-
-
-
public class RunConfiguration
extends Object
- - -

-Value class for persisting ConfExecutable instances -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static StringrconfigFile - -
-           
-  - - - - - - - - - - - - - -
-Constructor Summary
RunConfiguration() - -
-           
RunConfiguration(ConfExecutable<?> cexec) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- StringgetError() - -
-           
- StringgetInput() - -
-           
- StringgetOutput() - -
-           
- CommandBuilder<?>getParameters() - -
-           
- StringgetRunnerClassName() - -
-           
- inthashCode() - -
-           
-static RunConfigurationload(InputStream input) - -
-           
- voidsetError(String error) - -
-           
- voidsetInput(String input) - -
-           
- voidsetOutput(String output) - -
-           
- voidsetParameters(CommandBuilder<?> parameters) - -
-           
- StringtoString() - -
-           
-static booleanwrite(RunConfiguration rconf) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-rconfigFile

-
-public static final String rconfigFile
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-RunConfiguration

-
-public RunConfiguration()
-
-
-
- -

-RunConfiguration

-
-public RunConfiguration(ConfExecutable<?> cexec)
-
-
- - - - - - - - -
-Method Detail
- -

-write

-
-public static boolean write(RunConfiguration rconf)
-                     throws IOException
-
-
- -
Throws: -
IOException
-
-
-
- -

-load

-
-public static RunConfiguration load(InputStream input)
-                             throws IOException
-
-
- -
Throws: -
IOException
-
-
-
- -

-setOutput

-
-public void setOutput(String output)
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<?> getParameters()
-
-
-
-
-
-
- -

-setParameters

-
-public void setParameters(CommandBuilder<?> parameters)
-
-
-
-
-
-
- -

-getOutput

-
-public String getOutput()
-
-
-
-
-
-
- -

-setError

-
-public void setError(String error)
-
-
-
-
-
-
- -

-getError

-
-public String getError()
-
-
-
-
-
-
- -

-getInput

-
-public String getInput()
-
-
-
-
-
-
- -

-setInput

-
-public void setInput(String input)
-
-
-
-
-
-
- -

-getRunnerClassName

-
-public String getRunnerClassName()
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html deleted file mode 100644 index c8ac243..0000000 --- a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html +++ /dev/null @@ -1,782 +0,0 @@ - - - - - - -SkeletalExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Class SkeletalExecutable<T>

-
-java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<T>
-
-
-
All Implemented Interfaces:
Executable<T>
-
-
-
Direct Known Subclasses:
AACon, ClustalO, ClustalW, Disembl, GlobPlot, IUPred, Jronn, Mafft, Muscle, Probcons, Tcoffee
-
-
-
-
public abstract class SkeletalExecutable<T>
extends Object
implements Executable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static StringERROR - -
-           
-static StringINPUT - -
-           
-static StringOUTPUT - -
-           
-  - - - - - - - - - - - - - -
-Constructor Summary
SkeletalExecutable() - -
-           
SkeletalExecutable(String parameterKeyValueDelimiter) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(List<String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- booleanequals(Object obj) - -
-           
-static intgetClusterCpuNum(Class<? extends Executable<?>> type) - -
-           
- StringgetClusterJobSettings() - -
-           
- List<String>getCreatedFiles() - -
-          This method cannot really tell whether the files has actually been - created or not.
- StringgetError() - -
-           
- StringgetInput() - -
-           
- Limit<T>getLimit(String presetName) - -
-           
- LimitsManager<T>getLimits() - -
-           
- StringgetOutput() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
-abstract  Class<T>getType() - -
-           
- inthashCode() - -
-           
- Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
-           
- SkeletalExecutable<T>setError(String errFile) - -
-           
- SkeletalExecutable<T>setInput(String inFile) - -
-           
- SkeletalExecutable<T>setOutput(String outFile) - -
-           
- Executable<T>setParameter(String parameter) - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
getResults
-  -

- - - - - - - - -
-Field Detail
- -

-INPUT

-
-public static final String INPUT
-
-
-
See Also:
Constant Field Values
-
-
- -

-OUTPUT

-
-public static final String OUTPUT
-
-
-
See Also:
Constant Field Values
-
-
- -

-ERROR

-
-public static final String ERROR
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-SkeletalExecutable

-
-public SkeletalExecutable()
-
-
-
- -

-SkeletalExecutable

-
-public SkeletalExecutable(String parameterKeyValueDelimiter)
-
-
- - - - - - - - -
-Method Detail
- -

-setInput

-
-public SkeletalExecutable<T> setInput(String inFile)
-
-
-
-
-
-
-
-
-
- -

-setOutput

-
-public SkeletalExecutable<T> setOutput(String outFile)
-
-
-
-
-
-
-
-
-
- -

-setError

-
-public SkeletalExecutable<T> setError(String errFile)
-
-
-
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
Specified by:
getParameters in interface Executable<T>
-
-
-
-
-
-
- -

-addParameters

-
-public Executable<T> addParameters(List<String> parameters)
-
-
Description copied from interface: Executable
-
Adds parameter to the list of parameters for a native executable -

-

-
Specified by:
addParameters in interface Executable<T>
-
-
- -
Returns:
this Executable
-
-
-
- -

-setParameter

-
-public Executable<T> setParameter(String parameter)
-
-
-
-
-
-
-
-
-
- -

-getCreatedFiles

-
-public List<String> getCreatedFiles()
-
-
This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

-

-
Specified by:
getCreatedFiles in interface Executable<T>
-
-
-
See Also:
Executable.getCreatedFiles()
-
-
-
- -

-getInput

-
-public String getInput()
-
-
-
Specified by:
getInput in interface Executable<T>
-
-
-
-
-
-
- -

-getOutput

-
-public String getOutput()
-
-
-
Specified by:
getOutput in interface Executable<T>
-
-
-
-
-
-
- -

-getError

-
-public String getError()
-
-
-
Specified by:
getError in interface Executable<T>
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-loadRunConfiguration

-
-public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
-
-
-
Specified by:
loadRunConfiguration in interface Executable<T>
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-getClusterJobSettings

-
-public String getClusterJobSettings()
-
-
-
Specified by:
getClusterJobSettings in interface Executable<T>
-
-
-
-
-
-
- -

-getClusterCpuNum

-
-public static int getClusterCpuNum(Class<? extends Executable<?>> type)
-
-
-
-
-
- -
Returns:
number of cpus to use on the cluster or 0 if the value is - undefined
-
-
-
- -

-getLimit

-
-public Limit<T> getLimit(String presetName)
-
-
-
Specified by:
getLimit in interface Executable<T>
-
-
-
-
-
-
- -

-getLimits

-
-public LimitsManager<T> getLimits()
-
-
-
Specified by:
getLimits in interface Executable<T>
-
-
-
-
-
-
- -

-getType

-
-public abstract Class<T> getType()
-
-
-
-
-
- -
Returns:
subclasses must return their type
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/Util.html b/website/full_javadoc/compbio/engine/client/Util.html deleted file mode 100644 index c55b11d..0000000 --- a/website/full_javadoc/compbio/engine/client/Util.html +++ /dev/null @@ -1,588 +0,0 @@ - - - - - - -Util - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.client -
-Class Util

-
-java.lang.Object
-  extended by compbio.engine.client.Util
-
-
-
-
public final class Util
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Util() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static StringconvertToAbsolute(String relativePath) - -
-           
-static StringgetCommand(Executable.ExecProvider provider, - Class<?> clazz) - -
-           
-static StringgetExecProperty(String propertySpec, - Class<?> clazz) - -
-           
-static StringgetExecProperty(String propertySpec, - Executable<?> exec) - -
-           
-static StringgetFullPath(String workDirectory, - String fileName) - -
-           
-static StringgetJava() - -
-          Returns the absolute path to the Java executable from JAVA_HOME
-static - - - - -
-<T> LimitsManager<T>
-		getLimits(Class<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
-static Executable.ExecProvidergetSupportedRuntimes(Class<?> clazz) - -
-           
-static booleanisJavaLibrary(Class<?> clazz) - -
-          Returns true of executableName.jar.file property has some value in the - Executable.properties file, false otherwise.
-static booleanisMarked(String workDirectory, - JobStatus marker) - -
-           
-static booleanisValidJobId(String key) - -
-           
-static ConfiguredExecutable<?>loadExecutable(String taskId) - -
-           
-static Map<String,String>mergeEnvVariables(Map<String,String> sysEnvTobeModified, - Map<String,String> variables) - -
-           
-static voidwriteFile(String workDirectory, - String fileAndEventName, - String content, - boolean override) - -
-           
-static booleanwriteMarker(String workDirectory, - JobStatus fileType) - -
-           
-static voidwriteStatFile(String workDirectory, - String fileAndEventName) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Util

-
-public Util()
-
-
- - - - - - - - -
-Method Detail
- -

-isValidJobId

-
-public static boolean isValidJobId(String key)
-
-
-
-
-
-
- -

-writeStatFile

-
-public static void writeStatFile(String workDirectory,
-                                 String fileAndEventName)
-
-
-
-
-
-
- -

-writeFile

-
-public static void writeFile(String workDirectory,
-                             String fileAndEventName,
-                             String content,
-                             boolean override)
-
-
-
-
-
-
- -

-writeMarker

-
-public static final boolean writeMarker(String workDirectory,
-                                        JobStatus fileType)
-
-
-
-
-
-
- -

-isMarked

-
-public static boolean isMarked(String workDirectory,
-                               JobStatus marker)
-
-
-
-
-
-
- -

-mergeEnvVariables

-
-public static Map<String,String> mergeEnvVariables(Map<String,String> sysEnvTobeModified,
-                                                   Map<String,String> variables)
-
-
-
-
-
-
- -

-convertToAbsolute

-
-public static String convertToAbsolute(String relativePath)
-
-
-
-
-
-
- -

-getExecProperty

-
-public static String getExecProperty(String propertySpec,
-                                     Executable<?> exec)
-
-
-
-
-
-
- -

-getExecProperty

-
-public static String getExecProperty(String propertySpec,
-                                     Class<?> clazz)
-
-
-
-
-
-
- -

-getFullPath

-
-public static String getFullPath(String workDirectory,
-                                 String fileName)
-
-
-
-
-
-
- -

-getCommand

-
-public static String getCommand(Executable.ExecProvider provider,
-                                Class<?> clazz)
-
-
-
-
-
-
- -

-isJavaLibrary

-
-public static boolean isJavaLibrary(Class<?> clazz)
-
-
Returns true of executableName.jar.file property has some value in the - Executable.properties file, false otherwise. -

-

-
Parameters:
clazz - -
Returns:
-
-
-
- -

-getJava

-
-public static String getJava()
-
-
Returns the absolute path to the Java executable from JAVA_HOME -

-

- -
Returns:
returns the absolute path to the Java executable from JAVA_HOME
-
-
-
- -

-getSupportedRuntimes

-
-public static Executable.ExecProvider getSupportedRuntimes(Class<?> clazz)
-
-
-
-
-
-
- -

-loadExecutable

-
-public static ConfiguredExecutable<?> loadExecutable(String taskId)
-                                              throws ResultNotAvailableException
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getLimits

-
-public static <T> LimitsManager<T> getLimits(Class<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; }
-
-
- -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html deleted file mode 100644 index cd5993b..0000000 --- a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html +++ /dev/null @@ -1,405 +0,0 @@ - - - - - - -Uses of Class compbio.engine.client.CommandBuilder - - - - - - - - - - - - -
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-

-Uses of Class
compbio.engine.client.CommandBuilder

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use CommandBuilder
compbio.engine.client  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of CommandBuilder in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return CommandBuilder
- CommandBuilder<?>RunConfiguration.getParameters() - -
-           
- CommandBuilder<T>ConfiguredExecutable.getParameters() - -
-           
- CommandBuilder<T>ConfExecutable.getParameters() - -
-           
- CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> CommandBuilder<T>
-		CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments, - String nameValueSeparator) - -
-          This produces the same result as getCommands method.
-  -

- - - - - - - - - -
Methods in compbio.engine.client with parameters of type CommandBuilder
- voidRunConfiguration.setParameters(CommandBuilder<?> parameters) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return CommandBuilder
- CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
-          Deprecated.  
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner._impl
-  -

- - - - - - - - - -
Methods in compbio.runner._impl that return CommandBuilder
- CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner.conservation
-  -

- - - - - - - - - -
Methods in compbio.runner.conservation that return CommandBuilder
- CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner.disorder
-  -

- - - - - - - - - -
Methods in compbio.runner.disorder that return CommandBuilder
- CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner.msa
-  -

- - - - - - - - - - - - - -
Methods in compbio.runner.msa that return CommandBuilder
- CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.ConfExecutable

-
- - - - - - - - - -
-Packages that use ConfExecutable
compbio.engine.client  
-  -

- - - - - -
-Uses of ConfExecutable in compbio.engine.client
-  -

- - - - - - - - -
Constructors in compbio.engine.client with parameters of type ConfExecutable
RunConfiguration(ConfExecutable<?> cexec) - -
-           
-  -

-

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-Uses of Interface
compbio.engine.client.ConfiguredExecutable

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use ConfiguredExecutable
compbio.engine  
compbio.engine.client  
compbio.engine.cluster.drmaa  
compbio.engine.local  
compbio.runnerUtilities commonly used by all runners. 
compbio.ws.server  
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine that return ConfiguredExecutable
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
-           
- ConfiguredExecutable<?>Job.getConfExecutable() - -
-           
- ConfiguredExecutable<?>AsyncExecutor.getResults(String jobId) - -
-          Retrieve the results of the job.
- ConfiguredExecutable<?>SyncExecutor.waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  -

- - - - - - - - - -
Methods in compbio.engine that return types with arguments of type ConfiguredExecutable
-static Future<ConfiguredExecutable<?>>SubmissionManager.getTask(String taskId) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine with parameters of type ConfiguredExecutable
-static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, - Future<ConfiguredExecutable<?>> future) - -
-           
-static booleanCleaner.deleteFiles(ConfiguredExecutable<?> exec) - -
-          Deprecated. This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty)
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static voidSubmissionManager.removeTask(ConfiguredExecutable<?> executable) - -
-           
- StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  -

- - - - - - - - - -
Method parameters in compbio.engine with type arguments of type ConfiguredExecutable
-static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, - Future<ConfiguredExecutable<?>> future) - -
-           
-  -

- - - - - - - - -
Constructors in compbio.engine with parameters of type ConfiguredExecutable
Job(String taskId, - String jobId, - ConfiguredExecutable<?> cexecutable) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine.client
-  -

- - - - - - - - - -
Classes in compbio.engine.client that implement ConfiguredExecutable
- classConfExecutable<T> - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return ConfiguredExecutable
-static ConfiguredExecutable<?>Util.loadExecutable(String taskId) - -
-           
- ConfiguredExecutable<?>ConfiguredExecutable.loadRunConfiguration(InputStream input) - -
-           
- ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(InputStream input) - -
-           
- ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) - -
-           
-static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return ConfiguredExecutable
- ConfiguredExecutable<?>ClusterSession.getResults(String taskId) - -
-           
- ConfiguredExecutable<?>AsyncJobRunner.getResults(String jobId) - -
-           
- ConfiguredExecutable<?>JobRunner.waitForResult() - -
-           
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
-static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
-           
- StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
-           
-  -

- - - - - - - - -
Constructors in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
JobRunner(ConfiguredExecutable<?> confExec) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine.local
-  -

- - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.local that return ConfiguredExecutable
- ConfiguredExecutable<?>ExecutableWrapper.call() - -
-          It is vital that output and error streams are captured immediately for - this call() to succeed.
-static ConfiguredExecutable<?>LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
-           
- ConfiguredExecutable<?>AsyncLocalRunner.getResults(String taskId) - -
-           
- ConfiguredExecutable<?>LocalRunner.waitForResult() - -
-           
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.local with parameters of type ConfiguredExecutable
-static booleanLocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable) - -
-           
- StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable
-static booleanLocalEngineUtil.cancelJob(Future<ConfiguredExecutable<?>> future, - String workDirectory) - -
-           
-static JobStatusLocalEngineUtil.getJobStatus(Future<ConfiguredExecutable<?>> future) - -
-           
-static ConfiguredExecutable<?>LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
-           
-  -

- - - - - - - - - - - -
Constructors in compbio.engine.local with parameters of type ConfiguredExecutable
ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
-           
LocalRunner(ConfiguredExecutable<?> executable) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner with parameters of type ConfiguredExecutable
-static voidUtil.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.ws.server with parameters of type ConfiguredExecutable
-static - - - - -
-<T> String
-		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
-           
-static - - - - -
-<T> String
-		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
-           
-static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.EnvVariableProcessor

-
-No usage of compbio.engine.client.EnvVariableProcessor -

-

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-Uses of Class
compbio.engine.client.Executable.ExecProvider

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use Executable.ExecProvider
compbio.engine  
compbio.engine.client  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.engine
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine that return Executable.ExecProvider
-static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		LoadBalancer.getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine with parameters of type Executable.ExecProvider
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return Executable.ExecProvider
- Executable.ExecProviderConfiguredExecutable.getExecProvider() - -
-           
- Executable.ExecProviderConfExecutable.getExecProvider() - -
-           
- Executable.ExecProviderConfiguredExecutable.getSupportedRuntimes() - -
-           
- Executable.ExecProviderConfExecutable.getSupportedRuntimes() - -
-           
-static Executable.ExecProviderUtil.getSupportedRuntimes(Class<?> clazz) - -
-           
-static Executable.ExecProviderExecutable.ExecProvider.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static Executable.ExecProvider[]Executable.ExecProvider.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client with parameters of type Executable.ExecProvider
- StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
-           
- StringConfExecutable.getCommand(Executable.ExecProvider provider) - -
-           
-static StringUtil.getCommand(Executable.ExecProvider provider, - Class<?> clazz) - -
-           
- CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) - -
-           
- voidConfExecutable.setExecProvider(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner with parameters of type Executable.ExecProvider
- CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
-          Deprecated.  
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner._impl
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.runner._impl with parameters of type Executable.ExecProvider
- StringRPSBlast.getCommand(Executable.ExecProvider provider) - -
-           
- StringPSIBlast.getCommand(Executable.ExecProvider provider) - -
-           
- StringRonn.getCommand(Executable.ExecProvider provider) - -
-           
- StringMcl.getCommand(Executable.ExecProvider provider) - -
-           
- StringBlastAll.getCommand(Executable.ExecProvider provider) - -
-           
- CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner.conservation
-  -

- - - - - - - - - -
Methods in compbio.runner.conservation with parameters of type Executable.ExecProvider
- CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner.disorder
-  -

- - - - - - - - - -
Methods in compbio.runner.disorder with parameters of type Executable.ExecProvider
- CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner.msa
-  -

- - - - - - - - - - - - - -
Methods in compbio.runner.msa with parameters of type Executable.ExecProvider
- CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) - -
-           
-  -

-

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-Uses of Interface
compbio.engine.client.Executable

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use Executable
compbio.engine  
compbio.engine.client  
compbio.engine.conf  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - -
-Uses of Executable in compbio.engine
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine with parameters of type Executable
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
-           
-static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		LoadBalancer.getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.engine.client
-  -

- - - - - - - - - - - - - -
Subinterfaces of Executable in compbio.engine.client
- interfaceConfiguredExecutable<T> - -
-           
- interfacePipedExecutable<T> - -
-          This is a marker interface to indicate that the output of the process must be - captured.
-  -

- - - - - - - - - - - - - -
Classes in compbio.engine.client that implement Executable
- classConfExecutable<T> - -
-           
- classSkeletalExecutable<T> - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return Executable
- Executable<T>Executable.addParameters(List<String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- Executable<T>SkeletalExecutable.addParameters(List<String> parameters) - -
-           
- Executable<T>ConfExecutable.addParameters(List<String> parameters) - -
-           
- Executable<T>ConfiguredExecutable.getExecutable() - -
-           
- Executable<T>ConfExecutable.getExecutable() - -
-           
- Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- Executable<T>SkeletalExecutable.setParameter(String parameter) - -
-           
-  -

- - - - - - - - - -
Methods in compbio.engine.client with parameters of type Executable
-static StringUtil.getExecProperty(String propertySpec, - Executable<?> exec) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.engine.client with type arguments of type Executable
-static intSkeletalExecutable.getClusterCpuNum(Class<? extends Executable<?>> type) - -
-           
-static - - - - -
-<V> RunnerConfig<V>
-		ConfExecutable.getRunnerOptions(Class<? extends Executable<V>> clazz) - -
-           
-static - - - - -
-<V> PresetManager<V>
-		ConfExecutable.getRunnerPresets(Class<? extends Executable<V>> clazz) - -
-           
-  -

- - - - - - - - -
Constructors in compbio.engine.client with parameters of type Executable
ConfExecutable(Executable<T> executable, - String taskDirectory) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.engine.conf
-  -

- - - - - - - - - -
Methods in compbio.engine.conf that return types with arguments of type Executable
-static Class<Executable<?>>DirectoryManager.getClass(String taskId) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner
-  -

- - - - - - - - - -
Classes in compbio.runner that implement Executable
- class_SkeletalCommandBuilder - -
-          Deprecated. 
-  -

- - - - - - - - - -
Methods in compbio.runner that return Executable
- Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) - -
-          Deprecated.  
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.runner with type arguments of type Executable
-static List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
-           
-static - - - - -
-<T> PresetManager<T>
-		Util.getPresets(Class<? extends Executable<T>> clazz) - -
-           
-static - - - - -
-<T> RunnerConfig<T>
-		Util.getSupportedOptions(Class<? extends Executable<T>> clazz) - -
-           
-  -

- - - - - - - - -
Constructor parameters in compbio.runner with type arguments of type Executable
OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner._impl
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.runner._impl that implement Executable
- classBlastAll - -
-           
- classMcl - -
-           
- classNetNglyc - -
-           
- classOB - -
-          TODO this needs fixing! Executable does not work
- classPSIBlast - -
-           
- classRonn - -
-           
- classRPSBlast - -
-           
-  -

- - - - - - - - - -
Methods in compbio.runner._impl that return Executable
- Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner.conservation
-  -

- - - - - - - - - -
Classes in compbio.runner.conservation that implement Executable
- classAACon - -
-          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
-  -

- - - - - -
-Uses of Executable in compbio.runner.disorder
-  -

- - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.runner.disorder that implement Executable
- classDisembl - -
-          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
- classGlobPlot - -
-          ./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.
- classIUPred - -
-          iupred sequenceFile - - Maximum sequence length is 40000 chars.
- classJronn - -
-          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
-  -

- - - - - -
-Uses of Executable in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.runner.msa that implement Executable
- classClustalO - -
-           
- classClustalW - -
-           
- classMafft - -
-           
- classMuscle - -
-           
- classProbcons - -
-           
- classTcoffee - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.ws.client
-  -

- - - - - - - - - - - - - -
Methods in compbio.ws.client that return types with arguments of type Executable
-static Class<? extends Executable<?>>ServicesUtil.getRunnerByJobDirectory(File jobdir) - -
-           
-static Class<? extends Executable<?>>ServicesUtil.getServiceImpl(Services service) - -
-           
-  -

- - - - - - - - - -
Method parameters in compbio.ws.client with type arguments of type Executable
-static ServicesServicesUtil.getServiceByRunner(Class<Executable<?>> runnerClassName) - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.PathValidator

-
-No usage of compbio.engine.client.PathValidator -

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-Uses of Interface
compbio.engine.client.PipedExecutable

-
- - - - - - - - - - - - - - - - - -
-Packages that use PipedExecutable
compbio.engine.client  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of PipedExecutable in compbio.engine.client
-  -

- - - - - - - - - -
Subinterfaces of PipedExecutable in compbio.engine.client
- interfaceConfiguredExecutable<T> - -
-           
-  -

- - - - - - - - - -
Classes in compbio.engine.client that implement PipedExecutable
- classConfExecutable<T> - -
-           
-  -

- - - - - -
-Uses of PipedExecutable in compbio.runner.disorder
-  -

- - - - - - - - - - - - - -
Classes in compbio.runner.disorder that implement PipedExecutable
- classDisembl - -
-          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
- classGlobPlot - -
-          ./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.
-  -

- - - - - -
-Uses of PipedExecutable in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - -
Classes in compbio.runner.msa that implement PipedExecutable
- classMafft - -
-           
- classProbcons - -
-           
- classTcoffee - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.RunConfiguration

-
- - - - - - - - - - - - - - - - - -
-Packages that use RunConfiguration
compbio.engine.client  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
-  -

- - - - - -
-Uses of RunConfiguration in compbio.engine.client
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.client that return RunConfiguration
- RunConfigurationConfExecutable.getRunConfiguration() - -
-           
-static RunConfigurationRunConfiguration.load(InputStream input) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client with parameters of type RunConfiguration
- Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) - -
-           
-static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) - -
-           
-static booleanRunConfiguration.write(RunConfiguration rconf) - -
-           
-  -

- - - - - -
-Uses of RunConfiguration in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner with parameters of type RunConfiguration
- Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) - -
-          Deprecated.  
-  -

- - - - - -
-Uses of RunConfiguration in compbio.runner._impl
-  -

- - - - - - - - - -
Methods in compbio.runner._impl with parameters of type RunConfiguration
- Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.SkeletalExecutable

-
- - - - - - - - - - - - - - - - - - - - - -
-Packages that use SkeletalExecutable
compbio.engine.client  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return SkeletalExecutable
- SkeletalExecutable<T>SkeletalExecutable.setError(String errFile) - -
-           
- SkeletalExecutable<T>SkeletalExecutable.setInput(String inFile) - -
-           
- SkeletalExecutable<T>SkeletalExecutable.setOutput(String outFile) - -
-           
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.runner.conservation
-  -

- - - - - - - - - -
Subclasses of SkeletalExecutable in compbio.runner.conservation
- classAACon - -
-          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.runner.disorder
-  -

- - - - - - - - - - - - - - - - - - - - - -
Subclasses of SkeletalExecutable in compbio.runner.disorder
- classDisembl - -
-          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
- classGlobPlot - -
-          ./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.
- classIUPred - -
-          iupred sequenceFile - - Maximum sequence length is 40000 chars.
- classJronn - -
-          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Subclasses of SkeletalExecutable in compbio.runner.msa
- classClustalO - -
-           
- classClustalW - -
-           
- classMafft - -
-           
- classMuscle - -
-           
- classProbcons - -
-           
- classTcoffee - -
-           
-  -

-

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-Interface Summary
ConfiguredExecutable<T> 
Executable<T>Interface to a native executable.
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-Class Summary
CommandBuilder<T> 
ConfExecutable<T> 
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PathValidator 
RunConfigurationValue class for persisting ConfExecutable instances
SkeletalExecutable<T> 
Util 
-  - -

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Executable.ExecProvider 
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compbio.engine.client

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use compbio.engine.client
compbio.engine  
compbio.engine.client  
compbio.engine.cluster.drmaa  
compbio.engine.conf  
compbio.engine.local  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
compbio.ws.server  
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine
ConfiguredExecutable - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.client
CommandBuilder - -
-           
ConfExecutable - -
-           
ConfiguredExecutable - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
PipedExecutable - -
-          This is a marker interface to indicate that the output of the process must be - captured.
RunConfiguration - -
-          Value class for persisting ConfExecutable instances
SkeletalExecutable - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.cluster.drmaa
ConfiguredExecutable - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.conf
Executable - -
-          Interface to a native executable.
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.local
ConfiguredExecutable - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner
CommandBuilder - -
-           
ConfiguredExecutable - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
RunConfiguration - -
-          Value class for persisting ConfExecutable instances
-  -

- - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner._impl
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
RunConfiguration - -
-          Value class for persisting ConfExecutable instances
-  -

- - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner.conservation
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
SkeletalExecutable - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner.disorder
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
PipedExecutable - -
-          This is a marker interface to indicate that the output of the process must be - captured.
SkeletalExecutable - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner.msa
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
PipedExecutable - -
-          This is a marker interface to indicate that the output of the process must be - captured.
SkeletalExecutable - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.ws.client
Executable - -
-          Interface to a native executable.
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.ws.server
ConfiguredExecutable - -
-           
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-

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- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class AsyncJobRunner

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.AsyncJobRunner
-
-
-
All Implemented Interfaces:
AsyncExecutor
-
-
-
-
public class AsyncJobRunner
extends Object
implements AsyncExecutor
- - -

-Single cluster job runner class -

- -

-

-
Version:
-
1.0 August 2009 - - TODO after call to submitJob() no setters really work as the job - template gets deleted, this needs to be taken into account in this - class design!
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
AsyncJobRunner() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(String jobId) - -
-          Stop running job.
- booleancleanup(String jobId) - -
-          Remove all files and a job directory for a jobid.
- JobStatusgetJobStatus(String jobId) - -
-          This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed.
- ConfiguredExecutable<?>getResults(String jobId) - -
-          Retrieve the results of the job.
- StringgetWorkDirectory(String jobId) - -
-           
- StringsubmitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-AsyncJobRunner

-
-public AsyncJobRunner()
-
-
- - - - - - - - -
-Method Detail
- -

-submitJob

-
-public String submitJob(ConfiguredExecutable<?> executable)
-                 throws JobSubmissionException
-
-
Description copied from interface: AsyncExecutor
-
Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

-

-
Specified by:
submitJob in interface AsyncExecutor
-
-
- -
Returns:
unique job identifier -
Throws: -
JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
-
-
-
- -

-cancelJob

-
-public boolean cancelJob(String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

-

-
Specified by:
cancelJob in interface AsyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus(String jobId)
-
-
This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed. Cancelled jobs needs to be - tracked manually! -

-

-
Specified by:
getJobStatus in interface AsyncExecutor
-
-
- -
Returns:
The JobStatus object representing the status of the job
See Also:
JobStatus
-
-
-
- -

-cleanup

-
-public boolean cleanup(String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Remove all files and a job directory for a jobid. -

-

-
Specified by:
cleanup in interface AsyncExecutor
-
-
- -
Returns:
true if job directory was successfully removed, false otherwise.
-
-
-
- -

-getResults

-
-public ConfiguredExecutable<?> getResults(String jobId)
-                                   throws ResultNotAvailableException
-
-
Description copied from interface: AsyncExecutor
-
Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

-

-
Specified by:
getResults in interface AsyncExecutor
-
-
-
Parameters:
jobId - job identifier obtained at the job submission -
Returns:
ConfiguredExecutable object from which result can be obtained -
Throws: -
ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
-
-
-
- -

-getWorkDirectory

-
-public String getWorkDirectory(String jobId)
-
-
-
Specified by:
getWorkDirectory in interface AsyncExecutor
-
-
-
Parameters:
jobId - unique job identifier -
Returns:
task working directory
-
-
- -
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- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class ClusterSession

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.ClusterSession
-
-
-
-
public final class ClusterSession
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static StringJOBID - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidclose() - -
-           
-static ClusterJobIdgetClusterJobId(String taskId) - -
-           
- intgetJobStatus(ClusterJobId jobId) - -
-          Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed.
-static StringgetJobStatus(int status) - -
-          Deprecated. 
- ConfiguredExecutable<?>getResults(String taskId) - -
-           
- org.ggf.drmaa.SessiongetSession() - -
-           
-static StatisticManagergetStatistics(org.ggf.drmaa.JobInfo status) - -
-           
- voidremoveJob(String taskId) - -
-           
- org.ggf.drmaa.JobInfowaitForJob(String taskId) - -
-           
- org.ggf.drmaa.JobInfowaitForJob(String jobId, - long waitingTime) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-JOBID

-
-public static final String JOBID
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Method Detail
- -

-getSession

-
-public org.ggf.drmaa.Session getSession()
-
-
-
-
-
-
- -

-close

-
-public void close()
-
-
-
-
-
-
- -

-removeJob

-
-public void removeJob(String taskId)
-
-
-
-
-
-
- -

-waitForJob

-
-public org.ggf.drmaa.JobInfo waitForJob(String taskId)
-                                 throws org.ggf.drmaa.DrmaaException,
-                                        IOException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException -
IOException
-
-
-
- -

-getClusterJobId

-
-public static ClusterJobId getClusterJobId(String taskId)
-                                    throws IOException
-
-
- -
Throws: -
IOException
-
-
-
- -

-waitForJob

-
-public org.ggf.drmaa.JobInfo waitForJob(String jobId,
-                                        long waitingTime)
-                                 throws org.ggf.drmaa.DrmaaException,
-                                        IOException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException -
IOException
-
-
-
- -

-getResults

-
-public ConfiguredExecutable<?> getResults(String taskId)
-                                   throws org.ggf.drmaa.DrmaaException,
-                                          ResultNotAvailableException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException -
ResultNotAvailableException
-
-
-
- -

-getStatistics

-
-public static StatisticManager getStatistics(org.ggf.drmaa.JobInfo status)
-                                      throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getJobStatus

-
-public int getJobStatus(ClusterJobId jobId)
-                 throws org.ggf.drmaa.DrmaaException,
-                        org.ggf.drmaa.InvalidJobException
-
-
Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed. -

-

- -
Throws: -
org.ggf.drmaa.InvalidJobException - if the job is no longer in the queue or running. basically it - will throw this exception for all finished or cancelled jobs -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getJobStatus

-
-@Deprecated
-public static String getJobStatus(int status)
-                           throws org.ggf.drmaa.DrmaaException
-
-
Deprecated.  -

-

Method for getting jobs status by quering the cluster, It returns status - in therms of a Sessions, not a JobStatus Should only be used for testing! -

-

-
Parameters:
status - -
Returns:
job status -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
- -
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- - - -
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- -

- -compbio.engine.cluster.drmaa -
-Class ClusterUtil

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.ClusterUtil
-
-
-
-
public class ClusterUtil
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static NumberFormatCLUSTER_STAT_IN_SEC - -
-           
-  - - - - - - - - - - -
-Constructor Summary
ClusterUtil() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static booleancancelJob(String jobId, - ClusterSession csession) - -
-           
-static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, - String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-CLUSTER_STAT_IN_SEC

-
-public static final NumberFormat CLUSTER_STAT_IN_SEC
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-ClusterUtil

-
-public ClusterUtil()
-
-
- - - - - - - - -
-Method Detail
- -

-cancelJob

-
-public static final boolean cancelJob(String jobId,
-                                      ClusterSession csession)
-
-
-
-
-
-
- -

-waitForResult

-
-public static final org.ggf.drmaa.JobInfo waitForResult(ClusterSession csession,
-                                                        String jobId)
-                                                 throws JobExecutionException
-
-
- -
Throws: -
JobExecutionException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html deleted file mode 100644 index 5336570..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html +++ /dev/null @@ -1,487 +0,0 @@ - - - - - - -JobRunner - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class JobRunner

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.JobRunner
-
-
-
All Implemented Interfaces:
SyncExecutor
-
-
-
-
public class JobRunner
extends Object
implements SyncExecutor
- - -

-Single cluster job runner class -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
JobRunner(ConfiguredExecutable<?> confExec) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob() - -
-          Stops running job.
- booleancleanup() - -
-          Clean up after the job
- booleandeepClean() - -
-           
- voidexecuteJob() - -
-          Execute the job
-static JobRunnergetInstance(ConfiguredExecutable<?> executable) - -
-           
- org.ggf.drmaa.JobInfogetJobInfo() - -
-          This method will block before the calculation has completed and then - return the object containing a job execution statistics
- JobStatusgetJobStatus() - -
-          Query the status of the job by its id.
- StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobRunner

-
-public JobRunner(ConfiguredExecutable<?> confExec)
-          throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
- - - - - - - - -
-Method Detail
- -

-deepClean

-
-public boolean deepClean()
-
-
-
-
-
-
-
-
-
- -

-cleanup

-
-public boolean cleanup()
-
-
Description copied from interface: SyncExecutor
-
Clean up after the job -

-

-
Specified by:
cleanup in interface SyncExecutor
-
-
- -
Returns:
true if all the files created by this job have been removed successfully, false otherwise
-
-
-
- -

-cancelJob

-
-public boolean cancelJob()
-
-
Description copied from interface: SyncExecutor
-
Stops running job. - Clean up is not performed. -

-

-
Specified by:
cancelJob in interface SyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getWorkDirectory

-
-public String getWorkDirectory()
-
-
-
Specified by:
getWorkDirectory in interface SyncExecutor
-
-
- -
Returns:
working directory if the task
-
-
-
- -

-executeJob

-
-public void executeJob()
-                throws JobSubmissionException
-
-
Description copied from interface: SyncExecutor
-
Execute the job -

-

-
Specified by:
executeJob in interface SyncExecutor
-
-
- -
Throws: -
JobSubmissionException - if submission fails
-
-
-
- -

-getJobInfo

-
-public org.ggf.drmaa.JobInfo getJobInfo()
-                                 throws JobExecutionException
-
-
This method will block before the calculation has completed and then - return the object containing a job execution statistics -

-

-
-
-
- -
Returns:
-
Throws: -
JobExecutionException
-
-
-
- -

-waitForResult

-
-public ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
-
-
Description copied from interface: SyncExecutor
-
Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

-

-
Specified by:
waitForResult in interface SyncExecutor
-
-
- -
Returns:
object from wich the result can be obtained -
Throws: -
JobExecutionException
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus()
-
-
Description copied from interface: SyncExecutor
-
Query the status of the job by its id. -

-

-
Specified by:
getJobStatus in interface SyncExecutor
-
-
- -
Returns:
- JobStatus
-
-
-
- -

-getInstance

-
-public static JobRunner getInstance(ConfiguredExecutable<?> executable)
-                             throws JobSubmissionException
-
-
-
-
-
- -
Throws: -
JobSubmissionException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.engine.cluster.drmaa -
-Class StatisticManager

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.StatisticManager
-
-
-
-
public class StatisticManager
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
StatisticManager(org.ggf.drmaa.JobInfo status) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- StringgetAllStats() - -
-           
- StringgetCalculationTime() - -
-           
- StringgetCPUTimeStat() - -
-           
- StringgetCPUUsageTime() - -
-           
- StringgetDataTransfered() - -
-           
- StringgetEndTime() - -
-           
- StringgetExecutionStat() - -
-           
- StringgetExitStatus() - -
-           
- StringgetIOWait() - -
-           
- StringgetJobId() - -
-           
- StringgetJobPriority() - -
-           
- StringgetMaxVMem() - -
-           
- StringgetMemoryStat() - -
-           
- Map<String,String>getRawUsage() - -
-           
- StringgetStartTime() - -
-           
- StringgetSubmissionTime() - -
-           
- StringgetTimeStat() - -
-           
- StringgetUsedSysTime() - -
-           
- StringgetUsedUserTime() - -
-           
- StringgetVMem() - -
-           
- booleanhasDump() - -
-           
- booleanhasExited() - -
-           
- booleanhasSignaled() - -
-           
- StringtermSignal() - -
-           
- StringtoString() - -
-           
- booleanwasAborted() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-StatisticManager

-
-public StatisticManager(org.ggf.drmaa.JobInfo status)
-                 throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public String getJobId()
-                throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-hasExited

-
-public boolean hasExited()
-                  throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-hasSignaled

-
-public boolean hasSignaled()
-                    throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-hasDump

-
-public boolean hasDump()
-                throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-termSignal

-
-public String termSignal()
-                  throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-wasAborted

-
-public boolean wasAborted()
-                   throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getSubmissionTime

-
-public String getSubmissionTime()
-
-
-
-
-
-
- -

-getVMem

-
-public String getVMem()
-
-
-
-
-
-
- -

-getMaxVMem

-
-public String getMaxVMem()
-
-
-
-
-
-
- -

-getUsedSysTime

-
-public String getUsedSysTime()
-
-
-
-
-
-
- -

-getUsedUserTime

-
-public String getUsedUserTime()
-
-
-
-
-
-
- -

-getCalculationTime

-
-public String getCalculationTime()
-
-
-
-
-
-
- -

-getEndTime

-
-public String getEndTime()
-
-
-
-
-
-
- -

-getStartTime

-
-public String getStartTime()
-
-
-
-
-
-
- -

-getIOWait

-
-public String getIOWait()
-
-
-
-
-
-
- -

-getCPUUsageTime

-
-public String getCPUUsageTime()
-
-
-
-
-
-
- -

-getDataTransfered

-
-public String getDataTransfered()
-
-
-
-
-
-
- -

-getJobPriority

-
-public String getJobPriority()
-
-
-
-
-
-
- -

-getExitStatus

-
-public String getExitStatus()
-
-
-
-
-
-
- -

-getAllStats

-
-public String getAllStats()
-                   throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getExecutionStat

-
-public String getExecutionStat()
-                        throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getMemoryStat

-
-public String getMemoryStat()
-
-
-
-
-
-
- -

-getCPUTimeStat

-
-public String getCPUTimeStat()
-
-
-
-
-
-
- -

-getTimeStat

-
-public String getTimeStat()
-
-
-
-
-
-
- -

-getRawUsage

-
-public Map<String,String> getRawUsage()
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
- -
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-Uses of Class
compbio.engine.cluster.drmaa.AsyncJobRunner

-
-No usage of compbio.engine.cluster.drmaa.AsyncJobRunner -

-

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- - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterSession.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterSession.html deleted file mode 100644 index 9d38f9b..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterSession.html +++ /dev/null @@ -1,190 +0,0 @@ - - - - - - -Uses of Class compbio.engine.cluster.drmaa.ClusterSession - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.cluster.drmaa.ClusterSession

