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+ + +
+ + +
+ +

JABAWS Javadoc

+

Data model javadoc- read this if your are coding against JABA Web Services

+

Complete javadoc - for developers who want to use JABAWS framework and use Engines and Executables directly

+

Starting up from the source code

+

SVN source repository:https://svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA_r1
+The repository contains a complete JABAWS Eclipse project. To use Eclipse with this repository you need to install Eclipse SVN plugin which could be found here: http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA. Eclipse update web site address is http://subclipse.tigris.org/update_1.4.x Take care to install 1.4.x version of the plugin, as SVN repository will not work with more recent clients. it would help to install TestNG plugin as well which could be downloaded from http://testng.org/doc/download.html. Please note however that no generated code is stored in the repository. That is to say that if you like to obtain client or server packages it is better to download them from the download section of this web site. Of cause If you want to make a modification to the source code you would need to generate distributives yourself. To do that first generate JAX-WS artifacts using build-server task from wsbuild.xml ant script, than you could use build.xml tasks to generate any of the distributives you need.

+

Structure of the project

+JABAWS layers +

Layers in the source code are defined in a different source folders which are: +
/webservices
+ /runner
+ /engine
+ /datamodel

+

JABAWS project is split into 4 layers. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So, to be able to use JABAWS one needs to have these classes. At the same time classes on this layer does not have any dependencies on the layers above.

+

The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. The code on this level code engine. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster. Thus currently code on this layer contain two engines. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above.

+

The third layer consists of the wrappers for the native executables and classes to handle their configuration. It depends on the engines and the data model, but know nothing about the web services.

+

Finally, the upper layer contains the web services, that depend on all the layers below.

+

The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. Any violation of the layer boundaries results in the compilation failure. Use Ant "Compile" or "Complile_with_debug" tasks to perform the staged compilation.

+

A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.

+ +

Running tests

+

The test results for the JABAWS package offered for download can be found here: Test Results
+JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases.

+

The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. +Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster. +Several testing groups are supported: +

    +
  • All tests (Test)
    • +
  • Cluster tests (Run_cluster_dependent_test)
    • +
  • Cluster independent tests ()
    • +
  • Windows only tests (All_cluster_independent_windows_only_tests)
    • +
  • Performance and stability tests (Long_tests)
    • +
  • Re-run failed tests (Rerun_failed_tests)
    • +
  • Run custom test (CustomTest)
    • +
+

To run the tests you need to download all sources from repository. Once you have done that, enter into the command line mode, change directory to the project directory and type: + ant -f build.xml <test group name>

+

. Make sure you have Apache Ant + installed and path to ant executable is defined in your path environmental variable. + Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests + use the following + command: ant -f build.xml Run_cluster_dependent_test + If you work under Linux you could use a simple script from the root folder of repository called runtests.sh This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse. +

+

+

A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in test-output/testng-failed.xml. and is used in the ant task called Rerun_failed_tests. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: ant -f build.xml Rerun_failed_tests CustomTest runs the test defined in the project root directory file called temp-testng-customsuite.xml. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure.

+

For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.

+ +

Preparing distributive's

+

There are a number of ant tasks aimed for preparing distributives for download. + Currently a few types of JABAWS packages are offered +

    +
  1. Client only (contains classes required to access JABA Web Services)
    2. +
  2. Platform specific JABAWS (windows and other)
    3. +
  3. JABA Web Services without JAXWS libraries ( a the runtime dependency)
    4. +
  4. JABAWS without binaries
    5. +
  5. JABAWS without binaries and jax-ws
    6. +
  6. JABAWS framework
    7. +
+

+ Corresponding build task names are: +
    +
  1. min-jaba-client
    2. +
  2. jaba-windows, jaba-complete
    3. +
  3. jaba-without-jaxws
    4. +
  4. jaba-no-binaries
    5. +
  5. jaba-no-jaxws-no-binaries
    6. +
  6. full-jaba-client
    7. +
+ +

The easiest way to build all distributives is to call build-all ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.

+

If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below.

+

Building web services artifacts

+

Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in webservices/compbio/ws/server/resource directory. It is not necessary to edit them if any of the JABAWS clients are used. However, if you would like to generate portable artifacts using wsimport based on the generated WSDL files then, <soap:address location="REPLACE_WITH_ACTUAL_URL"/>

+ +

must be replaced with an actual server URL including the web services context path. For example:

+

http://www.compbio.ac.uk:8080/ws

+

JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible.

+
+ + +
+
+ + + + + + diff --git a/website/dm_javadoc/allclasses-frame.html b/website/dm_javadoc/allclasses-frame.html new file mode 100644 index 0000000..8e9068d --- /dev/null +++ b/website/dm_javadoc/allclasses-frame.html @@ -0,0 +1,87 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
+ + + + + +
Alignment +
+AlignmentMetadata +
+Argument +
+ChunkHolder +
+ClustalAlignmentUtil +
+FastaSequence +
+JobExecutionException +
+JobStatus +
+JobSubmissionException +
+Jws2Client +
+Limit +
+LimitExceededException +
+LimitsManager +
+MsaWS +
+Option +
+Parameter +
+Preset +
+PresetManager +
+Program +
+ResultNotAvailableException +
+RunnerConfig +
+SequenceUtil +
+Services +
+UnknownFileFormatException +
+UnsupportedRuntimeException +
+ValueConstrain +
+ValueConstrain.Type +
+WrongParameterException +
+WSTester +
+
+ + + diff --git a/website/dm_javadoc/allclasses-noframe.html b/website/dm_javadoc/allclasses-noframe.html new file mode 100644 index 0000000..c4eee2f --- /dev/null +++ b/website/dm_javadoc/allclasses-noframe.html @@ -0,0 +1,87 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
+ + + + + +
Alignment +
+AlignmentMetadata +
+Argument +
+ChunkHolder +
+ClustalAlignmentUtil +
+FastaSequence +
+JobExecutionException +
+JobStatus +
+JobSubmissionException +
+Jws2Client +
+Limit +
+LimitExceededException +
+LimitsManager +
+MsaWS +
+Option +
+Parameter +
+Preset +
+PresetManager +
+Program +
+ResultNotAvailableException +
+RunnerConfig +
+SequenceUtil +
+Services +
+UnknownFileFormatException +
+UnsupportedRuntimeException +
+ValueConstrain +
+ValueConstrain.Type +
+WrongParameterException +
+WSTester +
+
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/MsaWS.html b/website/dm_javadoc/compbio/data/msa/MsaWS.html new file mode 100644 index 0000000..2578550 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/MsaWS.html @@ -0,0 +1,556 @@ + + + + + + +MsaWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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 MsaWS<T>

+
+
Type Parameters:
T - executable type / web service type
+
+
+
public interface MsaWS<T>
+ + +