-
- - - - - - - - - -
-Packages that use ClusterSession
compbio.engine.cluster.drmaa  
-  -

- - - - - -
-Uses of ClusterSession in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.cluster.drmaa with parameters of type ClusterSession
-static booleanClusterUtil.cancelJob(String jobId, - ClusterSession csession) - -
-           
-static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, - String jobId) - -
-           
-  -

-

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compbio.engine.cluster.drmaa.ClusterUtil

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-

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compbio.engine.cluster.drmaa.JobRunner

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- - - - - - - - - -
-Packages that use JobRunner
compbio.engine.cluster.drmaa  
-  -

- - - - - -
-Uses of JobRunner in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return JobRunner
-static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.cluster.drmaa.StatisticManager

-
- - - - - - - - - -
-Packages that use StatisticManager
compbio.engine.cluster.drmaa  
-  -

- - - - - -
-Uses of StatisticManager in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return StatisticManager
-static StatisticManagerClusterSession.getStatistics(org.ggf.drmaa.JobInfo status) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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-Classes  - -
-AsyncJobRunner -
-ClusterSession -
-ClusterUtil -
-JobRunner -
-StatisticManager
- - - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html deleted file mode 100644 index 823a12b..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html +++ /dev/null @@ -1,173 +0,0 @@ - - - - - - -compbio.engine.cluster.drmaa - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
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-

-Package compbio.engine.cluster.drmaa -

- - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
AsyncJobRunnerSingle cluster job runner class
ClusterSession 
ClusterUtil 
JobRunnerSingle cluster job runner class
StatisticManager 
-  - -

-

-
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-Hierarchy For Package compbio.engine.cluster.drmaa -

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-Class Hierarchy -

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-Uses of Package
compbio.engine.cluster.drmaa

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-Packages that use compbio.engine.cluster.drmaa
compbio.engine.cluster.drmaa  
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.engine.cluster.drmaa used by compbio.engine.cluster.drmaa
ClusterSession - -
-           
JobRunner - -
-          Single cluster job runner class
StatisticManager - -
-           
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html deleted file mode 100644 index 01ece1b..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html +++ /dev/null @@ -1,520 +0,0 @@ - - - - - - -_Queue - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.engine.cluster.dundee -
-Enum _Queue

-
-java.lang.Object
-  extended by java.lang.Enum<_Queue>
-      extended by compbio.engine.cluster.dundee._Queue
-
-
-
All Implemented Interfaces:
Serializable, Comparable<_Queue>
-
-
-Deprecated. -

-

-
@Deprecated
-public enum _Queue
extends Enum<_Queue>
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
BIGINT - -
-          Deprecated.  
BIGMEM - -
-          Deprecated.  
BIT64 - -
-          Deprecated.  
DEVEL - -
-          Deprecated. Order of the constraint reflect the priority of the queue
PRIBIT64 - -
-          Deprecated.  
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetMemoryLimit() - -
-          Deprecated. return max memory limit in Mb
-static _QueuegetQueue(int maxMemory, - int timeLimitInHours) - -
-          Deprecated.  
- _QueuegetQueue(String queueName) - -
-          Deprecated.  
-static _QueuegetQueueByMemoryRequirements(int maxMemory) - -
-          Deprecated.  
- intgetTimeLimit() - -
-          Deprecated. 0 - unlimited
- booleanhasTimeLimit() - -
-          Deprecated.  
- StringtoString() - -
-          Deprecated.  
-static _QueuevalueOf(String name) - -
-          Deprecated. Returns the enum constant of this type with the specified name.
-static _Queue[]values() - -
-          Deprecated. Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-DEVEL

-
-public static final _Queue DEVEL
-
-
Deprecated. 
Order of the constraint reflect the priority of the queue -

-

-
-
-
- -

-PRIBIT64

-
-public static final _Queue PRIBIT64
-
-
Deprecated. 
-
-
-
- -

-BIT64

-
-public static final _Queue BIT64
-
-
Deprecated. 
-
-
-
- -

-BIGINT

-
-public static final _Queue BIGINT
-
-
Deprecated. 
-
-
-
- -

-BIGMEM

-
-public static final _Queue BIGMEM
-
-
Deprecated. 
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static _Queue[] values()
-
-
Deprecated. 
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (_Queue c : _Queue.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static _Queue valueOf(String name)
-
-
Deprecated. 
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
-
- -

-toString

-
-public String toString()
-
-
Deprecated. 
-
Overrides:
toString in class Enum<_Queue>
-
-
-
-
-
-
- -

-getTimeLimit

-
-public int getTimeLimit()
-
-
Deprecated. 
0 - unlimited -

-

- -
Returns:
max runtime in hours
-
-
-
- -

-hasTimeLimit

-
-public boolean hasTimeLimit()
-
-
Deprecated. 
- -
Returns:
true if the queue has time limit, false overwise
-
-
-
- -

-getMemoryLimit

-
-public int getMemoryLimit()
-
-
Deprecated. 
return max memory limit in Mb -

-

- -
Returns:
-
-
-
- -

-getQueueByMemoryRequirements

-
-public static _Queue getQueueByMemoryRequirements(int maxMemory)
-
-
Deprecated. 
-
-
-
-
- -

-getQueue

-
-public static _Queue getQueue(int maxMemory,
-                              int timeLimitInHours)
-
-
Deprecated. 
-
-
-
-
- -

-getQueue

-
-public _Queue getQueue(String queueName)
-
-
Deprecated. 
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html deleted file mode 100644 index 2dbc4f2..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - -Uses of Class compbio.engine.cluster.dundee._Queue - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.cluster.dundee._Queue

-
- - - - - - - - - - - - - -
-Packages that use _Queue
compbio.engine.cluster.dundee  
compbio.runnerUtilities commonly used by all runners. 
-  -

- - - - - -
-Uses of _Queue in compbio.engine.cluster.dundee
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.cluster.dundee that return _Queue
-static _Queue_Queue.getQueue(int maxMemory, - int timeLimitInHours) - -
-          Deprecated.  
- _Queue_Queue.getQueue(String queueName) - -
-          Deprecated.  
-static _Queue_Queue.getQueueByMemoryRequirements(int maxMemory) - -
-          Deprecated.  
-static _Queue_Queue.valueOf(String name) - -
-          Deprecated. Returns the enum constant of this type with the specified name.
-static _Queue[]_Queue.values() - -
-          Deprecated. Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

- - - - - -
-Uses of _Queue in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return _Queue
- _Queue_NativeSpecHelper.getApproprieteQueue() - -
-          Deprecated.  
-  -

-

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-Enums  - -
-_Queue
- - - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html deleted file mode 100644 index cc78eb8..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - -compbio.engine.cluster.dundee - - - - - - - - - - - - -
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-Package compbio.engine.cluster.dundee -

- - - - - - - - - -
-Enum Summary
_QueueDeprecated.
-  - -

-

-
-
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-Hierarchy For Package compbio.engine.cluster.dundee -

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-Uses of Package
compbio.engine.cluster.dundee

-
- - - - - - - - - - - - - -
-Packages that use compbio.engine.cluster.dundee
compbio.engine.cluster.dundee  
compbio.runnerUtilities commonly used by all runners. 
-  -

- - - - - - - - -
-Classes in compbio.engine.cluster.dundee used by compbio.engine.cluster.dundee
_Queue - -
-          Deprecated. 
-  -

- - - - - - - - -
-Classes in compbio.engine.cluster.dundee used by compbio.runner
_Queue - -
-          Deprecated. 
-  -

-

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- - - -
- -

- -compbio.engine.conf -
-Class DirectoryManager

-
-java.lang.Object
-  extended by compbio.engine.conf.DirectoryManager
-
-
-
-
public class DirectoryManager
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static StringDELIM - -
-           
-  - - - - - - - - - - -
-Constructor Summary
DirectoryManager() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static Class<Executable<?>>getClass(String taskId) - -
-           
-static StringgetTaskDirectory(Class<?> clazz) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-DELIM

-
-public static final String DELIM
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-DirectoryManager

-
-public DirectoryManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getTaskDirectory

-
-public static String getTaskDirectory(Class<?> clazz)
-
-
-
-
-
-
- -

-getClass

-
-public static Class<Executable<?>> getClass(String taskId)
-
-
-
-
-
- -
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- - - diff --git a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html deleted file mode 100644 index f0a5f69..0000000 --- a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html +++ /dev/null @@ -1,332 +0,0 @@ - - - - - - -PropertyHelperManager - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.conf -
-Class PropertyHelperManager

-
-java.lang.Object
-  extended by compbio.engine.conf.PropertyHelperManager
-
-
-
-
public final class PropertyHelperManager
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static StringconfDir - -
-           
-  - - - - - - - - - - -
-Constructor Summary
PropertyHelperManager() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static StringgetLocalPath() - -
-          Method return the absolute path to the project root directory.
-static compbio.util.PropertyHelpergetPropertyHelper() - -
-          Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-confDir

-
-public static final String confDir
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-PropertyHelperManager

-
-public PropertyHelperManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getPropertyHelper

-
-public static compbio.util.PropertyHelper getPropertyHelper()
-
-
Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class. Then prepend this absolute path to the rest of - paths pros: no input from user cons: relocation of the source may cause - problems 2) Require users to add configuration directories to the class - path and then load entries from it. pros: cons: Many paths needs to be - added. Put significant burden on the user. Hard to tell web appl server - to add these entries to its class path. 3) Ask for project source - directory explicitly in the configuration. pros cons: similar to 1, but - this initial configuration file must reside in well known location! Why - ask users what can be found automatically? 4) Have everything in the - location already in class path for tomcat. cons: only classes and - lib/*.jar are added, eclipse will remove non classses from classes dir. - - Try 1 - succeed. -

-

- -
Returns:
an instance
-
-
-
- -

-getLocalPath

-
-public static String getLocalPath()
-
-
Method return the absolute path to the project root directory. It assumes - the following structure of the project project root conf settings - binaries WEB-INF classes compbio engine conf If the structure changes it - must be reflected in this method -

-

- -
Returns:
the local path -
Throws: -
RuntimeException - if cannot determine the local path
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html deleted file mode 100644 index 6bbfb95..0000000 --- a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html +++ /dev/null @@ -1,507 +0,0 @@ - - - - - - -RunnerConfigMarshaller - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.conf -
-Class RunnerConfigMarshaller<T>

-
-java.lang.Object
-  extended by compbio.engine.conf.RunnerConfigMarshaller<T>
-
-
-
-
public class RunnerConfigMarshaller<T>
extends Object
- - -

-

- -

- - - - - - - - - - - - - - -
-Constructor Summary
RunnerConfigMarshaller(Class<?> rootClass) - -
-           
RunnerConfigMarshaller(Class<?> rootClass, - Class<?>... classes) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static SchemagetSchema(String schemafile) - -
-           
-static ValidatorgetValidator(Schema schema) - -
-           
-static ValidatorgetValidator(String schemafile) - -
-           
- - - - - -
-<V> V
-		read(InputStream instream, - Class<V> resultElemType) - -
-           
- - - - - -
-<V> V
-		read(InputStream instream, - Class<V> resultElemType, - Class<?>... classes) - -
-           
- - - - - -
-<V> V
-		readAndValidate(InputStream document, - Class<V> resultElemType) - -
-           
-static booleanvalidate(Validator validator, - String document) - -
-           
- voidwrite(Object xmlRootElement, - OutputStream out) - -
-           
- voidwriteAndValidate(Object xmlRootElement, - String schemafile, - OutputStream out) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-RunnerConfigMarshaller

-
-public RunnerConfigMarshaller(Class<?> rootClass)
-                       throws JAXBException
-
-
- -
Throws: -
JAXBException
-
-
- -

-RunnerConfigMarshaller

-
-public RunnerConfigMarshaller(Class<?> rootClass,
-                              Class<?>... classes)
-                       throws JAXBException
-
-
- -
Throws: -
JAXBException
-
- - - - - - - - -
-Method Detail
- -

-write

-
-public void write(Object xmlRootElement,
-                  OutputStream out)
-           throws JAXBException,
-                  IOException
-
-
- -
Throws: -
JAXBException -
IOException
-
-
-
- -

-writeAndValidate

-
-public void writeAndValidate(Object xmlRootElement,
-                             String schemafile,
-                             OutputStream out)
-                      throws JAXBException,
-                             IOException,
-                             SAXException
-
-
- -
Throws: -
JAXBException -
IOException -
SAXException
-
-
-
- -

-getSchema

-
-public static Schema getSchema(String schemafile)
-                        throws SAXException
-
-
- -
Throws: -
SAXException
-
-
-
- -

-getValidator

-
-public static Validator getValidator(String schemafile)
-                              throws SAXException
-
-
- -
Returns:
validator instance -
Throws: -
SAXException
-
-
-
- -

-getValidator

-
-public static Validator getValidator(Schema schema)
-                              throws SAXException
-
-
- -
Throws: -
SAXException
-
-
-
- -

-validate

-
-public static boolean validate(Validator validator,
-                               String document)
-                        throws IOException,
-                               SAXException
-
-
- -
Throws: -
IOException -
SAXException
-
-
-
- -

-readAndValidate

-
-public <V> V readAndValidate(InputStream document,
-                             Class<V> resultElemType)
-                  throws JAXBException,
-                         IOException,
-                         SAXException
-
-
- -
Throws: -
JAXBException -
IOException -
SAXException
-
-
-
- -

-read

-
-public <V> V read(InputStream instream,
-                  Class<V> resultElemType)
-       throws JAXBException
-
-
- -
Throws: -
JAXBException
-
-
-
- -

-read

-
-public <V> V read(InputStream instream,
-                  Class<V> resultElemType,
-                  Class<?>... classes)
-       throws JAXBException
-
-
- -
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JAXBException
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- -compbio.engine.conf -
-Class _Key

-
-java.lang.Object
-  extended by compbio.engine.conf._Key
-
-
-Deprecated. -

-

-
@Deprecated
-public final class _Key
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static StringDELIM - -
-          Deprecated.  
-  - - - - - - - - - - -
-Constructor Summary
_Key(Class<?> clazz) - -
-          Deprecated.  
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-          Deprecated.  
- inthashCode() - -
-          Deprecated.  
-static _Keyparse(String key) - -
-          Deprecated.  
- StringtoString() - -
-          Deprecated.  
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-DELIM

-
-public static final String DELIM
-
-
Deprecated. 
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-_Key

-
-public _Key(Class<?> clazz)
-
-
Deprecated. 
- - - - - - - - -
-Method Detail
- -

-equals

-
-public boolean equals(Object obj)
-
-
Deprecated. 
-
Overrides:
equals in class Object
-
-
-
-
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-
- -

-toString

-
-public String toString()
-
-
Deprecated. 
-
Overrides:
toString in class Object
-
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-
-
-
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- -

-hashCode

-
-public int hashCode()
-
-
Deprecated. 
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-parse

-
-public static _Key parse(String key)
-
-
Deprecated. 
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- - - diff --git a/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html deleted file mode 100644 index 16c29b0..0000000 --- a/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.engine.conf.DirectoryManager - - - - - - - - - - - - -
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compbio.engine.conf.DirectoryManager

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-

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compbio.engine.conf.PropertyHelperManager

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-

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compbio.engine.conf.RunnerConfigMarshaller

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-No usage of compbio.engine.conf.RunnerConfigMarshaller -

-

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-Uses of Class
compbio.engine.conf._Key

-
- - - - - - - - - -
-Packages that use _Key
compbio.engine.conf  
-  -

- - - - - -
-Uses of _Key in compbio.engine.conf
-  -

- - - - - - - - - -
Methods in compbio.engine.conf that return _Key
-static _Key_Key.parse(String key) - -
-          Deprecated.  
-  -

-

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-Classes  - -
-_Key -
-DirectoryManager -
-PropertyHelperManager -
-RunnerConfigMarshaller
- - - - diff --git a/website/full_javadoc/compbio/engine/conf/package-summary.html b/website/full_javadoc/compbio/engine/conf/package-summary.html deleted file mode 100644 index ae382e1..0000000 --- a/website/full_javadoc/compbio/engine/conf/package-summary.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - - - -compbio.engine.conf - - - - - - - - - - - - -
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-Package compbio.engine.conf -

- - - - - - - - - - - - - - - - - - - - - -
-Class Summary
_KeyDeprecated.
DirectoryManager 
PropertyHelperManager 
RunnerConfigMarshaller<T> 
-  - -

-

-
-
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-Hierarchy For Package compbio.engine.conf -

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-Class Hierarchy -

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compbio.engine.conf

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compbio.engine.conf  
-  -

- - - - - - - - -
-Classes in compbio.engine.conf used by compbio.engine.conf
_Key - -
-          Deprecated. 
-  -

-

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- - - -
- -

- -compbio.engine.local -
-Class AsyncLocalRunner

-
-java.lang.Object
-  extended by compbio.engine.local.AsyncLocalRunner
-
-
-
All Implemented Interfaces:
AsyncExecutor
-
-
-
-
public final class AsyncLocalRunner
extends Object
implements AsyncExecutor
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
AsyncLocalRunner() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(String jobId) - -
-          Stop running job.
- booleancleanup(String jobId) - -
-          Remove all files and a job directory for a jobid.
- JobStatusgetJobStatus(String jobId) - -
-          Query the status of the job
- ConfiguredExecutable<?>getResults(String taskId) - -
-          Retrieve the results of the job.
- StringgetWorkDirectory(String jobId) - -
-           
- StringsubmitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-AsyncLocalRunner

-
-public AsyncLocalRunner()
-
-
- - - - - - - - -
-Method Detail
- -

-getWorkDirectory

-
-public String getWorkDirectory(String jobId)
-
-
-
Specified by:
getWorkDirectory in interface AsyncExecutor
-
-
-
Parameters:
jobId - unique job identifier -
Returns:
task working directory
-
-
-
- -

-cancelJob

-
-public boolean cancelJob(String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

-

-
Specified by:
cancelJob in interface AsyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus(String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Query the status of the job -

-

-
Specified by:
getJobStatus in interface AsyncExecutor
-
-
- -
Returns:
The JobStatus object representing the status of the job
See Also:
JobStatus
-
-
-
- -

-submitJob

-
-public String submitJob(ConfiguredExecutable<?> executable)
-                 throws JobSubmissionException
-
-
Description copied from interface: AsyncExecutor
-
Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

-

-
Specified by:
submitJob in interface AsyncExecutor
-
-
- -
Returns:
unique job identifier -
Throws: -
JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
-
-
-
- -

-cleanup

-
-public boolean cleanup(String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Remove all files and a job directory for a jobid. -

-

-
Specified by:
cleanup in interface AsyncExecutor
-
-
-
Parameters:
jobId - -
Returns:
true if all files were removed, false otherwise
-
-
-
- -

-getResults

-
-public ConfiguredExecutable<?> getResults(String taskId)
-                                   throws ResultNotAvailableException
-
-
Description copied from interface: AsyncExecutor
-
Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

-

-
Specified by:
getResults in interface AsyncExecutor
-
-
-
Parameters:
taskId - job identifier obtained at the job submission -
Returns:
ConfiguredExecutable object from which result can be obtained -
Throws: -
ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html b/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html deleted file mode 100644 index 49b8381..0000000 --- a/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html +++ /dev/null @@ -1,359 +0,0 @@ - - - - - - -ExecutableWrapper - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.local -
-Class ExecutableWrapper

-
-java.lang.Object
-  extended by compbio.engine.local.ExecutableWrapper
-
-
-
All Implemented Interfaces:
Callable<ConfiguredExecutable<?>>
-
-
-
-
@Immutable
-public final class ExecutableWrapper
extends Object
implements Callable<ConfiguredExecutable<?>>
- - -

-

- -

- - - - - - - - - - - - - - - -
-Field Summary
-static StringPROC_ERR_FILE - -
-           
-static StringPROC_OUT_FILE - -
-           
-  - - - - - - - - - - -
-Constructor Summary
ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ConfiguredExecutable<?>call() - -
-          It is vital that output and error streams are captured immediately for - this call() to succeed.
-static voidshutdownService() - -
-          Stops internal executor service which captures streams of native - executables.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-PROC_OUT_FILE

-
-public static final String PROC_OUT_FILE
-
-
-
See Also:
Constant Field Values
-
-
- -

-PROC_ERR_FILE

-
-public static final String PROC_ERR_FILE
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-ExecutableWrapper

-
-public ExecutableWrapper(ConfiguredExecutable<?> executable,
-                         String workDirectory)
-                  throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
- - - - - - - - -
-Method Detail
- -

-shutdownService

-
-public static final void shutdownService()
-
-
Stops internal executor service which captures streams of native - executables. This method is intended for stopping service if deployed in - the web application content. There is NO NEED of using this method - otherwise as the executor service is taken care of internally. -

-

-
-
-
-
-
-
-
- -

-call

-
-public ConfiguredExecutable<?> call()
-                             throws IOException
-
-
It is vital that output and error streams are captured immediately for - this call() to succeed. Thus each instance if ExecutableWrapper has 2 its - own thread ready to capture the output. If executor could not execute - capture immediately this could lead to the call method to stale, as - execution could not proceed without output being captured. Every call to - call() method will use 2 threads -

-

-
Specified by:
call in interface Callable<ConfiguredExecutable<?>>
-
-
- -
Throws: -
IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html deleted file mode 100644 index ca17a85..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - - -LocalEngineUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.local -
-Class LocalEngineUtil

-
-java.lang.Object
-  extended by compbio.engine.local.LocalEngineUtil
-
-
-
-
public final class LocalEngineUtil
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
LocalEngineUtil() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleancancelJob(Future<ConfiguredExecutable<?>> future, - String workDirectory) - -
-           
-static booleancleanup(ConfiguredExecutable<?> confExecutable) - -
-           
-static JobStatusgetJobStatus(Future<ConfiguredExecutable<?>> future) - -
-           
-static JobStatusgetRecordedJobStatus(String jobId) - -
-           
-static ConfiguredExecutable<?>getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LocalEngineUtil

-
-public LocalEngineUtil()
-
-
- - - - - - - - -
-Method Detail
- -

-cancelJob

-
-public static boolean cancelJob(Future<ConfiguredExecutable<?>> future,
-                                String workDirectory)
-
-
-
-
-
-
- -

-getJobStatus

-
-public static JobStatus getJobStatus(Future<ConfiguredExecutable<?>> future)
-
-
-
-
-
-
- -

-getRecordedJobStatus

-
-public static JobStatus getRecordedJobStatus(String jobId)
-
-
-
-
-
-
- -

-cleanup

-
-public static boolean cleanup(ConfiguredExecutable<?> confExecutable)
-
-
-
-
-
-
- -

-getResults

-
-public static ConfiguredExecutable<?> getResults(Future<ConfiguredExecutable<?>> future,
-                                                 String taskId)
-                                          throws ResultNotAvailableException
-
-
- -
Throws: -
ResultNotAvailableException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html deleted file mode 100644 index d65318e..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html +++ /dev/null @@ -1,315 +0,0 @@ - - - - - - -LocalExecutorService - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.local -
-Class LocalExecutorService

-
-java.lang.Object
-  extended by java.util.concurrent.AbstractExecutorService
-      extended by java.util.concurrent.ThreadPoolExecutor
-          extended by compbio.engine.local.LocalExecutorService
-
-
-
All Implemented Interfaces:
Executor, ExecutorService
-
-
-
-
public final class LocalExecutorService
extends ThreadPoolExecutor
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor
ThreadPoolExecutor.AbortPolicy, ThreadPoolExecutor.CallerRunsPolicy, ThreadPoolExecutor.DiscardOldestPolicy, ThreadPoolExecutor.DiscardPolicy
-  - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancanAcceptMoreWork() - -
-          If the Executor queue is empty
-static LocalExecutorServicegetExecutor() - -
-          This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally
-static voidshutDown() - -
-          This stops all executing processes via interruption.
-  - - - - - - - -
Methods inherited from class java.util.concurrent.ThreadPoolExecutor
allowCoreThreadTimeOut, allowsCoreThreadTimeOut, awaitTermination, execute, getActiveCount, getCompletedTaskCount, getCorePoolSize, getKeepAliveTime, getLargestPoolSize, getMaximumPoolSize, getPoolSize, getQueue, getRejectedExecutionHandler, getTaskCount, getThreadFactory, isShutdown, isTerminated, isTerminating, prestartAllCoreThreads, prestartCoreThread, purge, remove, setCorePoolSize, setKeepAliveTime, setMaximumPoolSize, setRejectedExecutionHandler, setThreadFactory, shutdown, shutdownNow
-  - - - - - - - -
Methods inherited from class java.util.concurrent.AbstractExecutorService
invokeAll, invokeAll, invokeAny, invokeAny, submit, submit, submit
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Method Detail
- -

-getExecutor

-
-public static LocalExecutorService getExecutor()
-
-
This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally -

-

- -
Returns:
the instance
-
-
-
- -

-shutDown

-
-public static void shutDown()
-
-
This stops all executing processes via interruption. Thus it is vital - that all processes that use this service respond to interruption - - Stops internal executor service which captures streams of native - executables. This method is intended for stopping service if deployed in - the web application context. There is NO NEED of using this method - otherwise as the executor service is taken care of internally. -

-

-
-
-
-
- -

-canAcceptMoreWork

-
-public boolean canAcceptMoreWork()
-
-
If the Executor queue is empty -

-

- -
Returns:
true is not all threads are busy, false otherwise
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/LocalRunner.html b/website/full_javadoc/compbio/engine/local/LocalRunner.html deleted file mode 100644 index 1e78431..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalRunner.html +++ /dev/null @@ -1,398 +0,0 @@ - - - - - - -LocalRunner - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.engine.local -
-Class LocalRunner

-
-java.lang.Object
-  extended by compbio.engine.local.LocalRunner
-
-
-
All Implemented Interfaces:
SyncExecutor
-
-
-
-
public final class LocalRunner
extends Object
implements SyncExecutor
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
LocalRunner(ConfiguredExecutable<?> executable) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob() - -
-          Stops running job.
- booleancleanup() - -
-          Clean up after the job
- voidexecuteJob() - -
-          Execute the job
- JobStatusgetJobStatus() - -
-          Query the status of the job by its id.
- StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LocalRunner

-
-public LocalRunner(ConfiguredExecutable<?> executable)
-
-
- - - - - - - - -
-Method Detail
- -

-getWorkDirectory

-
-public String getWorkDirectory()
-
-
-
Specified by:
getWorkDirectory in interface SyncExecutor
-
-
- -
Returns:
working directory if the task
-
-
-
- -

-cancelJob

-
-public boolean cancelJob()
-
-
Description copied from interface: SyncExecutor
-
Stops running job. - Clean up is not performed. -

-

-
Specified by:
cancelJob in interface SyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus()
-
-
Description copied from interface: SyncExecutor
-
Query the status of the job by its id. -

-

-
Specified by:
getJobStatus in interface SyncExecutor
-
-
- -
Returns:
- JobStatus
-
-
-
- -

-executeJob

-
-public void executeJob()
-                throws JobSubmissionException
-
-
Description copied from interface: SyncExecutor
-
Execute the job -

-

-
Specified by:
executeJob in interface SyncExecutor
-
-
- -
Throws: -
JobSubmissionException - if submission fails
-
-
-
- -

-waitForResult

-
-public ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
-
-
Description copied from interface: SyncExecutor
-
Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

-

-
Specified by:
waitForResult in interface SyncExecutor
-
-
- -
Returns:
object from wich the result can be obtained -
Throws: -
CancellationException -
JobExecutionException
-
-
-
- -

-cleanup

-
-public boolean cleanup()
-
-
Description copied from interface: SyncExecutor
-
Clean up after the job -

-

-
Specified by:
cleanup in interface SyncExecutor
-
-
- -
Returns:
true if all the files created by this job have been removed successfully, false otherwise
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/StreamGobbler.html deleted file mode 100644 index 0cdba6e..0000000 --- a/website/full_javadoc/compbio/engine/local/StreamGobbler.html +++ /dev/null @@ -1,226 +0,0 @@ - - - - - - -StreamGobbler - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.local -
-Class StreamGobbler

-
-java.lang.Object
-  extended by compbio.engine.local.StreamGobbler
-
-
-
All Implemented Interfaces:
Runnable
-
-
-
-
@ThreadSafe
-public class StreamGobbler
extends Object
implements Runnable
- - -

-

- -

- - - - - - - - - - - - -
-Method Summary
- voidrun() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Method Detail
- -

-run

-
-public void run()
-
-
-
Specified by:
run in interface Runnable
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html deleted file mode 100644 index e257a9e..0000000 --- a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.engine.local.AsyncLocalRunner - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.local.AsyncLocalRunner

-
-No usage of compbio.engine.local.AsyncLocalRunner -

-

- - - - - - - - - - - - - - - -
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compbio.engine.local.ExecutableWrapper

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-

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compbio.engine.local.LocalEngineUtil

-
-No usage of compbio.engine.local.LocalEngineUtil -

-

- - - - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.local.LocalExecutorService

-
- - - - - - - - - -
-Packages that use LocalExecutorService
compbio.engine.local  
-  -

- - - - - -
-Uses of LocalExecutorService in compbio.engine.local
-  -

- - - - - - - - - -
Methods in compbio.engine.local that return LocalExecutorService
-static LocalExecutorServiceLocalExecutorService.getExecutor() - -
-          This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally
-  -

-

- - - - - - - - - - - - - - - -
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compbio.engine.local.LocalRunner

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-

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-Classes  - -
-AsyncLocalRunner -
-ExecutableWrapper -
-LocalEngineUtil -
-LocalExecutorService -
-LocalRunner -
-StreamGobbler
- - - - diff --git a/website/full_javadoc/compbio/engine/local/package-summary.html b/website/full_javadoc/compbio/engine/local/package-summary.html deleted file mode 100644 index 6a0b02a..0000000 --- a/website/full_javadoc/compbio/engine/local/package-summary.html +++ /dev/null @@ -1,177 +0,0 @@ - - - - - - -compbio.engine.local - - - - - - - - - - - - -
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-

-Package compbio.engine.local -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
AsyncLocalRunner 
ExecutableWrapper 
LocalEngineUtil 
LocalExecutorService 
LocalRunner 
StreamGobbler 
-  - -

-

-
-
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compbio.engine.local  
-  -

- - - - - - - - -
-Classes in compbio.engine.local used by compbio.engine.local
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-Interfaces  - -
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- - - - - - -
-Classes  - -
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- - - - diff --git a/website/full_javadoc/compbio/engine/package-summary.html b/website/full_javadoc/compbio/engine/package-summary.html deleted file mode 100644 index 08d94fb..0000000 --- a/website/full_javadoc/compbio/engine/package-summary.html +++ /dev/null @@ -1,208 +0,0 @@ - - - - - - -compbio.engine - - - - - - - - - - - - -
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-Package compbio.engine -

- - - - - - - - - - - - - -
-Interface Summary
AsyncExecutorAn asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
SyncExecutorSynchronous executor, is an engine to run the Executable synchronously.
-  - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
CleanerDeprecated.
ClusterJobId 
Configurator 
FilePuller 
Job 
LoadBalancerThis class decides where to execute the job.
ProgressGetter 
PulledFileCache 
SubmissionManagerSubmit jobs for execution
-  - -

-

-
-
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-Uses of Package
compbio.engine

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-Packages that use compbio.engine
compbio.engine  
compbio.engine.cluster.drmaa  
compbio.engine.local  
compbio.ws.server  
-  -

- - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine used by compbio.engine
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
ClusterJobId - -
-           
FilePuller - -
-           
Job - -
-           
SyncExecutor - -
-          Synchronous executor, is an engine to run the Executable synchronously.
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.engine used by compbio.engine.cluster.drmaa
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
ClusterJobId - -
-           
SyncExecutor - -
-          Synchronous executor, is an engine to run the Executable synchronously.
-  -

- - - - - - - - - - - -
-Classes in compbio.engine used by compbio.engine.local
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
SyncExecutor - -
-          Synchronous executor, is an engine to run the Executable synchronously.
-  -

- - - - - - - - -
-Classes in compbio.engine used by compbio.ws.server
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
-  -

-

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- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.metadata -
-Interface Argument<T>

-
-
Type Parameters:
T - executable type
-
-
All Known Implementing Classes:
Option, Parameter
-
-
-
-
public interface Argument<T>
- - -

-An unmodifiable view for the options and parameters, with one exception - it - allows to set a value -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Parameter, -Option
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- StringgetDefaultValue() - -
-           
- StringgetDescription() - -
-           
- URLgetFurtherDetails() - -
-           
- StringgetName() - -
-           
- List<String>getPossibleValues() - -
-           
- voidsetValue(String defaultValue) - -
-          Set default values for the parameter or an option
-  -

- - - - - - - - -
-Method Detail
- -

-getFurtherDetails

-
-URL getFurtherDetails()
-
-
-
-
-
-
- -

-getDefaultValue

-
-String getDefaultValue()
-
-
-
-
-
-
- -

-getDescription

-
-String getDescription()
-
-
-
-
-
-
- -

-getName

-
-String getName()
-
-
-
-
-
-
- -

-getPossibleValues

-
-List<String> getPossibleValues()
-
-
- -
Returns:
List of values allowed for an Argument
-
-
-
- -

-setValue

-
-void setValue(String defaultValue)
-              throws WrongParameterException
-
-
Set default values for the parameter or an option -

-

-
Parameters:
defaultValue - the value to be set -
Throws: -
WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:
ValueConstrain
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/ChunkHolder.html b/website/full_javadoc/compbio/metadata/ChunkHolder.html deleted file mode 100644 index b8604f6..0000000 --- a/website/full_javadoc/compbio/metadata/ChunkHolder.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -ChunkHolder - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class ChunkHolder

-
-java.lang.Object
-  extended by compbio.metadata.ChunkHolder
-
-
-
-
public class ChunkHolder
extends Object
- - -

-Represents a chunk of a string data together with the position in a file for - the next read operation. -

- -

-

-
Version:
-
1.0 December 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
ChunkHolder(String chunk, - long position) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- StringgetChunk() - -
-           
- longgetNextPosition() - -
-           
- inthashCode() - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-ChunkHolder

-
-public ChunkHolder(String chunk,
-                   long position)
-
-
- - - - - - - - -
-Method Detail
- -

-getChunk

-
-public String getChunk()
-
-
-
-
-
-
- -

-getNextPosition

-
-public long getNextPosition()
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
- -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/JobExecutionException.html b/website/full_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index 331bf18..0000000 --- a/website/full_javadoc/compbio/metadata/JobExecutionException.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - -JobExecutionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class JobExecutionException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobExecutionException
-
-
-
All Implemented Interfaces:
Serializable
-
-
-
-
public class JobExecutionException
extends Exception
- - -

-JobExecutionException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides DrmaaException -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - -
-Constructor Summary
JobExecutionException(String message) - -
-           
JobExecutionException(String message, - Throwable cause) - -
-           
JobExecutionException(Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobExecutionException

-
-public JobExecutionException(String message)
-
-
-
- -

-JobExecutionException

-
-public JobExecutionException(Throwable cause)
-
-
-
- -

-JobExecutionException

-
-public JobExecutionException(String message,
-                             Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/JobStatus.html b/website/full_javadoc/compbio/metadata/JobStatus.html deleted file mode 100644 index 1d26f50..0000000 --- a/website/full_javadoc/compbio/metadata/JobStatus.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -JobStatus - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.metadata -
-Enum JobStatus

-
-java.lang.Object
-  extended by java.lang.Enum<JobStatus>
-      extended by compbio.metadata.JobStatus
-
-
-
All Implemented Interfaces:
Serializable, Comparable<JobStatus>
-
-
-
-
public enum JobStatus
extends Enum<JobStatus>
- - -

-The status of the job. -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CANCELLED - -
-          Jobs that has been cancelled
COLLECTED - -
-          Results has been collected
FAILED - -
-          Failed jobs
FINISHED - -
-          Finished jobs
PENDING - -
-          Jobs which are in the queue and awaiting execution reported for cluster - jobs only
RUNNING - -
-          Jobs that are running
STARTED - -
-          Job calculation has been started.
SUBMITTED - -
-          Job has been submitted.
UNDEFINED - -
-          Represents jobs with unknown status
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JobStatusvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static JobStatus[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-PENDING

-
-public static final JobStatus PENDING
-
-
Jobs which are in the queue and awaiting execution reported for cluster - jobs only -

-

-
-
-
- -

-RUNNING

-
-public static final JobStatus RUNNING
-
-
Jobs that are running -

-

-
-
-
- -

-CANCELLED

-
-public static final JobStatus CANCELLED
-
-
Jobs that has been cancelled -

-

-
-
-
- -

-FINISHED

-
-public static final JobStatus FINISHED
-
-
Finished jobs -

-

-
-
-
- -

-FAILED

-
-public static final JobStatus FAILED
-
-
Failed jobs -

-

-
-
-
- -

-UNDEFINED

-
-public static final JobStatus UNDEFINED
-
-
Represents jobs with unknown status -

-

-
-
-
- -

-STARTED

-
-public static final JobStatus STARTED
-
-
Job calculation has been started. First status reported by the local - engine -

-

-
-
-
- -

-SUBMITTED

-
-public static final JobStatus SUBMITTED
-
-
Job has been submitted. This status is only set for cluster jobs -

-

-
-
-
- -

-COLLECTED

-
-public static final JobStatus COLLECTED
-
-
Results has been collected -

-

-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static JobStatus[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (JobStatus c : JobStatus.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static JobStatus valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/JobSubmissionException.html deleted file mode 100644 index 2e99e5d..0000000 --- a/website/full_javadoc/compbio/metadata/JobSubmissionException.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -JobSubmissionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.metadata -
-Class JobSubmissionException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-
-
-
All Implemented Interfaces:
Serializable
-
-
-
Direct Known Subclasses:
LimitExceededException, UnsupportedRuntimeException
-
-
-
-
public class JobSubmissionException
extends Exception
- - -

-Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException. If - this exception is thrown the task has not been calculated -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - -
-Constructor Summary
JobSubmissionException(String message) - -
-           
JobSubmissionException(String message, - Throwable cause) - -
-           
JobSubmissionException(Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobSubmissionException

-
-public JobSubmissionException(String message)
-
-
-
- -

-JobSubmissionException

-
-public JobSubmissionException(Throwable cause)
-
-
-
- -

-JobSubmissionException

-
-public JobSubmissionException(String message,
-                              Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Limit.html b/website/full_javadoc/compbio/metadata/Limit.html deleted file mode 100644 index a61f937..0000000 --- a/website/full_javadoc/compbio/metadata/Limit.html +++ /dev/null @@ -1,478 +0,0 @@ - - - - - - -Limit - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class Limit<T>

-
-java.lang.Object
-  extended by compbio.metadata.Limit<T>
-
-
-
Type Parameters:
T - the type of an executable for which this limit is defined.
-
-
-
public class Limit<T>
extends Object
- - -

-A value object containing a maximum number of sequences and a maximum average - sequence length for a preset. Also contains static method for determining the - number of sequence and their average length in the List -

- -

-

-
Version:
-
1.0 January 2010
-
Author:
-
pvtroshin
-
See Also:
LimitsManager
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
Limit(int seqNumber, - int seqLength, - String preset) - -
-          Instantiate the limit
Limit(int seqNumber, - int seqLength, - String preset, - boolean isDefault) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- intgetAvgSeqLength() - -
-           
-static intgetAvgSequenceLength(List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- StringgetPreset() - -
-           
- intgetSeqNumber() - -
-           
- inthashCode() - -
-           
- booleanisDefault() - -
-           
- booleanisExceeded(List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Limit

-
-public Limit(int seqNumber,
-             int seqLength,
-             String preset)
-
-
Instantiate the limit -

-

-
Parameters:
seqNumber - the maximum number of sequences allowed for calculation. - Required
seqLength - the average length of the sequence, optional
preset - the name of preset if any, optional -
Throws: -
IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
-
-
- -

-Limit

-
-public Limit(int seqNumber,
-             int seqLength,
-             String preset,
-             boolean isDefault)
-
-
- - - - - - - - -
-Method Detail
- -

-getPreset

-
-public String getPreset()
-
-
-
-
-
-
- -

-getAvgSeqLength

-
-public int getAvgSeqLength()
-
-
- -
Returns:
the allowed average sequence length
-
-
-
- -

-getSeqNumber

-
-public int getSeqNumber()
-
-
- -
Returns:
the maximum number of sequences allowed
-
-
-
- -

-isDefault

-
-public boolean isDefault()
-
-
- -
Returns:
true is this is a default limit to be used, false otherwise
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-isExceeded

-
-public boolean isExceeded(List<FastaSequence> data)
-
-
Checks if the number of sequences or their average length in the dataset - exceeds this limit. -

-

-
Parameters:
data - the dataset to measure -
Returns:
true if a limit is exceeded (what is the dataset is larger then - the limit), false otherwise. First check the number of sequences - in the dataset and if it exceeds the limit return true - irrespective of the average length. If the number of sequences in - the dataset is less than the limit and average length is defined, - then check whether the total number of letters (number of - sequence multiplied by the average sequence length) is greater - then the total number of letters in the dataset. Returns true if - the total number of letters in the dataset is greater than the - limit, false otherwise.
-
-
-
- -

-getAvgSequenceLength

-
-public static int getAvgSequenceLength(List<FastaSequence> data)
-
-
Calculates an average sequence length of the dataset -

-

-
Parameters:
data - -
Returns:
an average sequence length in the input dataset
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/LimitExceededException.html b/website/full_javadoc/compbio/metadata/LimitExceededException.html deleted file mode 100644 index 8dee72a..0000000 --- a/website/full_javadoc/compbio/metadata/LimitExceededException.html +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - -LimitExceededException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class LimitExceededException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.LimitExceededException
-
-
-
All Implemented Interfaces:
Serializable
-
-
-
-
public class LimitExceededException
extends JobSubmissionException
- - -

-This exception is thrown if the task larger in size that the limit that - applies to the calculation. -

- -

-

-
Version:
-
1.0 February 2010
-
Author:
-
pvtroshin
-
See Also:
Limit, -Serialized Form
-
- -

- - - - - - - - - - - -
-Constructor Summary
LimitExceededException(String message) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetActualNumberofSequences() - -
-           
- intgetNumberOfSequencesAllowed() - -
-           
- intgetSequenceLenghtActual() - -
-           
- intgetSequenceLenghtAllowed() - -
-           
-static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LimitExceededException

-
-public LimitExceededException(String message)
-
-
- - - - - - - - -
-Method Detail
- -

-newLimitExceeded

-
-public static LimitExceededException newLimitExceeded(Limit<?> limit,
-                                                      List<FastaSequence> seqs)
-
-
-
-
-
-
- -

-getNumberOfSequencesAllowed

-
-public int getNumberOfSequencesAllowed()
-
-
-
-
-
-
- -

-getActualNumberofSequences

-
-public int getActualNumberofSequences()
-
-
-
-
-
-
- -

-getSequenceLenghtAllowed

-
-public int getSequenceLenghtAllowed()
-
-
-
-
-
-
- -

-getSequenceLenghtActual

-
-public int getSequenceLenghtActual()
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/LimitsManager.html b/website/full_javadoc/compbio/metadata/LimitsManager.html deleted file mode 100644 index 22dd5a5..0000000 --- a/website/full_javadoc/compbio/metadata/LimitsManager.html +++ /dev/null @@ -1,363 +0,0 @@ - - - - - - -LimitsManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class LimitsManager<T>

-
-java.lang.Object
-  extended by compbio.metadata.LimitsManager<T>
-
-
-
Type Parameters:
T - executable type
-
-
-
public class LimitsManager<T>
extends Object
- - -

-A collection of Limits -

- -

-

-
Version:
-
1.0 January 2010
-
Author:
-
pvtroshin
-
See Also:
Limit
-
- -

- - - - - - - - - - - -
-Constructor Summary
LimitsManager() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Limit<T>getDefaultLimit() - -
-           
- Limit<T>getLimitByName(String presetName) - -
-           
- List<Limit<T>>getLimits() - -
-           
- StringtoString() - -
-           
- voidvalidate(PresetManager<T> presets) - -
-          Validate Limits
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LimitsManager

-
-public LimitsManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getLimits

-
-public List<Limit<T>> getLimits()
-
-
- -
Returns:
all limits defined for an executable T
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-getLimitByName

-
-public Limit<T> getLimitByName(String presetName)
-
-
-
Parameters:
presetName - -
Returns:
Limit defined for the executable T and presetName. If no limit is - defined for the presetName then default Limit is returned. If - presetName is empty or null than the default Limit will be - returned. If not limit defined for the type T than NULL will be - returned
-
-
-
- -

-getDefaultLimit

-
-public Limit<T> getDefaultLimit()
-
-
- -
Returns:
the default Limit for an executable type T
-
-
-
- -

-validate

-
-public void validate(PresetManager<T> presets)
-              throws ValidationException
-
-
Validate Limits -

-

-
Parameters:
presets - -
Throws: -
ValidationException - if any of the Limit defined is found to be invalid. That is - when - - 1) No default limit is defined - - 2) More than 1 default limit is defined - - 3) Limit's preset name does not match any presets for type T
See Also:
Limit, -Preset
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Option.html b/website/full_javadoc/compbio/metadata/Option.html deleted file mode 100644 index 604862d..0000000 --- a/website/full_javadoc/compbio/metadata/Option.html +++ /dev/null @@ -1,714 +0,0 @@ - - - - - - -Option - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class Option<T>

-
-java.lang.Object
-  extended by compbio.metadata.Option<T>
-
-
-
Type Parameters:
T - type of executable
-
-
All Implemented Interfaces:
Argument<T>
-
-
-
Direct Known Subclasses:
Parameter
-
-
-
-
public class Option<T>
extends Object
implements Argument<T>
- - -

-Command line option/flag or multiple exclusive options with no value. Example - -protein, -dna, -auto -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
Option(String name, - String description) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Set<String>addOptionNames(String... value) - -
-          Adds an option to the optionName list
- booleanequals(Object obj) - -
-           
- StringgetDefaultValue() - -
-          A default value of the option.
- StringgetDescription() - -
-          A long description of the Option
- URLgetFurtherDetails() - -
-          The URL where further details about the option can be found
- StringgetName() - -
-          Human readable name of the option
- List<String>getOptionNames() - -
-           
- List<String>getPossibleValues() - -
-          List of possible optionNames
- inthashCode() - -
-           
- booleanisRequired() - -
-          Flag that indicated that this option must be specified in the command - line for an executable to run
- voidsetDefaultValue(String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- voidsetDescription(String description) - -
-           
- voidsetFurtherDetails(URL furtherDetails) - -
-           
- voidsetName(String name) - -
-           
- voidsetOptionNames(Set<String> optionNames) - -
-           
- voidsetRequired(boolean isRequired) - -
-           
- voidsetValue(String dValue) - -
-          Set default values for the parameter or an option
- StringtoCommand(String nameValueSeparator) - -
-          Convert the option to the command string.
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Option

-
-public Option(String name,
-              String description)
-
-
- - - - - - - - -
-Method Detail
- -

-getName

-
-public String getName()
-
-
Human readable name of the option -

-

-
Specified by:
getName in interface Argument<T>
-
-
-
-
-
-
- -

-setName

-
-public void setName(String name)
-
-
-
-
-
-
-
-
-
- -

-getDescription

-
-public String getDescription()
-
-
A long description of the Option -

-

-
Specified by:
getDescription in interface Argument<T>
-
-
-
-
-
-
- -

-setDescription

-
-public void setDescription(String description)
-
-
-
-
-
-
-
-
-
- -

-getFurtherDetails

-
-public URL getFurtherDetails()
-
-
The URL where further details about the option can be found -

-

-
Specified by:
getFurtherDetails in interface Argument<T>
-
-
-
-
-
-
- -

-setFurtherDetails

-
-public void setFurtherDetails(URL furtherDetails)
-
-
-
-
-
-
-
-
-
- -

-getDefaultValue

-
-public String getDefaultValue()
-
-
A default value of the option. Defaults to command line argument name - e.g. -auto -

-

-
Specified by:
getDefaultValue in interface Argument<T>
-
-
-
-
-
-
- -

-setDefaultValue

-
-public void setDefaultValue(String defaultVal)
-                     throws WrongParameterException
-
-
Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

-

-
-
-
-
Parameters:
defaultVal - -
Throws: -
WrongParameterException - is thrown if the defaultValue is not found in optionList
-
-
-
- -

-isRequired

-
-public boolean isRequired()
-
-
Flag that indicated that this option must be specified in the command - line for an executable to run -

-

-
-
-
- -
Returns:
true is the option is required, false otherwise
-
-
-
- -

-setRequired

-
-public void setRequired(boolean isRequired)
-
-
-
-
-
-
-
-
-
- -

-getOptionNames

-
-public List<String> getOptionNames()
-
-
-
-
-
- -
Returns:
List of option names
-
-
-
- -

-setOptionNames

-
-public void setOptionNames(Set<String> optionNames)
-
-
-
-
-
-
-
-
-
- -

-addOptionNames

-
-public Set<String> addOptionNames(String... value)
-
-
Adds an option to the optionName list -

-

-
-
-
-
Parameters:
value - -
Returns:
modified optionName list
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-toCommand

-
-public String toCommand(String nameValueSeparator)
-
-
Convert the option to the command string. -

-

-
-
-
- -
Returns:
If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-getPossibleValues

-
-public List<String> getPossibleValues()
-
-
List of possible optionNames -

-

-
Specified by:
getPossibleValues in interface Argument<T>
-
-
- -
Returns:
List of values allowed for an Argument
-
-
-
- -

-setValue

-
-public void setValue(String dValue)
-              throws WrongParameterException
-
-
Description copied from interface: Argument
-
Set default values for the parameter or an option -

-

-
Specified by:
setValue in interface Argument<T>
-
-
-
Parameters:
dValue - the value to be set -
Throws: -
WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:
ValueConstrain
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Parameter.html b/website/full_javadoc/compbio/metadata/Parameter.html deleted file mode 100644 index 9e6d56f..0000000 --- a/website/full_javadoc/compbio/metadata/Parameter.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -Parameter - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class Parameter<T>

-
-java.lang.Object
-  extended by compbio.metadata.Option<T>
-      extended by compbio.metadata.Parameter<T>
-
-
-
All Implemented Interfaces:
Argument<T>
-
-
-
-
public class Parameter<T>
extends Option<T>
- - -

-A single value containing an option supported by the web service e.g. - seqType=protein. Where seqType is a optionName and protein is one of - possibleValues -

- -

-

-
Version:
-
1.0 November 2009
-
Author:
-
pvtroshin
-
See Also:
Option, -Argument
-
- -

- - - - - - - - - - - -
-Constructor Summary
Parameter(String name, - String description) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Set<String>addOptionNames(String... value) - -
-          Adds an option to the optionName list
- Set<String>addPossibleValues(String... value) - -
-           
- booleanequals(Object obj) - -
-           
- StringgetOptionName() - -
-           
- List<String>getPossibleValues() - -
-          List is more convenient to work with
- ValueConstraingetValidValue() - -
-           
- inthashCode() - -
-           
- voidsetDefaultValue(String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- voidsetOptionName(String optionName) - -
-           
- voidsetOptionNames(Set<String> optionName) - -
-           
- voidsetPossibleValues(Set<String> possibleValues) - -
-           
- voidsetValidValue(ValueConstrain validValue) - -
-           
- StringtoCommand(String nameValueSeparator) - -
-          Convert the option to the command string.
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class compbio.metadata.Option
getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Parameter

-
-public Parameter(String name,
-                 String description)
-
-
- - - - - - - - -
-Method Detail
- -

-getValidValue

-
-public ValueConstrain getValidValue()
-
-
-
-
-
-
- -

-setValidValue

-
-public void setValidValue(ValueConstrain validValue)
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Option<T>
-
-
-
-
-
-
- -

-toCommand

-
-public String toCommand(String nameValueSeparator)
-
-
Description copied from class: Option
-
Convert the option to the command string. -

-

-
Overrides:
toCommand in class Option<T>
-
-
- -
Returns:
If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Option<T>
-
-
-
-
-
-
- -

-getPossibleValues

-
-public List<String> getPossibleValues()
-
-
List is more convenient to work with -

-

-
Specified by:
getPossibleValues in interface Argument<T>
Overrides:
getPossibleValues in class Option<T>
-
-
- -
Returns:
List of String
-
-
-
- -

-setPossibleValues

-
-public void setPossibleValues(Set<String> possibleValues)
-
-
-
-
-
-
- -

-addPossibleValues

-
-public Set<String> addPossibleValues(String... value)
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Option<T>
-
-
-
-
-
-
- -

-setOptionNames

-
-public void setOptionNames(Set<String> optionName)
-
-
-
Overrides:
setOptionNames in class Option<T>
-
-
-
-
-
-
- -

-addOptionNames

-
-public Set<String> addOptionNames(String... value)
-
-
Description copied from class: Option
-
Adds an option to the optionName list -

-

-
Overrides:
addOptionNames in class Option<T>
-
-
- -
Returns:
modified optionName list
-
-
-
- -

-getOptionName

-
-public String getOptionName()
-
-
-
-
-
-
- -

-setOptionName

-
-public void setOptionName(String optionName)
-
-
-
-
-
-
- -

-setDefaultValue

-
-public void setDefaultValue(String defaultVal)
-                     throws WrongParameterException
-
-
Description copied from class: Option
-
Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

-

-
Overrides:
setDefaultValue in class Option<T>
-
-
- -
Throws: -
WrongParameterException - is thrown if the defaultValue is not found in optionList
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Preset.html b/website/full_javadoc/compbio/metadata/Preset.html deleted file mode 100644 index c9c39bf..0000000 --- a/website/full_javadoc/compbio/metadata/Preset.html +++ /dev/null @@ -1,455 +0,0 @@ - - - - - - -Preset - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class Preset<T>

-
-java.lang.Object
-  extended by compbio.metadata.Preset<T>
-
-
-
Type Parameters:
T - executable type
-
-
-
public class Preset<T>
extends Object
- - -

-Collection of Options and Parameters with their values -

- -

-

-
Version:
-
1.0 December 2009
-
Author:
-
pvtroshin
-
See Also:
Option, -Parameter
-
- -

- - - - - - - - - - - -
-Constructor Summary
Preset() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(Object obj) - -
-           
- List<Option<T>>getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- StringgetDescription() - -
-           
- StringgetName() - -
-           
- List<String>getOptions() - -
-           
- inthashCode() - -
-           
- voidsetDescription(String description) - -
-           
- voidsetName(String name) - -
-           
- voidsetOptions(List<String> option) - -
-           
- StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Preset

-
-public Preset()
-
-
- - - - - - - - -
-Method Detail
- -

-setOptions

-
-public void setOptions(List<String> option)
-
-
-
-
-
-
- -

-setName

-
-public void setName(String name)
-
-
-
-
-
-
- -

-setDescription

-
-public void setDescription(String description)
-
-
-
-
-
-
- -

-getOptions

-
-public List<String> getOptions()
-
-
- -
Returns:
a List of Options as a String
-
-
-
- -

-getName

-
-public String getName()
-
-
- -
Returns:
- name of the Preset
-
-
-
- -

-getDescription

-
-public String getDescription()
-
-
- -
Returns:
- a long description of the Preset
-
-
-
- -

-getArguments

-
-public List<Option<T>> getArguments(RunnerConfig<T> rconfig)
-                             throws WrongParameterException
-
-
Converts list of options as String to type Option -

-

-
Parameters:
rconfig - -
Returns:
List of Options -
Throws: -
WrongParameterException - if the value of the parameter is invalid @see - Parameter
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/PresetManager.html b/website/full_javadoc/compbio/metadata/PresetManager.html deleted file mode 100644 index 6adfaa5..0000000 --- a/website/full_javadoc/compbio/metadata/PresetManager.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - -PresetManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class PresetManager<T>

-
-java.lang.Object
-  extended by compbio.metadata.PresetManager<T>
-
-
-
Type Parameters:
T - type of executable.
-
-
-
public class PresetManager<T>
extends Object
- - -

-Collection of presets and methods to manipulate them @see Preset -

- -

-

-
Version:
-
1.0 December 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static StringLOCAL_ENGINE_LIMIT_PRESET - -
-           
-  - - - - - - - - - - -
-Constructor Summary
PresetManager() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Preset<T>getPresetByName(String presetName) - -
-           
- List<Preset<T>>getPresets() - -
-           
- StringgetRunnerClassName() - -
-           
- voidsetPresets(List<Preset<T>> presets) - -
-           
- voidsetRunnerClassName(String runnerClassName) - -
-           
- StringtoString() - -
-           
- voidvalidate(RunnerConfig<T> options) - -
-          Checks whether preset option and parameter are defined in RunnerConfig - object.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-LOCAL_ENGINE_LIMIT_PRESET

-
-public static final String LOCAL_ENGINE_LIMIT_PRESET
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-PresetManager

-
-public PresetManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getPresets

-
-public List<Preset<T>> getPresets()
-
-
-
-
-
-
- -

-setPresets

-
-public void setPresets(List<Preset<T>> presets)
-
-
-
-
-
-
- -

-getRunnerClassName

-
-public String getRunnerClassName()
-
-
- -
Returns:
fully qualified class name of type T
-
-
-
- -

-setRunnerClassName

-
-public void setRunnerClassName(String runnerClassName)
-
-
-
-
-
-
- -

-getPresetByName

-
-public Preset<T> getPresetByName(String presetName)
-
-
-
Parameters:
presetName - -
Returns:
preset by its name, null if no preset found
-
-
-
- -

-validate

-
-public void validate(RunnerConfig<T> options)
-              throws ValidationException
-
-
Checks whether preset option and parameter are defined in RunnerConfig - object. - - TODO handle parameters with values properly! -

-

- -
Throws: -
ValidationException - if preset is found to be invalid.
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html deleted file mode 100644 index 7888bb3..0000000 --- a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -ResultNotAvailableException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class ResultNotAvailableException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.ResultNotAvailableException
-
-
-
All Implemented Interfaces:
Serializable
-
-
-
-
public class ResultNotAvailableException
extends Exception
- - -

-ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides lower level exceptions - like DrmaaException -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - -
-Constructor Summary
ResultNotAvailableException(String message) - -
-           
ResultNotAvailableException(String message, - Throwable cause) - -
-           
ResultNotAvailableException(Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(String message)
-
-
-
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(Throwable cause)
-
-
-
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(String message,
-                                   Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/RunnerConfig.html b/website/full_javadoc/compbio/metadata/RunnerConfig.html deleted file mode 100644 index a853932..0000000 --- a/website/full_javadoc/compbio/metadata/RunnerConfig.html +++ /dev/null @@ -1,706 +0,0 @@ - - - - - - -RunnerConfig - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.metadata -
-Class RunnerConfig<T>

-
-java.lang.Object
-  extended by compbio.metadata.RunnerConfig<T>
-
-
-
Type Parameters:
T - type of an Executable
-
-
-
@NotThreadSafe
-public class RunnerConfig<T>
extends Object
- - -

-The list of Parameters and Options supported by executable. - The lists is defined in and loaded from Parameters.xml file. -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
RunnerConfig() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidaddOption(Option<T> option) - -
-          Adds Option to the internal list of options
- voidaddParameter(Parameter<T> param) - -
-          Adds parameter to the internal parameter list
- RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
-           
- booleanequals(Object obj) - -
-           
- Option<T>getArgument(String name) - -
-          Returns the argument by its name if found, NULL otherwise.
- Option<T>getArgumentByOptionName(String optionName) - -
-          Returns the argument by option name, NULL if the argument is not found
- List<Option<T>>getArguments() - -
-          Returns list of Parameter and Option supported by current - runner
- List<Option<T>>getOptions() - -
-          Returns the list of the Options supported by the executable of type T
- List<Parameter<T>>getParameters() - -
-          Returns the list of parameters supported executable of type T.
- StringgetPrmSeparator() - -
-           
- StringgetRunnerClassName() - -
-           
- booleanremoveArgument(String name) - -
-          Removes the argument Argument if found.
- booleanremoveArgumentByOptionName(String optionName) - -
-          Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor.
- voidsetOptions(List<Option<T>> parameters) - -
-          Adds the list of options or parameters to the internal list of options
- voidsetParameters(List<Parameter<T>> parameters) - -
-          Sets the list of parameters as internal list
- voidsetPrmSeparator(String prmSeparator) - -
-          Sets name value separator character
- voidsetRunnerClassName(String runnerClassName) - -
-          Set the name of a runner class
- StringtoString() - -
-           
- voidvalidate() - -
-          Validate the value of the argument.
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-RunnerConfig

-
-public RunnerConfig()
-
-
- - - - - - - - -
-Method Detail
- -

-copyAndValidateRConfig

-
-public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
-
-
-
-
-
-
- -

-getOptions

-
-public List<Option<T>> getOptions()
-
-
Returns the list of the Options supported by the executable of type T -

-

- -
Returns:
list of Option supported by type T
See Also:
Option
-
-
-
- -

-addParameter

-
-public void addParameter(Parameter<T> param)
-
-
Adds parameter to the internal parameter list -

-

-
Parameters:
param - the Parameter to add
See Also:
Parameter
-
-
-
- -

-addOption

-
-public void addOption(Option<T> option)
-
-
Adds Option to the internal list of options -

-

-
Parameters:
option - the Option to add
-
-
-
- -

-getArguments

-
-public List<Option<T>> getArguments()
-
-
Returns list of Parameter and Option supported by current - runner -

-

- -
Returns:
list of Option and Parameter supported by type T
-
-
-
- -

-getPrmSeparator

-
-public String getPrmSeparator()
-
-
- -
Returns:
name value separator character
-
-
-
- -

-setPrmSeparator

-
-public void setPrmSeparator(String prmSeparator)
-
-
Sets name value separator character -

-

-
Parameters:
prmSeparator - the separator char
-
-
-
- -

-setOptions

-
-public void setOptions(List<Option<T>> parameters)
-
-
Adds the list of options or parameters to the internal list of options -

-

-
Parameters:
parameters - the list of parameters to add
-
-
-
- -

-getRunnerClassName

-
-public String getRunnerClassName()
-
-
- -
Returns:
fully qualified class name for type T
-
-
-
- -

-setRunnerClassName

-
-public void setRunnerClassName(String runnerClassName)
-
-
Set the name of a runner class -

-

-
Parameters:
runnerClassName - the name of the executable wrapping class
-
-
-
- -

-setParameters

-
-public void setParameters(List<Parameter<T>> parameters)
-
-
Sets the list of parameters as internal list -

-

-
Parameters:
parameters - the list of parameters
-
-
-
- -

-getParameters

-
-public List<Parameter<T>> getParameters()
-
-
Returns the list of parameters supported executable of type T. Where - Parameter is an Option with value. -

-

- -
Returns:
List of Parameter supported by type T.
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
-
-
-
-
-
-
- -

-getArgument

-
-public Option<T> getArgument(String name)
-
-
Returns the argument by its name if found, NULL otherwise. Where the - Argument is a common interface for Option and Parameter - therefore this method can return either. If you need to retrieve the - Option by its optionNames use @link - getArgumentByOptionName(String) method. The - difference between option name and optionName is explained by the - following example: - - 
- Sequence type
-         
-         --nuc - Assume the sequences are nucleotide.
-         --amino - Assume the sequences are amino acid. 
-         --amino
-         --nuc
-         --auto
-
- - In the example, the "Sequence type" is a name whereas --amino, --nuc and - --auto are all optionNames. This dichotomy only manifests in - Option never in Parameters as the latter can - only have single element -

-

-
Parameters:
name - the Parameter of Option name -
Returns:
Argument
-
-
-
- -

-removeArgument

-
-public boolean removeArgument(String name)
-
-
Removes the argument Argument if found. Where Argument is either - Option or Parameter. -

-

-
Parameters:
name - of the argument -
Returns:
true if argument was removed, false otherwise
-
-
-
- -

-getArgumentByOptionName

-
-public Option<T> getArgumentByOptionName(String optionName)
-
-
Returns the argument by option name, NULL if the argument is not found -

-

-
Parameters:
optionName - - the optionName. This is not the same as an Option name. - - For example: - - 
-            Output sequences order
-                          --inputorder - Output order: same as input. 
-                           --reorder - Output order: aligned. Default: same as input
-                          --inputorder
-                          --reorder
-
- - The name of the option in the example is - "Output sequences order" whereas optionNames are - "--inputorder" and "--reorder". If you need to retrieve the - Option or Parameter by its names use - getArgument(String) method -
Returns:
Option
-
-
-
- -

-removeArgumentByOptionName

-
-public boolean removeArgumentByOptionName(String optionName)
-
-
Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -

-

-
Parameters:
optionName - the optionName of the option, do not confuse with the name! -
Returns:
true if argument with optionName exists and was removed, false - otherwise
See Also:
for destinctions - between optionNames and the name of the Option
-
-
-
- -

-validate

-
-public void validate()
-              throws ValidationException
-
-
Validate the value of the argument. Checks whether the argument value is - in the valid values range. -

-

- -
Throws: -
ValidationException - if any of the arguments found invalid which is when -
-
  • Parameter value outside ValueConstrain boundary
    • -
  • Parameter name is not listed in possible values
    • -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html deleted file mode 100644 index 80ebc81..0000000 --- a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class UnsupportedRuntimeException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.UnsupportedRuntimeException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    - - -

    -Indicates that the server could not execute native executables. e.g. If Mafft - (unix executable) is asked to be run on Windows. In context of JABAWS this - exception indicates that the service is deployed but is not able to run. -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date February 2010
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    UnsupportedRuntimeException(String message) - -
    -           
    UnsupportedRuntimeException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(String message)
    -
    -
    -
    - -

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html deleted file mode 100644 index 5902b6e..0000000 --- a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - -ValueConstrain.Type - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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    - - - -
    - -

    - -compbio.metadata -
    -Enum ValueConstrain.Type

    -
    -java.lang.Object
-  extended by java.lang.Enum<ValueConstrain.Type>
-      extended by compbio.metadata.ValueConstrain.Type
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<ValueConstrain.Type>
    -
    -
    -
    Enclosing class:
    ValueConstrain
    -
    -
    -
    -
    public static enum ValueConstrain.Type
    extends Enum<ValueConstrain.Type>
    - - -

    -

    - -

    - - - - - - - - - - - - - -
    -Enum Constant Summary
    Float - -
    -           
    Integer - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static ValueConstrain.TypevalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -Integer

    -
    -public static final ValueConstrain.Type Integer
    -
    -
    -
    -
    -
    - -

    -Float

    -
    -public static final ValueConstrain.Type Float
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static ValueConstrain.Type[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (ValueConstrain.Type c : ValueConstrain.Type.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static ValueConstrain.Type valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.html b/website/full_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index 016953c..0000000 --- a/website/full_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -ValueConstrain - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class ValueConstrain

    -
    -java.lang.Object
-  extended by compbio.metadata.ValueConstrain
-
    -
    -
    -
    public class ValueConstrain
    extends Object
    - - -

    -The type and the lower and upper boundaries for numerical value. -

    - -

    -

    -
    Version:
    -
    1.0 November 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classValueConstrain.Type - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ValueConstrain() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - NumbergetMax() - -
    -           
    - NumbergetMin() - -
    -           
    - ValueConstrain.TypegetType() - -
    -           
    - inthashCode() - -
    -           
    - voidsetMax(String max) - -
    -           
    - voidsetMin(String min) - -
    -           
    - voidsetType(ValueConstrain.Type type) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ValueConstrain

    -
    -public ValueConstrain()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getType

    -
    -public ValueConstrain.Type getType()
    -
    -
    -
    -
    -
    -
    - -

    -setType

    -
    -public void setType(ValueConstrain.Type type)
    -
    -
    -
    -
    -
    -
    - -

    -getMax

    -
    -public Number getMax()
    -
    -
    -
    -
    -
    -
    - -

    -setMax

    -
    -public void setMax(String max)
    -
    -
    -
    -
    -
    -
    - -

    -getMin

    -
    -public Number getMin()
    -
    -
    -
    -
    -
    -
    - -

    -setMin

    -
    -public void setMin(String min)
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/WrongParameterException.html b/website/full_javadoc/compbio/metadata/WrongParameterException.html deleted file mode 100644 index 9791652..0000000 --- a/website/full_javadoc/compbio/metadata/WrongParameterException.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -WrongParameterException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class WrongParameterException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.WrongParameterException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class WrongParameterException
    extends Exception
    - - -

    -WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value. -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    WrongParameterException(Option<?> option) - -
    -           
    WrongParameterException(String message) - -
    -           
    WrongParameterException(String message, - Throwable cause) - -
    -           
    WrongParameterException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -WrongParameterException

    -
    -public WrongParameterException(Option<?> option)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(String message)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(Throwable cause)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(String message,
-                               Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/Argument.html b/website/full_javadoc/compbio/metadata/class-use/Argument.html deleted file mode 100644 index 9fe69bf..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/Argument.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.metadata.Argument - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Interface
    compbio.metadata.Argument

    -
    - - - - - - - - - -
    -Packages that use Argument
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Argument in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Classes in compbio.metadata that implement Argument
    - classOption<T> - -
    -          Command line option/flag or multiple exclusive options with no value.
    - classParameter<T> - -
    -          A single value containing an option supported by the web service e.g.
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html deleted file mode 100644 index 02aadc8..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,385 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.ChunkHolder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.ChunkHolder

    -
    - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use ChunkHolder
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return ChunkHolder
    - ChunkHolderJManagement.pullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return ChunkHolder
    - ChunkHolderPullExecStatisticsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type ChunkHolder
    - voidPullExecStatisticsResponse.setReturn(ChunkHolder _return) - -
    -           
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return ChunkHolder
    - ChunkHolderFilePuller.pull(long position) - -
    -           
    -static ChunkHolderProgressGetter.pull(String file, - long position) - -
    -           
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return ChunkHolder
    - ChunkHolderGenericMetadataService.pullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    - ChunkHolderClustalWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolder_MsaService.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderAAConWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderMuscleWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderJronnWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderMafftWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderTcoffeeWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderProbconsWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderClustalOWS.pullExecStatistics(String jobId, - long position) - -
    -           
    -static ChunkHolderWSUtil.pullFile(String file, - long position) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.JobExecutionException

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use JobExecutionException
    compbio.engine  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that throw JobExecutionException
    - ConfiguredExecutable<?>SyncExecutor.waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw JobExecutionException
    - org.ggf.drmaa.JobInfoJobRunner.getJobInfo() - -
    -          This method will block before the calculation has completed and then - return the object containing a job execution statistics
    - ConfiguredExecutable<?>JobRunner.waitForResult() - -
    -           
    -static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, - String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine.local
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.local that throw JobExecutionException
    - ConfiguredExecutable<?>LocalRunner.waitForResult() - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.JobStatus

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use JobStatus
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return JobStatus
    - JobStatusJManagement.getJobStatus(String jobId) - -
    -          Return the status of the job.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return JobStatus
    - JobStatusGetJobStatusResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type JobStatus
    - voidGetJobStatusResponse.setReturn(JobStatus _return) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return JobStatus
    - JobStatusSyncExecutor.getJobStatus() - -
    -          Query the status of the job by its id.
    - JobStatusAsyncExecutor.getJobStatus(String jobId) - -
    -          Query the status of the job
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type JobStatus
    -static booleanUtil.isMarked(String workDirectory, - JobStatus marker) - -
    -           
    -static booleanUtil.writeMarker(String workDirectory, - JobStatus fileType) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return JobStatus
    - JobStatusJobRunner.getJobStatus() - -
    -           
    - JobStatusAsyncJobRunner.getJobStatus(String jobId) - -
    -          This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.local
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.local that return JobStatus
    - JobStatusLocalRunner.getJobStatus() - -
    -           
    -static JobStatusLocalEngineUtil.getJobStatus(Future<ConfiguredExecutable<?>> future) - -
    -           
    - JobStatusAsyncLocalRunner.getJobStatus(String jobId) - -
    -           
    -static JobStatusLocalEngineUtil.getRecordedJobStatus(String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return JobStatus
    -static JobStatusJobStatus.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JobStatus[]JobStatus.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return JobStatus
    - JobStatusGenericMetadataService.getJobStatus(String jobId) - -
    -           
    - JobStatusClustalWS.getJobStatus(String jobId) - -
    -           
    - JobStatusMuscleWS.getJobStatus(String jobId) - -
    -           
    - JobStatusMafftWS.getJobStatus(String jobId) - -
    -           
    - JobStatusTcoffeeWS.getJobStatus(String jobId) - -
    -           
    - JobStatusProbconsWS.getJobStatus(String jobId) - -
    -           
    - JobStatusClustalOWS.getJobStatus(String jobId) - -
    -           
    -static JobStatusWSUtil.getJobStatus(String jobId) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.JobSubmissionException

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use JobSubmissionException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw JobSubmissionException
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine that throw JobSubmissionException
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
    -           
    - voidSyncExecutor.executeJob() - -
    -          Execute the job
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    - StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that throw JobSubmissionException
    - StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException
    - voidJobRunner.executeJob() - -
    -           
    -static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
    -           
    - StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException
    JobRunner(ConfiguredExecutable<?> confExec) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.local
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local that throw JobSubmissionException
    - voidLocalRunner.executeJob() - -
    -           
    - StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.local that throw JobSubmissionException
    ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Subclasses of JobSubmissionException in compbio.metadata
    - classLimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    - classUnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that throw JobSubmissionException
    -static voidUtil.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw JobSubmissionException
    - StringClustalWS.align(List<FastaSequence> sequences) - -
    -           
    - String_MsaService.align(List<FastaSequence> sequences) - -
    -           
    - StringMuscleWS.align(List<FastaSequence> sequences) - -
    -           
    - StringMafftWS.align(List<FastaSequence> sequences) - -
    -           
    - StringTcoffeeWS.align(List<FastaSequence> sequences) - -
    -           
    - StringProbconsWS.align(List<FastaSequence> sequences) - -
    -           
    - StringClustalOWS.align(List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -static voidWSUtil.validateAAConInput(List<FastaSequence> sequences) - -
    -           
    -static voidWSUtil.validateFastaInput(List<FastaSequence> sequences) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.Limit

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Limit
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Limit in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return Limit
    - Limit<T>Metadata.getLimit(String presetName) - -
    -          Get a Limit for a preset.
    -  -

    - - - - - -
    -Uses of Limit in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Limit
    - LimitGetLimitResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Limit
    - voidGetLimitResponse.setReturn(Limit _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return Limit
    - Limit<T>Executable.getLimit(String presetName) - -
    -           
    - Limit<T>SkeletalExecutable.getLimit(String presetName) - -
    -           
    - Limit<T>ConfExecutable.getLimit(String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Limit
    - Limit<T>LimitsManager.getDefaultLimit() - -
    -           
    - Limit<T>LimitsManager.getLimitByName(String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Limit
    - List<Limit<T>>LimitsManager.getLimits() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Limit
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return Limit
    - Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(String presetName) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Limit
    - Limit<NetNglyc>NetNglyc.getLimit(String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return Limit
    - Limit<T>GenericMetadataService.getLimit(String presetName) - -
    -           
    - Limit<ClustalW>ClustalWS.getLimit(String presetName) - -
    -           
    - Limit<Muscle>MuscleWS.getLimit(String presetName) - -
    -           
    - Limit<Mafft>MafftWS.getLimit(String presetName) - -
    -           
    - Limit<Tcoffee>TcoffeeWS.getLimit(String presetName) - -
    -           
    - Limit<Probcons>ProbconsWS.getLimit(String presetName) - -
    -           
    - Limit<ClustalO>ClustalOWS.getLimit(String presetName) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Limit
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.LimitExceededException

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use LimitExceededException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw LimitExceededException
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return LimitExceededException
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw LimitExceededException
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.LimitsManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use LimitsManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return LimitsManager
    - LimitsManager<T>Metadata.getLimits() - -
    -          List Limits supported by a web service.
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return LimitsManager
    - LimitsManagerGetLimitsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type LimitsManager
    - voidGetLimitsResponse.setReturn(LimitsManager _return) - -
    -           
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return LimitsManager
    - LimitsManager<T>Executable.getLimits() - -
    -           
    - LimitsManager<T>SkeletalExecutable.getLimits() - -
    -           
    - LimitsManager<T>ConfExecutable.getLimits() - -
    -           
    -static - - - - -
    -<T> LimitsManager<T>
    -    		Util.getLimits(Class<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
    -static - - - - -
    -<V> LimitsManager<V>
    -    		ConfExecutable.getRunnerLimits(Class<V> clazz) - -
    -          This method should be executed once and result of its execution reused.
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return LimitsManager
    - LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return LimitsManager
    - LimitsManager<NetNglyc>NetNglyc.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return LimitsManager
    - LimitsManager<T>GenericMetadataService.getLimits() - -
    -           
    - LimitsManager<ClustalW>ClustalWS.getLimits() - -
    -           
    - LimitsManager<Muscle>MuscleWS.getLimits() - -
    -           
    - LimitsManager<Mafft>MafftWS.getLimits() - -
    -           
    - LimitsManager<Tcoffee>TcoffeeWS.getLimits() - -
    -           
    - LimitsManager<Probcons>ProbconsWS.getLimits() - -
    -           
    - LimitsManager<ClustalO>ClustalOWS.getLimits() - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.Option

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    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Option
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Option in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa with type arguments of type Option
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    -  -

    - - - - - -
    -Uses of Option in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Option
    - List<Option>CustomAnalize.getOptions() - -
    -           
    - List<Option>CustomAlign.getOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Option
    - voidCustomAnalize.setOptions(List<Option> options) - -
    -           
    - voidCustomAlign.setOptions(List<Option> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.engine.client
    -  -

    - - - - - - - - - -
    Method parameters in compbio.engine.client with type arguments of type Option
    -static - - - - -
    -<T> CommandBuilder<T>
    -    		CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments, - String nameValueSeparator) - -
    -          This produces the same result as getCommands method.
    -  -

    - - - - - -
    -Uses of Option in compbio.metadata
    -  -

    - - - - - - - - - -
    Subclasses of Option in compbio.metadata
    - classParameter<T> - -
    -          A single value containing an option supported by the web service e.g.
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Option
    - Option<T>RunnerConfig.getArgument(String name) - -
    -          Returns the argument by its name if found, NULL otherwise.
    - Option<T>RunnerConfig.getArgumentByOptionName(String optionName) - -
    -          Returns the argument by option name, NULL if the argument is not found
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Option
    - List<Option<T>>RunnerConfig.getArguments() - -
    -          Returns list of Parameter and Option supported by current - runner
    - List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - List<Option<T>>RunnerConfig.getOptions() - -
    -          Returns the list of the Options supported by the executable of type T
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Option
    - voidRunnerConfig.addOption(Option<T> option) - -
    -          Adds Option to the internal list of options
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Option
    - voidRunnerConfig.setOptions(List<Option<T>> parameters) - -
    -          Adds the list of options or parameters to the internal list of options
    -  -

    - - - - - - - - -
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Option
    - List<Option<?>>OptionCombinator.getAllOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Option
    - List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments) - -
    -           
    -static List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    - List<String>OptionCombinator.optionsToCommandString(List<Option<?>> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Option
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    -static - - - - -
    -<T> List<String>
    -    		WSUtil.getCommands(List<Option<T>> options, - String keyValueSeparator) - -
    -           
    -  -

    -

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    -Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    -  -

    - - - - - -
    -Uses of Parameter in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Parameter
    - List<Parameter<T>>RunnerConfig.getParameters() - -
    -          Returns the list of parameters supported executable of type T.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Parameter
    - voidRunnerConfig.addParameter(Parameter<T> param) - -
    -          Adds parameter to the internal parameter list
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Parameter
    - voidRunnerConfig.setParameters(List<Parameter<T>> parameters) - -
    -          Sets the list of parameters as internal list
    -  -

    - - - - - -
    -Uses of Parameter in compbio.runner
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Parameter
    - Map<Parameter<?>,String>OptionCombinator.getAllConstrainedParametersWithBorderValues(boolean minValue) - -
    -           
    - Map<Parameter<?>,String>OptionCombinator.getAllConstrainedParametersWithRandomValues() - -
    -           
    - List<Parameter<?>>OptionCombinator.getAllParameters() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Parameter
    - List<String>OptionCombinator.parametersToCommandString(List<Parameter<?>> orderedList, - Map<Parameter<?>,String> prmValue) - -
    -           
    - List<String>OptionCombinator.parametersToCommandString(List<Parameter<?>> orderedList, - Map<Parameter<?>,String> prmValue) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.Preset

    -
    - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Preset
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Preset in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Preset
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of Preset in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Preset
    - PresetPresetAnalize.getPreset() - -
    -           
    - PresetPresetAlign.getPreset() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Preset
    - voidPresetAnalize.setPreset(Preset preset) - -
    -           
    - voidPresetAlign.setPreset(Preset preset) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return Preset
    - Preset<T>PresetManager.getPresetByName(String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Preset
    - List<Preset<T>>PresetManager.getPresets() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Preset
    - voidPresetManager.setPresets(List<Preset<T>> presets) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Preset
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.PresetManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use PresetManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return PresetManager
    - PresetManager<T>Metadata.getPresets() - -
    -          Get presets supported by a web service
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return PresetManager
    - PresetManagerGetPresetsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type PresetManager
    - voidGetPresetsResponse.setReturn(PresetManager _return) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that return PresetManager
    -static - - - - -
    -<V> PresetManager<V>
    -    		ConfExecutable.getRunnerPresets(Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type PresetManager
    - voidLimitsManager.validate(PresetManager<T> presets) - -
    -          Validate Limits
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return PresetManager
    -static - - - - -
    -<T> PresetManager<T>
    -    		Util.getPresets(Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return PresetManager
    - PresetManager<T>GenericMetadataService.getPresets() - -
    -           
    - PresetManager<ClustalW>ClustalWS.getPresets() - -
    -           
    - PresetManager<Muscle>MuscleWS.getPresets() - -
    -           
    - PresetManager<Mafft>MafftWS.getPresets() - -
    -           
    - PresetManager<Tcoffee>TcoffeeWS.getPresets() - -
    -           
    - PresetManager<Probcons>ProbconsWS.getPresets() - -
    -           
    - PresetManager<ClustalO>ClustalOWS.getPresets() - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.ResultNotAvailableException