+Multiple Sequence Alignment (MSA) Web Services Interface +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ booleancancelJob(java.lang.String jobId) + +
+          Stop running the job jobId but leave its output untouched
+ java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
+          Align a list of sequences with options.
+ JobStatusgetJobStatus(java.lang.String jobId) + +
+          Return the status of the job.
+ Limit<T>getLimit(java.lang.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
+ AlignmentgetResult(java.lang.String jobId) + +
+          Return the result of the job.
+ RunnerConfig<T>getRunnerOptions() + +
+          Get options supported by a web service
+ java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+ ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
+          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
+  +

+ + + + + + + + +
+Method Detail
+ +

+align

+
+java.lang.String align(java.util.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. +
java.security.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

+
+java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                             java.util.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. +
java.security.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

+
+java.lang.String presetAlign(java.util.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. +
java.security.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(java.lang.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. +
java.security.InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid + format
+
+
+
+ +

+cancelJob

+
+boolean cancelJob(java.lang.String jobId)
+
+
Stop running the job jobId but leave its output untouched +

+

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

+getJobStatus

+
+JobStatus getJobStatus(java.lang.String jobId)
+
+
Return the status of the job. +

+

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

+pullExecStatistics

+
+ChunkHolder pullExecStatistics(java.lang.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: +
java.security.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
+
+
+
+ +

+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(java.lang.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/dm_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html new file mode 100644 index 0000000..0d7adda --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Interface compbio.data.msa.MsaWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+
+

+Uses of Interface
compbio.data.msa.MsaWS

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

+ + + + + +
+Uses of MsaWS in compbio.ws.client
+  +

+ + + + + + + + + +
Methods in compbio.ws.client that return MsaWS
+static + + + + +
+<T> MsaWS<T>
+		Jws2Client.connect(java.lang.String host, + Services service) + +
+          Connects to a web service by the host and the service name
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-frame.html b/website/dm_javadoc/compbio/data/msa/package-frame.html new file mode 100644 index 0000000..4ed7be0 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-frame.html @@ -0,0 +1,32 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + +compbio.data.msa + + + + +
+Interfaces  + +
+MsaWS
+ + + + diff --git a/website/dm_javadoc/compbio/data/msa/package-summary.html b/website/dm_javadoc/compbio/data/msa/package-summary.html new file mode 100644 index 0000000..a0eb501 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-summary.html @@ -0,0 +1,176 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+

+Package compbio.data.msa +

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

+See: +
+          Description +

+ + + + + + + + + +
+Interface Summary
MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
+  + +

+

+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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+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-tree.html b/website/dm_javadoc/compbio/data/msa/package-tree.html new file mode 100644 index 0000000..b17702d --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-tree.html @@ -0,0 +1,151 @@ + + + + + + +compbio.data.msa Class Hierarchy + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Hierarchy For Package compbio.data.msa +

+
+
+
Package Hierarchies:
All Packages
+
+

+Interface Hierarchy +

+
    +
  • compbio.data.msa.MsaWS<T>
+
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-use.html b/website/dm_javadoc/compbio/data/msa/package-use.html new file mode 100644 index 0000000..b4a22d9 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-use.html @@ -0,0 +1,171 @@ + + + + + + +Uses of Package compbio.data.msa + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Uses of Package
compbio.data.msa

+
+ + + + + + + + + +
+Packages that use compbio.data.msa
compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + + + + +
+Classes in compbio.data.msa used by compbio.ws.client
MsaWS + +
+          Multiple Sequence Alignment (MSA) Web Services Interface
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..b2f0dc5 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,403 @@ + + + + + + +Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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 Alignment

+
+java.lang.Object
+  extended by compbio.data.sequence.Alignment
+
+
+
+
@Immutable
+public final class Alignment
extends java.lang.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(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
Alignment(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(java.lang.Object obj) + +
+          Please note that this implementation does not take the order of sequences + into account!
+ AlignmentMetadatagetMetadata() + +
+           
+ java.util.List<FastaSequence>getSequences() + +
+           
+ intgetSize() + +
+           
+ inthashCode() + +
+           
+ java.lang.StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Alignment

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

+Alignment

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

+getSequences

+
+public java.util.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 java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

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

+

+
Overrides:
equals in class java.lang.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/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..10400ce --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,329 @@ + + + + + + +AlignmentMetadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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 AlignmentMetadata

+
+java.lang.Object
+  extended by compbio.data.sequence.AlignmentMetadata
+
+
+
+
@Immutable
+public class AlignmentMetadata
extends java.lang.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(java.lang.Object obj) + +
+           
+ chargetGapchar() + +
+           
+ ProgramgetProgram() + +
+           
+ inthashCode() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, 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(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..39bba28 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,387 @@ + + + + + + +ClustalAlignmentUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ +

+ +compbio.data.sequence +
+Class ClustalAlignmentUtil

+
+java.lang.Object
+  extended by compbio.data.sequence.ClustalAlignmentUtil
+
+
+
+
public final class ClustalAlignmentUtil
extends java.lang.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(java.io.InputStream input) + +
+          Please note this method closes the input stream provided as a parameter
+static AlignmentreadClustalFile(java.io.File file) + +
+           
+static AlignmentreadClustalFile(java.io.InputStream instream) + +
+          Read Clustal formatted alignment.
+static voidwriteClustalAlignment(java.io.OutputStream outStream, + Alignment alignment) + +
+          Write Clustal formatted alignment Limitations: does not record the + consensus.
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, 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(java.io.InputStream instream)
+                                 throws java.io.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} +
java.io.IOException +
UnknownFileFormatException
+
+
+
+ +

+isValidClustalFile

+
+public static boolean isValidClustalFile(java.io.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(java.io.OutputStream outStream,
+                                         Alignment alignment)
+                                  throws java.io.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:
outStream -
alignment - +
Throws: +
java.io.IOException
+
+
+
+ +

+readClustalFile

+
+public static Alignment readClustalFile(java.io.File file)
+                                 throws UnknownFileFormatException,
+                                        java.io.IOException
+
+
+ +
Throws: +
UnknownFileFormatException +
java.io.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/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..c9a97f6 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,471 @@ + + + + + + +FastaSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ 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 java.lang.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(java.lang.String id, + java.lang.String sequence) + +
+          Upon construction the any whitespace characters are removed from the + sequence
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static intcountMatchesInSequence(java.lang.String theString, + java.lang.String theRegExp) + +
+           
+ booleanequals(java.lang.Object obj) + +
+           
+ java.lang.StringgetFormatedSequence(int width) + +
+          Format sequence per width letter in one string.
+ java.lang.StringgetFormattedFasta() + +
+           
+ java.lang.StringgetId() + +
+          Gets the value of id
+ intgetLength() + +
+           
+ java.lang.StringgetOnelineFasta() + +
+           
+ java.lang.StringgetSequence() + +
+          Gets the value of sequence
+ inthashCode() + +
+           
+ java.lang.StringtoString() + +
+          Same as oneLineFasta
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+FastaSequence

+
+public FastaSequence(java.lang.String id,
+                     java.lang.String sequence)
+
+
Upon construction the any whitespace characters are removed from the + sequence +

+

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

+getId

+
+public java.lang.String getId()
+
+
Gets the value of id +

+

+ +
Returns:
the value of id
+
+
+
+ +

+getSequence

+
+public java.lang.String getSequence()
+
+
Gets the value of sequence +

+

+ +
Returns:
the value of sequence
+
+
+
+ +

+countMatchesInSequence

+
+public static int countMatchesInSequence(java.lang.String theString,
+                                         java.lang.String theRegExp)
+
+
+
+
+
+
+ +

+getFormattedFasta

+
+public java.lang.String getFormattedFasta()
+
+
+
+
+
+
+ +

+getOnelineFasta

+
+public java.lang.String getOnelineFasta()
+
+
+ +
Returns:
one line name, next line sequence, no matter what the sequence + length is
+
+
+
+ +

+getFormatedSequence

+
+public java.lang.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 java.lang.String toString()
+
+
Same as oneLineFasta +

+

+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.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/dm_javadoc/compbio/data/sequence/Program.html b/website/dm_javadoc/compbio/data/sequence/Program.html new file mode 100644 index 0000000..4a41196 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,388 @@ + + + + + + +Program + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ 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:
java.io.Serializable, java.lang.Comparable<Program>
+
+
+
+
public enum Program
extends java.lang.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(java.lang.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
clone, compareTo, equals, finalize, 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(java.lang.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: +
java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
java.lang.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/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..81a6209 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,673 @@ + + + + + + +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 java.lang.Object
+ + +

+Utility class for operations on sequences +

+ +

+

+
Version:
+
1.0
+
Author:
+
Petr Troshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Field Summary
+static java.util.regex.PatternAA + +
+          Valid Amino acids
+static java.util.regex.PatternAMBIGUOUS_AA + +
+          Same as AA pattern but with two additional letters - XU
+static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE + +
+          Ambiguous nucleotide
+static java.util.regex.PatternDIGIT + +
+          A digit
+static java.util.regex.PatternNON_AA + +
+          inversion of AA pattern
+static java.util.regex.PatternNON_NUCLEOTIDE + +
+          Non nucleotide
+static java.util.regex.PatternNONWORD + +
+          Non word
+static java.util.regex.PatternNUCLEOTIDE + +
+          Nucleotides a, t, g, c, u
+static java.util.regex.PatternWHITE_SPACE + +
+          A whitespace character: [\t\n\x0B\f\r]
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static java.lang.StringcleanSequence(java.lang.String sequence) + +
+          Removes all whitespace chars in the sequence string
+static voidcloseSilently(java.util.logging.Logger log, + java.io.Closeable stream) + +
+          Closes the Closable and logs the exception if any
+static java.lang.StringdeepCleanSequence(java.lang.String sequence) + +
+          Removes all special characters and digits as well as whitespace chars + from the sequence
+static booleanisAmbiguosProtein(java.lang.String sequence) + +
+          Check whether the sequence confirms to amboguous protein sequence
+static booleanisNonAmbNucleotideSequence(java.lang.String sequence) + +
+          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
+static booleanisNucleotideSequence(FastaSequence s) + +
+           
+static booleanisProteinSequence(java.lang.String sequence) + +
+           
+static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) + +
+          Reads fasta sequences from inStream into the list of FastaSequence + objects
+static voidwriteFasta(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) + +
+          Writes FastaSequence in the file, each sequence will take one line only
+static voidwriteFasta(java.io.OutputStream outstream, + java.util.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(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

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

+WHITE_SPACE

+
+public static final java.util.regex.Pattern WHITE_SPACE
+
+
A whitespace character: [\t\n\x0B\f\r] +

+

+
+
+
+ +

+DIGIT

+
+public static final java.util.regex.Pattern DIGIT
+
+
A digit +

+

+
+
+
+ +

+NONWORD

+
+public static final java.util.regex.Pattern NONWORD
+
+
Non word +

+

+
+
+
+ +

+AA

+
+public static final java.util.regex.Pattern AA
+
+
Valid Amino acids +

+

+
+
+
+ +

+NON_AA

+
+public static final java.util.regex.Pattern NON_AA
+
+
inversion of AA pattern +

+

+
+
+
+ +

+AMBIGUOUS_AA

+
+public static final java.util.regex.Pattern AMBIGUOUS_AA
+
+
Same as AA pattern but with two additional letters - XU +

+

+
+
+
+ +

+NUCLEOTIDE

+
+public static final java.util.regex.Pattern NUCLEOTIDE
+
+
Nucleotides a, t, g, c, u +

+

+
+
+
+ +

+AMBIGUOUS_NUCLEOTIDE

+
+public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
+
+
Ambiguous nucleotide +

+

+
+
+
+ +

+NON_NUCLEOTIDE

+
+public static final java.util.regex.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(java.lang.String sequence)
+
+
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +

+

+
+
+
+
+ +

+cleanSequence

+
+public static java.lang.String cleanSequence(java.lang.String sequence)
+
+
Removes all whitespace chars in the sequence string +

+

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

+deepCleanSequence

+
+public static java.lang.String deepCleanSequence(java.lang.String sequence)
+
+
Removes all special characters and digits as well as whitespace chars + from the sequence +

+

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

+isProteinSequence

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

+isAmbiguosProtein

+
+public static boolean isAmbiguosProtein(java.lang.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(java.io.OutputStream outstream,
+                              java.util.List<FastaSequence> sequences,
+                              int width)
+                       throws java.io.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: +
java.io.IOException
+
+
+
+ +

+writeFastaKeepTheStream

+
+public static void writeFastaKeepTheStream(java.io.OutputStream outstream,
+                                           java.util.List<FastaSequence> sequences,
+                                           int width)
+                                    throws java.io.IOException
+
+
+ +
Throws: +
java.io.IOException
+
+
+
+ +

+readFasta

+
+public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
+                                               throws java.io.IOException
+
+
Reads fasta sequences from inStream into the list of FastaSequence + objects +

+

+
Parameters:
inStream - from +
Returns:
list of FastaSequence objects +
Throws: +
java.io.IOException
+
+
+
+ +

+writeFasta

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

+

+
Parameters:
os -
sequences - +
Throws: +
java.io.IOException
+
+
+
+ +

+closeSilently

+
+public static final void closeSilently(java.util.logging.Logger log,
+                                       java.io.Closeable stream)
+
+
Closes the Closable and logs the exception if any +

+

+
Parameters:
log -
stream -
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..e694f79 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,300 @@ + + + + + + +UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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 UnknownFileFormatException

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

+

+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + +
+Constructor Summary
UnknownFileFormatException() + +
+           
UnknownFileFormatException(java.io.File file, + java.lang.Throwable cause) + +
+           
UnknownFileFormatException(java.lang.String message) + +
+           
UnknownFileFormatException(java.lang.String message, + java.lang.Throwable cause) + +
+           
UnknownFileFormatException(java.lang.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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException()
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(java.io.File file,
+                                  java.lang.Throwable cause)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(java.lang.String message,
+                                  java.lang.Throwable cause)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(java.lang.String message)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(java.lang.Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..ac7e106 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,236 @@ + + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.Alignment