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use ResultNotAvailableException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw ResultNotAvailableException
    - ScoreManagerSequenceAnnotation.getAnnotation(String jobId) - -
    -          Return the result of the job.
    - AlignmentMsaWS.getResult(String jobId) - -
    -          Return the result of the job.
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that throw ResultNotAvailableException
    - ConfiguredExecutable<?>AsyncExecutor.getResults(String jobId) - -
    -          Retrieve the results of the job.
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that throw ResultNotAvailableException
    - - - - - -
    -<V> V
    -    		ConfiguredExecutable.getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		ConfExecutable.getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		Executable.getResults(String directory) - -
    -           
    - - - - - -
    -<V> V
    -    		ConfExecutable.getResults(String directory) - -
    -           
    -static ConfiguredExecutable<?>Util.loadExecutable(String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw ResultNotAvailableException
    - ConfiguredExecutable<?>ClusterSession.getResults(String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncJobRunner.getResults(String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.local
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local that throw ResultNotAvailableException
    -static ConfiguredExecutable<?>LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncLocalRunner.getResults(String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.conservation that throw ResultNotAvailableException
    - ScoreManagerAACon.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that throw ResultNotAvailableException
    - ScoreManagerJronn.getResults(String workDirectory) - -
    -           
    - ScoreManagerIUPred.getResults(String workDirectory) - -
    -           
    - ScoreManagerGlobPlot.getResults(String workDirectory) - -
    -           
    - ScoreManagerDisembl.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that throw ResultNotAvailableException
    - AlignmentMafft.getResults(String workDirectory) - -
    -           
    - AlignmentClustalW.getResults(String workDirectory) - -
    -           
    - AlignmentTcoffee.getResults(String workDirectory) - -
    -           
    - AlignmentMuscle.getResults(String workDirectory) - -
    -           
    - AlignmentClustalO.getResults(String workDirectory) - -
    -           
    - AlignmentProbcons.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw ResultNotAvailableException
    - ScoreManagerSequenceAnnotationService.getAnnotation(String jobId) - -
    -           
    -static - - - - -
    -<T> ScoreManager
    -    		WSUtil.getAnnotation(String jobId, - org.apache.log4j.Logger log) - -
    -           
    - AlignmentClustalWS.getResult(String jobId) - -
    -           
    - Alignment_MsaService.getResult(String jobId) - -
    -           
    - AlignmentMuscleWS.getResult(String jobId) - -
    -           
    - AlignmentMafftWS.getResult(String jobId) - -
    -           
    - AlignmentTcoffeeWS.getResult(String jobId) - -
    -           
    - AlignmentProbconsWS.getResult(String jobId) - -
    -           
    - AlignmentClustalOWS.getResult(String jobId) - -
    -           
    -  -

    -

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    compbio.metadata.RunnerConfig

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    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use RunnerConfig
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return RunnerConfig
    - RunnerConfig<T>Metadata.getRunnerOptions() - -
    -          Get options supported by a web service
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return RunnerConfig
    - RunnerConfigGetRunnerOptionsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type RunnerConfig
    - voidGetRunnerOptionsResponse.setReturn(RunnerConfig _return) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that return RunnerConfig
    -static - - - - -
    -<V> RunnerConfig<V>
    -    		ConfExecutable.getRunnerOptions(Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata with parameters of type RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    - List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidPresetManager.validate(RunnerConfig<T> options) - -
    -          Checks whether preset option and parameter are defined in RunnerConfig - object.
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return RunnerConfig
    -static - - - - -
    -<T> RunnerConfig<T>
    -    		Util.getSupportedOptions(Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner with parameters of type RunnerConfig
    -static List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.runner with parameters of type RunnerConfig
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return RunnerConfig
    - RunnerConfig<T>GenericMetadataService.getRunnerOptions() - -
    -           
    - RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Muscle>MuscleWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Mafft>MafftWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() - -
    -           
    - RunnerConfig<ClustalO>ClustalOWS.getRunnerOptions() - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.UnsupportedRuntimeException

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    -Packages that use UnsupportedRuntimeException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.engine.client  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that throw UnsupportedRuntimeException
    - StringConfExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw UnsupportedRuntimeException
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.ValueConstrain.Type

    -
    - - - - - - - - - -
    -Packages that use ValueConstrain.Type
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of ValueConstrain.Type in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain.Type
    - ValueConstrain.TypeValueConstrain.getType() - -
    -           
    -static ValueConstrain.TypeValueConstrain.Type.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]ValueConstrain.Type.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    - voidValueConstrain.setType(ValueConstrain.Type type) - -
    -           
    -  -

    -

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    compbio.metadata.ValueConstrain

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    -Packages that use ValueConstrain
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of ValueConstrain in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain
    - ValueConstrainParameter.getValidValue() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain
    - voidParameter.setValidValue(ValueConstrain validValue) - -
    -           
    -  -

    -

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    -Packages that use WrongParameterException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw WrongParameterException
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that throw WrongParameterException
    - List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidParameter.setDefaultValue(String defaultVal) - -
    -           
    - voidOption.setDefaultValue(String defaultVal) - -
    -          Sets one of the values defined in optionList as default.
    - voidArgument.setValue(String defaultValue) - -
    -          Set default values for the parameter or an option
    - voidOption.setValue(String dValue) - -
    -           
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw WrongParameterException
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

    -

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    -ValueConstrain
    - - - - - - -
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    - - - - - - -
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    -ResultNotAvailableException -
    -UnsupportedRuntimeException -
    -WrongParameterException
    - - - - diff --git a/website/full_javadoc/compbio/metadata/package-summary.html b/website/full_javadoc/compbio/metadata/package-summary.html deleted file mode 100644 index c135b59..0000000 --- a/website/full_javadoc/compbio/metadata/package-summary.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -compbio.metadata - - - - - - - - - - - - -
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    -Package compbio.metadata -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. -

    -See: -
    -          Description -

    - - - - - - - - - -
    -Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ChunkHolderRepresents a chunk of a string data together with the position in a file for - the next read operation.
    Limit<T>A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager<T>A collection of Limits
    Option<T>Command line option/flag or multiple exclusive options with no value.
    Parameter<T>A single value containing an option supported by the web service e.g.
    Preset<T>Collection of Options and Parameters with their values
    PresetManager<T>Collection of presets and methods to manipulate them @see Preset
    RunnerConfig<T>The list of Parameters and Options supported by executable.
    ValueConstrainThe type and the lower and upper boundaries for numerical value.
    -  - -

    - - - - - - - - - - - - - -
    -Enum Summary
    JobStatusThe status of the job.
    ValueConstrain.Type 
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Exception Summary
    JobExecutionExceptionJobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobSubmissionExceptionException for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    LimitExceededExceptionThis exception is thrown if the task larger in size that the limit that - applies to the calculation.
    ResultNotAvailableExceptionResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    UnsupportedRuntimeExceptionIndicates that the server could not execute native executables.
    WrongParameterExceptionWrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  - -

    -

    -Package compbio.metadata Description -

    - -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS) -

    - -

    -

    -
    Version:
    -
    1.0 January 2010
    -
    Author:
    -
    Peter Troshin
    -
    -
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    -Hierarchy For Package compbio.metadata -

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    -Uses of Package
    compbio.metadata

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use compbio.metadata
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa.jaxws
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.client
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.cluster.drmaa
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.local
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.metadata
    Argument - -
    -          An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Parameter - -
    -          A single value containing an option supported by the web service e.g.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    ValueConstrain - -
    -          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type - -
    -           
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Parameter - -
    -          A single value containing an option supported by the web service e.g.
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner._impl
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    -  -

    - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.conservation
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.disorder
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.msa
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.ws.server
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    -

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    - -compbio.pipeline._jpred -
    -Class BlastBlastComparator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastBlastComparator
-
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    -
    -
    public class BlastBlastComparator
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    BlastBlastComparator() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          args[0] is assumed to be the name of a Blast output file
    -  - - - - - - - -
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    -
    -public static void main(String[] args)
-                 throws FileNotFoundException,
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    - -compbio.pipeline._jpred -
    -Class BlastHmmerComparator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastHmmerComparator
-
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    extends Object
    - - -

    -

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    -Method Detail
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    -
    -public static void main(String[] args)
-                 throws XMLStreamException,
-                        IOException
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    - -compbio.pipeline._jpred -
    -Class BlastParser

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastParser
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    -
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    public class BlastParser
    extends Object
    - - -

    -

    - -

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    - -

    -BlastParser

    -
    -public BlastParser(String file)
-            throws FileNotFoundException,
-                   XMLStreamException
    -
    -
    - -
    Throws: -
    FileNotFoundException -
    XMLStreamException
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    - - - - - - - - -
    -Method Detail
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    -main

    -
    -public static void main(String[] args)
-                 throws FileNotFoundException,
-                        XMLStreamException
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    -
    args[0] is assumed to be the name of a Blast output file -

    -

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    -Class Hit.EvalueComporator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Hit.EvalueComporator
-
    -
    -
    All Implemented Interfaces:
    Comparator<Hit>
    -
    -
    -
    Enclosing class:
    Hit
    -
    -
    -
    -
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    extends Object
    implements Comparator<Hit>
    - - -

    -

    - -

    - - - - - - - - - - - -
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    -Hit.EvalueComporator

    -
    -public Hit.EvalueComporator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -compare

    -
    -public int compare(Hit o1,
-                   Hit o2)
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    -
    Specified by:
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    - -compbio.pipeline._jpred -
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    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Hit.NumberComporator
-
    -
    -
    All Implemented Interfaces:
    Comparator<Hit>
    -
    -
    -
    Enclosing class:
    Hit
    -
    -
    -
    -
    public static final class Hit.NumberComporator
    extends Object
    implements Comparator<Hit>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Hit.NumberComporator() - -
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    -
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    -Method Detail
    - -

    -compare

    -
    -public int compare(Hit o1,
-                   Hit o2)
    -
    -
    -
    Specified by:
    compare in interface Comparator<Hit>
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    - -compbio.pipeline._jpred -
    -Class Hit

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Hit
-
    -
    -
    -
    public class Hit
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - -
    -Nested Class Summary
    -static classHit.EvalueComporator - -
    -           
    -static classHit.NumberComporator - -
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    Hit() - -
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    - booleanequals(Object obj) - -
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    Overrides:
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    -
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    -
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    Overrides:
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    - -compbio.pipeline._jpred -
    -Class JackHmmerHitParser

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.JackHmmerHitParser
-
    -
    -
    -
    public class JackHmmerHitParser
    extends Object
    - - -

    -Parser for the following files: -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    JackHmmerHitParser(String file) - -
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    -JackHmmerHitParser

    -
    -public JackHmmerHitParser(String file)
-                   throws IOException
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    -
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-                 throws IOException
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    - -compbio.pipeline._jpred -
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    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Jpred4
-
    -
    -
    -
    public class Jpred4
    extends Object
    - - -

    -jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying. Default: uniref90 ( - /homes/www-jpred/databases/uniref90.filt) Please note that database must be - psi-blast indexed - - [--pred-nohits] Toggle allowing Jpred to make predictions even when there are - no PSI-BLAST hits. - - [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help] -

    - -

    -

    -
    Author:
    -
    pvtroshin
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    - voidrunPsiBlast() - -
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    - -compbio.pipeline._jpred -
    -Class PScore

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.PScore
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    public class PScore
    extends Object
    - - -

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    - - - - - - - - - - - - - -
    Methods in compbio.pipeline._jpred with parameters of type Hit
    - intHit.NumberComporator.compare(Hit o1, - Hit o2) - -
    -           
    - intHit.EvalueComporator.compare(Hit o1, - Hit o2) - -
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    -BlastBlastComparator -
    -BlastHmmerComparator -
    -BlastParser -
    -Hit -
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    -Hit.NumberComporator -
    -JackHmmerHitParser -
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    -Class Summary
    BlastBlastComparator 
    BlastHmmerComparator 
    BlastParser 
    Hit 
    Hit.EvalueComporator 
    Hit.NumberComporator 
    JackHmmerHitParserParser for the following files:
    Jpred4jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying.
    Pairwise 
    PScore 
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    compbio.pipeline._jpred  
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    -Classes in compbio.pipeline._jpred used by compbio.pipeline._jpred
    Hit - -
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    - -compbio.runner -
    -Class OptionCombinator

    -
    -java.lang.Object
-  extended by compbio.runner.OptionCombinator
-
    -
    -
    -
    @Immutable
-public final class OptionCombinator
    extends Object
    - - -

    -This class solve the following problems. Given the RunnerConfig - - 1) generate a valid option string with all options and parameters in it - - 2) Permute all possible combinations of options order and parameters values -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>argumentsToCommandString(List<? extends Option<?>> arguments) - -
    -           
    -static List<String>argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    - Map<Parameter<?>,String>getAllConstrainedParametersWithBorderValues(boolean minValue) - -
    -           
    - Map<Parameter<?>,String>getAllConstrainedParametersWithRandomValues() - -
    -           
    - List<Option<?>>getAllOptions() - -
    -           
    - List<Parameter<?>>getAllParameters() - -
    -           
    - List<String>getOptionsAtRandom() - -
    -           
    - List<String>optionsToCommandString(List<Option<?>> options) - -
    -           
    - List<String>parametersToCommandString(List<Parameter<?>> orderedList, - Map<Parameter<?>,String> prmValue) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -OptionCombinator

    -
    -public OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -optionsToCommandString

    -
    -public List<String> optionsToCommandString(List<Option<?>> options)
    -
    -
    -
    -
    -
    -
    - -

    -getOptionsAtRandom

    -
    -public List<String> getOptionsAtRandom()
    -
    -
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    -
    -
    -
    - -

    -getAllOptions

    -
    -public List<Option<?>> getAllOptions()
    -
    -
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    -getAllParameters

    -
    -public List<Parameter<?>> getAllParameters()
    -
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    -
    -
    -
    - -

    -argumentsToCommandString

    -
    -public List<String> argumentsToCommandString(List<? extends Option<?>> arguments)
    -
    -
    -
    -
    -
    -
    - -

    -argumentsToCommandString

    -
    -public static List<String> argumentsToCommandString(List<? extends Option<?>> arguments,
-                                                    RunnerConfig<? extends Executable<?>> rconfig)
    -
    -
    -
    -
    -
    -
    - -

    -parametersToCommandString

    -
    -public List<String> parametersToCommandString(List<Parameter<?>> orderedList,
-                                              Map<Parameter<?>,String> prmValue)
    -
    -
    -
    -
    -
    -
    - -

    -getAllConstrainedParametersWithBorderValues

    -
    -public Map<Parameter<?>,String> getAllConstrainedParametersWithBorderValues(boolean minValue)
    -
    -
    -
    -
    -
    -
    - -

    -getAllConstrainedParametersWithRandomValues

    -
    -public Map<Parameter<?>,String> getAllConstrainedParametersWithRandomValues()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/Util.html b/website/full_javadoc/compbio/runner/Util.html deleted file mode 100644 index 8db9c58..0000000 --- a/website/full_javadoc/compbio/runner/Util.html +++ /dev/null @@ -1,423 +0,0 @@ - - - - - - -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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html deleted file mode 100644 index 09b9e19..0000000 --- a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -_NativeSpecHelper - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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    - - - -
    - -

    - -compbio.runner -
    -Class _NativeSpecHelper

    -
    -java.lang.Object
-  extended by compbio.runner._NativeSpecHelper
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class _NativeSpecHelper
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    _NativeSpecHelper(int requiredMemory) - -
    -          Deprecated.  
    _NativeSpecHelper(int requiredMemory, - int maxCalculationTime) - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - _QueuegetApproprieteQueue() - -
    -          Deprecated.  
    - StringgetNativeSpec() - -
    -          Deprecated.  
    - StringgetQueue() - -
    -          Deprecated.  
    - voidsetQueue(String queue) - -
    -          Deprecated.  
    - voidsetRequiredMemory(int memory) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -_NativeSpecHelper

    -
    -public _NativeSpecHelper(int requiredMemory)
    -
    -
    Deprecated. 
    -
    - -

    -_NativeSpecHelper

    -
    -public _NativeSpecHelper(int requiredMemory,
-                         int maxCalculationTime)
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -setRequiredMemory

    -
    -public void setRequiredMemory(int memory)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -setQueue

    -
    -public void setQueue(String queue)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getQueue

    -
    -public String getQueue()
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getNativeSpec

    -
    -public String getNativeSpec()
-                     throws UnknownServiceException
    -
    -
    Deprecated. 
    - -
    Throws: -
    UnknownServiceException
    -
    -
    -
    - -

    -getApproprieteQueue

    -
    -public _Queue getApproprieteQueue()
    -
    -
    Deprecated. 
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html deleted file mode 100644 index 9296823..0000000 --- a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html +++ /dev/null @@ -1,611 +0,0 @@ - - - - - - -_SkeletalCommandBuilder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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 _SkeletalCommandBuilder

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    Direct Known Subclasses:
    BlastAll, Mcl, OB, PSIBlast, Ronn, RPSBlast
    -
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public abstract class _SkeletalCommandBuilder
    extends Object
    implements Executable<_SkeletalCommandBuilder>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    _SkeletalCommandBuilder() - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - _SkeletalCommandBuilderaddParameter(String parameter) - -
    -          Deprecated.  
    - _SkeletalCommandBuilderaddParameters(List<String> parameters) - -
    -          Deprecated. Adds parameter to the list of parameters for a native executable
    - _SkeletalCommandBuilderaddParameters(String[] parameters) - -
    -          Deprecated.  
    - StringgetClusterJobSettings() - -
    -          Deprecated.  
    - StringgetEmail() - -
    -          Deprecated.  
    - StringgetError() - -
    -          Deprecated.  
    - Limit<_SkeletalCommandBuilder>getLimit(String presetName) - -
    -          Deprecated.  
    - LimitsManager<_SkeletalCommandBuilder>getLimits() - -
    -          Deprecated.  
    - StringgetName() - -
    -          Deprecated.  
    - StringgetOutput() - -
    -          Deprecated.  
    - CommandBuilder<_SkeletalCommandBuilder>getParameters(Executable.ExecProvider provider) - -
    -          Deprecated.  
    - - - - - -
    -<V> V
    -    		getResults(String directory) - -
    -          Deprecated.  
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -          Deprecated.  
    - _SkeletalCommandBuildersetEmail(String email) - -
    -          Deprecated.  
    - _SkeletalCommandBuildersetName(String name) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    getCreatedFiles, getInput
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -_SkeletalCommandBuilder

    -
    -public _SkeletalCommandBuilder()
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -setEmail

    -
    -public _SkeletalCommandBuilder setEmail(String email)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -setName

    -
    -public _SkeletalCommandBuilder setName(String name)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -getName

    -
    -public String getName()
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -getEmail

    -
    -public String getEmail()
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public _SkeletalCommandBuilder addParameters(String[] parameters)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

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

    -

    -
    Specified by:
    addParameters in interface Executable<_SkeletalCommandBuilder>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)
    -
    -
    Deprecated. 
    -
    Specified by:
    getParameters in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -addParameter

    -
    -public _SkeletalCommandBuilder addParameter(String parameter)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public <V> V getResults(String directory)
    -
    -
    Deprecated. 
    -
    Specified by:
    getResults in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
    Deprecated. 
    -
    Specified by:
    loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    Deprecated. 
    -
    Specified by:
    getOutput in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public String getError()
    -
    -
    Deprecated. 
    -
    Specified by:
    getError in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<_SkeletalCommandBuilder> getLimit(String presetName)
    -
    -
    Deprecated. 
    -
    Specified by:
    getLimit in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -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>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/BlastAll.html deleted file mode 100644 index 62d0af1..0000000 --- a/website/full_javadoc/compbio/runner/_impl/BlastAll.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -BlastAll - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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._impl -
    -Class BlastAll

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.BlastAll
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class BlastAll
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    BlastAll(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    - booleanremoveOutput(String outfile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -BlastAll

    -
    -public BlastAll(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -removeOutput

    -
    -public boolean removeOutput(String outfile)
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public String getCommandName()
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html deleted file mode 100644 index d2497cb..0000000 --- a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html +++ /dev/null @@ -1,199 +0,0 @@ - - - - - - -BlastParameters - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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._impl -
    -Class BlastParameters

    -
    -java.lang.Object
-  extended by compbio.runner._impl.BlastParameters
-
    -
    -
    -
    public class BlastParameters
    extends Object
    - - -

    -Utility class for common Blast parameters -

    - -

    -

    -
    Author:
    -
    pvtroshin TODO
    -
    -
    - -

    - - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - -

    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Environment.html b/website/full_javadoc/compbio/runner/_impl/Environment.html deleted file mode 100644 index 502ed49..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Environment.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -Environment - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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._impl -
    -Class Environment

    -
    -java.lang.Object
-  extended by compbio.runner._impl.Environment
-
    -
    -
    -
    public final class Environment
    extends Object
    - - -

    -This is utility class to encapsulate environmental variables like directory paths -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static StringgetBlastBinDir() - -
    -           
    -static StringgetBlastDatabasesDir() - -
    -           
    -static StringgetRPSBlastDatabasesDir() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getBlastBinDir

    -
    -public static String getBlastBinDir()
    -
    -
    -
    -
    -
    -
    - -

    -getBlastDatabasesDir

    -
    -public static final String getBlastDatabasesDir()
    -
    -
    -
    -
    -
    -
    - -

    -getRPSBlastDatabasesDir

    -
    -public static final String getRPSBlastDatabasesDir()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Mcl.html b/website/full_javadoc/compbio/runner/_impl/Mcl.html deleted file mode 100644 index f22bae8..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Mcl.html +++ /dev/null @@ -1,379 +0,0 @@ - - - - - - -Mcl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class Mcl

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Mcl
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class Mcl
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Mcl(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    -static StringgetTestCommand() - -
    -           
    -static List<String>getTestParams() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Mcl

    -
    -public Mcl(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTestParams

    -
    -public static List<String> getTestParams()
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static String getTestCommand()
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public String getCommandName()
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
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    - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html deleted file mode 100644 index 5cd196e..0000000 --- a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html +++ /dev/null @@ -1,574 +0,0 @@ - - - - - - -NetNglyc - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class NetNglyc

    -
    -java.lang.Object
-  extended by compbio.runner._impl.NetNglyc
-
    -
    -
    All Implemented Interfaces:
    Executable<NetNglyc>
    -
    -
    -
    -
    public class NetNglyc
    extends Object
    implements Executable<NetNglyc>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    NetNglyc() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - NetNglycaddParameters(List<String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - StringgetClusterJobSettings() - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetError() - -
    -           
    - StringgetInput() - -
    -           
    - Limit<NetNglyc>getLimit(String presetName) - -
    -           
    - LimitsManager<NetNglyc>getLimits() - -
    -           
    - StringgetOutput() - -
    -           
    - CommandBuilder<NetNglyc>getParameters(Executable.ExecProvider provider) - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(String directory) - -
    -           
    -static List<String>getTestArgs() - -
    -           
    -static StringgetTestCommand() - -
    -           
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -NetNglyc

    -
    -public NetNglyc()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getParameters

    -
    -public CommandBuilder<NetNglyc> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getTestArgs

    -
    -public static List<String> getTestArgs()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public NetNglyc addParameters(List<String> parameters)
    -
    -
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<NetNglyc>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static String getTestCommand()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public String getCommandName()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    Specified by:
    getCreatedFiles in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    Specified by:
    getInput in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public <V> V getResults(String directory)
    -
    -
    -
    Specified by:
    getResults in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
    -
    Specified by:
    loadRunConfiguration in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public String getError()
    -
    -
    -
    Specified by:
    getError in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<NetNglyc> getLimit(String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<NetNglyc> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getClusterJobSettings

    -
    -public String getClusterJobSettings()
    -
    -
    -
    Specified by:
    getClusterJobSettings in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/OB.html b/website/full_javadoc/compbio/runner/_impl/OB.html deleted file mode 100644 index 7a95b09..0000000 --- a/website/full_javadoc/compbio/runner/_impl/OB.html +++ /dev/null @@ -1,382 +0,0 @@ - - - - - - -OB - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class OB

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.OB
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class OB
    extends _SkeletalCommandBuilder
    - - -

    -TODO this needs fixing! Executable does not work -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - -
    -Constructor Summary
    OB() - -
    -           
    OB(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    - List<String>getTestArgs() - -
    -           
    -static StringgetTestCommand() - -
    -           
    -static voidmain(String[] args) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -OB

    -
    -public OB()
    -
    -
    -
    - -

    -OB

    -
    -public OB(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTestCommand

    -
    -public static String getTestCommand()
    -
    -
    -
    -
    -
    -
    - -

    -getTestArgs

    -
    -public List<String> getTestArgs()
    -
    -
    -
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html deleted file mode 100644 index 3f9faab..0000000 --- a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -PSIBlast - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class PSIBlast

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.PSIBlast
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class PSIBlast
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    PSIBlast(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    - booleanremoveOutput(String outfile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PSIBlast

    -
    -public PSIBlast(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -removeOutput

    -
    -public boolean removeOutput(String outfile)
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public String getCommandName()
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html deleted file mode 100644 index 7981429..0000000 --- a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -RPSBlast - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class RPSBlast

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.RPSBlast
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class RPSBlast
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    RPSBlast(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    -static StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    -static StringgetTestCommand() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -RPSBlast

    -
    -public RPSBlast(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static String getTestCommand()
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public static String getCommandName()
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Ronn.html b/website/full_javadoc/compbio/runner/_impl/Ronn.html deleted file mode 100644 index c16e07f..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Ronn.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -Ronn - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class Ronn

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Ronn
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class Ronn
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Ronn(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    -static StringgetTestCommand() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Ronn

    -
    -public Ronn(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static String getTestCommand()
    -
    -
    -
    -
    -
    -
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    -getCommandName

    -
    -public String getCommandName()
    -
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    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Runners.html b/website/full_javadoc/compbio/runner/_impl/Runners.html deleted file mode 100644 index 29e902e..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Runners.html +++ /dev/null @@ -1,352 +0,0 @@ - - - - - - -Runners - - - - - - - - - - - - -
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    - -

    - -compbio.runner._impl -
    -Class Runners

    -
    -java.lang.Object
-  extended by compbio.runner._impl.Runners
-
    -
    -
    -
    public final class Runners
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static BlastAllgetBlastAllRunnable(String workDirectory) - -
    -           
    -static MclgetMclRunnable(String workDirectory) - -
    -           
    -static NetNglycgetNetNglycRunnable(String workDirectory) - -
    -           
    -static OBgetOBRunnable(String workDirectory) - -
    -           
    -static PSIBlastgetPSIBlastRunnable(String workDirectory) - -
    -           
    -static RonngetRonnRunnable(String workDirectory) - -
    -           
    -static RPSBlastgetRPSBlastRunnable(String workDirectory) - -
    -           
    -static compbio.runner._impl.Tmhmm2getTmhmm2Runnable(String workDirectory) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getMclRunnable

    -
    -public static Mcl getMclRunnable(String workDirectory)
    -
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    -
    - -

    -getOBRunnable

    -
    -public static OB getOBRunnable(String workDirectory)
    -
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    - -

    -getNetNglycRunnable

    -
    -public static NetNglyc getNetNglycRunnable(String workDirectory)
    -
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    - -

    -getRonnRunnable

    -
    -public static Ronn getRonnRunnable(String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getTmhmm2Runnable

    -
    -public static compbio.runner._impl.Tmhmm2 getTmhmm2Runnable(String workDirectory)
    -
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    -
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    -getRPSBlastRunnable

    -
    -public static RPSBlast getRPSBlastRunnable(String workDirectory)
    -
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    -
    -
    - -

    -getBlastAllRunnable

    -
    -public static BlastAll getBlastAllRunnable(String workDirectory)
    -
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    -
    -
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    - -

    -getPSIBlastRunnable

    -
    -public static PSIBlast getPSIBlastRunnable(String workDirectory)
    -
    -
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    -Uses of Class
    compbio.runner._impl.BlastAll

    -
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    -Packages that use BlastAll
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of BlastAll in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return BlastAll
    -static BlastAllRunners.getBlastAllRunnable(String workDirectory) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.runner._impl.BlastParameters

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    -No usage of compbio.runner._impl.BlastParameters -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.Mcl

    -
    - - - - - - - - - -
    -Packages that use Mcl
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of Mcl in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Mcl
    -static MclRunners.getMclRunnable(String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html deleted file mode 100644 index 3b4cafa..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.NetNglyc - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.NetNglyc

    -
    - - - - - - - - - -
    -Packages that use NetNglyc
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of NetNglyc in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner._impl that return NetNglyc
    - NetNglycNetNglyc.addParameters(List<String> parameters) - -
    -           
    -static NetNglycRunners.getNetNglycRunnable(String workDirectory) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner._impl that return types with arguments of type NetNglyc
    - Limit<NetNglyc>NetNglyc.getLimit(String presetName) - -
    -           
    - LimitsManager<NetNglyc>NetNglyc.getLimits() - -
    -           
    - CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    compbio.runner._impl.OB

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    -Packages that use OB
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of OB in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return OB
    -static OBRunners.getOBRunnable(String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.PSIBlast

    -
    - - - - - - - - - -
    -Packages that use PSIBlast
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of PSIBlast in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return PSIBlast
    -static PSIBlastRunners.getPSIBlastRunnable(String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.RPSBlast

    -
    - - - - - - - - - -
    -Packages that use RPSBlast
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of RPSBlast in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return RPSBlast
    -static RPSBlastRunners.getRPSBlastRunnable(String workDirectory) - -
    -           
    -  -

    -

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    -

    -Uses of Class
    compbio.runner._impl.Ronn

    -
    - - - - - - - - - -
    -Packages that use Ronn
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of Ronn in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Ronn
    -static RonnRunners.getRonnRunnable(String workDirectory) - -
    -           
    -  -

    -

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    compbio.runner._impl.Runners

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    -No usage of compbio.runner._impl.Runners -

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    -Classes  - -
    -BlastAll -
    -BlastParameters -
    -Environment -
    -Mcl -
    -NetNglyc -
    -OB -
    -PSIBlast -
    -Ronn -
    -RPSBlast -
    -Runners
    - - - - diff --git a/website/full_javadoc/compbio/runner/_impl/package-summary.html b/website/full_javadoc/compbio/runner/_impl/package-summary.html deleted file mode 100644 index 3355806..0000000 --- a/website/full_javadoc/compbio/runner/_impl/package-summary.html +++ /dev/null @@ -1,193 +0,0 @@ - - - - - - -compbio.runner._impl - - - - - - - - - - - - -
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    -Package compbio.runner._impl -

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    -Class Summary
    BlastAll 
    BlastParametersUtility class for common Blast parameters
    EnvironmentThis is utility class to encapsulate environmental variables like directory paths
    Mcl 
    NetNglyc 
    OBTODO this needs fixing! Executable does not work
    PSIBlast 
    Ronn 
    RPSBlast 
    Runners 
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    compbio.runner._impl  
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    -Classes in compbio.runner._impl used by compbio.runner._impl
    BlastAll - -
    -           
    Mcl - -
    -           
    NetNglyc - -
    -           
    OB - -
    -          TODO this needs fixing! Executable does not work
    PSIBlast - -
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    Ronn - -
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    - -compbio.runner._jpred -
    -Class _Jpred

    -
    -java.lang.Object
-  extended by compbio.runner._jpred._Jpred
-
    -
    -
    -
    public class _Jpred
    extends Object
    - - -

    -

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    -Constructor Summary
    _Jpred() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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    -Constructor Detail
    - -

    -_Jpred

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    -Classes  - -
    -_Jpred
    - - - - diff --git a/website/full_javadoc/compbio/runner/_jpred/package-summary.html b/website/full_javadoc/compbio/runner/_jpred/package-summary.html deleted file mode 100644 index 6c097c4..0000000 --- a/website/full_javadoc/compbio/runner/_jpred/package-summary.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - -compbio.runner._jpred - - - - - - - - - - - - -
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    _Jpred 
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    compbio.runner._SkeletalCommandBuilder

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    -Packages that use _SkeletalCommandBuilder
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of _SkeletalCommandBuilder in compbio.runner
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return _SkeletalCommandBuilder
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameter(String parameter) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(List<String> parameters) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(String[] parameters) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.setEmail(String email) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.setName(String name) - -
    -          Deprecated.  
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type _SkeletalCommandBuilder
    - Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(String presetName) - -
    -          Deprecated.  
    - LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() - -
    -          Deprecated.  
    - CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of _SkeletalCommandBuilder in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Subclasses of _SkeletalCommandBuilder in compbio.runner._impl
    - classBlastAll - -
    -           
    - classMcl - -
    -           
    - classOB - -
    -          TODO this needs fixing! Executable does not work
    - classPSIBlast - -
    -           
    - classRonn - -
    -           
    - classRPSBlast - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/conservation/AACon.html b/website/full_javadoc/compbio/runner/conservation/AACon.html deleted file mode 100644 index 2531d64..0000000 --- a/website/full_javadoc/compbio/runner/conservation/AACon.html +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - -AACon - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner.conservation -
    -Class AACon

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<AACon>
-      extended by compbio.runner.conservation.AACon
-
    -
    -
    All Implemented Interfaces:
    Executable<AACon>
    -
    -
    -
    -
    public class AACon
    extends SkeletalExecutable<AACon>
    - - -

    -Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -static StringSTAT_FILE - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    AACon() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - CommandBuilder<AACon>getParameters(Executable.ExecProvider provider) - -
    -           
    - ScoreManagergetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<AACon>getType() - -
    -           
    - AAConsetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    - AAConsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -STAT_FILE

    -
    -public static final String STAT_FILE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -AACon

    -
    -public AACon()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<AACon>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<AACon>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public AACon setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<AACon>
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public AACon setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<AACon>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<AACon> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<AACon>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<AACon> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<AACon>
    Overrides:
    getParameters in class SkeletalExecutable<AACon>
    -
    -
    -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
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    - - - diff --git a/website/full_javadoc/compbio/runner/conservation/class-use/AACon.html b/website/full_javadoc/compbio/runner/conservation/class-use/AACon.html deleted file mode 100644 index 94ec58c..0000000 --- a/website/full_javadoc/compbio/runner/conservation/class-use/AACon.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -Uses of Class compbio.runner.conservation.AACon - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.conservation.AACon

    -
    - - - - - - - - - -
    -Packages that use AACon
    compbio.runner.conservation  
    -  -

    - - - - - -
    -Uses of AACon in compbio.runner.conservation
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.conservation that return AACon
    - AAConAACon.setInput(String inFile) - -
    -           
    - AAConAACon.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.conservation that return types with arguments of type AACon
    - CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<AACon>AACon.getType() - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -AACon
    - - - - diff --git a/website/full_javadoc/compbio/runner/conservation/package-summary.html b/website/full_javadoc/compbio/runner/conservation/package-summary.html deleted file mode 100644 index 05396da..0000000 --- a/website/full_javadoc/compbio/runner/conservation/package-summary.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - -compbio.runner.conservation - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -

    -Package compbio.runner.conservation -

    - - - - - - - - - -
    -Class Summary
    AAConCommand line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  - -

    -

    -
    -
    - - - - - - - - - - - - - - - -
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    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/conservation/package-tree.html b/website/full_javadoc/compbio/runner/conservation/package-tree.html deleted file mode 100644 index d18097d..0000000 --- a/website/full_javadoc/compbio/runner/conservation/package-tree.html +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - -compbio.runner.conservation Class Hierarchy - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    -
    -

    -Hierarchy For Package compbio.runner.conservation -

    -
    -
    -
    Package Hierarchies:
    All Packages
    -
    -

    -Class Hierarchy -

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    - - - - - - - - - - - - - - - -
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    -Uses of Package
    compbio.runner.conservation

    -
    - - - - - - - - - -
    -Packages that use compbio.runner.conservation
    compbio.runner.conservation  
    -  -

    - - - - - - - - -
    -Classes in compbio.runner.conservation used by compbio.runner.conservation
    AACon - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/Disembl.html b/website/full_javadoc/compbio/runner/disorder/Disembl.html deleted file mode 100644 index 762436e..0000000 --- a/website/full_javadoc/compbio/runner/disorder/Disembl.html +++ /dev/null @@ -1,468 +0,0 @@ - - - - - - -Disembl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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 Disembl

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

    -DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script. - smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4 - fold_rem465=1.2 - - Changing these values are not recommended by developers, apart from smoothing - window. However, 5 orders of magnitude changes in this parameter does not - change the output so allowing this change also seems pointless. Finally, the - binary, DisEMBL depends on - Tisean is not happy with arbitruary changes to - these values, so changing them can lead to problems. - - - This is not a standard DisEMBL! The script has been modified! -

    - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    - doubleCOILS_EXPECTATION_THRESHOLD - -
    -          For the region to be considered disordered the values must exceed these
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    - doubleLOOPS_EXPECTATION_THRESHOLD - -
    -           
    - doubleREM_EXPECTATION_THRESHOLD - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Disembl() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - ScoreManagergetResults(String workDirectory) - -
    -           
    - Class<Disembl>getType() - -
    -           
    - DisemblsetInput(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
    -
    -
    - -

    -COILS_EXPECTATION_THRESHOLD

    -
    -public final double COILS_EXPECTATION_THRESHOLD
    -
    -
    For the region to be considered disordered the values must exceed these -

    -

    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -REM_EXPECTATION_THRESHOLD

    -
    -public final double REM_EXPECTATION_THRESHOLD
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -LOOPS_EXPECTATION_THRESHOLD

    -
    -public final double LOOPS_EXPECTATION_THRESHOLD
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Disembl

    -
    -public Disembl()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

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

    -setInput

    -
    -public Disembl setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Disembl>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Disembl> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Disembl>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/GlobPlot.html b/website/full_javadoc/compbio/runner/disorder/GlobPlot.html deleted file mode 100644 index 20a6f4f..0000000 --- a/website/full_javadoc/compbio/runner/disorder/GlobPlot.html +++ /dev/null @@ -1,405 +0,0 @@ - - - - - - -GlobPlot - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - 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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/IUPred.html b/website/full_javadoc/compbio/runner/disorder/IUPred.html deleted file mode 100644 index 52643a9..0000000 --- a/website/full_javadoc/compbio/runner/disorder/IUPred.html +++ /dev/null @@ -1,401 +0,0 @@ - - - - - - -IUPred - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.disorder -
    -Class IUPred

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<IUPred>
-      extended by compbio.runner.disorder.IUPred
-
    -
    -
    All Implemented Interfaces:
    Executable<IUPred>
    -
    -
    -
    -
    public class IUPred
    extends SkeletalExecutable<IUPred>
    - - -

    -iupred sequenceFile - - Maximum sequence length is 40000 chars. Single string length max is a 1000 - chars! -

    - -

    -

    - -

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

    - - - - - - - - -
    -Constructor Detail
    - -

    -IUPred

    -
    -public IUPred()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public IUPred setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<IUPred>
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public IUPred setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<IUPred>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<IUPred>
    Overrides:
    getOutput in class SkeletalExecutable<IUPred>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<IUPred> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<IUPred>
    -
    -
    - -
    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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/Jronn.html b/website/full_javadoc/compbio/runner/disorder/Jronn.html deleted file mode 100644 index 9a0b602..0000000 --- a/website/full_javadoc/compbio/runner/disorder/Jronn.html +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - -Jronn - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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 Jronn

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Jronn>
-      extended by compbio.runner.disorder.Jronn
-
    -
    -
    All Implemented Interfaces:
    Executable<Jronn>
    -
    -
    -
    -
    public class Jronn
    extends SkeletalExecutable<Jronn>
    - - -

    -Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -static StringSTAT_FILE - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Jronn() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - CommandBuilder<Jronn>getParameters(Executable.ExecProvider provider) - -
    -           
    - ScoreManagergetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<Jronn>getType() - -
    -           
    - JronnsetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    - JronnsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -STAT_FILE

    -
    -public static final String STAT_FILE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Jronn

    -
    -public Jronn()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Jronn>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Jronn>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public Jronn setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Jronn>
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public Jronn setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<Jronn>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Jronn> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Jronn>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<Jronn> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<Jronn>
    Overrides:
    getParameters in class SkeletalExecutable<Jronn>
    -
    -
    -
    -
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    - -
    - - - - - - - - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/Disembl.html b/website/full_javadoc/compbio/runner/disorder/class-use/Disembl.html deleted file mode 100644 index d87fb68..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/Disembl.html +++ /dev/null @@ -1,235 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.Disembl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.disorder.Disembl

    -
    - - - - - - - - - - - - - -
    -Packages that use Disembl
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Disembl in compbio.runner.disorder
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return Disembl
    - DisemblDisembl.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type Disembl
    - Class<Disembl>Disembl.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Disembl in compbio.ws.server
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Disembl
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/GlobPlot.html b/website/full_javadoc/compbio/runner/disorder/class-use/GlobPlot.html deleted file mode 100644 index 267ebac..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/GlobPlot.html +++ /dev/null @@ -1,235 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.GlobPlot - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.disorder.GlobPlot

    -
    - - - - - - - - - - - - - -
    -Packages that use GlobPlot
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of GlobPlot in compbio.runner.disorder
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return GlobPlot
    - GlobPlotGlobPlot.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type GlobPlot
    - Class<GlobPlot>GlobPlot.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of GlobPlot in compbio.ws.server
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type GlobPlot
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/IUPred.html b/website/full_javadoc/compbio/runner/disorder/class-use/IUPred.html deleted file mode 100644 index 8e6c178..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/IUPred.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.IUPred - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - -
    -
    -