+
+ + + + + + + + + + + + + +
+Packages that use Alignment
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

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

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

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

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

+ + + + + + + + + +
Methods in compbio.data.sequence with parameters of type Alignment
+static voidClustalAlignmentUtil.writeClustalAlignment(java.io.OutputStream outStream, + Alignment alignment) + +
+          Write Clustal formatted alignment Limitations: does not record the + consensus.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html new file mode 100644 index 0000000..fbc8221 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html @@ -0,0 +1,196 @@ + + + + + + +Uses of Class compbio.data.sequence.AlignmentMetadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+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(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html new file mode 100644 index 0000000..8317054 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.ClustalAlignmentUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

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

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html new file mode 100644 index 0000000..15dffc9 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,362 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.FastaSequence

+
+ + + + + + + + + + + + + + + + + +
+Packages that use FastaSequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
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 FastaSequence in compbio.data.msa
+  +

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.data.msa with type arguments of type FastaSequence
+ java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
+          Align a list of sequences with options.
+ java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+  +

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

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
+ java.util.List<FastaSequence>Alignment.getSequences() + +
+           
+static java.util.List<FastaSequence>SequenceUtil.readFasta(java.io.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(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) + +
+          Writes FastaSequence in the file, each sequence will take one line only
+static voidSequenceUtil.writeFasta(java.io.OutputStream outstream, + java.util.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(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) + +
+           
+  +

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

+ + + + + +
+Uses of FastaSequence in compbio.metadata
+  +

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

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Program.html b/website/dm_javadoc/compbio/data/sequence/class-use/Program.html new file mode 100644 index 0000000..5dcd170 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Program.html @@ -0,0 +1,221 @@ + + + + + + +Uses of Class compbio.data.sequence.Program + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+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(java.lang.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(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
AlignmentMetadata(Program program, + char gapchar) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html new file mode 100644 index 0000000..b07a50a --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.SequenceUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.SequenceUtil

+
+No usage of compbio.data.sequence.SequenceUtil +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html new file mode 100644 index 0000000..4816f77 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Class compbio.data.sequence.UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Uses of Class
compbio.data.sequence.UnknownFileFormatException

+
+ + + + + + + + + +
+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. 
+  +

+ + + + + +
+Uses of UnknownFileFormatException in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that throw UnknownFileFormatException
+static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) + +
+           
+static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) + +
+          Read Clustal formatted alignment.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-frame.html b/website/dm_javadoc/compbio/data/sequence/package-frame.html new file mode 100644 index 0000000..34e0fc6 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-frame.html @@ -0,0 +1,62 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + +compbio.data.sequence + + + + +
+Classes  + +
+Alignment +
+AlignmentMetadata +
+ClustalAlignmentUtil +
+FastaSequence +
+SequenceUtil
+ + + + + + +
+Enums  + +
+Program
+ + + + + + +
+Exceptions  + +
+UnknownFileFormatException
+ + + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-summary.html b/website/dm_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..879bbb2 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,224 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+

+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
FastaSequenceA FASTA formatted sequence.
SequenceUtilUtility class for operations on sequences
+  + +

+ + + + + + + + + +
+Enum Summary
ProgramThe list of programmes that can produce alignments
+  + +

+ + + + + + + + + +
+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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+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-tree.html b/website/dm_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..d2759d2 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,168 @@ + + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+
+

+Hierarchy For Package compbio.data.sequence +

+
+
+
Package Hierarchies:
All Packages
+
+

+Class Hierarchy +

+ +

+Enum Hierarchy +

+
    +
  • java.lang.Object
      +
    • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
    +
+
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+ + + + + + + + + + + + +
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+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-use.html b/website/dm_javadoc/compbio/data/sequence/package-use.html new file mode 100644 index 0000000..89c7cbb --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-use.html @@ -0,0 +1,240 @@ + + + + + + +Uses of Package compbio.data.sequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Uses of Package
compbio.data.sequence

+
+ + + + + + + + + + + + + + + + + +
+Packages that use compbio.data.sequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
+  +

+ + + + + + + + + + + +
+Classes in compbio.data.sequence used by compbio.data.msa
Alignment + +
+          Multiple sequence alignment.
FastaSequence + +
+          A FASTA formatted sequence.
+  +

+ + + + + + + + + + + + + + + + + + + + +
+Classes in compbio.data.sequence used by compbio.data.sequence
Alignment + +
+          Multiple sequence alignment.
AlignmentMetadata + +
+          Alignment metadata e.g.
FastaSequence + +
+          A FASTA formatted sequence.
Program + +
+          The list of programmes that can produce alignments
UnknownFileFormatException + +
+           
+  +

+ + + + + + + + +
+Classes in compbio.data.sequence used by compbio.metadata
FastaSequence + +
+          A FASTA formatted sequence.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Argument.html b/website/dm_javadoc/compbio/metadata/Argument.html new file mode 100644 index 0000000..c55be5f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Argument.html @@ -0,0 +1,327 @@ + + + + + + +Argument + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +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
+ java.lang.StringgetDefaultValue() + +
+           
+ java.lang.StringgetDescription() + +
+           
+ java.net.URLgetFurtherDetails() + +
+           
+ java.lang.StringgetName() + +
+           
+ java.util.List<java.lang.String>getPossibleValues() + +
+           
+ voidsetValue(java.lang.String defaultValue) + +
+          Set default values for the parameter or an option
+  +

+ + + + + + + + +
+Method Detail
+ +

+getFurtherDetails

+
+java.net.URL getFurtherDetails()
+
+
+
+
+
+
+ +

+getDefaultValue

+
+java.lang.String getDefaultValue()
+
+
+
+
+
+
+ +

+getDescription

+
+java.lang.String getDescription()
+
+
+
+
+
+
+ +

+getName

+
+java.lang.String getName()
+
+
+
+
+
+
+ +

+getPossibleValues

+
+java.util.List<java.lang.String> getPossibleValues()
+
+
+ +
Returns:
List of values allowed for an Argument
+
+
+
+ +

+setValue

+
+void setValue(java.lang.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
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..b443911 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,350 @@ + + + + + + +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
+ + + +
+ +

+ +compbio.metadata +
+Class ChunkHolder

+
+java.lang.Object
+  extended by compbio.metadata.ChunkHolder
+
+
+
+
public class ChunkHolder
extends java.lang.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(java.lang.String chunk, + long position) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(java.lang.Object obj) + +
+           
+ java.lang.StringgetChunk() + +
+           
+ longgetNextPosition() + +
+           
+ inthashCode() + +
+           
+ java.lang.StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+ChunkHolder

+
+public ChunkHolder(java.lang.String chunk,
+                   long position)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getChunk

+
+public java.lang.String getChunk()
+
+
+
+
+
+
+ +

+getNextPosition

+
+public long getNextPosition()
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.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/dm_javadoc/compbio/metadata/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..6037fe3 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,279 @@ + + + + + + +JobExecutionException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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 JobExecutionException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobExecutionException
+
+
+
All Implemented Interfaces:
java.io.Serializable
+
+
+
+
public class JobExecutionException
extends java.lang.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(java.lang.String message) + +
+           
JobExecutionException(java.lang.String message, + java.lang.Throwable cause) + +
+           
JobExecutionException(java.lang.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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JobExecutionException

+
+public JobExecutionException(java.lang.String message)
+
+
+
+ +

+JobExecutionException

+
+public JobExecutionException(java.lang.Throwable cause)
+
+
+
+ +

+JobExecutionException

+
+public JobExecutionException(java.lang.String message,
+                             java.lang.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/dm_javadoc/compbio/metadata/JobStatus.html b/website/dm_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..69cb3ea --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,465 @@ + + + + + + +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:
java.io.Serializable, java.lang.Comparable<JobStatus>
+
+
+
+
public enum JobStatus
extends java.lang.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(java.lang.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
clone, compareTo, equals, finalize, 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(java.lang.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: +
java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
java.lang.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/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html new file mode 100644 index 0000000..7cf5a8f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,283 @@ + + + + + + +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
+ + + +
+ +

+ +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:
java.io.Serializable
+
+
+
Direct Known Subclasses:
LimitExceededException, UnsupportedRuntimeException
+
+
+
+
public class JobSubmissionException
extends java.lang.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(java.lang.String message) + +
+           
JobSubmissionException(java.lang.String message, + java.lang.Throwable cause) + +
+           
JobSubmissionException(java.lang.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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JobSubmissionException

+
+public JobSubmissionException(java.lang.String message)
+
+
+
+ +

+JobSubmissionException

+
+public JobSubmissionException(java.lang.Throwable cause)
+
+
+
+ +

+JobSubmissionException

+
+public JobSubmissionException(java.lang.String message,
+                              java.lang.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/dm_javadoc/compbio/metadata/Limit.html b/website/dm_javadoc/compbio/metadata/Limit.html new file mode 100644 index 0000000..cc32e07 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,459 @@ + + + + + + +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 java.lang.Object
+ + +

+A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
pvtroshin
+
See Also:
LimitsManager
+
+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
Limit(int seqNumber, + int seqLength, + java.lang.String preset) + +
+           
Limit(int seqNumber, + int seqLength, + java.lang.String preset, + boolean isDefault) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(java.lang.Object obj) + +
+           
+ intgetAvgSeqLength() + +
+           
+static intgetAvgSequenceLength(java.util.List<FastaSequence> data) + +
+          Calculates an average sequence length of the dataset
+ java.lang.StringgetPreset() + +
+           
+ intgetSeqNumber() + +
+           
+ inthashCode() + +
+           
+ booleanisDefault() + +
+           
+ booleanisExceeded(java.util.List<FastaSequence> data) + +
+          Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit
+ java.lang.StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Limit

+
+public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset)
+
+
+
+ +

+Limit

+
+public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset,
+             boolean isDefault)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getPreset

+
+public java.lang.String getPreset()
+
+
+
+
+
+
+ +

+getAvgSeqLength

+
+public int getAvgSeqLength()
+
+
+
+
+
+
+ +

+getSeqNumber

+
+public int getSeqNumber()
+
+
+
+
+
+
+ +

+isDefault

+
+public boolean isDefault()
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+isExceeded

+
+public boolean isExceeded(java.util.List<FastaSequence> data)
+
+
Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit +

+

+
Parameters:
data - +
Returns:
true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise.
+
+
+
+ +

+getAvgSequenceLength

+
+public static int getAvgSequenceLength(java.util.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/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/LimitExceededException.html new file mode 100644 index 0000000..2432a4a --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,357 @@ + + + + + + +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:
java.io.Serializable
+
+
+
+
public class LimitExceededException
extends JobSubmissionException
+ + +

+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(java.lang.String message) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ intgetActualNumberofSequences() + +
+           
+ intgetNumberOfSequencesAllowed() + +
+           
+ intgetSequenceLenghtActual() + +
+           
+ intgetSequenceLenghtAllowed() + +
+           
+static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, + java.util.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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+LimitExceededException

+
+public LimitExceededException(java.lang.String message)
+
+
+ + + + + + + + +
+Method Detail
+ +

+newLimitExceeded

+
+public static LimitExceededException newLimitExceeded(Limit<?> limit,
+                                                      java.util.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/dm_javadoc/compbio/metadata/LimitsManager.html b/website/dm_javadoc/compbio/metadata/LimitsManager.html new file mode 100644 index 0000000..95142fa --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,363 @@ + + + + + + +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 java.lang.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(java.lang.String presetName) + +
+           
+ java.util.List<Limit<T>>getLimits() + +
+           
+ java.lang.StringtoString() + +
+           
+ voidvalidate(PresetManager<T> presets) + +
+          Validate Limits
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+LimitsManager

+
+public LimitsManager()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getLimits

+
+public java.util.List<Limit<T>> getLimits()
+
+
+ +
Returns:
all limits defined for an executable T
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+getLimitByName

+
+public Limit<T> getLimitByName(java.lang.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 javax.xml.bind.ValidationException
+
+
Validate Limits +

+

+
Parameters:
presets - +
Throws: +
javax.xml.bind.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/dm_javadoc/compbio/metadata/Option.html b/website/dm_javadoc/compbio/metadata/Option.html new file mode 100644 index 0000000..9f6722b --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Option.html @@ -0,0 +1,822 @@ + + + + + + +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 java.lang.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
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Field Summary
+protected  java.lang.StringdefaultValue + +
+           
+protected  java.lang.Stringdescription + +
+           
+protected  java.net.URLfurtherDetails + +
+           
+protected  booleanisRequired + +
+           
+protected  java.lang.Stringname + +
+           
+  + + + + + + + + + + +
+Constructor Summary
Option(java.lang.String name, + java.lang.String description) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) + +
+          Adds an option to the optionName list
+ booleanequals(java.lang.Object obj) + +
+           
+ java.lang.StringgetDefaultValue() + +
+          A default value of the option.
+ java.lang.StringgetDescription() + +
+          A long description of the Option
+ java.net.URLgetFurtherDetails() + +
+          The URL where further details about the option can be found
+ java.lang.StringgetName() + +
+          Human readable name of the option
+ java.util.List<java.lang.String>getOptionNames() + +
+           
+ java.util.List<java.lang.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(java.lang.String defaultVal) + +
+          Sets one of the values defined in optionList as default.
+ voidsetDescription(java.lang.String description) + +
+           
+ voidsetFurtherDetails(java.net.URL furtherDetails) + +
+           
+ voidsetName(java.lang.String name) + +
+           
+ voidsetOptionNames(java.util.Set<java.lang.String> optionNames) + +
+           
+ voidsetRequired(boolean isRequired) + +
+           
+ voidsetValue(java.lang.String dValue) + +
+          Set default values for the parameter or an option
+ java.lang.StringtoCommand(java.lang.String nameValueSeparator) + +
+          Convert the option to the command string.
+ java.lang.StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