    -Uses of Class
    compbio.runner.disorder.IUPred

    -
    - - - - - - - - - - - - - -
    -Packages that use IUPred
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of IUPred in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return IUPred
    - IUPredIUPred.setInput(String inFile) - -
    -           
    - IUPredIUPred.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type IUPred
    - Class<IUPred>IUPred.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of IUPred in compbio.ws.server
    -  -

    - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type IUPred
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/Jronn.html b/website/full_javadoc/compbio/runner/disorder/class-use/Jronn.html deleted file mode 100644 index 2ca614b..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/Jronn.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.Jronn - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -
    -

    -Uses of Class
    compbio.runner.disorder.Jronn

    -
    - - - - - - - - - -
    -Packages that use Jronn
    compbio.runner.disorder  
    -  -

    - - - - - -
    -Uses of Jronn in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return Jronn
    - JronnJronn.setInput(String inFile) - -
    -           
    - JronnJronn.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type Jronn
    - CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<Jronn>Jronn.getType() - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -Disembl -
    -GlobPlot -
    -IUPred -
    -Jronn
    - - - - diff --git a/website/full_javadoc/compbio/runner/disorder/package-summary.html b/website/full_javadoc/compbio/runner/disorder/package-summary.html deleted file mode 100644 index 18a8586..0000000 --- a/website/full_javadoc/compbio/runner/disorder/package-summary.html +++ /dev/null @@ -1,186 +0,0 @@ - - - - - - -compbio.runner.disorder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -

    -Package compbio.runner.disorder -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    DisemblDisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    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.
    IUPrediupred sequenceFile - - Maximum sequence length is 40000 chars.
    JronnCommand line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  - -

    -

    -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
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    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/package-tree.html b/website/full_javadoc/compbio/runner/disorder/package-tree.html deleted file mode 100644 index 52942ce..0000000 --- a/website/full_javadoc/compbio/runner/disorder/package-tree.html +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - -compbio.runner.disorder Class Hierarchy - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Hierarchy For Package compbio.runner.disorder -

    -
    -
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    Package Hierarchies:
    All Packages
    -
    -

    -Class Hierarchy -

    - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/package-use.html b/website/full_javadoc/compbio/runner/disorder/package-use.html deleted file mode 100644 index b5c3017..0000000 --- a/website/full_javadoc/compbio/runner/disorder/package-use.html +++ /dev/null @@ -1,251 +0,0 @@ - - - - - - -Uses of Package compbio.runner.disorder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - -
    -
    -

    -Uses of Package
    compbio.runner.disorder

    -
    - - - - - - - - - - - - - -
    -Packages that use compbio.runner.disorder
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.disorder used by compbio.runner.disorder
    Disembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    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.
    IUPred - -
    -          iupred sequenceFile - - Maximum sequence length is 40000 chars.
    Jronn - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.runner.disorder used by compbio.ws.server
    Disembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    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.
    IUPred - -
    -          iupred sequenceFile - - Maximum sequence length is 40000 chars.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/ClustalO.html b/website/full_javadoc/compbio/runner/msa/ClustalO.html deleted file mode 100644 index 9175571..0000000 --- a/website/full_javadoc/compbio/runner/msa/ClustalO.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -ClustalO - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class ClustalO

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<ClustalO>
-      extended by compbio.runner.msa.ClustalO
-
    -
    -
    All Implemented Interfaces:
    Executable<ClustalO>
    -
    -
    -
    -
    public class ClustalO
    extends SkeletalExecutable<ClustalO>
    - - -

    -

    - -

    - - - - - - - -
    -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
    ClustalO() - -
    -          --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - CommandBuilder<ClustalO>getParameters(Executable.ExecProvider provider) - -
    -           
    - AlignmentgetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<ClustalO>getType() - -
    -           
    - ClustalOsetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    - ClustalOsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

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

    -ClustalO

    -
    -public ClustalO()
    -
    -
    --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file -

    -

    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public ClustalO setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<ClustalO>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public ClustalO setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<ClustalO>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<ClustalO> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<ClustalO>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<ClustalO> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<ClustalO>
    Overrides:
    getParameters in class SkeletalExecutable<ClustalO>
    -
    -
    -
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html deleted file mode 100644 index 38602cb..0000000 --- a/website/full_javadoc/compbio/runner/msa/ClustalW.html +++ /dev/null @@ -1,445 +0,0 @@ - - - - - - -ClustalW - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.msa -
    -Class ClustalW

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<ClustalW>
-      extended by compbio.runner.msa.ClustalW
-
    -
    -
    All Implemented Interfaces:
    Executable<ClustalW>
    -
    -
    -
    -
    public class ClustalW
    extends SkeletalExecutable<ClustalW>
    - - -

    -

    - -

    - - - - - - - -
    -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
    ClustalW() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - AlignmentgetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<ClustalW>getType() - -
    -           
    - ClustalWsetInput(String inFile) - -
    -           
    - ClustalWsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

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

    -ClustalW

    -
    -public ClustalW()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public ClustalW setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<ClustalW>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public ClustalW setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<ClustalW>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<ClustalW>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<ClustalW>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<ClustalW> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<ClustalW>
    -
    -
    - -
    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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html deleted file mode 100644 index 45b6b8d..0000000 --- a/website/full_javadoc/compbio/runner/msa/Mafft.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -Mafft - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.msa -
    -Class Mafft

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

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -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
    Mafft() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - MafftaddParameters(List<String> parameters) - -
    -          Mafft input must always be the last parameter!
    - AlignmentgetResults(String workDirectory) - -
    -           
    - Class<Mafft>getType() - -
    -           
    - MafftsetInput(String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    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
    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
    - -

    -Mafft

    -
    -public Mafft()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Mafft>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public Mafft setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Mafft>
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public Mafft addParameters(List<String> parameters)
    -
    -
    Mafft input must always be the last parameter! -

    -

    -
    Specified by:
    addParameters in interface Executable<Mafft>
    Overrides:
    addParameters in class SkeletalExecutable<Mafft>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getType

    -
    -public Class<Mafft> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Mafft>
    -
    -
    - -
    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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Muscle.html b/website/full_javadoc/compbio/runner/msa/Muscle.html deleted file mode 100644 index 9e15084..0000000 --- a/website/full_javadoc/compbio/runner/msa/Muscle.html +++ /dev/null @@ -1,451 +0,0 @@ - - - - - - -Muscle - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.msa -
    -Class Muscle

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Muscle>
-      extended by compbio.runner.msa.Muscle
-
    -
    -
    All Implemented Interfaces:
    Executable<Muscle>
    -
    -
    -
    -
    public class Muscle
    extends SkeletalExecutable<Muscle>
    - - -

    -

    - -

    - - - - - - - -
    -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
    Muscle() - -
    -          Default options are - - -clwstrict - write output in clustal format
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - AlignmentgetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<Muscle>getType() - -
    -           
    - MusclesetInput(String inFile) - -
    -           
    - MusclesetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

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

    -Muscle

    -
    -public Muscle()
    -
    -
    Default options are - - -clwstrict - write output in clustal format -

    -

    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public Muscle setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public Muscle setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Muscle>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Muscle>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Muscle> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Muscle>
    -
    -
    - -
    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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Probcons.html b/website/full_javadoc/compbio/runner/msa/Probcons.html deleted file mode 100644 index 6c60f51..0000000 --- a/website/full_javadoc/compbio/runner/msa/Probcons.html +++ /dev/null @@ -1,416 +0,0 @@ - - - - - - -Probcons - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Probcons

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

    -

    - -

    - - - - - - - -
    -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
    Probcons() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - AlignmentgetResults(String workDirectory) - -
    -           
    - Class<Probcons>getType() - -
    -           
    - ProbconssetInput(String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, 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, 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
    - -

    -Probcons

    -
    -public Probcons()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Probcons>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Probcons>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Probcons>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public Probcons setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Probcons>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Probcons> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Probcons>
    -
    -
    - -
    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
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/Tcoffee.html deleted file mode 100644 index 1a2bfed..0000000 --- a/website/full_javadoc/compbio/runner/msa/Tcoffee.html +++ /dev/null @@ -1,460 +0,0 @@ - - - - - - -Tcoffee - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Tcoffee

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

    -

    - -

    - - - - - - - -
    -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
    Tcoffee() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - CommandBuilder<Tcoffee>getParameters(Executable.ExecProvider provider) - -
    -           
    - AlignmentgetResults(String workDirectory) - -
    -           
    - Class<Tcoffee>getType() - -
    -           
    - TcoffeesetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, 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, getError, getInput, getLimit, getLimits, getOutput, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

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

    -Tcoffee

    -
    -public Tcoffee()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setInput

    -
    -public Tcoffee setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Tcoffee>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Tcoffee>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<Tcoffee> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<Tcoffee>
    Overrides:
    getParameters in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Tcoffee> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Tcoffee>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalO.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalO.html deleted file mode 100644 index bb958c0..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/ClustalO.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.ClustalO - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.runner.msa.ClustalO

    -
    - - - - - - - - - - - - - -
    -Packages that use ClustalO
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ClustalO in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return ClustalO
    - ClustalOClustalO.setInput(String inFile) - -
    -           
    - ClustalOClustalO.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type ClustalO
    - CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<ClustalO>ClustalO.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of ClustalO in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type ClustalO
    - Limit<ClustalO>ClustalOWS.getLimit(String presetName) - -
    -           
    - LimitsManager<ClustalO>ClustalOWS.getLimits() - -
    -           
    - PresetManager<ClustalO>ClustalOWS.getPresets() - -
    -           
    - RunnerConfig<ClustalO>ClustalOWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type ClustalO
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html deleted file mode 100644 index 71ac043..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.ClustalW - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.runner.msa.ClustalW

    -
    - - - - - - - - - - - - - -
    -Packages that use ClustalW
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ClustalW in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return ClustalW
    - ClustalWClustalW.setInput(String inFile) - -
    -           
    - ClustalWClustalW.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type ClustalW
    - Class<ClustalW>ClustalW.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of ClustalW in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type ClustalW
    - Limit<ClustalW>ClustalWS.getLimit(String presetName) - -
    -           
    - LimitsManager<ClustalW>ClustalWS.getLimits() - -
    -           
    - PresetManager<ClustalW>ClustalWS.getPresets() - -
    -           
    - RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type ClustalW
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html deleted file mode 100644 index 75977c5..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Mafft - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Mafft

    -
    - - - - - - - - - - - - - -
    -Packages that use Mafft
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Mafft in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Mafft
    - MafftMafft.addParameters(List<String> parameters) - -
    -          Mafft input must always be the last parameter!
    - MafftMafft.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Mafft
    - Class<Mafft>Mafft.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Mafft in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Mafft
    - Limit<Mafft>MafftWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Mafft>MafftWS.getLimits() - -
    -           
    - PresetManager<Mafft>MafftWS.getPresets() - -
    -           
    - RunnerConfig<Mafft>MafftWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Mafft
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html deleted file mode 100644 index 258cdd1..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Muscle - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Muscle

    -
    - - - - - - - - - - - - - -
    -Packages that use Muscle
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Muscle in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Muscle
    - MuscleMuscle.setInput(String inFile) - -
    -           
    - MuscleMuscle.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Muscle
    - Class<Muscle>Muscle.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Muscle in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Muscle
    - Limit<Muscle>MuscleWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Muscle>MuscleWS.getLimits() - -
    -           
    - PresetManager<Muscle>MuscleWS.getPresets() - -
    -           
    - RunnerConfig<Muscle>MuscleWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Muscle
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html deleted file mode 100644 index 1804852..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Probcons - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Probcons

    -
    - - - - - - - - - - - - - -
    -Packages that use Probcons
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Probcons in compbio.runner.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return Probcons
    - ProbconsProbcons.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Probcons
    - Class<Probcons>Probcons.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Probcons in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Probcons
    - Limit<Probcons>ProbconsWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Probcons>ProbconsWS.getLimits() - -
    -           
    - PresetManager<Probcons>ProbconsWS.getPresets() - -
    -           
    - RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Probcons
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html deleted file mode 100644 index 2d533c7..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Tcoffee - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Tcoffee

    -
    - - - - - - - - - - - - - -
    -Packages that use Tcoffee
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Tcoffee in compbio.runner.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return Tcoffee
    - TcoffeeTcoffee.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Tcoffee
    - CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<Tcoffee>Tcoffee.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Tcoffee in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Tcoffee
    - Limit<Tcoffee>TcoffeeWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Tcoffee>TcoffeeWS.getLimits() - -
    -           
    - PresetManager<Tcoffee>TcoffeeWS.getPresets() - -
    -           
    - RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Tcoffee
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    -  -

    -

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    -Package compbio.runner.msa -

    -Wrappers for native executables for multiple sequence alignment (msa) -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ClustalO 
    ClustalW 
    Mafft 
    Muscle 
    Probcons 
    Tcoffee 
    -  - -

    -

    -Package compbio.runner.msa Description -

    - -

    -Wrappers for native executables for multiple sequence alignment (msa) -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
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    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.msa used by compbio.runner.msa
    ClustalO - -
    -           
    ClustalW - -
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    Mafft - -
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    Muscle - -
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    Probcons - -
    -           
    Tcoffee - -
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    -  -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.msa used by compbio.ws.server
    ClustalO - -
    -           
    ClustalW - -
    -           
    Mafft - -
    -           
    Muscle - -
    -           
    Probcons - -
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    -Classes  - -
    -_NativeSpecHelper -
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    - - - - diff --git a/website/full_javadoc/compbio/runner/package-summary.html b/website/full_javadoc/compbio/runner/package-summary.html deleted file mode 100644 index 60deb34..0000000 --- a/website/full_javadoc/compbio/runner/package-summary.html +++ /dev/null @@ -1,188 +0,0 @@ - - - - - - -compbio.runner - - - - - - - - - - - - -
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    -Package compbio.runner -

    -Utilities commonly used by all runners. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    _NativeSpecHelperDeprecated.
    _SkeletalCommandBuilderDeprecated.
    OptionCombinatorThis class solve the following problems.
    Util 
    -  - -

    -

    -Package compbio.runner Description -

    - -

    -Utilities commonly used by all runners. -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
    -
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    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    -  -

    - - - - - - - - -
    -Classes in compbio.runner used by compbio.runner
    _SkeletalCommandBuilder - -
    -          Deprecated. 
    -  -

    - - - - - - - - -
    -Classes in compbio.runner used by compbio.runner._impl
    _SkeletalCommandBuilder - -
    -          Deprecated. 
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    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.stat.collector -
    -Class ExecutionStatCollector

    -
    -java.lang.Object
-  extended by compbio.stat.collector.ExecutionStatCollector
-
    -
    -
    All Implemented Interfaces:
    Runnable
    -
    -
    -
    -
    public class ExecutionStatCollector
    extends Object
    implements Runnable
    - - -

    -Number of runs of each WS = number of folders with name - - Number of successful runs = all runs with no result file - - Per period of time = limit per file creating time Runtime (avg/max) = - - started time - finished time - - Task & result size = result.size - - Abandoned runs - not collected runs - - Cancelled runs - cancelled - - Cluster vs local runs - - Reasons for failure = look in the err out? - - - Metadata required: - - work directory for local and cluster tasks = from Helper or cmd parameter. WS - names - enumeration. Status file names and content. -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ExecutionStatCollector(String workDirectory, - int timeOutInHours) - -
    -          List subdirectories in the job directory
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          Not in use
    - voidrun() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ExecutionStatCollector

    -
    -public ExecutionStatCollector(String workDirectory,
-                              int timeOutInHours)
    -
    -
    List subdirectories in the job directory -

    -

    -
    Parameters:
    workDirectory -
    timeOutInHours -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
-                 throws IOException,
-                        SQLException
    -
    -
    Not in use -

    -

    -
    -
    -
    - -
    Throws: -
    IOException -
    SQLException
    -
    -
    -
    - -

    -run

    -
    -public void run()
    -
    -
    -
    Specified by:
    run in interface Runnable
    -
    -
    -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/stat/collector/JobStat.html b/website/full_javadoc/compbio/stat/collector/JobStat.html deleted file mode 100644 index 6704ad2..0000000 --- a/website/full_javadoc/compbio/stat/collector/JobStat.html +++ /dev/null @@ -1,551 +0,0 @@ - - - - - - -JobStat - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.collector -
    -Class JobStat

    -
    -java.lang.Object
-  extended by compbio.stat.collector.JobStat
-
    -
    -
    -
    public class JobStat
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - StringgetClusterJobId() - -
    -           
    - StringgetEscJobname() - -
    -           
    - StringgetFinish() - -
    -           
    - longgetInputSize() - -
    -           
    - booleangetIsCancelled() - -
    -           
    - booleangetIsCollected() - -
    -           
    - booleangetIsFinished() - -
    -           
    - StringgetJobname() - -
    -           
    - longgetResultSize() - -
    -           
    - intgetRuntime() - -
    -           
    - StringgetStart() - -
    -           
    - ServicesgetWebService() - -
    -           
    - inthashCode() - -
    -           
    - booleanhasResult() - -
    -           
    - booleanhasStarted() - -
    -           
    - booleanisClusterJob() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -isClusterJob

    -
    -public boolean isClusterJob()
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getRuntime

    -
    -public int getRuntime()
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getWebService

    -
    -public Services getWebService()
    -
    -
    -
    -
    -
    -
    - -

    -getClusterJobId

    -
    -public String getClusterJobId()
    -
    -
    -
    -
    -
    -
    - -

    -getJobname

    -
    -public String getJobname()
    -
    -
    -
    -
    -
    -
    - -

    -getEscJobname

    -
    -public String getEscJobname()
    -
    -
    -
    -
    -
    -
    - -

    -getStart

    -
    -public String getStart()
    -
    -
    -
    -
    -
    -
    - -

    -getFinish

    -
    -public String getFinish()
    -
    -
    -
    -
    -
    -
    - -

    -getInputSize

    -
    -public long getInputSize()
    -
    -
    -
    -
    -
    -
    - -

    -getResultSize

    -
    -public long getResultSize()
    -
    -
    -
    -
    -
    -
    - -

    -hasResult

    -
    -public boolean hasResult()
    -
    -
    -
    -
    -
    -
    - -

    -hasStarted

    -
    -public boolean hasStarted()
    -
    -
    -
    -
    -
    -
    - -

    -getIsCollected

    -
    -public boolean getIsCollected()
    -
    -
    -
    -
    -
    -
    - -

    -getIsCancelled

    -
    -public boolean getIsCancelled()
    -
    -
    -
    -
    -
    -
    - -

    -getIsFinished

    -
    -public boolean getIsFinished()
    -
    -
    -
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/collector/StatDB.html b/website/full_javadoc/compbio/stat/collector/StatDB.html deleted file mode 100644 index d2d4425..0000000 --- a/website/full_javadoc/compbio/stat/collector/StatDB.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -StatDB - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.stat.collector -
    -Class StatDB

    -
    -java.lang.Object
-  extended by compbio.stat.collector.StatDB
-
    -
    -
    -
    public class StatDB
    extends Object
    - - -

    -The database must be stored in the application root directory and called - "ExecutionStatistic" -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatDB() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetAbandonedCount(Timestamp from, - Timestamp to) - -
    -           
    - intgetCancelledCount(Timestamp from, - Timestamp to) - -
    -           
    - DategetEarliestRecord() - -
    -           
    - intgetIncompleteCount(Timestamp from, - Timestamp to) - -
    -           
    - intgetTotalJobsCount(Timestamp from, - Timestamp to) - -
    -           
    -static voidmain(String[] args) - -
    -           
    - List<JobStat>readData(Timestamp from, - Timestamp to, - Services wservice, - Boolean clusterOnly) - -
    -           
    - voidremoveRecordedJobs(Set<JobStat> fsJobs) - -
    -          Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs.
    -static voidshutdownDBServer() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatDB

    -
    -public StatDB()
-       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getEarliestRecord

    -
    -public Date getEarliestRecord()
-                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getTotalJobsCount

    -
    -public int getTotalJobsCount(Timestamp from,
-                             Timestamp to)
-                      throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getCancelledCount

    -
    -public int getCancelledCount(Timestamp from,
-                             Timestamp to)
-                      throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getAbandonedCount

    -
    -public int getAbandonedCount(Timestamp from,
-                             Timestamp to)
-                      throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getIncompleteCount

    -
    -public int getIncompleteCount(Timestamp from,
-                              Timestamp to)
-                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -readData

    -
    -public List<JobStat> readData(Timestamp from,
-                              Timestamp to,
-                              Services wservice,
-                              Boolean clusterOnly)
-                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -removeRecordedJobs

    -
    -public void removeRecordedJobs(Set<JobStat> fsJobs)
-                        throws SQLException
    -
    -
    Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs. -

    -

    -
    Parameters:
    fsJobs - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -shutdownDBServer

    -
    -public static final void shutdownDBServer()
    -
    -
    -
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/collector/StatProcessor.html b/website/full_javadoc/compbio/stat/collector/StatProcessor.html deleted file mode 100644 index d389b92..0000000 --- a/website/full_javadoc/compbio/stat/collector/StatProcessor.html +++ /dev/null @@ -1,527 +0,0 @@ - - - - - - -StatProcessor - - - - - - - - - - - - -
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    - -compbio.stat.collector -
    -Class StatProcessor

    -
    -java.lang.Object
-  extended by compbio.stat.collector.StatProcessor
-
    -
    -
    -
    public class StatProcessor
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatProcessor(List<JobStat> stats) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<JobStat>getAbandonedJobs() - -
    -          Not collected.
    - List<JobStat>getCancelledJobs() - -
    -           
    - List<JobStat>getClusterJobs() - -
    -           
    - List<JobStat>getFailedJobs() - -
    -          Started & finished but did not produce result
    - List<JobStat>getIncompleteJobs() - -
    -           
    - intgetJobNumber() - -
    -           
    - List<JobStat>getJobs() - -
    -           
    - List<JobStat>getLocalJobs() - -
    -           
    - StatProcessorgetSingleWSStat(Services webService) - -
    -           
    - longgetTotalRuntime() - -
    -           
    - StringreportStat() - -
    -           
    - List<JobStat>sortByResultSize() - -
    -           
    - List<JobStat>sortByRuntime() - -
    -           
    - List<JobStat>sortByStartTime() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatProcessor

    -
    -public StatProcessor(List<JobStat> stats)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getClusterJobs

    -
    -public List<JobStat> getClusterJobs()
    -
    -
    -
    -
    -
    -
    - -

    -getLocalJobs

    -
    -public List<JobStat> getLocalJobs()
    -
    -
    -
    -
    -
    -
    - -

    -getAbandonedJobs

    -
    -public List<JobStat> getAbandonedJobs()
    -
    -
    Not collected. Excludes all cancelled jobs, and jobs with no results as - these are reported separately. -

    -

    -
    -
    -
    -
    - -

    -getFailedJobs

    -
    -public List<JobStat> getFailedJobs()
    -
    -
    Started & finished but did not produce result -

    -

    - -
    Returns:
    -
    -
    -
    - -

    -getCancelledJobs

    -
    -public List<JobStat> getCancelledJobs()
    -
    -
    -
    -
    -
    -
    - -

    -sortByRuntime

    -
    -public List<JobStat> sortByRuntime()
    -
    -
    -
    -
    -
    -
    - -

    -sortByStartTime

    -
    -public List<JobStat> sortByStartTime()
    -
    -
    -
    -
    -
    -
    - -

    -sortByResultSize

    -
    -public List<JobStat> sortByResultSize()
    -
    -
    -
    -
    -
    -
    - -

    -getJobNumber

    -
    -public int getJobNumber()
    -
    -
    -
    -
    -
    -
    - -

    -getJobs

    -
    -public List<JobStat> getJobs()
    -
    -
    -
    -
    -
    -
    - -

    -getSingleWSStat

    -
    -public StatProcessor getSingleWSStat(Services webService)
    -
    -
    -
    -
    -
    -
    - -

    -getTotalRuntime

    -
    -public long getTotalRuntime()
    -
    -
    -
    -
    -
    -
    - -

    -getIncompleteJobs

    -
    -public List<JobStat> getIncompleteJobs()
    -
    -
    -
    -
    -
    -
    - -

    -reportStat

    -
    -public String reportStat()
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
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    -Packages that use JobStat
    compbio.stat.collector  
    -  -

    - - - - - -
    -Uses of JobStat in compbio.stat.collector
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.stat.collector that return types with arguments of type JobStat
    - List<JobStat>StatProcessor.getAbandonedJobs() - -
    -          Not collected.
    - List<JobStat>StatProcessor.getCancelledJobs() - -
    -           
    - List<JobStat>StatProcessor.getClusterJobs() - -
    -           
    - List<JobStat>StatProcessor.getFailedJobs() - -
    -          Started & finished but did not produce result
    - List<JobStat>StatProcessor.getIncompleteJobs() - -
    -           
    - List<JobStat>StatProcessor.getJobs() - -
    -           
    - List<JobStat>StatProcessor.getLocalJobs() - -
    -           
    - List<JobStat>StatDB.readData(Timestamp from, - Timestamp to, - Services wservice, - Boolean clusterOnly) - -
    -           
    - List<JobStat>StatProcessor.sortByResultSize() - -
    -           
    - List<JobStat>StatProcessor.sortByRuntime() - -
    -           
    - List<JobStat>StatProcessor.sortByStartTime() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.collector with type arguments of type JobStat
    - voidStatDB.removeRecordedJobs(Set<JobStat> fsJobs) - -
    -          Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs.
    -  -

    - - - - - - - - -
    Constructor parameters in compbio.stat.collector with type arguments of type JobStat
    StatProcessor(List<JobStat> stats) - -
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    -Packages that use StatProcessor
    compbio.stat.collector  
    compbio.stat.servlet.util  
    -  -

    - - - - - -
    -Uses of StatProcessor in compbio.stat.collector
    -  -

    - - - - - - - - - -
    Methods in compbio.stat.collector that return StatProcessor
    - StatProcessorStatProcessor.getSingleWSStat(Services webService) - -
    -           
    -  -

    - - - - - -
    -Uses of StatProcessor in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return types with arguments of type StatProcessor
    - Map<Services,StatProcessor>StatCollection.getAllStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getClusterStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getLocalStat() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.servlet.util with type arguments of type StatProcessor
    -static TotalsTotals.sumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  -

    -

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    -Classes  - -
    -ExecutionStatCollector -
    -JobStat -
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    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ExecutionStatCollectorNumber of runs of each WS = number of folders with name - - Number of successful runs = all runs with no result file - - Per period of time = limit per file creating time Runtime (avg/max) = - - started time - finished time - - Task & result size = result.size - - Abandoned runs - not collected runs - - Cancelled runs - cancelled - - Cluster vs local runs - - Reasons for failure = look in the err out? - - - Metadata required: - - work directory for local and cluster tasks = from Helper or cmd parameter.
    JobStat 
    StatDBThe database must be stored in the application root directory and called - "ExecutionStatistic"
    StatProcessor 
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    compbio.stat.collector  
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    - - - - - - - - - - - -
    -Classes in compbio.stat.collector used by compbio.stat.collector
    JobStat - -
    -           
    StatProcessor - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.stat.collector used by compbio.stat.servlet.util
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    - -compbio.stat.servlet -
    -Class AnnualStat

    -
    -java.lang.Object
-  extended by javax.servlet.GenericServlet
-      extended by javax.servlet.http.HttpServlet
-          extended by compbio.stat.servlet.AnnualStat
-
    -
    -
    All Implemented Interfaces:
    Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
    -
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    -
    -
    public class AnnualStat
    extends javax.servlet.http.HttpServlet
    - - -

    -

    -
    See Also:
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    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    AnnualStat() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class javax.servlet.http.HttpServlet
    service
    -  - - - - - - - -
    Methods inherited from class javax.servlet.GenericServlet
    destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AnnualStat

    -
    -public AnnualStat()
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/DisplayStat.html b/website/full_javadoc/compbio/stat/servlet/DisplayStat.html deleted file mode 100644 index ca7f106..0000000 --- a/website/full_javadoc/compbio/stat/servlet/DisplayStat.html +++ /dev/null @@ -1,249 +0,0 @@ - - - - - - -DisplayStat - - - - - - - - - - - - -
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    - -compbio.stat.servlet -
    -Class DisplayStat

    -
    -java.lang.Object
-  extended by javax.servlet.GenericServlet
-      extended by javax.servlet.http.HttpServlet
-          extended by compbio.stat.servlet.DisplayStat
-
    -
    -
    All Implemented Interfaces:
    Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
    -
    -
    -
    -
    public class DisplayStat
    extends javax.servlet.http.HttpServlet
    - - -

    -

    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    DisplayStat() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class javax.servlet.http.HttpServlet
    service
    -  - - - - - - - -
    Methods inherited from class javax.servlet.GenericServlet
    destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -DisplayStat

    -
    -public DisplayStat()
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    -Class Joblist

    -
    -java.lang.Object
-  extended by javax.servlet.GenericServlet
-      extended by javax.servlet.http.HttpServlet
-          extended by compbio.stat.servlet.Joblist
-
    -
    -
    All Implemented Interfaces:
    Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
    -
    -
    -
    -
    public class Joblist
    extends javax.servlet.http.HttpServlet
    - - -

    -

    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Joblist() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class javax.servlet.http.HttpServlet
    service
    -  - - - - - - - -
    Methods inherited from class javax.servlet.GenericServlet
    destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Joblist

    -
    -public Joblist()
    -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/StatisticCollector.html b/website/full_javadoc/compbio/stat/servlet/StatisticCollector.html deleted file mode 100644 index 9be9ef7..0000000 --- a/website/full_javadoc/compbio/stat/servlet/StatisticCollector.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -StatisticCollector - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.servlet -
    -Class StatisticCollector

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.StatisticCollector
-
    -
    -
    All Implemented Interfaces:
    EventListener, javax.servlet.ServletContextListener
    -
    -
    -
    -
    public class StatisticCollector
    extends Object
    implements javax.servlet.ServletContextListener
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatisticCollector() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - voidcontextDestroyed(javax.servlet.ServletContextEvent arg0) - -
    -           
    - voidcontextInitialized(javax.servlet.ServletContextEvent arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatisticCollector

    -
    -public StatisticCollector()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -contextDestroyed

    -
    -public void contextDestroyed(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextDestroyed in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
    -
    -
    - -

    -contextInitialized

    -
    -public void contextInitialized(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextInitialized in interface javax.servlet.ServletContextListener
    -
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    -Uses of Class
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    -
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    -

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    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -Uses of Class
    compbio.stat.servlet.StatisticCollector

    -
    -No usage of compbio.stat.servlet.StatisticCollector -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -AnnualStat -
    -DisplayStat -
    -Joblist -
    -StatisticCollector
    - - - - diff --git a/website/full_javadoc/compbio/stat/servlet/package-summary.html b/website/full_javadoc/compbio/stat/servlet/package-summary.html deleted file mode 100644 index 924a038..0000000 --- a/website/full_javadoc/compbio/stat/servlet/package-summary.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - - - -compbio.stat.servlet - - - - - - - - - - - - -
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    -

    -Package compbio.stat.servlet -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AnnualStat 
    DisplayStat 
    Joblist 
    StatisticCollector 
    -  - -

    -

    -
    -
    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/package-tree.html b/website/full_javadoc/compbio/stat/servlet/package-tree.html deleted file mode 100644 index f13ddc6..0000000 --- a/website/full_javadoc/compbio/stat/servlet/package-tree.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - - - -compbio.stat.servlet Class Hierarchy - - - - - - - - - - - - -
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    -

    -Hierarchy For Package compbio.stat.servlet -

    -
    -
    -
    Package Hierarchies:
    All Packages
    -
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    -Class Hierarchy -

    - -
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    -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/util/StatCollection.Stattype.html b/website/full_javadoc/compbio/stat/servlet/util/StatCollection.Stattype.html deleted file mode 100644 index 8194c9c..0000000 --- a/website/full_javadoc/compbio/stat/servlet/util/StatCollection.Stattype.html +++ /dev/null @@ -1,351 +0,0 @@ - - - - - - -StatCollection.Stattype - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.servlet.util -
    -Enum StatCollection.Stattype

    -
    -java.lang.Object
-  extended by java.lang.Enum<StatCollection.Stattype>
-      extended by compbio.stat.servlet.util.StatCollection.Stattype
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<StatCollection.Stattype>
    -
    -
    -
    Enclosing class:
    StatCollection
    -
    -
    -
    -
    public static enum StatCollection.Stattype
    extends Enum<StatCollection.Stattype>
    - - -

    -Total number of requests - - incomplete abandoned cancelled -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    ALL - -
    -           
    CLUSTER - -
    -           
    LOCAL - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static StatCollection.StattypevalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static StatCollection.Stattype[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -CLUSTER

    -
    -public static final StatCollection.Stattype CLUSTER
    -
    -
    -
    -
    -
    - -

    -LOCAL

    -
    -public static final StatCollection.Stattype LOCAL
    -
    -
    -
    -
    -
    - -

    -ALL

    -
    -public static final StatCollection.Stattype ALL
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static StatCollection.Stattype[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (StatCollection.Stattype c : StatCollection.Stattype.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static StatCollection.Stattype valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/util/StatCollection.html b/website/full_javadoc/compbio/stat/servlet/util/StatCollection.html deleted file mode 100644 index fc5d84e..0000000 --- a/website/full_javadoc/compbio/stat/servlet/util/StatCollection.html +++ /dev/null @@ -1,443 +0,0 @@ - - - - - - -StatCollection - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.servlet.util -
    -Class StatCollection

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.util.StatCollection
-
    -
    -
    -
    public class StatCollection
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classStatCollection.Stattype - -
    -          Total number of requests - - incomplete abandoned cancelled
    -  - - - - - - - - - - -
    -Constructor Summary
    StatCollection() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - Map<Services,StatProcessor>getAllStat() - -
    -           
    - Map<Services,StatProcessor>getClusterStat() - -
    -           
    - Map<Services,StatProcessor>getLocalStat() - -
    -           
    -static Map<Date,Totals>getStats(Date fromDate) - -
    -           
    -static Map<Date,Totals>getStats(int monthsToReport) - -
    -           
    - inthashCode() - -
    -           
    -static StatCollectionnewStatCollecton(Date startDate, - Date endDate) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatCollection

    -
    -public StatCollection()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getAllStat

    -
    -public Map<Services,StatProcessor> getAllStat()
    -
    -
    -
    -
    -
    -
    - -

    -getClusterStat

    -
    -public Map<Services,StatProcessor> getClusterStat()
    -
    -
    -
    -
    -
    -
    - -

    -getLocalStat

    -
    -public Map<Services,StatProcessor> getLocalStat()
    -
    -
    -
    -
    -
    -
    - -

    -getStats

    -
    -public static Map<Date,Totals> getStats(int monthsToReport)
-                                 throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getStats

    -
    -public static Map<Date,Totals> getStats(Date fromDate)
-                                 throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -newStatCollecton

    -
    -public static StatCollection newStatCollecton(Date startDate,
-                                              Date endDate)
-                                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/util/Totals.html b/website/full_javadoc/compbio/stat/servlet/util/Totals.html deleted file mode 100644 index ce5953f..0000000 --- a/website/full_javadoc/compbio/stat/servlet/util/Totals.html +++ /dev/null @@ -1,366 +0,0 @@ - - - - - - -Totals - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.servlet.util -
    -Class Totals

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.util.Totals
-
    -
    -
    -
    public class Totals
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Totals() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetAbandoned() - -
    -           
    - intgetCancelled() - -
    -           
    - intgetFailed() - -
    -           
    - intgetIncomplete() - -
    -           
    - intgetTotal() - -
    -           
    -static TotalssumOfTotals(Map<Date,Totals> stat) - -
    -           
    -static TotalssumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Totals

    -
    -public Totals()
    -
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    -Method Detail
    - -

    -getTotal

    -
    -public int getTotal()
    -
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    -
    - -

    -getIncomplete

    -
    -public int getIncomplete()
    -
    -
    -
    -
    -
    -
    - -

    -getAbandoned

    -
    -public int getAbandoned()
    -
    -
    -
    -
    -
    -
    - -

    -getCancelled

    -
    -public int getCancelled()
    -
    -
    -
    -
    -
    -
    - -

    -getFailed

    -
    -public int getFailed()
    -
    -
    -
    -
    -
    -
    - -

    -sumOfTotals

    -
    -public static Totals sumOfTotals(Map<Date,Totals> stat)
    -
    -
    -
    -
    -
    -
    - -

    -sumStats

    -
    -public static Totals sumStats(Map<Services,StatProcessor> stat)
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    -Packages that use StatCollection.Stattype
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    -  -

    - - - - - -
    -Uses of StatCollection.Stattype in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return StatCollection.Stattype
    -static StatCollection.StattypeStatCollection.Stattype.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static StatCollection.Stattype[]StatCollection.Stattype.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
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    compbio.stat.servlet.util  
    -  -

    - - - - - -
    -Uses of StatCollection in compbio.stat.servlet.util
    -  -

    - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return StatCollection
    -static StatCollectionStatCollection.newStatCollecton(Date startDate, - Date endDate) - -
    -           
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    -

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    -Packages that use Totals
    compbio.stat.servlet.util  
    -  -

    - - - - - -
    -Uses of Totals in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return Totals
    -static TotalsTotals.sumOfTotals(Map<Date,Totals> stat) - -
    -           
    -static TotalsTotals.sumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return types with arguments of type Totals
    -static Map<Date,Totals>StatCollection.getStats(Date fromDate) - -
    -           
    -static Map<Date,Totals>StatCollection.getStats(int monthsToReport) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.servlet.util with type arguments of type Totals
    -static TotalsTotals.sumOfTotals(Map<Date,Totals> stat) - -
    -           
    -  -

    -

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    -Classes  - -
    -StatCollection -
    -Totals
    - - - - - - -
    -Enums  - -
    -StatCollection.Stattype
    - - - - diff --git a/website/full_javadoc/compbio/stat/servlet/util/package-summary.html b/website/full_javadoc/compbio/stat/servlet/util/package-summary.html deleted file mode 100644 index 7a8ea22..0000000 --- a/website/full_javadoc/compbio/stat/servlet/util/package-summary.html +++ /dev/null @@ -1,177 +0,0 @@ - - - - - - -compbio.stat.servlet.util - - - - - - - - - - - - -
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    -Package compbio.stat.servlet.util -

    - - - - - - - - - - - - - -
    -Class Summary
    StatCollection 
    Totals 
    -  - -

    - - - - - - - - - -
    -Enum Summary
    StatCollection.StattypeTotal number of requests - - incomplete abandoned cancelled
    -  - -

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    -Packages that use compbio.stat.servlet.util
    compbio.stat.servlet.util  
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.stat.servlet.util used by compbio.stat.servlet.util
    StatCollection - -
    -           
    StatCollection.Stattype - -
    -          Total number of requests - - incomplete abandoned cancelled
    Totals - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/AAConClient.html b/website/full_javadoc/compbio/ws/client/AAConClient.html deleted file mode 100644 index 7d5bce0..0000000 --- a/website/full_javadoc/compbio/ws/client/AAConClient.html +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - -AAConClient - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class AAConClient

    -
    -java.lang.Object
-  extended by compbio.ws.client.AAConClient
-
    -
    -
    -
    public class AAConClient
    extends Object
    - - -

    -A command line client for AACon web service -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - -
    -Method Summary
    -static SequenceAnnotation<AAConWS>connect() - -
    -          Connects to a AACon web service by the host and the service name
    -static voidmain(String[] args) - -
    -          Starts command line client, if no parameters are supplied prints help.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -connect

    -
    -public static SequenceAnnotation<AAConWS> connect()
-                                           throws WebServiceException
    -
    -
    Connects to a AACon web service by the host and the service name -

    -

    - -
    Returns:
    AlignmentAnnotation -
    Throws: -
    WebServiceException - if cannot connect to a web service
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Starts command line client, if no parameters are supplied prints help. -

    -

    -
    Parameters:
    args - Usage: ACTION [OPTIONS] - - -i= - full path to fasta or Clustal formatted - alignment file - - -parameters - lists parameters supported by web service - - -presets - lists presets supported by web service - - -limits - lists web services limits. Please note that if input - file is specified other actions are ignored - - OPTIONS: (only for use with -i action): - - -r= - name of the preset to use - - -o= - full path to the file where to write results - -f= - the name of the file with the list - of parameters to use. Please note that -r and -f options - cannot be used together. Conservation is calculated with - either a preset or parameters from the file, but not both!
    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/IOHelper.html b/website/full_javadoc/compbio/ws/client/IOHelper.html deleted file mode 100644 index be3f785..0000000 --- a/website/full_javadoc/compbio/ws/client/IOHelper.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -IOHelper - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class IOHelper

    -
    -java.lang.Object
-  extended by compbio.ws.client.IOHelper
-
    -
    -
    -
    public class IOHelper
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    IOHelper() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IOHelper

    -
    -public IOHelper()
    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.html b/website/full_javadoc/compbio/ws/client/Jws2Client.html deleted file mode 100644 index 97556c6..0000000 --- a/website/full_javadoc/compbio/ws/client/Jws2Client.html +++ /dev/null @@ -1,399 +0,0 @@ - - - - - - -Jws2Client - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class Jws2Client

    -
    -java.lang.Object
-  extended by compbio.ws.client.Jws2Client
-
    -
    -
    -
    public class Jws2Client
    extends Object
    - - -