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

+description

+
+protected java.lang.String description
+
+
+
+
+
+ +

+name

+
+protected java.lang.String name
+
+
+
+
+
+ +

+isRequired

+
+protected boolean isRequired
+
+
+
+
+
+ +

+furtherDetails

+
+protected java.net.URL furtherDetails
+
+
+
+
+
+ +

+defaultValue

+
+protected java.lang.String defaultValue
+
+
+
+
+ + + + + + + + +
+Constructor Detail
+ +

+Option

+
+public Option(java.lang.String name,
+              java.lang.String description)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getName

+
+public java.lang.String getName()
+
+
Human readable name of the option +

+

+
Specified by:
getName in interface Argument<T>
+
+
+
+
+
+
+ +

+setName

+
+public void setName(java.lang.String name)
+
+
+
+
+
+
+
+
+
+ +

+getDescription

+
+public java.lang.String getDescription()
+
+
A long description of the Option +

+

+
Specified by:
getDescription in interface Argument<T>
+
+
+
+
+
+
+ +

+setDescription

+
+public void setDescription(java.lang.String description)
+
+
+
+
+
+
+
+
+
+ +

+getFurtherDetails

+
+public java.net.URL getFurtherDetails()
+
+
The URL where further details about the option can be found +

+

+
Specified by:
getFurtherDetails in interface Argument<T>
+
+
+
+
+
+
+ +

+setFurtherDetails

+
+public void setFurtherDetails(java.net.URL furtherDetails)
+
+
+
+
+
+
+
+
+
+ +

+getDefaultValue

+
+public java.lang.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(java.lang.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 java.util.List<java.lang.String> getOptionNames()
+
+
+
+
+
+ +
Returns:
List of option names
+
+
+
+ +

+setOptionNames

+
+public void setOptionNames(java.util.Set<java.lang.String> optionNames)
+
+
+
+
+
+
+
+
+
+ +

+addOptionNames

+
+public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
+
+
Adds an option to the optionName list +

+

+
+
+
+
Parameters:
value - +
Returns:
modified optionName list
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+toCommand

+
+public java.lang.String toCommand(java.lang.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(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+getPossibleValues

+
+public java.util.List<java.lang.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(java.lang.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/dm_javadoc/compbio/metadata/Parameter.html b/website/dm_javadoc/compbio/metadata/Parameter.html new file mode 100644 index 0000000..e929ee8 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,590 @@ + + + + + + +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
+
+ +

+ + + + + + + +
+Field Summary
+  + + + + + + + +
Fields inherited from class compbio.metadata.Option
defaultValue, description, furtherDetails, isRequired, name
+  + + + + + + + + + + +
+Constructor Summary
Parameter(java.lang.String name, + java.lang.String description) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) + +
+          Adds an option to the optionName list
+ java.util.Set<java.lang.String>addPossibleValues(java.lang.String... value) + +
+           
+ booleanequals(java.lang.Object obj) + +
+           
+ java.lang.StringgetOptionName() + +
+           
+ java.util.List<java.lang.String>getPossibleValues() + +
+          List is more convenient to work with
+ ValueConstraingetValidValue() + +
+           
+ inthashCode() + +
+           
+ voidsetDefaultValue(java.lang.String defaultVal) + +
+          Sets one of the values defined in optionList as default.
+ voidsetOptionName(java.lang.String optionName) + +
+           
+ voidsetOptionNames(java.util.Set<java.lang.String> optionName) + +
+           
+ voidsetPossibleValues(java.util.Set<java.lang.String> possibleValues) + +
+           
+ voidsetValidValue(ValueConstrain validValue) + +
+           
+ java.lang.StringtoCommand(java.lang.String nameValueSeparator) + +
+          Convert the option to the command string.
+ java.lang.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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Parameter

+
+public Parameter(java.lang.String name,
+                 java.lang.String description)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getValidValue

+
+public ValueConstrain getValidValue()
+
+
+
+
+
+
+ +

+setValidValue

+
+public void setValidValue(ValueConstrain validValue)
+
+
+
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class Option<T>
+
+
+
+
+
+
+ +

+toCommand

+
+public java.lang.String toCommand(java.lang.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(java.lang.Object obj)
+
+
+
Overrides:
equals in class Option<T>
+
+
+
+
+
+
+ +

+getPossibleValues

+
+public java.util.List<java.lang.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(java.util.Set<java.lang.String> possibleValues)
+
+
+
+
+
+
+ +

+addPossibleValues

+
+public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Option<T>
+
+
+
+
+
+
+ +

+setOptionNames

+
+public void setOptionNames(java.util.Set<java.lang.String> optionName)
+
+
+
Overrides:
setOptionNames in class Option<T>
+
+
+
+
+
+
+ +

+addOptionNames

+
+public java.util.Set<java.lang.String> addOptionNames(java.lang.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 java.lang.String getOptionName()
+
+
+
+
+
+
+ +

+setOptionName

+
+public void setOptionName(java.lang.String optionName)
+
+
+
+
+
+
+ +

+setDefaultValue

+
+public void setDefaultValue(java.lang.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/dm_javadoc/compbio/metadata/Preset.html b/website/dm_javadoc/compbio/metadata/Preset.html new file mode 100644 index 0000000..c2ded88 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,455 @@ + + + + + + +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 java.lang.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(java.lang.Object obj) + +
+           
+ java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) + +
+          Converts list of options as String to type Option
+ java.lang.StringgetDescription() + +
+           
+ java.lang.StringgetName() + +
+           
+ java.util.List<java.lang.String>getOptions() + +
+           
+ inthashCode() + +
+           
+ voidsetDescription(java.lang.String description) + +
+           
+ voidsetName(java.lang.String name) + +
+           
+ voidsetOptions(java.util.List<java.lang.String> option) + +
+           
+ java.lang.StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Preset

+
+public Preset()
+
+
+ + + + + + + + +
+Method Detail
+ +

+setOptions

+
+public void setOptions(java.util.List<java.lang.String> option)
+
+
+
+
+
+
+ +

+setName

+
+public void setName(java.lang.String name)
+
+
+
+
+
+
+ +

+setDescription

+
+public void setDescription(java.lang.String description)
+
+
+
+
+
+
+ +

+getOptions

+
+public java.util.List<java.lang.String> getOptions()
+
+
+ +
Returns:
a List of Options as a String
+
+
+
+ +

+getName

+
+public java.lang.String getName()
+
+
+ +
Returns:
- name of the Preset
+
+
+
+ +

+getDescription

+
+public java.lang.String getDescription()
+
+
+ +
Returns:
- a long description of the Preset
+
+
+
+ +

+getArguments

+
+public java.util.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 java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.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/dm_javadoc/compbio/metadata/PresetManager.html b/website/dm_javadoc/compbio/metadata/PresetManager.html new file mode 100644 index 0000000..465d36a --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,428 @@ + + + + + + +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 java.lang.Object
+ + +

+Collection of presets and methods to manipulate them @see Preset +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Field Summary
+static java.lang.StringLOCAL_ENGINE_LIMIT_PRESET + +
+           
+  + + + + + + + + + + +
+Constructor Summary
PresetManager() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Preset<T>getPresetByName(java.lang.String presetName) + +
+           
+ java.util.List<Preset<T>>getPresets() + +
+           
+ java.lang.StringgetRunnerClassName() + +
+           
+ voidsetPresets(java.util.List<Preset<T>> presets) + +
+           
+ voidsetRunnerClassName(java.lang.String runnerClassName) + +
+           
+ java.lang.StringtoString() + +
+           
+ voidvalidate(RunnerConfig<T> options) + +
+          Checks whether preset option and parameter are defined in RunnerConfig + object.
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

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

+LOCAL_ENGINE_LIMIT_PRESET

+
+public static final java.lang.String LOCAL_ENGINE_LIMIT_PRESET
+
+
+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Constructor Detail
+ +

+PresetManager

+
+public PresetManager()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getPresets

+
+public java.util.List<Preset<T>> getPresets()
+
+
+
+
+
+
+ +

+setPresets

+
+public void setPresets(java.util.List<Preset<T>> presets)
+
+
+
+
+
+
+ +

+getRunnerClassName

+
+public java.lang.String getRunnerClassName()
+
+
+ +
Returns:
fully qualified class name of type T
+
+
+
+ +

+setRunnerClassName

+
+public void setRunnerClassName(java.lang.String runnerClassName)
+
+
+
+
+
+
+ +

+getPresetByName

+
+public Preset<T> getPresetByName(java.lang.String presetName)
+
+
+
Parameters:
presetName - +
Returns:
preset by its name, null if no preset found
+
+
+
+ +

+validate

+
+public void validate(RunnerConfig<T> options)
+              throws javax.xml.bind.ValidationException
+
+
Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly! +

+

+ +
Throws: +
javax.xml.bind.ValidationException - if preset is found to be invalid.
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.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/dm_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html new file mode 100644 index 0000000..0cc0324 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,280 @@ + + + + + + +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:
java.io.Serializable
+
+
+
+
public class ResultNotAvailableException
extends java.lang.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(java.lang.String message) + +
+           
ResultNotAvailableException(java.lang.String message, + java.lang.Throwable cause) + +
+           
ResultNotAvailableException(java.lang.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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(java.lang.String message)
+
+
+
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(java.lang.Throwable cause)
+
+
+
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(java.lang.String message,
+                                   java.lang.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/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html new file mode 100644 index 0000000..cb761eb --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,706 @@ + + + + + + +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 java.lang.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(java.lang.Object obj) + +
+           
+ Option<T>getArgument(java.lang.String name) + +
+          Returns the argument by its name if found, NULL otherwise.
+ Option<T>getArgumentByOptionName(java.lang.String optionName) + +
+          Returns the argument by option name, NULL if the argument is not found
+ java.util.List<Option<T>>getArguments() + +
+          Returns list of Parameter and Option supported by current + runner
+ java.util.List<Option<T>>getOptions() + +
+          Returns the list of the Options supported by the executable of type T
+ java.util.List<Parameter<T>>getParameters() + +
+          Returns the list of parameters supported executable of type T.
+ java.lang.StringgetPrmSeparator() + +
+           
+ java.lang.StringgetRunnerClassName() + +
+           
+ booleanremoveArgument(java.lang.String name) + +
+          Removes the argument Argument if found.
+ booleanremoveArgumentByOptionName(java.lang.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(java.util.List<Option<T>> parameters) + +
+          Adds the list of options or parameters to the internal list of options
+ voidsetParameters(java.util.List<Parameter<T>> parameters) + +
+          Sets the list of parameters as internal list
+ voidsetPrmSeparator(java.lang.String prmSeparator) + +
+          Sets name value separator character
+ voidsetRunnerClassName(java.lang.String runnerClassName) + +
+          Set the name of a runner class
+ java.lang.StringtoString() + +
+           
+ voidvalidate() + +
+          Validate the value of the argument.
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+RunnerConfig

+
+public RunnerConfig()
+
+
+ + + + + + + + +
+Method Detail
+ +

+copyAndValidateRConfig

+
+public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
+
+
+
+
+
+
+ +

+getOptions

+
+public java.util.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 java.util.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 java.lang.String getPrmSeparator()
+
+
+ +
Returns:
name value separator character
+
+
+
+ +

+setPrmSeparator

+
+public void setPrmSeparator(java.lang.String prmSeparator)
+
+
Sets name value separator character +

+

+
Parameters:
prmSeparator - the separator char
+
+
+
+ +

+setOptions

+
+public void setOptions(java.util.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 java.lang.String getRunnerClassName()
+
+
+ +
Returns:
fully qualified class name for type T
+
+
+
+ +

+setRunnerClassName

+
+public void setRunnerClassName(java.lang.String runnerClassName)
+
+
Set the name of a runner class +

+

+
Parameters:
runnerClassName - the name of the executable wrapping class
+
+
+
+ +

+setParameters

+
+public void setParameters(java.util.List<Parameter<T>> parameters)
+
+
Sets the list of parameters as internal list +

+

+
Parameters:
parameters - the list of parameters
+
+
+
+ +

+getParameters

+
+public java.util.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 java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+
+ +

+getArgument

+
+public Option<T> getArgument(java.lang.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(java.lang.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(java.lang.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(java.lang.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 javax.xml.bind.ValidationException
+
+
Validate the value of the argument. Checks whether the argument value is + in the valid values range. +

+

+ +
Throws: +
javax.xml.bind.ValidationException - if any of the arguments found invalid which is when +
+
  • Parameter value outside ValueConstrain boundary
    • +
  • Parameter name is not listed in possible values
    • +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..82d35e6 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,265 @@ + + + + + + +UnsupportedRuntimeException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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:
    java.io.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(java.lang.String message) + +
    +           
    UnsupportedRuntimeException(java.lang.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
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(java.lang.String message)
    +
    +
    +
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/dm_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..12d1789 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,325 @@ + + + + + + +ValueConstrain.Type + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 ValueConstrain.Type

    +
    +java.lang.Object
+  extended by java.lang.Enum<ValueConstrain.Type>
+      extended by compbio.metadata.ValueConstrain.Type
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<ValueConstrain.Type>
    +
    +
    +
    Enclosing class:
    ValueConstrain
    +
    +
    +
    +
    public static enum ValueConstrain.Type
    extends java.lang.Enum<ValueConstrain.Type>
    + + +