    -A command line client for JAva Bioinformatics Analysis Web Services -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static JABAServiceconnect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -static RegistryWSconnectToRegistry(String host) - -
    -          Get a connection of JABAWS registry
    -static Set<Services>getServices(String hostname) - -
    -           
    -static voidmain(String[] args) - -
    -          Starts command line client, if no parameter are supported print help.
    -static voidtestService(String hostname, - Services service, - PrintWriter writer) - -
    -          Asks registry to test the service on the host hostname
    -static booleanvalidURL(String urlstr) - -
    -          Attempt to construct the URL object from the string
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -validURL

    -
    -public static boolean validURL(String urlstr)
    -
    -
    Attempt to construct the URL object from the string -

    -

    -
    Parameters:
    urlstr - -
    Returns:
    true if it succeed false otherwise
    -
    -
    -
    - -

    -testService

    -
    -public static void testService(String hostname,
-                               Services service,
-                               PrintWriter writer)
-                        throws ConnectException,
-                               WebServiceException
    -
    -
    Asks registry to test the service on the host hostname -

    -

    -
    Parameters:
    hostname -
    service -
    writer - -
    Throws: -
    ConnectException -
    WebServiceException
    -
    -
    -
    - -

    -getServices

    -
    -public static Set<Services> getServices(String hostname)
-                                 throws WebServiceException,
-                                        ConnectException
    -
    -
    - -
    Throws: -
    WebServiceException -
    ConnectException
    -
    -
    -
    - -

    -connect

    -
    -public static JABAService connect(String host,
-                                  Services service)
-                           throws WebServiceException,
-                                  ConnectException
    -
    -
    Connects to a web service by the host and the service name web service - type -

    -

    -
    Parameters:
    host - the fully qualified name of JABAWS server including JABAWS - context name e.g - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
    service - the name of the JABAWS service to connect to -
    Returns:
    JABAService -
    Throws: -
    WebServiceException -
    ConnectException - if fails to connect to the service on the host
    -
    -
    -
    - -

    -connectToRegistry

    -
    -public static RegistryWS connectToRegistry(String host)
-                                    throws WebServiceException,
-                                           ConnectException
    -
    -
    Get a connection of JABAWS registry -

    -

    -
    Parameters:
    host - the fully qualified name of JABAWS server including JABAWS - context name e.g - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba -
    Returns:
    compbio.data.msa.RegistryWS - instance of a RegistryWS web - service -
    Throws: -
    WebServiceException -
    ConnectException
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Starts command line client, if no parameter are supported print help. Two - parameters are required for successful call the JWS2 host name and a - service name. -

    -

    -
    Parameters:
    args - Usage: -h=host_and_context - -s=serviceName ACTION [OPTIONS] - - -h= - a full URL to the JWS2 web server - including context path e.g. http://10.31.1.159:8080/ws - - -s= - one of [MafftWS, MuscleWS, ClustalWS, - TcoffeeWS, ProbconsWS] ACTIONS: - - -i= - full path to fasta formatted sequence file, - from which to align sequences - - -parameters - lists parameters supported by web service - - -presets - lists presets supported by web service - - -limits - lists web services limits Please note that if input - file is specified other actions are ignored - - OPTIONS: (only for use with -i action): - - -r= - name of the preset to use - - -o= - full path to the file where to write an - alignment -f= - the name of the file with - the list of parameters to use. Please note that -r and -f - options cannot be used together. Alignment is done with either - preset or a parameters from the file, but not both!
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/MetadataHelper.html b/website/full_javadoc/compbio/ws/client/MetadataHelper.html deleted file mode 100644 index 206caf5..0000000 --- a/website/full_javadoc/compbio/ws/client/MetadataHelper.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -MetadataHelper - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class MetadataHelper

    -
    -java.lang.Object
-  extended by compbio.ws.client.MetadataHelper
-
    -
    -
    -
    public class MetadataHelper
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    MetadataHelper() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MetadataHelper

    -
    -public MetadataHelper()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/Services.html b/website/full_javadoc/compbio/ws/client/Services.html deleted file mode 100644 index 884fd28..0000000 --- a/website/full_javadoc/compbio/ws/client/Services.html +++ /dev/null @@ -1,508 +0,0 @@ - - - - - - -Services - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Enum Services

    -
    -java.lang.Object
-  extended by java.lang.Enum<Services>
-      extended by compbio.ws.client.Services
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<Services>
    -
    -
    -
    -
    public enum Services
    extends Enum<Services>
    - - -

    -List of web services currently supported by JABAWS version 2 -

    - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    AAConWS - -
    -           
    ClustalOWS - -
    -           
    ClustalWS - -
    -           
    DisemblWS - -
    -           
    GlobPlotWS - -
    -           
    IUPredWS - -
    -           
    JronnWS - -
    -           
    MafftWS - -
    -           
    MuscleWS - -
    -           
    ProbconsWS - -
    -           
    TcoffeeWS - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static ServicesgetService(String servName) - -
    -           
    -static StringtoString(Set<Services> services) - -
    -           
    -static ServicesvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Services[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -MafftWS

    -
    -public static final Services MafftWS
    -
    -
    -
    -
    -
    - -

    -MuscleWS

    -
    -public static final Services MuscleWS
    -
    -
    -
    -
    -
    - -

    -ClustalWS

    -
    -public static final Services ClustalWS
    -
    -
    -
    -
    -
    - -

    -ClustalOWS

    -
    -public static final Services ClustalOWS
    -
    -
    -
    -
    -
    - -

    -TcoffeeWS

    -
    -public static final Services TcoffeeWS
    -
    -
    -
    -
    -
    - -

    -ProbconsWS

    -
    -public static final Services ProbconsWS
    -
    -
    -
    -
    -
    - -

    -AAConWS

    -
    -public static final Services AAConWS
    -
    -
    -
    -
    -
    - -

    -JronnWS

    -
    -public static final Services JronnWS
    -
    -
    -
    -
    -
    - -

    -DisemblWS

    -
    -public static final Services DisemblWS
    -
    -
    -
    -
    -
    - -

    -GlobPlotWS

    -
    -public static final Services GlobPlotWS
    -
    -
    -
    -
    -
    - -

    -IUPredWS

    -
    -public static final Services IUPredWS
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static Services[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (Services c : Services.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static Services valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    -
    - -

    -getService

    -
    -public static Services getService(String servName)
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public static String toString(Set<Services> services)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/ServicesUtil.html b/website/full_javadoc/compbio/ws/client/ServicesUtil.html deleted file mode 100644 index 12ad89d..0000000 --- a/website/full_javadoc/compbio/ws/client/ServicesUtil.html +++ /dev/null @@ -1,309 +0,0 @@ - - - - - - -ServicesUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class ServicesUtil

    -
    -java.lang.Object
-  extended by compbio.ws.client.ServicesUtil
-
    -
    -
    -
    public class ServicesUtil
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ServicesUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static Class<? extends Executable<?>>getRunnerByJobDirectory(File jobdir) - -
    -           
    -static ServicesgetServiceByJobDirectory(File jobdir) - -
    -           
    -static ServicesgetServiceByRunner(Class<Executable<?>> runnerClassName) - -
    -           
    -static Class<? extends Executable<?>>getServiceImpl(Services service) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ServicesUtil

    -
    -public ServicesUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getServiceByRunner

    -
    -public static Services getServiceByRunner(Class<Executable<?>> runnerClassName)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceImpl

    -
    -public static Class<? extends Executable<?>> getServiceImpl(Services service)
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerByJobDirectory

    -
    -public static Class<? extends Executable<?>> getRunnerByJobDirectory(File jobdir)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceByJobDirectory

    -
    -public static Services getServiceByJobDirectory(File jobdir)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/WSTester.html b/website/full_javadoc/compbio/ws/client/WSTester.html deleted file mode 100644 index 72bca28..0000000 --- a/website/full_javadoc/compbio/ws/client/WSTester.html +++ /dev/null @@ -1,312 +0,0 @@ - - - - - - -WSTester - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class WSTester

    -
    -java.lang.Object
-  extended by compbio.ws.client.WSTester
-
    -
    -
    -
    public class WSTester
    extends Object
    - - -

    -Class for testing web services -

    - -

    -

    -
    Version:
    -
    1.0 February 2010
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    WSTester(String hostname, - PrintWriter writer) - -
    -          Construct an instance of JABAWS tester
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancheckService(Services service) - -
    -          Test JABA web service
    -static - - - - -
    -<T> void
    -    		main(String[] args) - -
    -          Test JWS2 web services
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -WSTester

    -
    -public WSTester(String hostname,
-                PrintWriter writer)
    -
    -
    Construct an instance of JABAWS tester -

    -

    -
    Parameters:
    hostname - - fully qualified host and context name of JABAWS e.g. - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
    writer - a PrintWriter instance to writer test log to.
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static <T> void main(String[] args)
-                 throws IOException
    -
    -
    Test JWS2 web services -

    -

    -
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= - - -s= which is optional. If service name is not - provided then all known JWS2 web services are tested -
    Throws: -
    IOException
    -
    -
    -
    - -

    -checkService

    -
    -public boolean checkService(Services service)
-                     throws ConnectException,
-                            WebServiceException
    -
    -
    Test JABA web service -

    -

    -
    Parameters:
    service - the service to test -
    Returns:
    true if the service works as expected, false otherwise -
    Throws: -
    WebServiceException -
    ConnectException
    -
    -
    - -
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    -Uses of Class
    compbio.ws.client.AAConClient

    -
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    -

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    -Uses of Class
    compbio.ws.client.IOHelper

    -
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    -

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    -Uses of Class
    compbio.ws.client.Jws2Client

    -
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    -

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    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    -
    -

    -Uses of Class
    compbio.ws.client.MetadataHelper

    -
    -No usage of compbio.ws.client.MetadataHelper -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/class-use/Services.html b/website/full_javadoc/compbio/ws/client/class-use/Services.html deleted file mode 100644 index 74e302d..0000000 --- a/website/full_javadoc/compbio/ws/client/class-use/Services.html +++ /dev/null @@ -1,679 +0,0 @@ - - - - - - -Uses of Class compbio.ws.client.Services - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.ws.client.Services

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Services
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.stat.collector  
    compbio.stat.servlet.util  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Services in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return types with arguments of type Services
    - Set<Services>RegistryWS.getSupportedServices() - -
    -          List of services that are functioning on the server.
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Services
    - intRegistryWS.getLastTested(Services service) - -
    -          Number of seconds since the last test.
    - DateRegistryWS.getLastTestedOn(Services service) - -
    -          The date and time the service has been verified to work last time
    - booleanRegistryWS.isOperating(Services service) - -
    -          Check whether a particular web service is working on this server
    - StringRegistryWS.testService(Services service) - -
    -          Test a particular service
    -  -

    - - - - - -
    -Uses of Services in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Services
    - ServicesTestService.getArg0() - -
    -           
    - ServicesIsOperating.getArg0() - -
    -           
    - ServicesGetLastTestedOn.getArg0() - -
    -           
    - ServicesGetLastTested.getArg0() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Services
    - Set<Services>GetSupportedServicesResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Services
    - voidTestService.setArg0(Services arg0) - -
    -           
    - voidIsOperating.setArg0(Services arg0) - -
    -           
    - voidGetLastTestedOn.setArg0(Services arg0) - -
    -           
    - voidGetLastTested.setArg0(Services arg0) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Services
    - voidGetSupportedServicesResponse.setReturn(Set<Services> _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.stat.collector
    -  -

    - - - - - - - - - -
    Methods in compbio.stat.collector that return Services
    - ServicesJobStat.getWebService() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.collector with parameters of type Services
    - StatProcessorStatProcessor.getSingleWSStat(Services webService) - -
    -           
    - List<JobStat>StatDB.readData(Timestamp from, - Timestamp to, - Services wservice, - Boolean clusterOnly) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return types with arguments of type Services
    - Map<Services,StatProcessor>StatCollection.getAllStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getClusterStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getLocalStat() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.servlet.util with type arguments of type Services
    -static TotalsTotals.sumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.ws.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return Services
    -static ServicesServices.getService(String servName) - -
    -           
    -static ServicesServicesUtil.getServiceByJobDirectory(File jobdir) - -
    -           
    -static ServicesServicesUtil.getServiceByRunner(Class<Executable<?>> runnerClassName) - -
    -           
    -static ServicesServices.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Services[]Services.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return types with arguments of type Services
    -static Set<Services>Jws2Client.getServices(String hostname) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client with parameters of type Services
    - booleanWSTester.checkService(Services service) - -
    -          Test JABA web service
    -static JABAServiceJws2Client.connect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -static Class<? extends Executable<?>>ServicesUtil.getServiceImpl(Services service) - -
    -           
    -static voidJws2Client.testService(String hostname, - Services service, - PrintWriter writer) - -
    -          Asks registry to test the service on the host hostname
    -  -

    - - - - - - - - - -
    Method parameters in compbio.ws.client with type arguments of type Services
    -static StringServices.toString(Set<Services> services) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.ws.server
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Services
    - Set<Services>RegistryWS.getSupportedServices() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Services
    - intRegistryWS.getLastTested(Services service) - -
    -           
    - DateRegistryWS.getLastTestedOn(Services service) - -
    -          Can potentially return null if the service has not been tested yet.
    -static _WSLogger_WSLogger.getStatLogger(Services service, - WebServiceContext wsContext) - -
    -          Deprecated.  
    - booleanRegistryWS.isOperating(Services service) - -
    -           
    - StringRegistryWS.testService(Services service) - -
    -           
    -  -

    -

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    -Classes  - -
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    - - - - diff --git a/website/full_javadoc/compbio/ws/client/package-summary.html b/website/full_javadoc/compbio/ws/client/package-summary.html deleted file mode 100644 index b6a9318..0000000 --- a/website/full_javadoc/compbio/ws/client/package-summary.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -compbio.ws.client - - - - - - - - - - - - -
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    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -

    -Package compbio.ws.client -

    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AAConClientA command line client for AACon web service
    IOHelper 
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    MetadataHelper 
    ServicesUtil 
    WSTesterClass for testing web services
    -  - -

    - - - - - - - - - -
    -Enum Summary
    ServicesList of web services currently supported by JABAWS version 2
    -  - -

    -

    -Package compbio.ws.client Description -

    - -

    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    - -

    -

    -
    Version:
    -
    1.0 April 2010
    -
    Author:
    -
    Peter Troshin
    -
    -
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    -Hierarchy For Package compbio.ws.client -

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    All Packages
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    -Uses of Package
    compbio.ws.client

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use compbio.ws.client
    compbio.data.msa.jaxws  
    compbio.stat.collector  
    compbio.stat.servlet.util  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.data.msa.jaxws
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.stat.collector
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.stat.servlet.util
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.ws.client
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.ws.server
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/server/AAConWS.html b/website/full_javadoc/compbio/ws/server/AAConWS.html deleted file mode 100644 index fe5b4a3..0000000 --- a/website/full_javadoc/compbio/ws/server/AAConWS.html +++ /dev/null @@ -1,380 +0,0 @@ - - - - - - -AAConWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class AAConWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<AACon>
-          extended by compbio.ws.server.AAConWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<AACon>, SequenceAnnotation<AACon>
    -
    -
    -
    -
    public class AAConWS
    extends SequenceAnnotationService<AACon>
    implements SequenceAnnotation<AACon>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    AAConWS() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringanalize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AAConWS

    -
    -public AAConWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -analize

    -
    -public String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences. The actual analysis algorithm is defined by the - type T. - - Any dataset containing a greater number of sequences or the average - length of the sequences are greater then defined in the default Limit - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    analize in interface SequenceAnnotation<AACon>
    Overrides:
    analize in class SequenceAnnotationService<AACon>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception.
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from class: GenericMetadataService
    -
    Assume statistics is not supported -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    Overrides:
    pullExecStatistics in class GenericMetadataService
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ClustalOWS.html b/website/full_javadoc/compbio/ws/server/ClustalOWS.html deleted file mode 100644 index f98ac15..0000000 --- a/website/full_javadoc/compbio/ws/server/ClustalOWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -ClustalOWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class ClustalOWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ClustalOWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<ClustalO>, MsaWS<ClustalO>
    -
    -
    -
    -
    public class ClustalOWS
    extends Object
    implements MsaWS<ClustalO>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalOWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<ClustalO>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<ClustalO>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<ClustalO>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<ClustalO>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalOWS

    -
    -public ClustalOWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<ClustalO> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<ClustalO>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<ClustalO> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<ClustalO>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<ClustalO> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<ClustalO>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<ClustalO> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<ClustalO>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<ClustalO> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<ClustalO>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ClustalWS.html b/website/full_javadoc/compbio/ws/server/ClustalWS.html deleted file mode 100644 index 3ef9306..0000000 --- a/website/full_javadoc/compbio/ws/server/ClustalWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -ClustalWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class ClustalWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ClustalWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<ClustalW>, MsaWS<ClustalW>
    -
    -
    -
    -
    public class ClustalWS
    extends Object
    implements MsaWS<ClustalW>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<ClustalW>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<ClustalW>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<ClustalW>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<ClustalW>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalWS

    -
    -public ClustalWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<ClustalW> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<ClustalW>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<ClustalW> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<ClustalW>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<ClustalW> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<ClustalW>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<ClustalW> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<ClustalW>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<ClustalW> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<ClustalW>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/DisemblWS.html b/website/full_javadoc/compbio/ws/server/DisemblWS.html deleted file mode 100644 index 5ea4721..0000000 --- a/website/full_javadoc/compbio/ws/server/DisemblWS.html +++ /dev/null @@ -1,414 +0,0 @@ - - - - - - -DisemblWS - - - - - - - - - - - - -
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    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class DisemblWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<Disembl>
-          extended by compbio.ws.server.DisemblWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Disembl>, SequenceAnnotation<Disembl>
    -
    -
    -
    -
    public class DisemblWS
    extends SequenceAnnotationService<Disembl>
    implements SequenceAnnotation<Disembl>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    DisemblWS() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -DisemblWS

    -
    -public DisemblWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -customAnalize

    -
    -public String customAnalize(List<FastaSequence> sequences,
-                            List<Option<Disembl>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

    -

    -
    Specified by:
    customAnalize in interface SequenceAnnotation<Disembl>
    Overrides:
    customAnalize in class SequenceAnnotationService<Disembl>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Option
    -
    -
    -
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<Disembl> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAnalize in interface SequenceAnnotation<Disembl>
    Overrides:
    presetAnalize in class SequenceAnnotationService<Disembl>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/GenericMetadataService.html b/website/full_javadoc/compbio/ws/server/GenericMetadataService.html deleted file mode 100644 index 10aaf20..0000000 --- a/website/full_javadoc/compbio/ws/server/GenericMetadataService.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -GenericMetadataService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.ws.server -
    -Class GenericMetadataService<T>

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService<T>
-
    -
    -
    Direct Known Subclasses:
    _MsaService, SequenceAnnotationService
    -
    -
    -
    -
    public abstract class GenericMetadataService<T>
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob(String jobId) - -
    -           
    - JobStatusgetJobStatus(String jobId) - -
    -           
    - Limit<T>getLimit(String presetName) - -
    -           
    - LimitsManager<T>getLimits() - -
    -           
    - PresetManager<T>getPresets() - -
    -           
    - RunnerConfig<T>getRunnerOptions() - -
    -           
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<T> getLimit(String presetName)
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<T> getLimits()
    -
    -
    -
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<T> getPresets()
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<T> getRunnerOptions()
    -
    -
    -
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Assume statistics is not supported -

    -

    -
    Parameters:
    jobId -
    position - -
    Returns:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/GlobPlotWS.html b/website/full_javadoc/compbio/ws/server/GlobPlotWS.html deleted file mode 100644 index 7511a31..0000000 --- a/website/full_javadoc/compbio/ws/server/GlobPlotWS.html +++ /dev/null @@ -1,414 +0,0 @@ - - - - - - -GlobPlotWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class GlobPlotWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<GlobPlot>
-          extended by compbio.ws.server.GlobPlotWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<GlobPlot>, SequenceAnnotation<GlobPlot>
    -
    -
    -
    -
    public class GlobPlotWS
    extends SequenceAnnotationService<GlobPlot>
    implements SequenceAnnotation<GlobPlot>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    GlobPlotWS() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GlobPlotWS

    -
    -public GlobPlotWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -customAnalize

    -
    -public String customAnalize(List<FastaSequence> sequences,
-                            List<Option<GlobPlot>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

    -

    -
    Specified by:
    customAnalize in interface SequenceAnnotation<GlobPlot>
    Overrides:
    customAnalize in class SequenceAnnotationService<GlobPlot>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Option
    -
    -
    -
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<GlobPlot> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAnalize in interface SequenceAnnotation<GlobPlot>
    Overrides:
    presetAnalize in class SequenceAnnotationService<GlobPlot>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/IUPredWS.html b/website/full_javadoc/compbio/ws/server/IUPredWS.html deleted file mode 100644 index a67c6eb..0000000 --- a/website/full_javadoc/compbio/ws/server/IUPredWS.html +++ /dev/null @@ -1,358 +0,0 @@ - - - - - - -IUPredWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class IUPredWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<IUPred>
-          extended by compbio.ws.server.IUPredWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<IUPred>, SequenceAnnotation<IUPred>
    -
    -
    -
    -
    public class IUPredWS
    extends SequenceAnnotationService<IUPred>
    implements SequenceAnnotation<IUPred>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    IUPredWS() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, customAnalize, getAnnotation
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, customAnalize, getAnnotation
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IUPredWS

    -
    -public IUPredWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<IUPred> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAnalize in interface SequenceAnnotation<IUPred>
    Overrides:
    presetAnalize in class SequenceAnnotationService<IUPred>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/JronnWS.html b/website/full_javadoc/compbio/ws/server/JronnWS.html deleted file mode 100644 index 4b8a827..0000000 --- a/website/full_javadoc/compbio/ws/server/JronnWS.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -JronnWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class JronnWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<Jronn>
-          extended by compbio.ws.server.JronnWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Jronn>, SequenceAnnotation<Jronn>
    -
    -
    -
    -
    public class JronnWS
    extends SequenceAnnotationService<Jronn>
    implements SequenceAnnotation<Jronn>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    JronnWS() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JronnWS

    -
    -public JronnWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from class: GenericMetadataService
    -
    Assume statistics is not supported -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    Overrides:
    pullExecStatistics in class GenericMetadataService
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/MafftWS.html b/website/full_javadoc/compbio/ws/server/MafftWS.html deleted file mode 100644 index f9f3b8a..0000000 --- a/website/full_javadoc/compbio/ws/server/MafftWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -MafftWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.ws.server -
    -Class MafftWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.MafftWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Mafft>, MsaWS<Mafft>
    -
    -
    -
    -
    public class MafftWS
    extends Object
    implements MsaWS<Mafft>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    MafftWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Mafft>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Mafft>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Mafft>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Mafft>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MafftWS

    -
    -public MafftWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Mafft>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Mafft> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Mafft> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Mafft>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Mafft> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Mafft>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Mafft> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Mafft>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Mafft> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Mafft>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/MuscleWS.html b/website/full_javadoc/compbio/ws/server/MuscleWS.html deleted file mode 100644 index 8b458c4..0000000 --- a/website/full_javadoc/compbio/ws/server/MuscleWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -MuscleWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.ws.server -
    -Class MuscleWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.MuscleWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Muscle>, MsaWS<Muscle>
    -
    -
    -
    -
    public class MuscleWS
    extends Object
    implements MsaWS<Muscle>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    MuscleWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Muscle>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Muscle>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Muscle>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Muscle>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MuscleWS

    -
    -public MuscleWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Muscle>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Muscle> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Muscle> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Muscle>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Muscle> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Muscle>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Muscle> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Muscle>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Muscle> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Muscle>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/ProbconsWS.html deleted file mode 100644 index ba76bed..0000000 --- a/website/full_javadoc/compbio/ws/server/ProbconsWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -ProbconsWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.ws.server -
    -Class ProbconsWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ProbconsWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Probcons>, MsaWS<Probcons>
    -
    -
    -
    -
    public class ProbconsWS
    extends Object
    implements MsaWS<Probcons>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    ProbconsWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Probcons>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Probcons>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Probcons>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Probcons>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ProbconsWS

    -
    -public ProbconsWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Probcons>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Probcons> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Probcons> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Probcons>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Probcons> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Probcons>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Probcons> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Probcons>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Probcons> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Probcons>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/RegistryWS.html b/website/full_javadoc/compbio/ws/server/RegistryWS.html deleted file mode 100644 index a8151e3..0000000 --- a/website/full_javadoc/compbio/ws/server/RegistryWS.html +++ /dev/null @@ -1,422 +0,0 @@ - - - - - - -RegistryWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class RegistryWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.RegistryWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, RegistryWS
    -
    -
    -
    -
    public class RegistryWS
    extends Object
    implements RegistryWS, JABAService
    - - -

    -JABAWS services registry -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    RegistryWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetLastTested(Services service) - -
    -          Number of seconds since the last test.
    - DategetLastTestedOn(Services service) - -
    -          Can potentially return null if the service has not been tested yet.
    - Set<Services>getSupportedServices() - -
    -          List of services that are functioning on the server.
    - booleanisOperating(Services service) - -
    -          Check whether a particular web service is working on this server
    - StringtestAllServices() - -
    -          TODO improve reporting.
    - StringtestService(Services service) - -
    -          Test a particular service
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -RegistryWS

    -
    -public RegistryWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getSupportedServices

    -
    -public Set<Services> getSupportedServices()
    -
    -
    Description copied from interface: RegistryWS
    -
    List of services that are functioning on the server. This function - returns the results of testing performed some time ago by - RegistryWS.testAllServices() or RegistryWS.testService(Services) methods. The - time of last check can be obtained from - RegistryWS.getLastTestedOn(Services) method -

    -

    -
    Specified by:
    getSupportedServices in interface RegistryWS
    -
    -
    - -
    Returns:
    the Set of Services which are functioning on the server
    See Also:
    RegistryWS.testAllServices()
    -
    -
    -
    - -

    -getLastTested

    -
    -public int getLastTested(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Number of seconds since the last test. Returns 0 if the service was not - tested or tested less then a one second ago. -

    -

    -
    Specified by:
    getLastTested in interface RegistryWS
    -
    -
    - -
    Returns:
    when last time tested
    -
    -
    -
    - -

    -getLastTestedOn

    -
    -public Date getLastTestedOn(Services service)
    -
    -
    Can potentially return null if the service has not been tested yet. -

    -

    -
    Specified by:
    getLastTestedOn in interface RegistryWS
    -
    -
    - -
    Returns:
    the Date and time on which the service was last tested
    -
    -
    -
    - -

    -testAllServices

    -
    -public String testAllServices()
    -
    -
    TODO improve reporting. stop testing service on unsupported runtime env - exception -

    -

    -
    Specified by:
    testAllServices in interface RegistryWS
    -
    -
    - -
    Returns:
    the test log
    -
    -
    -
    - -

    -testService

    -
    -public String testService(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Test a particular service -

    -

    -
    Specified by:
    testService in interface RegistryWS
    -
    -
    - -
    Returns:
    the testing log
    -
    -
    -
    - -

    -isOperating

    -
    -public boolean isOperating(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Check whether a particular web service is working on this server -

    -

    -
    Specified by:
    isOperating in interface RegistryWS
    -
    -
    - -
    Returns:
    true if the service was functioning in time of last testing.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/SequenceAnnotationService.html b/website/full_javadoc/compbio/ws/server/SequenceAnnotationService.html deleted file mode 100644 index 6caab68..0000000 --- a/website/full_javadoc/compbio/ws/server/SequenceAnnotationService.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - - -SequenceAnnotationService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class SequenceAnnotationService<T>

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<T>
-
    -
    -
    Type Parameters:
    T -
    -
    -
    Direct Known Subclasses:
    AAConWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS
    -
    -
    -
    -
    public abstract class SequenceAnnotationService<T>
    extends GenericMetadataService
    - - -

    -Common methods for all SequenceAnnotation web services -

    - -

    -

    -
    Since:
    -
    2.0
    -
    Version:
    -
    1.0 June 2011
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringanalize(List<FastaSequence> sequences) - -
    -           
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - ScoreManagergetAnnotation(String jobId) - -
    -           
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getAnnotation

    -
    -public ScoreManager getAnnotation(String jobId)
-                           throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -analize

    -
    -public String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException -
    LimitExceededException -
    JobSubmissionException
    -
    -
    -
    - -

    -customAnalize

    -
    -public String customAnalize(List<FastaSequence> sequences,
-                            List<Option<T>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException -
    LimitExceededException -
    JobSubmissionException -
    WrongParameterException
    -
    -
    -
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<T> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException -
    LimitExceededException -
    JobSubmissionException -
    WrongParameterException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ShutdownEngines.html b/website/full_javadoc/compbio/ws/server/ShutdownEngines.html deleted file mode 100644 index 3841244..0000000 --- a/website/full_javadoc/compbio/ws/server/ShutdownEngines.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -ShutdownEngines - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class ShutdownEngines

    -
    -java.lang.Object
-  extended by compbio.ws.server.ShutdownEngines
-
    -
    -
    All Implemented Interfaces:
    EventListener, javax.servlet.ServletContextListener
    -
    -
    -
    -
    public class ShutdownEngines
    extends Object
    implements javax.servlet.ServletContextListener
    - - -

    -Switch off engines if JABAWS web application is undeployed, or web server is - shutdown -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    Peter Troshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ShutdownEngines() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - voidcontextDestroyed(javax.servlet.ServletContextEvent ignored) - -
    -           
    - voidcontextInitialized(javax.servlet.ServletContextEvent arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ShutdownEngines

    -
    -public ShutdownEngines()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -contextDestroyed

    -
    -public void contextDestroyed(javax.servlet.ServletContextEvent ignored)
    -
    -
    -
    Specified by:
    contextDestroyed in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
    -
    -
    - -

    -contextInitialized

    -
    -public void contextInitialized(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextInitialized in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html deleted file mode 100644 index 939aad6..0000000 --- a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html +++ /dev/null @@ -1,266 +0,0 @@ - - - - - - -SimpleWSPublisher - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class SimpleWSPublisher

    -
    -java.lang.Object
-  extended by compbio.ws.server.SimpleWSPublisher
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class SimpleWSPublisher
    extends Object
    - - -

    -This class publish a web service. This is not a production implementation. - Should be used only for during development and testing -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    SimpleWSPublisher(Object exec, - String context) - -
    -          Deprecated.  
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -SimpleWSPublisher

    -
    -public SimpleWSPublisher(Object exec,
-                         String context)
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Deprecated. 
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html deleted file mode 100644 index e44fe88..0000000 --- a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -TcoffeeWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class TcoffeeWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.TcoffeeWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Tcoffee>, MsaWS<Tcoffee>
    -
    -
    -
    -
    public class TcoffeeWS
    extends Object
    implements MsaWS<Tcoffee>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    TcoffeeWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Tcoffee>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Tcoffee>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Tcoffee>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Tcoffee>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -TcoffeeWS

    -
    -public TcoffeeWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Tcoffee>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Tcoffee> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Tcoffee> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Tcoffee>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Tcoffee> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Tcoffee>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Tcoffee> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Tcoffee>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Tcoffee> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Tcoffee>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/WSUtil.html b/website/full_javadoc/compbio/ws/server/WSUtil.html deleted file mode 100644 index ed060f0..0000000 --- a/website/full_javadoc/compbio/ws/server/WSUtil.html +++ /dev/null @@ -1,531 +0,0 @@ - - - - - - -WSUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class WSUtil

    -
    -java.lang.Object
-  extended by compbio.ws.server.WSUtil
-
    -
    -
    -
    public final class WSUtil
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    WSUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> String
    -    		align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    -static - - - - -
    -<T> String
    -    		analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    -static booleancancelJob(String jobId) - -
    -           
    -static - - - - -
    -<T> ScoreManager
    -    		getAnnotation(String jobId, - org.apache.log4j.Logger log) - -
    -           
    -static - - - - -
    -<T> List<String>
    -    		getCommands(List<Option<T>> options, - String keyValueSeparator) - -
    -           
    -static AsyncExecutorgetEngine(ConfiguredExecutable<?> confClustal) - -
    -           
    -static JobStatusgetJobStatus(String jobId) - -
    -           
    -static bytegetProgress(String jobId) - -
    -           
    -static ChunkHolderpullFile(String file, - long position) - -
    -           
    -static voidvalidateAAConInput(List<FastaSequence> sequences) - -
    -           
    -static voidvalidateFastaInput(List<FastaSequence> sequences) - -
    -           
    -static voidvalidateJobId(String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -WSUtil

    -
    -public WSUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -validateJobId

    -
    -public static final void validateJobId(String jobId)
-                                throws InvalidParameterException
    -
    -
    - -
    Throws: -
    InvalidParameterException
    -
    -
    -
    - -

    -validateFastaInput

    -
    -public static final void validateFastaInput(List<FastaSequence> sequences)
-                                     throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getJobStatus

    -
    -public static JobStatus getJobStatus(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -pullFile

    -
    -public static ChunkHolder pullFile(String file,
-                                   long position)
    -
    -
    -
    -
    -
    -
    - -

    -getProgress

    -
    -public static byte getProgress(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getEngine

    -
    -public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal)
    -
    -
    -
    -
    -
    -
    - -

    -cancelJob

    -
    -public static boolean cancelJob(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -align

    -
    -public static <T> String align(List<FastaSequence> sequences,
-                               ConfiguredExecutable<T> confExec,
-                               org.apache.log4j.Logger logger,
-                               String callingMethod,
-                               Limit<T> limit)
-                    throws LimitExceededException,
-                           JobSubmissionException
    -
    -
    - -
    Throws: -
    LimitExceededException -
    JobSubmissionException
    -
    -
    -
    - -

    -analize

    -
    -public static <T> String analize(List<FastaSequence> sequences,
-                                 ConfiguredExecutable<T> confExec,
-                                 org.apache.log4j.Logger log,
-                                 String method,
-                                 Limit<T> limit)
-                      throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getCommands

    -
    -public static final <T> List<String> getCommands(List<Option<T>> options,
-                                                 String keyValueSeparator)
    -
    -
    -
    -
    -
    -
    - -

    -validateAAConInput

    -
    -public static void validateAAConInput(List<FastaSequence> sequences)
-                               throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getAnnotation

    -
    -public static <T> ScoreManager getAnnotation(String jobId,
-                                             org.apache.log4j.Logger log)
-                                  throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/_MsaService.html b/website/full_javadoc/compbio/ws/server/_MsaService.html deleted file mode 100644 index 085b91b..0000000 --- a/website/full_javadoc/compbio/ws/server/_MsaService.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -_MsaService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.ws.server -
    -Class _MsaService<T>

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server._MsaService<T>
-
    -
    -
    Type Parameters:
    T -
    -
    -
    -
    public abstract class _MsaService<T>
    extends GenericMetadataService
    - - -

    -TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services -

    - -

    -

    -
    Since:
    -
    2.0
    -
    Version:
    -
    1.0 June 2011
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -           
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - AlignmentgetResult(String jobId) - -
    -           
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<T> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    - -
    Throws: -
    JobSubmissionException -
    WrongParameterException
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<T>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    - -
    Throws: -
    JobSubmissionException -
    WrongParameterException
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from class: GenericMetadataService
    -
    Assume statistics is not supported -

    -

    -
    Overrides:
    pullExecStatistics in class GenericMetadataService
    -
    -
    - -
    Returns:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/_WSLogger.html b/website/full_javadoc/compbio/ws/server/_WSLogger.html deleted file mode 100644 index 817d82b..0000000 --- a/website/full_javadoc/compbio/ws/server/_WSLogger.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -_WSLogger - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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.ws.server -
    -Class _WSLogger

    -
    -java.lang.Object
-  extended by compbio.ws.server._WSLogger
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class _WSLogger
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetRemoteAddress() - -
    -          Deprecated.  
    -static _WSLoggergetStatLogger(Services service, - WebServiceContext wsContext) - -
    -          Deprecated.  
    - voidlog(compbio.util.Timer timer, - String activity) - -
    -          Deprecated.  
    - voidlog(compbio.util.Timer timer, - String activity, - String jobId) - -
    -          Deprecated.  
    - voidlogAll(compbio.util.Timer timer, - String activity) - -
    -          Deprecated.  
    - voidlogFine(compbio.util.Timer timer, - String activity) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getStatLogger

    -
    -public static final _WSLogger getStatLogger(Services service,
-                                            WebServiceContext wsContext)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -logAll

    -
    -public void logAll(compbio.util.Timer timer,
-                   String activity)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -logFine

    -
    -public void logFine(compbio.util.Timer timer,
-                    String activity)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -log

    -
    -public void log(compbio.util.Timer timer,
-                String activity)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -log

    -
    -public void log(compbio.util.Timer timer,
-                String activity,
-                String jobId)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getRemoteAddress

    -
    -public String getRemoteAddress()
    -
    -
    Deprecated. 
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/class-use/AAConWS.html b/website/full_javadoc/compbio/ws/server/class-use/AAConWS.html deleted file mode 100644 index 78c5fa1..0000000 --- a/website/full_javadoc/compbio/ws/server/class-use/AAConWS.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - -Uses of Class compbio.ws.server.AAConWS - - - - - - - - - - - - -
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    -Uses of Class
    compbio.ws.server.AAConWS

    -
    - - - - - - - - - -
    -Packages that use AAConWS
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

    - - - - - -
    -Uses of AAConWS in compbio.ws.client
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return types with arguments of type AAConWS
    -static SequenceAnnotation<AAConWS>AAConClient.connect() - -
    -          Connects to a AACon web service by the host and the service name
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.ws.server.ClustalOWS

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    -

    - - - - - - - - - - - - - - - -
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    compbio.ws.server.ClustalWS

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    -

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    compbio.ws.server.DisemblWS

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    -

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    -Uses of Class
    compbio.ws.server.GenericMetadataService

    -
    - - - - - - - - - -
    -Packages that use GenericMetadataService
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of GenericMetadataService in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Subclasses of GenericMetadataService in compbio.ws.server
    - class_MsaService<T> - -
    -          TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services
    - classAAConWS - -
    -           
    - classDisemblWS - -
    -           
    - classGlobPlotWS - -
    -           
    - classIUPredWS - -
    -           
    - classJronnWS - -
    -           
    - classSequenceAnnotationService<T> - -
    -          Common methods for all SequenceAnnotation web services
    -  -

    -

    - - - - - - - - - - - - - - - -
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    compbio.ws.server.GlobPlotWS

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    -

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    compbio.ws.server.IUPredWS

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    -

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    compbio.ws.server.JronnWS

    -
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    -

    - - - - - - - - - - - - - - - -
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    compbio.ws.server.MafftWS

    -
    -No usage of compbio.ws.server.MafftWS -

    -

    - - - - - - - - - - - - - - - -
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    compbio.ws.server.MuscleWS

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    -

    - - - - - - - - - - - - - - - -
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    compbio.ws.server.ProbconsWS

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    -

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    compbio.ws.server.RegistryWS

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    -

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    compbio.ws.server.SequenceAnnotationService

    -
    - - - - - - - - - -
    -Packages that use SequenceAnnotationService
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of SequenceAnnotationService in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Subclasses of SequenceAnnotationService in compbio.ws.server
    - classAAConWS - -
    -           
    - classDisemblWS - -
    -           
    - classGlobPlotWS - -
    -           
    - classIUPredWS - -
    -           
    - classJronnWS - -
    -           
    -  -

    -

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    compbio.ws.server.ShutdownEngines

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    compbio.ws.server.SimpleWSPublisher

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    compbio.ws.server.TcoffeeWS

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    compbio.ws.server.WSUtil

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    _MsaService<T>TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services
    _WSLoggerDeprecated.
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    ClustalWS 
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    RegistryWSJABAWS services registry
    SequenceAnnotationService<T>Common methods for all SequenceAnnotation web services
    ShutdownEnginesSwitch off engines if JABAWS web application is undeployed, or web server is - shutdown
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    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
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    compbio.data.sequence.ClustalAlignmentUtil
    -public static final chargapchar45
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    -public static final doubleDEFAULT_GAP_THRESHOLD0.1
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    -public static final StringKEY_VALUE_SEPARATOR"="
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    compbio.runner.disorder.Disembl
    -public final doubleCOILS_EXPECTATION_THRESHOLD0.43
    -public static final StringKEY_VALUE_SEPARATOR" "
    -public final doubleLOOPS_EXPECTATION_THRESHOLD0.086
    -public final doubleREM_EXPECTATION_THRESHOLD0.5
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    -public static final StringKEY_VALUE_SEPARATOR" "
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    -A

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    -
    AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Valid Amino acids -
    AACon - Class in compbio.runner.conservation
    Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    AACon() - -Constructor for class compbio.runner.conservation.AACon -
      -
    AAConClient - Class in compbio.ws.client
    A command line client for AACon web service
    AAConWS - Class in compbio.ws.server
     
    AAConWS() - -Constructor for class compbio.ws.server.AAConWS -
      -
    addOption(Option<T>) - -Method in class compbio.metadata.RunnerConfig -
    Adds Option to the internal list of options -
    addOptionNames(String...) - -Method in class compbio.metadata.Option -
    Adds an option to the optionName list -
    addOptionNames(String...) - -Method in class compbio.metadata.Parameter -
      -
    addParameter(Parameter<T>) - -Method in class compbio.metadata.RunnerConfig -
    Adds parameter to the internal parameter list -
    addParameter(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    addParameters(List<String>) - -Method in class compbio.engine.client.ConfExecutable -
      -
    addParameters(List<String>) - -Method in interface compbio.engine.client.Executable -
    Adds parameter to the list of parameters for a native executable -
    addParameters(List<String>) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    addParameters(List<String>) - -Method in class compbio.runner._impl.NetNglyc -
      -
    addParameters(String[]) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    addParameters(List<String>) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    addParameters(List<String>) - -Method in class compbio.runner.msa.Mafft -
    Mafft input must always be the last parameter! -
    addParams(List<String>) - -Method in class compbio.engine.client.CommandBuilder -
      -
    addPossibleValues(String...) - -Method in class compbio.metadata.Parameter -
      -
    addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - -Static method in class compbio.engine.SubmissionManager -
      -
    Align - Class in compbio.data.msa.jaxws
     
    Align() - -Constructor for class compbio.data.msa.jaxws.Align -
      -
    align(List<FastaSequence>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with default settings. -
    align(List<FastaSequence>) - -Method in class compbio.ws.server._MsaService -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ClustalOWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ClustalWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.MafftWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.MuscleWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - -Static method in class compbio.ws.server.WSUtil -
      -
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - -Constructor for class compbio.data.sequence.Alignment -
      -
    Alignment(List<FastaSequence>, AlignmentMetadata) - -Constructor for class compbio.data.sequence.Alignment -
      -
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - -Constructor for class compbio.data.sequence.AlignmentMetadata -
      -
    AlignResponse - Class in compbio.data.msa.jaxws
     
    AlignResponse() - -Constructor for class compbio.data.msa.jaxws.AlignResponse -
      -
    AMBIGUOUS_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Same as AA pattern but with two additional letters - XU -
    AMBIGUOUS_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Ambiguous nucleotide -
    Analize - Class in compbio.data.msa.jaxws
     
    Analize() - -Constructor for class compbio.data.msa.jaxws.Analize -
      -
    analize(List<FastaSequence>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences. -
    analize(List<FastaSequence>) - -Method in class compbio.ws.server.AAConWS -
      -
    analize(List<FastaSequence>) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - -Static method in class compbio.ws.server.WSUtil -
      -
    AnalizeResponse - Class in compbio.data.msa.jaxws
     
    AnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.AnalizeResponse -
      -
    AnnualStat - Class in compbio.stat.servlet
     
    AnnualStat() - -Constructor for class compbio.stat.servlet.AnnualStat -
      -
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    argumentsToCommandString(List<? extends Option<?>>) - -Method in class compbio.runner.OptionCombinator -
      -
    argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - -Static method in class compbio.runner.OptionCombinator -
      -
    asMap() - -Method in class compbio.data.sequence.ScoreManager -
      -
    asSet() - -Method in class compbio.data.sequence.ScoreManager -
      -
    AsyncExecutor - Interface in compbio.engine
    An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    AsyncJobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    AsyncJobRunner() - -Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    AsyncLocalRunner - Class in compbio.engine.local
     
    AsyncLocalRunner() - -Constructor for class compbio.engine.local.AsyncLocalRunner -
      -
    -
    - - - - - - - - - - - - - - - -
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    JABAService - Interface in compbio.data.msa
    This is a marker interface, contains no methods
    JackHmmerHitParser - Class in compbio.pipeline._jpred
    Parser for the following files:
    JackHmmerHitParser(String) - -Constructor for class compbio.pipeline._jpred.JackHmmerHitParser -
      -
    JManagement - Interface in compbio.data.msa
     
    JnetAnnotation - Enum in compbio.data._structure
     
    Job - Class in compbio.engine
     
    Job(String, String, ConfiguredExecutable<?>) - -Constructor for class compbio.engine.Job -
      -
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobExecutionException(String) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(String, Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JOBID - -Static variable in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    Joblist - Class in compbio.stat.servlet
     
    Joblist() - -Constructor for class compbio.stat.servlet.Joblist -
      -
    JobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    JobRunner(ConfiguredExecutable<?>) - -Constructor for class compbio.engine.cluster.drmaa.JobRunner -
      -
    JobStat - Class in compbio.stat.collector
     
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(String, Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobSubmissionExceptionBean() - -Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    Jpred4 - Class in compbio.pipeline._jpred
    jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying.
    Jpred4() - -Constructor for class compbio.pipeline._jpred.Jpred4 -
      -
    JpredAnnotation - Enum in compbio.data._structure
     
    JpredResult - Class in compbio.data._structure
    Jnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
    JpredResult() - -Constructor for class compbio.data._structure.JpredResult -
      -
    Jronn - Class in compbio.runner.disorder
    Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    Jronn() - -Constructor for class compbio.runner.disorder.Jronn -
      -
    JronnWS - Class in compbio.ws.server
     
    JronnWS() - -Constructor for class compbio.ws.server.JronnWS -
      -
    Jws2Client - Class in compbio.ws.client
    A command line client for JAva Bioinformatics Analysis Web Services
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.conservation.AACon -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.disorder.Disembl -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.disorder.GlobPlot -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.disorder.Jronn -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.ClustalO -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.ClustalW -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Mafft -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Muscle -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Probcons -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Tcoffee -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    Limit(int, int, String) - -Constructor for class compbio.metadata.Limit -
    Instantiate the limit -
    Limit(int, int, String, boolean) - -Constructor for class compbio.metadata.Limit -
      -
    LimitExceededException - Exception in compbio.metadata
    This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitExceededException(String) - -Constructor for exception compbio.metadata.LimitExceededException -
      -
    LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    LimitExceededExceptionBean() - -Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - -Constructor for class compbio.metadata.LimitsManager -
      -
    load(InputStream) - -Static method in class compbio.engine.client.RunConfiguration -
      -
    LoadBalancer - Class in compbio.engine
    This class decides where to execute the job.
    loadExecutable(String) - -Static method in class compbio.engine.client.Util -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.engine.client.ConfExecutable -
      -
    loadRunConfiguration(InputStream) - -Method in class compbio.engine.client.ConfExecutable -
      -
    loadRunConfiguration(InputStream) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in interface compbio.engine.client.Executable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.runner._impl.NetNglyc -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    LOCAL_ENGINE_LIMIT_PRESET - -Static variable in class compbio.metadata.PresetManager -
      -
    LOCAL_WORK_DIRECTORY - -Static variable in class compbio.engine.Configurator -
      -
    LocalEngineUtil - Class in compbio.engine.local
     
    LocalEngineUtil() - -Constructor for class compbio.engine.local.LocalEngineUtil -
      -
    LocalExecutorService - Class in compbio.engine.local
     
    LocalRunner - Class in compbio.engine.local
     
    LocalRunner(ConfiguredExecutable<?>) - -Constructor for class compbio.engine.local.LocalRunner -
      -
    log - -Static variable in class compbio.runner.Util -
      -
    log(Timer, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    log(Timer, String, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    logAll(Timer, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    logFine(Timer, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    LOOPS_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -
      -
    -
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    -
    -
    Mafft - Class in compbio.runner.msa
     
    Mafft() - -Constructor for class compbio.runner.msa.Mafft -
      -
    MafftWS - Class in compbio.ws.server
     
    MafftWS() - -Constructor for class compbio.ws.server.MafftWS -
      -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastBlastComparator -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastHmmerComparator -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastParser -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.JackHmmerHitParser -
      -
    main(String[]) - -Static method in class compbio.pipeline._jpred.Pairwise -
      -
    main(String[]) - -Static method in class compbio.runner._impl.OB -
      -
    main(String[]) - -Static method in class compbio.stat.collector.ExecutionStatCollector -
    Not in use -
    main(String[]) - -Static method in class compbio.stat.collector.StatDB -
      -
    main(String[]) - -Static method in class compbio.ws.client.AAConClient -
    Starts command line client, if no parameters are supplied prints help. -
    main(String[]) - -Static method in class compbio.ws.client.Jws2Client -
    Starts command line client, if no parameter are supported print help. -
    main(String[]) - -Static method in class compbio.ws.client.WSTester -
    Test JWS2 web services -
    main(String[]) - -Static method in class compbio.ws.server.SimpleWSPublisher -
    Deprecated.   -
    Mcl - Class in compbio.runner._impl
     
    Mcl(String) - -Constructor for class compbio.runner._impl.Mcl -
      -
    mergeEnvVariables(Map<String, String>, Map<String, String>) - -Static method in class compbio.engine.client.Util -
      -
    Metadata<T> - Interface in compbio.data.msa
     
    MetadataHelper - Class in compbio.ws.client
     
    MetadataHelper() - -Constructor for class compbio.ws.client.MetadataHelper -
      -
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    Muscle - Class in compbio.runner.msa
     
    Muscle() - -Constructor for class compbio.runner.msa.Muscle -
    Default options are - - -clwstrict - write output in clustal format -
    MuscleWS - Class in compbio.ws.server
     
    MuscleWS() - -Constructor for class compbio.ws.server.MuscleWS -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    NetNglyc - Class in compbio.runner._impl
     
    NetNglyc() - -Constructor for class compbio.runner._impl.NetNglyc -
      -
    newCommandBuilder(List<? extends Option<T>>, String) - -Static method in class compbio.engine.client.CommandBuilder -
    This produces the same result as getCommands method. -
    newConfExecutable(RunConfiguration) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    newFilePuller(String, int) - -Static method in class compbio.engine.FilePuller -
      -
    newInstance(Map<String, Set<Score>>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newInstanceSingleScore(Map<String, Score>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newInstanceSingleSequence(Set<Score>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newLimitExceeded(Limit<?>, List<FastaSequence>) - -Static method in exception compbio.metadata.LimitExceededException -
      -
    newProgressPuller(String) - -Static method in class compbio.engine.FilePuller -
    Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more. -
    newStatCollecton(Date, Date) - -Static method in class compbio.stat.servlet.util.StatCollection -
      -
    next() - -Method in class compbio.data.sequence.FastaReader -
    Reads the next FastaSequence from the input -
    NON_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    inversion of AA pattern -
    NON_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non nucleotide -
    NONWORD - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non word -
    NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Nucleotides a, t, g, c, u -
    -
    - - - - - - - - - - - - - - - -
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    -O

    -
    -
    OB - Class in compbio.runner._impl
    TODO this needs fixing! Executable does not work
    OB() - -Constructor for class compbio.runner._impl.OB -
      -
    OB(String) - -Constructor for class compbio.runner._impl.OB -
      -
    openInputStream(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects -
    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - -Constructor for class compbio.metadata.Option -
      -
    OptionCombinator - Class in compbio.runner
    This class solve the following problems.
    OptionCombinator(RunnerConfig<? extends Executable<?>>) - -Constructor for class compbio.runner.OptionCombinator -
      -
    optionsToCommandString(List<Option<?>>) - -Method in class compbio.runner.OptionCombinator -
      -
    OUTPUT - -Static variable in class compbio.engine.client.SkeletalExecutable -
      -
    -
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    -
    -
    Pairwise - Class in compbio.pipeline._jpred
     
    Pairwise(List<FastaSequence>) - -Constructor for class compbio.pipeline._jpred.Pairwise -
      -
    Parameter<T> - Class in compbio.metadata
    A single value containing an option supported by the web service e.g.
    Parameter(String, String) - -Constructor for class compbio.metadata.Parameter -
      -
    parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - -Method in class compbio.runner.OptionCombinator -
      -
    parse(String) - -Static method in class compbio.engine.conf._Key -
    Deprecated.   -
    PATH - -Static variable in class compbio.engine.client.EnvVariableProcessor -
    Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable -
    PathValidator - Class in compbio.engine.client
     
    PathValidator() - -Constructor for class compbio.engine.client.PathValidator -
      -
    PipedExecutable<T> - Interface in compbio.engine.client
    This is a marker interface to indicate that the output of the process must be - captured.
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - -Constructor for class compbio.metadata.Preset -
      -
    PresetAlign - Class in compbio.data.msa.jaxws
     
    PresetAlign() - -Constructor for class compbio.data.msa.jaxws.PresetAlign -
      -
    presetAlign(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with preset. -
    presetAlign(List<FastaSequence>, Preset<T>) - -Method in class compbio.ws.server._MsaService -
      -
    presetAlign(List<FastaSequence>, Preset<ClustalO>) - -Method in class compbio.ws.server.ClustalOWS -
      -
    presetAlign(List<FastaSequence>, Preset<ClustalW>) - -Method in class compbio.ws.server.ClustalWS -
      -
    presetAlign(List<FastaSequence>, Preset<Mafft>) - -Method in class compbio.ws.server.MafftWS -
      -
    presetAlign(List<FastaSequence>, Preset<Muscle>) - -Method in class compbio.ws.server.MuscleWS -
      -
    presetAlign(List<FastaSequence>, Preset<Probcons>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    presetAlign(List<FastaSequence>, Preset<Tcoffee>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    PresetAlignResponse - Class in compbio.data.msa.jaxws
     
    PresetAlignResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    PresetAnalize - Class in compbio.data.msa.jaxws
     
    PresetAnalize() - -Constructor for class compbio.data.msa.jaxws.PresetAnalize -
      -
    presetAnalize(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences according to the preset settings. -
    presetAnalize(List<FastaSequence>, Preset<Disembl>) - -Method in class compbio.ws.server.DisemblWS -
      -
    presetAnalize(List<FastaSequence>, Preset<GlobPlot>) - -Method in class compbio.ws.server.GlobPlotWS -
      -
    presetAnalize(List<FastaSequence>, Preset<IUPred>) - -Method in class compbio.ws.server.IUPredWS -
      -
    presetAnalize(List<FastaSequence>, Preset<T>) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    PresetAnalizeResponse - Class in compbio.data.msa.jaxws
     
    PresetAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - -Constructor for class compbio.metadata.PresetManager -
      -
    Probcons - Class in compbio.runner.msa
     
    Probcons() - -Constructor for class compbio.runner.msa.Probcons -
      -
    ProbconsWS - Class in compbio.ws.server
     
    ProbconsWS() - -Constructor for class compbio.ws.server.ProbconsWS -
      -
    PROC_ERR_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -
      -
    PROC_OUT_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -
      -
    Program - Enum in compbio.data.sequence
    The list of programmes that can produce alignments
    ProgressGetter - Class in compbio.engine
     
    ProgressGetter() - -Constructor for class compbio.engine.ProgressGetter -
      -
    PropertyHelperManager - Class in compbio.engine.conf
     
    PropertyHelperManager() - -Constructor for class compbio.engine.conf.PropertyHelperManager -
      -
    PScore - Class in compbio.pipeline._jpred
     
    PScore() - -Constructor for class compbio.pipeline._jpred.PScore -
      -
    PSIBlast - Class in compbio.runner._impl
     
    PSIBlast(String) - -Constructor for class compbio.runner._impl.PSIBlast -
      -
    pull(long) - -Method in class compbio.engine.FilePuller -
      -
    pull(String, long) - -Static method in class compbio.engine.ProgressGetter -
      -
    PulledFileCache - Class in compbio.engine
     
    PulledFileCache() - -Constructor for class compbio.engine.PulledFileCache -
      -
    PullExecStatistics - Class in compbio.data.msa.jaxws
     
    PullExecStatistics() - -Constructor for class compbio.data.msa.jaxws.PullExecStatistics -
      -
    pullExecStatistics(String, long) - -Method in interface compbio.data.msa.JManagement -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server._MsaService -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.AAConWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ClustalOWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ClustalWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.GenericMetadataService -
    Assume statistics is not supported -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.JronnWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.MafftWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.MuscleWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ProbconsWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
     
    PullExecStatisticsResponse() - -Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    pullFile(String, long) - -Static method in class compbio.ws.server.WSUtil -
      -
    put(FilePuller) - -Static method in class compbio.engine.PulledFileCache -
    This method allows duplicates to be added. -
    -
    - - - - - - - - - - - - - - - -
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    Range - Class in compbio.data.sequence
     
    Range(int, int) - -Constructor for class compbio.data.sequence.Range -
      -
    Range(String[]) - -Constructor for class compbio.data.sequence.Range -
      -
    rconfigFile - -Static variable in class compbio.engine.client.RunConfiguration -
      -
    read(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    read(InputStream, Class<V>, Class<?>...) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    readAAConResults(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Read AACon result with no alignment files. -
    readAndValidate(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    readClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Read Clustal formatted alignment. -
    readClustalFile(File) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
      -
    readClustalFile(String, String) - -Static method in class compbio.runner.Util -
      -
    readData(Timestamp, Timestamp, Services, Boolean) - -Method in class compbio.stat.collector.StatDB -
      -
    readDisembl(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
    readFasta(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads fasta sequences from inStream into the list of FastaSequence - objects -
    readGlobPlot(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
    readIUPred(File) - -Static method in class compbio.data.sequence.SequenceUtil -
    Read IUPred output -
    readJRonn(File) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    readJRonn(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reader for JRonn horizontal file format -
    readJronnFile(String, String) - -Static method in class compbio.runner.Util -
      -
    RegistryWS - Interface in compbio.data.msa
    JABAWS services registry
    RegistryWS - Class in compbio.ws.server
    JABAWS services registry
    RegistryWS() - -Constructor for class compbio.ws.server.RegistryWS -
      -
    REM_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -
      -
    remove() - -Method in class compbio.data.sequence.FastaReader -
    Not implemented -
    removeArgument(String) - -Method in class compbio.metadata.RunnerConfig -
    Removes the argument Argument if found. -
    removeArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -
    Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -
    removeJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    removeOutput(String) - -Method in class compbio.runner._impl.BlastAll -
      -
    removeOutput(String) - -Method in class compbio.runner._impl.PSIBlast -
      -
    removeParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    removeRecordedJobs(Set<JobStat>) - -Method in class compbio.stat.collector.StatDB -
    Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs. -
    removeTask(ConfiguredExecutable<?>) - -Static method in class compbio.engine.SubmissionManager -
      -
    removeTask(String) - -Static method in class compbio.engine.SubmissionManager -
      -
    reportStat() - -Method in class compbio.stat.collector.StatProcessor -
      -
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    ResultNotAvailableException(String) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(String, Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    ResultNotAvailableExceptionBean() - -Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    Ronn - Class in compbio.runner._impl
     
    Ronn(String) - -Constructor for class compbio.runner._impl.Ronn -
      -
    RPSBlast - Class in compbio.runner._impl
     
    RPSBlast(String) - -Constructor for class compbio.runner._impl.RPSBlast -
      -
    run() - -Method in class compbio.engine.local.StreamGobbler -
      -
    run() - -Method in class compbio.stat.collector.ExecutionStatCollector -
      -
    RunConfiguration - Class in compbio.engine.client
    Value class for persisting ConfExecutable instances
    RunConfiguration() - -Constructor for class compbio.engine.client.RunConfiguration -
      -
    RunConfiguration(ConfExecutable<?>) - -Constructor for class compbio.engine.client.RunConfiguration -
      -
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - -Constructor for class compbio.metadata.RunnerConfig -
      -
    RunnerConfigMarshaller<T> - Class in compbio.engine.conf
     
    RunnerConfigMarshaller(Class<?>) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -
      -
    RunnerConfigMarshaller(Class<?>, Class<?>...) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -
      -
    Runners - Class in compbio.runner._impl
     
    runPsiBlast() - -Method in class compbio.pipeline._jpred.Jpred4 -
      -
    -
    - - - - - - - - - - - - - - - -
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    -S

    -
    -
    saveRunConfiguration() - -Method in class compbio.engine.client.ConfExecutable -
      -
    saveRunConfiguration() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    Score - Class in compbio.data.sequence
    A value class for AACon annotation results storage.
    Score(Enum<?>, ArrayList<Float>) - -Constructor for class compbio.data.sequence.Score -
    Instantiate the Score -
    Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - -Constructor for class compbio.data.sequence.Score -
      -
    Score(Enum<?>, TreeSet<Range>) - -Constructor for class compbio.data.sequence.Score -
      -
    Score(Enum<?>, float[]) - -Constructor for class compbio.data.sequence.Score -
      -
    ScoreManager - Class in compbio.data.sequence
     
    ScoreManager.ScoreHolder - Class in compbio.data.sequence
     
    scores - -Variable in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    SequenceAnnotation<T> - Interface in compbio.data.msa
    Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    SequenceAnnotationService<T> - Class in compbio.ws.server
    Common methods for all SequenceAnnotation web services
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    SERVICE_NAMESPACE - -Static variable in interface compbio.data.msa.JABAService -
      -
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 2
    ServicesUtil - Class in compbio.ws.client
     
    ServicesUtil() - -Constructor for class compbio.ws.client.ServicesUtil -
      -
    setActualNumberofSequences(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetLastTested -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.IsOperating -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.TestService -
      -
    setDefaultValue(String) - -Method in class compbio.metadata.Option -
    Sets one of the values defined in optionList as default. -
    setDefaultValue(String) - -Method in class compbio.metadata.Parameter -
      -
    setDescription(String) - -Method in class compbio.metadata.Option -
      -
    setDescription(String) - -Method in class compbio.metadata.Preset -
      -
    setEmail(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    setError(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setError(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setExecProvider(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Align -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Analize -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    setFirst(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setFurtherDetails(URL) - -Method in class compbio.metadata.Option -
      -
    setInput(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setInput(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setInput(String) - -Method in class compbio.runner.conservation.AACon -
      -
    setInput(String) - -Method in class compbio.runner.disorder.Disembl -
      -
    setInput(String) - -Method in class compbio.runner.disorder.GlobPlot -
      -
    setInput(String) - -Method in class compbio.runner.disorder.IUPred -
      -
    setInput(String) - -Method in class compbio.runner.disorder.Jronn -
      -
    setInput(String) - -Method in class compbio.runner.msa.ClustalO -
      -
    setInput(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    setInput(String) - -Method in class compbio.runner.msa.Mafft -
      -
    setInput(String) - -Method in class compbio.runner.msa.Muscle -
      -
    setInput(String) - -Method in class compbio.runner.msa.Probcons -
      -
    setInput(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetAnnotation -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setLast(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setLast(String, String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setMax(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    setMin(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setName(String) - -Method in class compbio.metadata.Option -
      -
    setName(String) - -Method in class compbio.metadata.Preset -
      -
    setName(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    setNCore(int) - -Method in class compbio.runner.conservation.AACon -
      -
    setNCore(int) - -Method in class compbio.runner.disorder.Jronn -
      -
    setNCore(int) - -Method in class compbio.runner.msa.ClustalO -
      -
    setNCore(int) - -Method in class compbio.runner.msa.Tcoffee -
      -
    setNumberOfSequencesAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setOptionName(String) - -Method in class compbio.metadata.Parameter -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Option -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    setOptions(List<String>) - -Method in class compbio.metadata.Preset -
      -
    setOptions(List<Option<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Adds the list of options or parameters to the internal list of options -
    setOutput(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setOutput(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setOutput(String) - -Method in class compbio.runner.conservation.AACon -
      -
    setOutput(String) - -Method in class compbio.runner.disorder.IUPred -
      -
    setOutput(String) - -Method in class compbio.runner.disorder.Jronn -
      -
    setOutput(String) - -Method in class compbio.runner.msa.ClustalO -
      -
    setOutput(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    setOutput(String) - -Method in class compbio.runner.msa.Muscle -
      -
    setParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setParam(String, String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setParameter(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setParameters(CommandBuilder<?>) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setParameters(List<Parameter<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Sets the list of parameters as internal list -
    setParams(List<String>) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setPosition(long) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setPossibleValues(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    setPresetName(String) - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    setPresets(List<Preset<T>>) - -Method in class compbio.metadata.PresetManager -
      -
    setPrmSeparator(String) - -Method in class compbio.metadata.RunnerConfig -
    Sets name value separator character -
    setQueue(String) - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    setRanges(TreeSet<Range>) - -Method in class compbio.data.sequence.Score -
      -
    setRequired(boolean) - -Method in class compbio.metadata.Option -
      -
    setRequiredMemory(int) - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AnalizeResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    setReturn(ScoreManager) - -Method in class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    setReturn(JobStatus) - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    setReturn(Date) - -Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    setReturn(int) - -Method in class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    setReturn(Limit) - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    setReturn(LimitsManager) - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    setReturn(PresetManager) - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    setReturn(Alignment) - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    setReturn(RunnerConfig) - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    setReturn(Set<Services>) - -Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    setReturn(ChunkHolder) - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.TestServiceResponse -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.PresetManager -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.RunnerConfig -
    Set the name of a runner class -
    setSequenceLenghtActual(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setSequenceLenghtAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setType(ValueConstrain.Type) - -Method in class compbio.metadata.ValueConstrain -
      -
    setValidValue(ValueConstrain) - -Method in class compbio.metadata.Parameter -
      -
    setValue(String) - -Method in interface compbio.metadata.Argument -
    Set default values for the parameter or an option -
    setValue(String) - -Method in class compbio.metadata.Option -
      -
    setWorkDirectory(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    setWorkDirectory(String) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    shutDown() - -Static method in class compbio.engine.local.LocalExecutorService -
    This stops all executing processes via interruption. -
    shutdownDBServer() - -Static method in class compbio.stat.collector.StatDB -
      -
    ShutdownEngines - Class in compbio.ws.server
    Switch off engines if JABAWS web application is undeployed, or web server is - shutdown
    ShutdownEngines() - -Constructor for class compbio.ws.server.ShutdownEngines -
      -
    shutdownService() - -Static method in class compbio.engine.local.ExecutableWrapper -
    Stops internal executor service which captures streams of native - executables. -
    SimpleWSPublisher - Class in compbio.ws.server
    Deprecated. 
    SimpleWSPublisher(Object, String) - -Constructor for class compbio.ws.server.SimpleWSPublisher -
    Deprecated.   -
    SINGLE_ENTRY_KEY - -Static variable in class compbio.data.sequence.ScoreManager -
      -
    size() - -Method in class compbio.engine.client.CommandBuilder -
      -
    SkeletalExecutable<T> - Class in compbio.engine.client
     
    SkeletalExecutable() - -Constructor for class compbio.engine.client.SkeletalExecutable -
      -
    SkeletalExecutable(String) - -Constructor for class compbio.engine.client.SkeletalExecutable -
      -
    SMERFSConstraints - Enum in compbio.data.sequence
    Enumeration defining two constraints for SMERFS columns score calculation.
    sortByResultSize() - -Method in class compbio.stat.collector.StatProcessor -
      -
    sortByRuntime() - -Method in class compbio.stat.collector.StatProcessor -
      -
    sortByStartTime() - -Method in class compbio.stat.collector.StatProcessor -
      -
    SPACE - -Static variable in class compbio.runner.Util -
      -
    STAT_FILE - -Static variable in class compbio.runner.conservation.AACon -
      -
    STAT_FILE - -Static variable in class compbio.runner.disorder.Jronn -
      -
    StatCollection - Class in compbio.stat.servlet.util
     
    StatCollection() - -Constructor for class compbio.stat.servlet.util.StatCollection -
      -
    StatCollection.Stattype - Enum in compbio.stat.servlet.util
    Total number of requests - - incomplete abandoned cancelled
    StatDB - Class in compbio.stat.collector
    The database must be stored in the application root directory and called - "ExecutionStatistic"
    StatDB() - -Constructor for class compbio.stat.collector.StatDB -
      -
    StatisticCollector - Class in compbio.stat.servlet
     
    StatisticCollector() - -Constructor for class compbio.stat.servlet.StatisticCollector -
      -
    StatisticManager - Class in compbio.engine.cluster.drmaa
     
    StatisticManager(JobInfo) - -Constructor for class compbio.engine.cluster.drmaa.StatisticManager -
      -
    StatProcessor - Class in compbio.stat.collector
     
    StatProcessor(List<JobStat>) - -Constructor for class compbio.stat.collector.StatProcessor -
      -
    StreamGobbler - Class in compbio.engine.local
     
    SubmissionManager - Class in compbio.engine
    Submit jobs for execution
    submitJob(ConfiguredExecutable<?>) - -Method in interface compbio.engine.AsyncExecutor -
    Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. -
    submitJob(ConfiguredExecutable<?>) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    submitJob(ConfiguredExecutable<?>) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    sumOfTotals(Map<Date, Totals>) - -Static method in class compbio.stat.servlet.util.Totals -
      -
    sumStats(Map<Services, StatProcessor>) - -Static method in class compbio.stat.servlet.util.Totals -
      -
    SyncExecutor - Interface in compbio.engine
    Synchronous executor, is an engine to run the Executable synchronously.
    -
    - - - - - - - - - - - - - - - -
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    Tcoffee - Class in compbio.runner.msa
     
    Tcoffee() - -Constructor for class compbio.runner.msa.Tcoffee -
      -
    TcoffeeWS - Class in compbio.ws.server
     
    TcoffeeWS() - -Constructor for class compbio.ws.server.TcoffeeWS -
      -
    termSignal() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    TestAllServices - Class in compbio.data.msa.jaxws
     
    TestAllServices() - -Constructor for class compbio.data.msa.jaxws.TestAllServices -
      -
    testAllServices() - -Method in interface compbio.data.msa.RegistryWS -
    Test all JABAWS services on the server -
    testAllServices() - -Method in class compbio.ws.server.RegistryWS -
    TODO improve reporting. -
    TestAllServicesResponse - Class in compbio.data.msa.jaxws
     
    TestAllServicesResponse() - -Constructor for class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    TestService - Class in compbio.data.msa.jaxws
     
    TestService() - -Constructor for class compbio.data.msa.jaxws.TestService -
      -
    testService(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Test a particular service -
    testService(String, Services, PrintWriter) - -Static method in class compbio.ws.client.Jws2Client -
    Asks registry to test the service on the host hostname -
    testService(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    TestServiceResponse - Class in compbio.data.msa.jaxws
     
    TestServiceResponse() - -Constructor for class compbio.data.msa.jaxws.TestServiceResponse -
      -
    to - -Variable in class compbio.data.sequence.Range -
      -
    toCommand(String) - -Method in class compbio.metadata.Option -
    Convert the option to the command string. -
    toCommand(String) - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.data.sequence.Alignment -
      -
    toString() - -Method in class compbio.data.sequence.FastaSequence -
    Same as oneLineFasta -
    toString() - -Method in class compbio.data.sequence.Range -
      -
    toString() - -Method in class compbio.data.sequence.Score -
      -
    toString() - -Method in class compbio.engine.client.CommandBuilder -
      -
    toString() - -Method in class compbio.engine.client.ConfExecutable -
      -
    toString() - -Method in class compbio.engine.client.RunConfiguration -
      -
    toString() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    toString() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    toString() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    toString() - -Method in class compbio.engine.conf._Key -
    Deprecated.   -
    toString() - -Method in class compbio.engine.FilePuller -
      -
    toString() - -Method in class compbio.engine.Job -
      -
    toString() - -Method in class compbio.metadata.ChunkHolder -
      -
    toString() - -Method in class compbio.metadata.Limit -
      -
    toString() - -Method in class compbio.metadata.LimitsManager -
      -
    toString() - -Method in class compbio.metadata.Option -
      -
    toString() - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.metadata.Preset -
      -
    toString() - -Method in class compbio.metadata.PresetManager -
      -
    toString() - -Method in class compbio.metadata.RunnerConfig -
      -
    toString() - -Method in class compbio.metadata.ValueConstrain -
      -
    toString() - -Method in class compbio.pipeline._jpred.Hit -
      -
    toString() - -Method in class compbio.pipeline._jpred.PScore -
      -
    toString() - -Method in class compbio.stat.collector.JobStat -
      -
    toString() - -Method in class compbio.stat.collector.StatProcessor -
      -
    toString() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    toString(Set<Services>) - -Static method in enum compbio.ws.client.Services -
      -
    Totals - Class in compbio.stat.servlet.util
     
    Totals() - -Constructor for class compbio.stat.servlet.util.Totals -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
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    BlastAll - Class in compbio.runner._impl
     
    BlastAll(String) - -Constructor for class compbio.runner._impl.BlastAll -
      -
    BlastBlastComparator - Class in compbio.pipeline._jpred
     
    BlastBlastComparator() - -Constructor for class compbio.pipeline._jpred.BlastBlastComparator -
      -
    BlastHmmerComparator - Class in compbio.pipeline._jpred
     
    BlastHmmerComparator() - -Constructor for class compbio.pipeline._jpred.BlastHmmerComparator -
      -
    BlastParameters - Class in compbio.runner._impl
    Utility class for common Blast parameters
    BlastParser - Class in compbio.pipeline._jpred
     
    BlastParser(String) - -Constructor for class compbio.pipeline._jpred.BlastParser -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(File, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeException(Throwable) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBean() - -Constructor for class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    Util - Class in compbio.engine.client
     
    Util() - -Constructor for class compbio.engine.client.Util -
      -
    Util - Class in compbio.runner
     
    Util() - -Constructor for class compbio.runner.Util -
      -
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    -
    -
    V2_SERVICE_NAMESPACE - -Static variable in interface compbio.data.msa.JABAService -
      -
    validate(Validator, String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    validate(PresetManager<T>) - -Method in class compbio.metadata.LimitsManager -
    Validate Limits -
    validate(RunnerConfig<T>) - -Method in class compbio.metadata.PresetManager -
    Checks whether preset option and parameter are defined in RunnerConfig - object. -
    validate() - -Method in class compbio.metadata.RunnerConfig -
    Validate the value of the argument. -
    validateAAConInput(List<FastaSequence>) - -Static method in class compbio.ws.server.WSUtil -
      -
    validateDirectory(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validateExecutable(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validateFastaInput(List<FastaSequence>) - -Static method in class compbio.ws.server.WSUtil -
      -
    validateJobId(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    validatePathNames(List<String>, String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validURL(String) - -Static method in class compbio.ws.client.Jws2Client -
    Attempt to construct the URL object from the string -
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - -Constructor for class compbio.metadata.ValueConstrain -
      -
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - -Static method in enum compbio.data._structure.JnetAnnotation -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data._structure.JpredAnnotation -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.ConservationMethod -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.DisorderMethod -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.Program -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.SMERFSConstraints -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.engine.client.Executable.ExecProvider -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.metadata.JobStatus -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.metadata.ValueConstrain.Type -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.stat.servlet.util.StatCollection.Stattype -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.ws.client.Services -
    Returns the enum constant of this type with the specified name. -
    values() - -Static method in enum compbio.data._structure.JnetAnnotation -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data._structure.JpredAnnotation -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.ConservationMethod -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.DisorderMethod -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.Program -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.SMERFSConstraints -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.engine.client.Executable.ExecProvider -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.metadata.JobStatus -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.metadata.ValueConstrain.Type -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.stat.servlet.util.StatCollection.Stattype -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.ws.client.Services -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
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    waitForFile(long) - -Method in class compbio.engine.FilePuller -
      -
    waitForJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    waitForJob(String, long) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    waitForResult(ClusterSession, String) - -Static method in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    waitForResult() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    waitForResult() - -Method in class compbio.engine.local.LocalRunner -
      -
    waitForResult() - -Method in interface compbio.engine.SyncExecutor -
    Call to this method block for as long as it is required for an executable to finish its job. -
    wasAborted() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    WHITE_SPACE - -Static variable in class compbio.data.sequence.SequenceUtil -
    A whitespace character: [\t\n\x0B\f\r] -
    write(TreeSet<Score>, Writer) - -Static method in class compbio.data.sequence.Score -
    Outputs the List of Score objects into the Output stream. -
    write(RunConfiguration) - -Static method in class compbio.engine.client.RunConfiguration -
      -
    write(Object, OutputStream) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    writeAndValidate(Object, String, OutputStream) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    writeClustalAlignment(Writer, Alignment) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Write Clustal formatted alignment Limitations: does not record the - consensus. -
    writeFasta(OutputStream, List<FastaSequence>, int) - -Static method in class compbio.data.sequence.SequenceUtil -
    Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -
    writeFasta(OutputStream, List<FastaSequence>) - -Static method in class compbio.data.sequence.SequenceUtil -
    Writes FastaSequence in the file, each sequence will take one line only -
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    writeFile(String, String, String, boolean) - -Static method in class compbio.engine.client.Util -
      -
    writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - -Static method in class compbio.runner.Util -
      -
    writeMarker(String, JobStatus) - -Static method in class compbio.engine.client.Util -
      -
    writeOut(Writer) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    writeOut(Writer) - -Method in class compbio.data.sequence.ScoreManager -
      -
    writeStatFile(String, String) - -Static method in class compbio.engine.client.Util -
      -
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    WrongParameterException(Option<?>) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String, Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    WrongParameterExceptionBean() - -Constructor for class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester(String, PrintWriter) - -Constructor for class compbio.ws.client.WSTester -
    Construct an instance of JABAWS tester -
    WSUtil - Class in compbio.ws.server
     
    WSUtil() - -Constructor for class compbio.ws.server.WSUtil -
      -
    -
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    _Jpred - Class in compbio.runner._jpred
     
    _Jpred() - -Constructor for class compbio.runner._jpred._Jpred -
      -
    _Key - Class in compbio.engine.conf
    Deprecated. 
    _Key(Class<?>) - -Constructor for class compbio.engine.conf._Key -
    Deprecated.   -
    _MsaService<T> - Class in compbio.ws.server
    TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services
    _NativeSpecHelper - Class in compbio.runner
    Deprecated. 
    _NativeSpecHelper(int) - -Constructor for class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    _NativeSpecHelper(int, int) - -Constructor for class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    _Queue - Enum in compbio.engine.cluster.dundee
    Deprecated. 
    _SkeletalCommandBuilder - Class in compbio.runner
    Deprecated. 
    _SkeletalCommandBuilder() - -Constructor for class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    _WSLogger - Class in compbio.ws.server
    Deprecated. 
    -
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    -C

    -
    -
    call() - -Method in class compbio.engine.local.ExecutableWrapper -
    It is vital that output and error streams are captured immediately for - this call() to succeed. -
    canAcceptMoreWork() - -Method in class compbio.engine.local.LocalExecutorService -
    If the Executor queue is empty -
    CancelJob - Class in compbio.data.msa.jaxws
     
    CancelJob() - -Constructor for class compbio.data.msa.jaxws.CancelJob -
      -
    cancelJob(String) - -Method in interface compbio.data.msa.JManagement -
    Stop running the job jobId but leave its output untouched -
    cancelJob(String) - -Method in interface compbio.engine.AsyncExecutor -
    Stop running job. -
    cancelJob(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    cancelJob(String, ClusterSession) - -Static method in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    cancelJob() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    cancelJob(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    cancelJob(Future<ConfiguredExecutable<?>>, String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    cancelJob() - -Method in class compbio.engine.local.LocalRunner -
      -
    cancelJob() - -Method in interface compbio.engine.SyncExecutor -
    Stops running job. -
    cancelJob(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.GenericMetadataService -
      -
    cancelJob(String) - -Method in class compbio.ws.server.MafftWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    cancelJob(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    CancelJobResponse - Class in compbio.data.msa.jaxws
     
    CancelJobResponse() - -Constructor for class compbio.data.msa.jaxws.CancelJobResponse -
      -
    checkService(Services) - -Method in class compbio.ws.client.WSTester -
    Test JABA web service -
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of a string data together with the position in a file for - the next read operation.
    ChunkHolder(String, long) - -Constructor for class compbio.metadata.ChunkHolder -
      -
    Cleaner - Class in compbio.engine
    Deprecated. 
    Cleaner() - -Constructor for class compbio.engine.Cleaner -
    Deprecated.   -
    cleanProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Remove all non AA chars from the sequence -
    cleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all whitespace chars in the sequence string -
    cleanup(String) - -Method in interface compbio.engine.AsyncExecutor -
    Remove all files and a job directory for a jobid. -
    cleanup(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    cleanup() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    cleanup(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    cleanup(ConfiguredExecutable<?>) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    cleanup() - -Method in class compbio.engine.local.LocalRunner -
      -
    cleanup() - -Method in interface compbio.engine.SyncExecutor -
    Clean up after the job -
    close() - -Method in class compbio.data.sequence.FastaReader -
    Call this method to close the connection to the input file if you want to - free up the resources. -
    close() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    closeSilently(Logger, Closeable) - -Static method in class compbio.data.sequence.SequenceUtil -
    Closes the Closable and logs the exception if any -
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - -Constructor for class compbio.data.sequence.ClustalAlignmentUtil -
      -
    ClustalO - Class in compbio.runner.msa
     
    ClustalO() - -Constructor for class compbio.runner.msa.ClustalO -
    --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file -
    ClustalOWS - Class in compbio.ws.server
     
    ClustalOWS() - -Constructor for class compbio.ws.server.ClustalOWS -
      -
    ClustalW - Class in compbio.runner.msa
     
    ClustalW() - -Constructor for class compbio.runner.msa.ClustalW -
      -
    ClustalWS - Class in compbio.ws.server
     
    ClustalWS() - -Constructor for class compbio.ws.server.ClustalWS -
      -
    CLUSTER_STAT_IN_SEC - -Static variable in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    CLUSTER_TASK_ID_PREFIX - -Static variable in class compbio.engine.client.ConfExecutable -
      -
    CLUSTER_WORK_DIRECTORY - -Static variable in class compbio.engine.Configurator -
      -
    ClusterJobId - Class in compbio.engine
     
    ClusterJobId(String) - -Constructor for class compbio.engine.ClusterJobId -
      -
    ClusterSession - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil() - -Constructor for class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    COILS_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -
    For the region to be considered disordered the values must exceed these -
    CommandBuilder<T> - Class in compbio.engine.client
     
    CommandBuilder(String) - -Constructor for class compbio.engine.client.CommandBuilder -
      -
    compare(Hit, Hit) - -Method in class compbio.pipeline._jpred.Hit.EvalueComporator -
      -
    compare(Hit, Hit) - -Method in class compbio.pipeline._jpred.Hit.NumberComporator -
      -
    compareTo(Range) - -Method in class compbio.data.sequence.Range -
      -
    compareTo(Score) - -Method in class compbio.data.sequence.Score -
      -
    compareTo(Delayed) - -Method in class compbio.engine.FilePuller -
      -
    compbio.data._structure - package compbio.data._structure
     
    compbio.data.msa - package compbio.data.msa
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
     
    compbio.pipeline._jpred - package compbio.pipeline._jpred
     
    compbio.runner._jpred - package compbio.runner._jpred
     
    confDir - -Static variable in class compbio.engine.conf.PropertyHelperManager -
      -
    ConfExecutable<T> - Class in compbio.engine.client
     
    ConfExecutable(Executable<T>, String) - -Constructor for class compbio.engine.client.ConfExecutable -
      -
    Configurator - Class in compbio.engine
     
    Configurator() - -Constructor for class compbio.engine.Configurator -
      -
    ConfiguredExecutable<T> - Interface in compbio.engine.client
     
    configureExecutable(Executable<T>) - -Static method in class compbio.engine.Configurator -
      -
    configureExecutable(Executable<T>, List<FastaSequence>) - -Static method in class compbio.engine.Configurator -
      -
    configureExecutable(Executable<T>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    connect() - -Static method in class compbio.ws.client.AAConClient -
    Connects to a AACon web service by the host and the service name -
    connect(String, Services) - -Static method in class compbio.ws.client.Jws2Client -
    Connects to a web service by the host and the service name web service - type -
    connectToRegistry(String) - -Static method in class compbio.ws.client.Jws2Client -
    Get a connection of JABAWS registry -
    ConservationMethod - Enum in compbio.data.sequence
    Enumeration listing of all the supported methods.
    contextDestroyed(ServletContextEvent) - -Method in class compbio.stat.servlet.StatisticCollector -
      -
    contextDestroyed(ServletContextEvent) - -Method in class compbio.ws.server.ShutdownEngines -
      -
    contextInitialized(ServletContextEvent) - -Method in class compbio.stat.servlet.StatisticCollector -
      -
    contextInitialized(ServletContextEvent) - -Method in class compbio.ws.server.ShutdownEngines -
      -
    convertToAbsolute(String) - -Static method in class compbio.engine.client.Util -
      -
    copyAndValidateRConfig(RunnerConfig<?>) - -Method in class compbio.metadata.RunnerConfig -
      -
    countMatchesInSequence(String, String) - -Static method in class compbio.data.sequence.FastaSequence -
      -
    CustomAlign - Class in compbio.data.msa.jaxws
     
    CustomAlign() - -Constructor for class compbio.data.msa.jaxws.CustomAlign -
      -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with options. -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in class compbio.ws.server._MsaService -
      -
    customAlign(List<FastaSequence>, List<Option<ClustalO>>) - -Method in class compbio.ws.server.ClustalOWS -
      -
    customAlign(List<FastaSequence>, List<Option<ClustalW>>) - -Method in class compbio.ws.server.ClustalWS -
      -
    customAlign(List<FastaSequence>, List<Option<Mafft>>) - -Method in class compbio.ws.server.MafftWS -
      -
    customAlign(List<FastaSequence>, List<Option<Muscle>>) - -Method in class compbio.ws.server.MuscleWS -
      -
    customAlign(List<FastaSequence>, List<Option<Probcons>>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    customAlign(List<FastaSequence>, List<Option<Tcoffee>>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    CustomAlignResponse - Class in compbio.data.msa.jaxws
     
    CustomAlignResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    CustomAnalize - Class in compbio.data.msa.jaxws
     
    CustomAnalize() - -Constructor for class compbio.data.msa.jaxws.CustomAnalize -
      -
    customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences according to custom settings defined in options - list. -
    customAnalize(List<FastaSequence>, List<Option<Disembl>>) - -Method in class compbio.ws.server.DisemblWS -
      -
    customAnalize(List<FastaSequence>, List<Option<GlobPlot>>) - -Method in class compbio.ws.server.GlobPlotWS -
      -
    customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    CustomAnalizeResponse - Class in compbio.data.msa.jaxws
     
    CustomAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    -
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    -
    -
    deepClean() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    deepCleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all special characters and digits as well as whitespace chars - from the sequence -
    DEFAULT_COLUMN_SCORE - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default column scoring schema -
    DEFAULT_GAP_THRESHOLD - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default gap threshold value for SMERFS algorithm -
    DEFAULT_WINDOW_SIZE - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default window size value for SMERFS algorithm -
    deleteAllFiles(String) - -Static method in class compbio.engine.Cleaner -
    Deprecated.   -
    deleteFiles(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Cleaner -
    Deprecated. This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty) -
    DELIM - -Static variable in class compbio.engine.conf._Key -
    Deprecated.   -
    DELIM - -Static variable in class compbio.engine.conf.DirectoryManager -
      -
    DIGIT - -Static variable in class compbio.data.sequence.SequenceUtil -
    A digit -
    DirectoryManager - Class in compbio.engine.conf
     
    DirectoryManager() - -Constructor for class compbio.engine.conf.DirectoryManager -
      -
    disconnect() - -Method in class compbio.engine.FilePuller -
      -
    Disembl - Class in compbio.runner.disorder
    DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    Disembl() - -Constructor for class compbio.runner.disorder.Disembl -
      -
    DisemblWS - Class in compbio.ws.server
     
    DisemblWS() - -Constructor for class compbio.ws.server.DisemblWS -
      -
    DisorderMethod - Enum in compbio.data.sequence
     
    DisplayStat - Class in compbio.stat.servlet
     
    DisplayStat() - -Constructor for class compbio.stat.servlet.DisplayStat -
      -
    -
    - - - - - - - - - - - - - - - -
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    Environment - Class in compbio.runner._impl
    This is utility class to encapsulate environmental variables like directory paths
    EnvVariableProcessor - Class in compbio.engine.client
     
    EnvVariableProcessor() - -Constructor for class compbio.engine.client.EnvVariableProcessor -
      -
    equals(Object) - -Method in class compbio.data.sequence.Alignment -
    Please note that this implementation does not take the order of sequences - into account! -
    equals(Object) - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    equals(Object) - -Method in class compbio.data.sequence.FastaSequence -
      -
    equals(Object) - -Method in class compbio.data.sequence.Range -
      -
    equals(Object) - -Method in class compbio.data.sequence.Score -
      -
    equals(Object) - -Method in class compbio.data.sequence.ScoreManager -
      -
    equals(Object) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    equals(Object) - -Method in class compbio.engine.client.CommandBuilder -
      -
    equals(Object) - -Method in class compbio.engine.client.RunConfiguration -
      -
    equals(Object) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    equals(Object) - -Method in class compbio.engine.ClusterJobId -
      -
    equals(Object) - -Method in class compbio.engine.conf._Key -
    Deprecated.   -
    equals(Object) - -Method in class compbio.engine.FilePuller -
      -
    equals(Object) - -Method in class compbio.engine.Job -
      -
    equals(Object) - -Method in class compbio.metadata.ChunkHolder -
      -
    equals(Object) - -Method in class compbio.metadata.Limit -
      -
    equals(Object) - -Method in class compbio.metadata.Option -
      -
    equals(Object) - -Method in class compbio.metadata.Parameter -
      -
    equals(Object) - -Method in class compbio.metadata.Preset -
      -
    equals(Object) - -Method in class compbio.metadata.RunnerConfig -
      -
    equals(Object) - -Method in class compbio.metadata.ValueConstrain -
      -
    equals(Object) - -Method in class compbio.pipeline._jpred.Hit -
      -
    equals(Object) - -Method in class compbio.pipeline._jpred.PScore -
      -
    equals(Object) - -Method in class compbio.stat.collector.JobStat -
      -
    equals(Object) - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    ERROR - -Static variable in class compbio.engine.client.SkeletalExecutable -
      -
    Executable<T> - Interface in compbio.engine.client
    Interface to a native executable.
    Executable.ExecProvider - Enum in compbio.engine.client
     
    ExecutableWrapper - Class in compbio.engine.local
     
    ExecutableWrapper(ConfiguredExecutable<?>, String) - -Constructor for class compbio.engine.local.ExecutableWrapper -
      -
    executeJob() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    executeJob() - -Method in class compbio.engine.local.LocalRunner -
      -
    executeJob() - -Method in interface compbio.engine.SyncExecutor -
    Execute the job -
    ExecutionStatCollector - Class in compbio.stat.collector
    Number of runs of each WS = number of folders with name - - Number of successful runs = all runs with no result file - - Per period of time = limit per file creating time Runtime (avg/max) = - - started time - finished time - - Task & result size = result.size - - Abandoned runs - not collected runs - - Cancelled runs - cancelled - - Cluster vs local runs - - Reasons for failure = look in the err out? - - - Metadata required: - - work directory for local and cluster tasks = from Helper or cmd parameter.
    ExecutionStatCollector(String, int) - -Constructor for class compbio.stat.collector.ExecutionStatCollector -
    List subdirectories in the job directory -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    -    		 - -
    - PREV LETTER  - NEXT LETTER - FRAMES   - NO FRAMES   -  - - - -
    - - - -A B C D E F G H I J K L M N O P R S T U V W _
    - - - diff --git a/website/full_javadoc/index-files/index-6.html b/website/full_javadoc/index-files/index-6.html deleted file mode 100644 index 6400d3c..0000000 --- a/website/full_javadoc/index-files/index-6.html +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - -F-Index - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    - PREV LETTER  - NEXT LETTER - FRAMES   - NO FRAMES   -  - - - -
    - - - -A B C D E F G H I J K L M N O P R S T U V W _
    -

    -F

    -
    -
    FastaReader - Class in compbio.data.sequence
    Reads files with FASTA formatted sequences.
    FastaReader(String) - -Constructor for class compbio.data.sequence.FastaReader -
    Header data can contain non-ASCII symbols and read in UTF8 -
    FastaReader(InputStream) - -Constructor for class compbio.data.sequence.FastaReader -
    This class will not close the incoming stream! So the client should do - so. -
    FastaSequence - Class in compbio.data.sequence
    A FASTA formatted sequence.
    FastaSequence(String, String) - -Constructor for class compbio.data.sequence.FastaSequence -
    Upon construction the any whitespace characters are removed from the - sequence -
    FilePuller - Class in compbio.engine
     
    from - -Variable in class compbio.data.sequence.Range -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    -    		 - -
    - PREV LETTER  - NEXT LETTER - FRAMES   - NO FRAMES   -  - - - -
    - - - -A B C D E F G H I J K L M N O P R S T U V W _
    - - - diff --git a/website/full_javadoc/index-files/index-7.html b/website/full_javadoc/index-files/index-7.html deleted file mode 100644 index c4ce20a..0000000 --- a/website/full_javadoc/index-files/index-7.html +++ /dev/null @@ -1,1644 +0,0 @@ - - - - - - -G-Index - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    - PREV LETTER  - NEXT LETTER - FRAMES   - NO FRAMES   -  - - - -
    - - - -A B C D E F G H I J K L M N O P R S T U V W _
    -

    -G

    -
    -
    gapchar - -Static variable in class compbio.data.sequence.ClustalAlignmentUtil -
    Dash char to be used as gap char in the alignments -
    GenericMetadataService<T> - Class in compbio.ws.server
     
    get(String) - -Static method in class compbio.engine.PulledFileCache -
      -
    getAbandoned() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getAbandonedCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getAbandonedJobs() - -Method in class compbio.stat.collector.StatProcessor -
    Not collected. -
    getActualNumberofSequences() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getActualNumberofSequences() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getAllConstrainedParametersWithBorderValues(boolean) - -Method in class compbio.runner.OptionCombinator -
      -
    getAllConstrainedParametersWithRandomValues() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllOptions() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllParameters() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllStat() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    getAllStats() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    GetAnnotation - Class in compbio.data.msa.jaxws
     
    GetAnnotation() - -Constructor for class compbio.data.msa.jaxws.GetAnnotation -
      -
    getAnnotation(String) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Return the result of the job. -
    getAnnotation(String) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    getAnnotation(String, Logger) - -Static method in class compbio.ws.server.WSUtil -
      -
    getAnnotationForSequence(String) - -Method in class compbio.data.sequence.ScoreManager -
      -
    GetAnnotationResponse - Class in compbio.data.msa.jaxws
     
    GetAnnotationResponse() - -Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    getApproprieteQueue() - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetLastTested -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.IsOperating -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.TestService -
      -
    getArgument(String) - -Method in class compbio.metadata.RunnerConfig -
    Returns the argument by its name if found, NULL otherwise. -
    getArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -
    Returns the argument by option name, NULL if the argument is not found -
    getArguments(RunnerConfig<T>) - -Method in class compbio.metadata.Preset -
    Converts list of options as String to type Option -
    getArguments() - -Method in class compbio.metadata.RunnerConfig -
    Returns list of Parameter and Option supported by current - runner -
    getAsyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    getAsyncEngine(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Configurator -
      -
    getAsyncEngine(String) - -Static method in class compbio.engine.Configurator -
      -
    getAvgSeqLength() - -Method in class compbio.metadata.Limit -
      -
    getAvgSequenceLength(List<FastaSequence>) - -Static method in class compbio.metadata.Limit -
    Calculates an average sequence length of the dataset -
    getBlastAllRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getBlastBinDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getBlastDatabasesDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getByJobId(String, List<Job>) - -Static method in class compbio.engine.Job -
      -
    getByTaskId(String, List<Job>) - -Static method in class compbio.engine.Job -
      -
    getCalculationTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCancelled() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getCancelledCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getCancelledJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getChunk() - -Method in class compbio.metadata.ChunkHolder -
      -
    getClass(String) - -Static method in class compbio.engine.conf.DirectoryManager -
      -
    getClusterCpuNum(Class<? extends Executable<?>>) - -Static method in class compbio.engine.client.SkeletalExecutable -
      -
    getClusterJobId(String) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getClusterJobId() - -Method in class compbio.stat.collector.JobStat -
      -
    getClusterJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getClusterJobSettings() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getClusterJobSettings() - -Method in interface compbio.engine.client.Executable -
      -
    getClusterJobSettings() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getClusterJobSettings() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getClusterJobSettings() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getClusterStat() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getCommand(Executable.ExecProvider) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getCommand(Executable.ExecProvider, Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.BlastAll -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Mcl -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Ronn -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.RPSBlast -
      -
    getCommandName() - -Method in class compbio.runner._impl.BlastAll -
      -
    getCommandName() - -Method in class compbio.runner._impl.Mcl -
      -
    getCommandName() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getCommandName() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCommandName() - -Method in class compbio.runner._impl.Ronn -
      -
    getCommandName() - -Static method in class compbio.runner._impl.RPSBlast -
      -
    getCommands() - -Method in class compbio.engine.client.CommandBuilder -
      -
    getCommands(List<Option<T>>, String) - -Static method in class compbio.ws.server.WSUtil -
      -
    getCommandString() - -Method in class compbio.engine.client.CommandBuilder -
      -
    getConfExecutable() - -Method in class compbio.engine.Job -
      -
    getCPUTimeStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCPUUsageTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCreatedFiles() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getCreatedFiles() - -Method in interface compbio.engine.client.Executable -
    Deprecated.  -
    getCreatedFiles() - -Method in class compbio.engine.client.SkeletalExecutable -
    This method cannot really tell whether the files has actually been - created or not. -
    getCreatedFiles() - -Method in class compbio.runner._impl.BlastAll -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Mcl -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.OB -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Ronn -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.RPSBlast -
      -
    getCreatedFiles() - -Method in class compbio.runner.conservation.AACon -
      -
    getCreatedFiles() - -Method in class compbio.runner.disorder.Jronn -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.ClustalW -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Muscle -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Probcons -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getDataTransfered() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getDefaultLimit() - -Method in class compbio.metadata.LimitsManager -
      -
    getDefaultValue() - -Method in interface compbio.metadata.Argument -
      -
    getDefaultValue() - -Method in class compbio.metadata.Option -
    A default value of the option. -
    getDelay(TimeUnit) - -Method in class compbio.engine.FilePuller -
      -
    getDescription() - -Method in interface compbio.metadata.Argument -
      -
    getDescription() - -Method in class compbio.metadata.Option -
    A long description of the Option -
    getDescription() - -Method in class compbio.metadata.Preset -
      -
    getEarliestRecord() - -Method in class compbio.stat.collector.StatDB -
      -
    getEmail() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getEndTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getEngine(Executable<?>) - -Static method in class compbio.engine.LoadBalancer -
      -
    getEngine(Executable<V>, List<FastaSequence>) - -Static method in class compbio.engine.LoadBalancer -
      -
    getEngine(ConfiguredExecutable<?>) - -Static method in class compbio.ws.server.WSUtil -
      -
    getEnvironment() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getEnvironment() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getEnvVariables(String, Class<?>) - -Static method in class compbio.engine.client.EnvVariableProcessor -
      -
    getError() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getError() - -Method in interface compbio.engine.client.Executable -
      -
    getError() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getError() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getError() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getError() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getEscJobname() - -Method in class compbio.stat.collector.JobStat -
      -
    getExecProperty(String, Executable<?>) - -Static method in class compbio.engine.client.Util -
      -
    getExecProperty(String, Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getExecProvider() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getExecProvider() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getExecutable() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getExecutable() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getExecutionStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getExecutor() - -Static method in class compbio.engine.local.LocalExecutorService -
    This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally -
    getExitStatus() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getFailed() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getFailedJobs() - -Method in class compbio.stat.collector.StatProcessor -
    Started & finished but did not produce result -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Align -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Analize -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    getFile() - -Method in class compbio.engine.FilePuller -
      -
    getFinish() - -Method in class compbio.stat.collector.JobStat -
      -
    getFormatedSequence(int) - -Method in class compbio.data.sequence.FastaSequence -
    Format sequence per width letter in one string. -
    getFormattedFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getFullPath(String, String) - -Static method in class compbio.engine.client.Util -
      -
    getFurtherDetails() - -Method in interface compbio.metadata.Argument -
      -
    getFurtherDetails() - -Method in class compbio.metadata.Option -
    The URL where further details about the option can be found -
    getGapchar() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getId() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of id -
    getIncomplete() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getIncompleteCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getIncompleteJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getInput() - -Method in class compbio.engine.client.ConfExecutable -
    Not all input paths are relative! Input path could be absolute! -
    getInput() - -Method in interface compbio.engine.client.Executable -
      -
    getInput() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getInput() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getInput() - -Method in class compbio.runner._impl.BlastAll -
      -
    getInput() - -Method in class compbio.runner._impl.Mcl -
      -
    getInput() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getInput() - -Method in class compbio.runner._impl.OB -
      -
    getInput() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getInput() - -Method in class compbio.runner._impl.Ronn -
      -
    getInput() - -Method in class compbio.runner._impl.RPSBlast -
      -
    getInputSize() - -Method in class compbio.stat.collector.JobStat -
      -
    getInstance(ConfiguredExecutable<?>) - -Static method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getIOWait() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getIsCancelled() - -Method in class compbio.stat.collector.JobStat -
      -
    getIsCollected() - -Method in class compbio.stat.collector.JobStat -
      -
    getIsFinished() - -Method in class compbio.stat.collector.JobStat -
      -
    getJava() - -Static method in class compbio.engine.client.Util -
    Returns the absolute path to the Java executable from JAVA_HOME -
    getJobId() - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetAnnotation -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getJobId() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getJobId() - -Method in class compbio.engine.ClusterJobId -
      -
    getJobId() - -Method in class compbio.engine.Job -
      -
    getJobInfo() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
    This method will block before the calculation has completed and then - return the object containing a job execution statistics -
    getJobname() - -Method in class compbio.stat.collector.JobStat -
      -
    getJobNumber() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getJobPriority() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    GetJobStatus - Class in compbio.data.msa.jaxws
     
    GetJobStatus() - -Constructor for class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobStatus(String) - -Method in interface compbio.data.msa.JManagement -
    Return the status of the job. -
    getJobStatus(String) - -Method in interface compbio.engine.AsyncExecutor -
    Query the status of the job -
    getJobStatus(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed. -
    getJobStatus(ClusterJobId) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
    Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed. -
    getJobStatus(int) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
    Deprecated.  -
    getJobStatus() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getJobStatus(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getJobStatus(Future<ConfiguredExecutable<?>>) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getJobStatus() - -Method in class compbio.engine.local.LocalRunner -
      -
    getJobStatus() - -Method in interface compbio.engine.SyncExecutor -
    Query the status of the job by its id. -
    getJobStatus(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    getJobStatus(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    GetJobStatusResponse - Class in compbio.data.msa.jaxws
     
    GetJobStatusResponse() - -Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    GetLastTested - Class in compbio.data.msa.jaxws
     
    GetLastTested() - -Constructor for class compbio.data.msa.jaxws.GetLastTested -
      -
    getLastTested(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Number of seconds since the last test. -
    getLastTested(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    GetLastTestedOn - Class in compbio.data.msa.jaxws
     
    GetLastTestedOn() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    getLastTestedOn(Services) - -Method in interface compbio.data.msa.RegistryWS -
    The date and time the service has been verified to work last time -
    getLastTestedOn(Services) - -Method in class compbio.ws.server.RegistryWS -
    Can potentially return null if the service has not been tested yet. -
    GetLastTestedOnResponse - Class in compbio.data.msa.jaxws
     
    GetLastTestedOnResponse() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    GetLastTestedResponse - Class in compbio.data.msa.jaxws
     
    GetLastTestedResponse() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    getLength() - -Method in class compbio.data.sequence.FastaSequence -
      -
    GetLimit - Class in compbio.data.msa.jaxws
     
    GetLimit() - -Constructor for class compbio.data.msa.jaxws.GetLimit -
      -
    getLimit(String) - -Method in interface compbio.data.msa.Metadata -
    Get a Limit for a preset. -
    getLimit(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getLimit(String) - -Method in interface compbio.engine.client.Executable -
      -
    getLimit(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getLimit(String) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getLimit(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getLimit(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getLimit(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    getLimitByName(String) - -Method in class compbio.metadata.LimitsManager -
      -
    GetLimitResponse - Class in compbio.data.msa.jaxws
     
    GetLimitResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitResponse -
      -
    GetLimits - Class in compbio.data.msa.jaxws
     
    GetLimits() - -Constructor for class compbio.data.msa.jaxws.GetLimits -
      -
    getLimits() - -Method in interface compbio.data.msa.Metadata -
    List Limits supported by a web service. -
    getLimits() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getLimits() - -Method in interface compbio.engine.client.Executable -
      -
    getLimits() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getLimits(Class<T>) - -Static method in class compbio.engine.client.Util -
    For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then -
    getLimits() - -Method in class compbio.metadata.LimitsManager -
      -
    getLimits() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getLimits() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getLimits() - -Method in class compbio.ws.server.ClustalOWS -
      -
    getLimits() - -Method in class compbio.ws.server.ClustalWS -
      -
    getLimits() - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getLimits() - -Method in class compbio.ws.server.MafftWS -
      -
    getLimits() - -Method in class compbio.ws.server.MuscleWS -
      -
    getLimits() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getLimits() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetLimitsResponse - Class in compbio.data.msa.jaxws
     
    GetLimitsResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getLocalJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getLocalPath() - -Static method in class compbio.engine.conf.PropertyHelperManager -
    Method return the absolute path to the project root directory. -
    getLocalStat() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    getMax() - -Method in class compbio.metadata.ValueConstrain -
      -
    getMaxVMem() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getMclRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getMemoryLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. return max memory limit in Mb -
    getMemoryStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    getMetadata() - -Method in class compbio.data.sequence.Alignment -
      -
    getMethod(String) - -Static method in enum compbio.data.sequence.ConservationMethod -
      -
    getMethod() - -Method in class compbio.data.sequence.Score -
    Returns the ConservationMethod -
    getMin() - -Method in class compbio.metadata.ValueConstrain -
      -
    getName() - -Method in interface compbio.metadata.Argument -
      -
    getName() - -Method in class compbio.metadata.Option -
    Human readable name of the option -
    getName() - -Method in class compbio.metadata.Preset -
      -
    getName() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getNativeSpec() - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    getNetNglycRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getNextPosition() - -Method in class compbio.metadata.ChunkHolder -
      -
    getNumberOfScores() - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getNumberOfSeq() - -Method in class compbio.data.sequence.ScoreManager -
      -
    getNumberOfSequencesAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getNumberOfSequencesAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getOBRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getOnelineFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getOptionName() - -Method in class compbio.metadata.Parameter -
      -
    getOptionNames() - -Method in class compbio.metadata.Option -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    getOptions() - -Method in class compbio.metadata.Preset -
      -
    getOptions() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of the Options supported by the executable of type T -
    getOptionsAtRandom() - -Method in class compbio.runner.OptionCombinator -
      -
    getOutput() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getOutput() - -Method in interface compbio.engine.client.Executable -
      -
    getOutput() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getOutput() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getOutput() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getOutput() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getOutput() - -Method in class compbio.runner.disorder.IUPred -
      -
    getParameters() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getParameters() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getParameters(Executable.ExecProvider) - -Method in interface compbio.engine.client.Executable -
      -
    getParameters() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getParameters() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of parameters supported executable of type T. -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.conservation.AACon -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.disorder.Jronn -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.msa.ClustalO -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getParamValue(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    getPosition() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getPossibleValues() - -Method in interface compbio.metadata.Argument -
      -
    getPossibleValues() - -Method in class compbio.metadata.Option -
    List of possible optionNames -
    getPossibleValues() - -Method in class compbio.metadata.Parameter -
    List is more convenient to work with -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    getPreset() - -Method in class compbio.metadata.Limit -
      -
    getPresetByName(String) - -Method in class compbio.metadata.PresetManager -
      -
    getPresetName() - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    GetPresets - Class in compbio.data.msa.jaxws
     
    GetPresets() - -Constructor for class compbio.data.msa.jaxws.GetPresets -
      -
    getPresets() - -Method in interface compbio.data.msa.Metadata -
    Get presets supported by a web service -
    getPresets() - -Method in class compbio.metadata.PresetManager -
      -
    getPresets(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
      -
    getPresets() - -Method in class compbio.ws.server.ClustalOWS -
      -
    getPresets() - -Method in class compbio.ws.server.ClustalWS -
      -
    getPresets() - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getPresets() - -Method in class compbio.ws.server.MafftWS -
      -
    getPresets() - -Method in class compbio.ws.server.MuscleWS -
      -
    getPresets() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getPresets() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetPresetsResponse - Class in compbio.data.msa.jaxws
     
    GetPresetsResponse() - -Constructor for class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getPrmSeparator() - -Method in class compbio.metadata.RunnerConfig -
      -
    getProgram() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getProgress() - -Method in class compbio.engine.FilePuller -
      -
    getProgress(String) - -Static method in class compbio.engine.ProgressGetter -
      -
    getProgress(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    getPropertyHelper() - -Static method in class compbio.engine.conf.PropertyHelperManager -
    Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class. -
    getPSIBlastRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getQueue(int, int) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    getQueue(String) - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    getQueue() - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    getQueueByMemoryRequirements(int) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    getRanges() - -Method in class compbio.data.sequence.Score -
    Return Ranges if any Collections.EMPTY_SET otherwise -
    getRawUsage() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getRecordedJobStatus(String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getRemoteAddress() - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    GetResult - Class in compbio.data.msa.jaxws
     
    GetResult() - -Constructor for class compbio.data.msa.jaxws.GetResult -
      -
    getResult(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the result of the job. -
    getResult(String) - -Method in class compbio.ws.server._MsaService -
      -
    getResult(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    getResult(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getResult(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getResult(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getResult(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getResult(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetResultResponse - Class in compbio.data.msa.jaxws
     
    GetResultResponse() - -Constructor for class compbio.data.msa.jaxws.GetResultResponse -
      -
    getResults(String) - -Method in interface compbio.engine.AsyncExecutor -
    Retrieve the results of the job. -
    getResults() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getResults(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getResults() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getResults(String) - -Method in interface compbio.engine.client.Executable -
      -
    getResults(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    getResults(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getResults(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getResults(Future<ConfiguredExecutable<?>>, String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getResults(String) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getResults(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getResults(String) - -Method in class compbio.runner.conservation.AACon -
      -
    getResults(String) - -Method in class compbio.runner.disorder.Disembl -
      -
    getResults(String) - -Method in class compbio.runner.disorder.GlobPlot -
      -
    getResults(String) - -Method in class compbio.runner.disorder.IUPred -
      -
    getResults(String) - -Method in class compbio.runner.disorder.Jronn -
      -
    getResults(String) - -Method in class compbio.runner.msa.ClustalO -
      -
    getResults(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    getResults(String) - -Method in class compbio.runner.msa.Mafft -
      -
    getResults(String) - -Method in class compbio.runner.msa.Muscle -
      -
    getResults(String) - -Method in class compbio.runner.msa.Probcons -
      -
    getResults(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getResultSize() - -Method in class compbio.stat.collector.JobStat -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.TestServiceResponse -
      -
    getRonnRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getRPSBlastDatabasesDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getRPSBlastRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getRunConfiguration() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getRunnerByJobDirectory(File) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getRunnerClassName() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getRunnerClassName() - -Method in class compbio.metadata.PresetManager -
      -
    getRunnerClassName() - -Method in class compbio.metadata.RunnerConfig -
      -
    getRunnerLimits(Class<V>) - -Static method in class compbio.engine.client.ConfExecutable -
    This method should be executed once and result of its execution reused. -
    GetRunnerOptions - Class in compbio.data.msa.jaxws
     
    GetRunnerOptions() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptions -
      -
    getRunnerOptions() - -Method in interface compbio.data.msa.Metadata -
    Get options supported by a web service -
    getRunnerOptions(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ClustalOWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ClustalWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.MafftWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.MuscleWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws
     
    GetRunnerOptionsResponse() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getRunnerPresets(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    getRuntime() - -Method in class compbio.stat.collector.JobStat -
      -
    getSchema(String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getScoreByMethod(Enum<?>) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getScoreByMethod(String) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getScores() - -Method in class compbio.data.sequence.Score -
    The column scores for the alignment -
    getSeqNumber() - -Method in class compbio.metadata.Limit -
      -
    getSequence() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of sequence -
    getSequenceLenghtActual() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtActual() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequenceLenghtAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequences() - -Method in class compbio.data.sequence.Alignment -
      -
    getService(String) - -Static method in enum compbio.ws.client.Services -
      -
    getServiceByJobDirectory(File) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceByRunner(Class<Executable<?>>) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceImpl(Services) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServices(String) - -Static method in class compbio.ws.client.Jws2Client -
      -
    getSession() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getSingleWSStat(Services) - -Method in class compbio.stat.collector.StatProcessor -
      -
    getSize() - -Method in class compbio.data.sequence.Alignment -
      -
    getSMERFSColumnScore(String) - -Static method in enum compbio.data.sequence.SMERFSConstraints -
      -
    getStart() - -Method in class compbio.stat.collector.JobStat -
      -
    getStartTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getStatFile() - -Static method in class compbio.runner.conservation.AACon -
      -
    getStatFile() - -Static method in class compbio.runner.disorder.Jronn -
      -
    getStatFile() - -Static method in class compbio.runner.msa.ClustalO -
      -
    getStatFile() - -Static method in class compbio.runner.msa.ClustalW -
      -
    getStatFile() - -Static method in class compbio.runner.msa.Muscle -
      -
    getStatistics(JobInfo) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getStatLogger(Services, WebServiceContext) - -Static method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    getStats(int) - -Static method in class compbio.stat.servlet.util.StatCollection -
      -
    getStats(Date) - -Static method in class compbio.stat.servlet.util.StatCollection -
      -
    getSubmissionTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getSupportedOptions(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
      -
    getSupportedRuntimes() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getSupportedRuntimes() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getSupportedRuntimes(Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    GetSupportedServices - Class in compbio.data.msa.jaxws
     
    GetSupportedServices() - -Constructor for class compbio.data.msa.jaxws.GetSupportedServices -
      -
    getSupportedServices() - -Method in interface compbio.data.msa.RegistryWS -
    List of services that are functioning on the server. -
    getSupportedServices() - -Method in class compbio.ws.server.RegistryWS -
      -
    GetSupportedServicesResponse - Class in compbio.data.msa.jaxws
     
    GetSupportedServicesResponse() - -Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    getSyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    getSyncEngine(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Configurator -
      -
    getTask(String) - -Static method in class compbio.engine.SubmissionManager -
      -
    getTaskDirectory(Class<?>) - -Static method in class compbio.engine.conf.DirectoryManager -
      -
    getTaskId() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getTaskId() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getTaskId() - -Method in class compbio.engine.Job -
      -
    getTestArgs() - -Static method in class compbio.runner._impl.NetNglyc -
      -
    getTestArgs() - -Method in class compbio.runner._impl.OB -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Mcl -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.NetNglyc -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.OB -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Ronn -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.RPSBlast -
      -
    getTestParams() - -Static method in class compbio.runner._impl.Mcl -
      -
    getTimeLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. 0 - unlimited -
    getTimeStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getTmhmm2Runnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getTotal() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getTotalJobsCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getTotalRuntime() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getType() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getType() - -Method in class compbio.metadata.ValueConstrain -
      -
    getType() - -Method in class compbio.runner.conservation.AACon -
      -
    getType() - -Method in class compbio.runner.disorder.Disembl -
      -
    getType() - -Method in class compbio.runner.disorder.GlobPlot -
      -
    getType() - -Method in class compbio.runner.disorder.IUPred -
      -
    getType() - -Method in class compbio.runner.disorder.Jronn -
      -
    getType() - -Method in class compbio.runner.msa.ClustalO -
      -
    getType() - -Method in class compbio.runner.msa.ClustalW -
      -
    getType() - -Method in class compbio.runner.msa.Mafft -
      -
    getType() - -Method in class compbio.runner.msa.Muscle -
      -
    getType() - -Method in class compbio.runner.msa.Probcons -
      -
    getType() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getUsedSysTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getUsedUserTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getValidator(String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getValidator(Schema) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getValidValue() - -Method in class compbio.metadata.Parameter -
      -
    getVMem() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getWebService() - -Method in class compbio.stat.collector.JobStat -
      -
    getWorkDirectory(String) - -Method in interface compbio.engine.AsyncExecutor -
      -
    getWorkDirectory() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getWorkDirectory() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getWorkDirectory(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    getWorkDirectory() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getWorkDirectory(String) - -Static method in class compbio.engine.Configurator -
      -
    getWorkDirectory(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getWorkDirectory() - -Method in class compbio.engine.local.LocalRunner -
      -
    getWorkDirectory() - -Method in interface compbio.engine.SyncExecutor -
      -
    GlobPlot - Class in compbio.runner.disorder
    ./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.
    GlobPlot() - -Constructor for class compbio.runner.disorder.GlobPlot -
      -
    GlobPlotWS - Class in compbio.ws.server
     
    GlobPlotWS() - -Constructor for class compbio.ws.server.GlobPlotWS -
      -
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    hasDump() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hasExited() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hashCode() - -Method in class compbio.data.sequence.Alignment -
      -
    hashCode() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    hashCode() - -Method in class compbio.data.sequence.FastaSequence -
      -
    hashCode() - -Method in class compbio.data.sequence.Range -
      -
    hashCode() - -Method in class compbio.data.sequence.Score -
      -
    hashCode() - -Method in class compbio.data.sequence.ScoreManager -
      -
    hashCode() - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    hashCode() - -Method in class compbio.engine.client.CommandBuilder -
      -
    hashCode() - -Method in class compbio.engine.client.RunConfiguration -
      -
    hashCode() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    hashCode() - -Method in class compbio.engine.ClusterJobId -
      -
    hashCode() - -Method in class compbio.engine.conf._Key -
    Deprecated.   -
    hashCode() - -Method in class compbio.engine.FilePuller -
      -
    hashCode() - -Method in class compbio.engine.Job -
      -
    hashCode() - -Method in class compbio.metadata.ChunkHolder -
      -
    hashCode() - -Method in class compbio.metadata.Limit -
      -
    hashCode() - -Method in class compbio.metadata.Option -
      -
    hashCode() - -Method in class compbio.metadata.Parameter -
      -
    hashCode() - -Method in class compbio.metadata.Preset -
      -
    hashCode() - -Method in class compbio.metadata.ValueConstrain -
      -
    hashCode() - -Method in class compbio.pipeline._jpred.Hit -
      -
    hashCode() - -Method in class compbio.pipeline._jpred.PScore -
      -
    hashCode() - -Method in class compbio.stat.collector.JobStat -
      -
    hashCode() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    hasMoreData() - -Method in class compbio.engine.FilePuller -
      -
    hasNext() - -Method in class compbio.data.sequence.FastaReader -
    -
    hasParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    hasResult() - -Method in class compbio.stat.collector.JobStat -
      -
    hasSignaled() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hasStarted() - -Method in class compbio.stat.collector.JobStat -
      -
    hasTimeLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    Hit - Class in compbio.pipeline._jpred
     
    Hit() - -Constructor for class compbio.pipeline._jpred.Hit -
      -
    Hit.EvalueComporator - Class in compbio.pipeline._jpred
     
    Hit.EvalueComporator() - -Constructor for class compbio.pipeline._jpred.Hit.EvalueComporator -
      -
    Hit.NumberComporator - Class in compbio.pipeline._jpred
     
    Hit.NumberComporator() - -Constructor for class compbio.pipeline._jpred.Hit.NumberComporator -
      -
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    id - -Variable in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    initPull() - -Method in class compbio.engine.FilePuller -
      -
    INPUT - -Static variable in class compbio.engine.client.SkeletalExecutable -
      -
    IOHelper - Class in compbio.ws.client
     
    IOHelper() - -Constructor for class compbio.ws.client.IOHelper -
      -
    IS_CLUSTER_ENGINE_ENABLED - -Static variable in class compbio.engine.Configurator -
      -
    IS_LOCAL_ENGINE_ENABLED - -Static variable in class compbio.engine.Configurator -
      -
    isAbsolutePath(String) - -Static method in class compbio.engine.client.PathValidator -
    Whether a certain path is absolute or not is operation system dependent! -
    isAmbiguosProtein(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Check whether the sequence confirms to amboguous protein sequence -
    isClusterJob() - -Method in class compbio.stat.collector.JobStat -
      -
    isDefault() - -Method in class compbio.metadata.Limit -
      -
    isExceeded(List<FastaSequence>) - -Method in class compbio.metadata.Limit -
    Checks if the number of sequences or their average length in the dataset - exceeds this limit. -
    isFileCreated() - -Method in class compbio.engine.FilePuller -
      -
    isJavaLibrary(Class<?>) - -Static method in class compbio.engine.client.Util -
    Returns true of executableName.jar.file property has some value in the - Executable.properties file, false otherwise. -
    isMarked(String, JobStatus) - -Static method in class compbio.engine.client.Util -
      -
    isNonAmbNucleotideSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -
    isNucleotideSequence(FastaSequence) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    IsOperating - Class in compbio.data.msa.jaxws
     
    IsOperating() - -Constructor for class compbio.data.msa.jaxws.IsOperating -
      -
    isOperating(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Check whether a particular web service is working on this server -
    isOperating(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    IsOperatingResponse - Class in compbio.data.msa.jaxws
     
    IsOperatingResponse() - -Constructor for class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    isProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    isRequired() - -Method in class compbio.metadata.Option -
    Flag that indicated that this option must be specified in the command - line for an executable to run -
    isReturn() - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    isReturn() - -Method in class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    isValidClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Please note this method closes the input stream provided as a parameter -
    isValidDirectory(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    isValidExecutable(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    isValidJobId(String) - -Static method in class compbio.engine.client.Util -
      -
    IUPred - Class in compbio.runner.disorder
    iupred sequenceFile - - Maximum sequence length is 40000 chars.
    IUPred() - -Constructor for class compbio.runner.disorder.IUPred -
      -
    IUPredWS - Class in compbio.ws.server
     
    IUPredWS() - -Constructor for class compbio.ws.server.IUPredWS -
      -
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    compbio.data._structure 
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.data.msa.jaxws 
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model.
    compbio.engine 
    compbio.engine.client 
    compbio.engine.cluster.drmaa 
    compbio.engine.cluster.dundee 
    compbio.engine.conf 
    compbio.engine.local 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project.
    compbio.pipeline._jpred 
    compbio.runnerUtilities commonly used by all runners.
    compbio.runner._impl 
    compbio.runner._jpred 
    compbio.runner.conservation 
    compbio.runner.disorder 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa)
    compbio.stat.collector 
    compbio.stat.servlet 
    compbio.stat.servlet.util 
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services.
    compbio.ws.server 
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    -
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    -
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    -
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    -int aSequenceLenghtActual
    -
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    -Class compbio.metadata.ResultNotAvailableException extends Exception implements Serializable
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    -serialVersionUID: -5475613614578761L - -

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    -Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    - -

    -serialVersionUID: -86624836785110293L - -

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    - - - - - -
    -Class compbio.metadata.WrongParameterException extends Exception implements Serializable
    - -

    -serialVersionUID: -547775417557345769L - -

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    -Class compbio.stat.servlet.DisplayStat extends javax.servlet.http.HttpServlet implements Serializable
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