    +

    + +

    + + + + + + + + + + + + + +
    +Enum Constant Summary
    Float + +
    +           
    Integer + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ValueConstrain.TypevalueOf(java.lang.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
    clone, compareTo, equals, finalize, 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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..de6a77f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,440 @@ + + + + + + +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
    + + + +
    + +

    + +compbio.metadata +
    +Class ValueConstrain

    +
    +java.lang.Object
+  extended by compbio.metadata.ValueConstrain
+
    +
    +
    +
    public class ValueConstrain
    extends java.lang.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(java.lang.Object obj) + +
    +           
    + java.lang.NumbergetMax() + +
    +           
    + java.lang.NumbergetMin() + +
    +           
    + ValueConstrain.TypegetType() + +
    +           
    + inthashCode() + +
    +           
    + voidsetMax(java.lang.String max) + +
    +           
    + voidsetMin(java.lang.String min) + +
    +           
    + voidsetType(ValueConstrain.Type type) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, finalize, 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 java.lang.Number getMax()
    +
    +
    +
    +
    +
    +
    + +

    +setMax

    +
    +public void setMax(java.lang.String max)
    +
    +
    +
    +
    +
    +
    + +

    +getMin

    +
    +public java.lang.Number getMin()
    +
    +
    +
    +
    +
    +
    + +

    +setMin

    +
    +public void setMin(java.lang.String min)
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.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/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..95222ef --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,294 @@ + + + + + + +WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 WrongParameterException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.WrongParameterException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class WrongParameterException
    extends java.lang.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(java.lang.String message) + +
    +           
    WrongParameterException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    WrongParameterException(java.lang.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
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WrongParameterException

    +
    +public WrongParameterException(Option<?> option)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.String message)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.String message,
+                               java.lang.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/dm_javadoc/compbio/metadata/class-use/Argument.html b/website/dm_javadoc/compbio/metadata/class-use/Argument.html new file mode 100644 index 0000000..5c956cf --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Argument.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Interface compbio.metadata.Argument + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html new file mode 100644 index 0000000..64d348d --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html @@ -0,0 +1,182 @@ + + + + + + +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. 
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return ChunkHolder
    + ChunkHolderMsaWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html new file mode 100644 index 0000000..afe8d0f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.metadata.JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobExecutionException

    +
    +No usage of compbio.metadata.JobExecutionException +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html new file mode 100644 index 0000000..d3f85a0 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html @@ -0,0 +1,219 @@ + + + + + + +Uses of Class compbio.metadata.JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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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.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 JobStatus in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return JobStatus
    + JobStatusMsaWS.getJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return JobStatus
    +static JobStatusJobStatus.valueOf(java.lang.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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html new file mode 100644 index 0000000..883bcfb --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html @@ -0,0 +1,237 @@ + + + + + + +Uses of Class compbio.metadata.JobSubmissionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobSubmissionException

    +
    + + + + + + + + + + + + + +
    +Packages that use JobSubmissionException
    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. 
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw JobSubmissionException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Subclasses of JobSubmissionException in compbio.metadata
    + classLimitExceededException + +
    +          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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Limit.html b/website/dm_javadoc/compbio/metadata/class-use/Limit.html new file mode 100644 index 0000000..8af3925 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Limit.html @@ -0,0 +1,251 @@ + + + + + + +Uses of Class compbio.metadata.Limit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.Limit

    +
    + + + + + + + + + + + + + +
    +Packages that use Limit
    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. 
    +  +

    + + + + + +
    +Uses of Limit in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return Limit
    + Limit<T>MsaWS.getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    +  +

    + + + + + +
    +Uses of Limit in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Limit
    + Limit<T>LimitsManager.getDefaultLimit() + +
    +           
    + Limit<T>LimitsManager.getLimitByName(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Limit
    + java.util.List<Limit<T>>LimitsManager.getLimits() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Limit
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +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. 
    +  +

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    +Uses of LimitExceededException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw LimitExceededException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return LimitExceededException
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.LimitsManager

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    +Packages that use LimitsManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return LimitsManager
    + LimitsManager<T>MsaWS.getLimits() + +
    +          List Limits supported by a web service.
    +  +

    +

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    +Packages that use Option
    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. 
    +  +

    + + + + + +
    +Uses of Option in compbio.data.msa
    +  +

    + + + + + + + + + +
    Method parameters in compbio.data.msa with type arguments of type Option
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    +  +

    + + + + + +
    +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(java.lang.String name) + +
    +          Returns the argument by its name if found, NULL otherwise.
    + Option<T>RunnerConfig.getArgumentByOptionName(java.lang.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
    + java.util.List<Option<T>>RunnerConfig.getArguments() + +
    +          Returns list of Parameter and Option supported by current + runner
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + java.util.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(java.util.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) + +
    +           
    +  +

    +

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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. 
    +  +

    + + + + + +
    +Uses of Parameter in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Parameter
    + java.util.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(java.util.List<Parameter<T>> parameters) + +
    +          Sets the list of parameters as internal list
    +  +

    +

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    +
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    +Packages that use Preset
    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. 
    +  +

    + + + + + +
    +Uses of Preset in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa with parameters of type Preset
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of Preset in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return Preset
    + Preset<T>PresetManager.getPresetByName(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Preset
    + java.util.List<Preset<T>>PresetManager.getPresets() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Preset
    + voidPresetManager.setPresets(java.util.List<Preset<T>> presets) + +
    +           
    +  +

    +

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    +Uses of Class
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    +Packages that use PresetManager
    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. 
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return PresetManager
    + PresetManager<T>MsaWS.getPresets() + +
    +          Get presets supported by a web service
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type PresetManager
    + voidLimitsManager.validate(PresetManager<T> presets) + +
    +          Validate Limits
    +  +

    +

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    +Packages that use ResultNotAvailableException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that throw ResultNotAvailableException
    + AlignmentMsaWS.getResult(java.lang.String jobId) + +
    +          Return the result of the job.
    +  +

    +

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    +Packages that use RunnerConfig
    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. 
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return RunnerConfig
    + RunnerConfig<T>MsaWS.getRunnerOptions() + +
    +          Get options supported by a web service
    +  +

    + + + + + +
    +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) + +
    +           
    + java.util.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.
    +  +

    +

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    compbio.metadata.UnsupportedRuntimeException

    +
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    +Packages that use UnsupportedRuntimeException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    +

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    compbio.metadata.ValueConstrain.Type

    +
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    +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(java.lang.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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    +Uses of Class
    compbio.metadata.ValueConstrain

    +
    + + + + + + + + + +
    +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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    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html new file mode 100644 index 0000000..debc65d --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html @@ -0,0 +1,252 @@ + + + + + + +Uses of Class compbio.metadata.WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.WrongParameterException

    +
    + + + + + + + + + + + + + +
    +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. 
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw WrongParameterException
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that throw WrongParameterException
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidParameter.setDefaultValue(java.lang.String defaultVal) + +
    +           
    + voidOption.setDefaultValue(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidArgument.setValue(java.lang.String defaultValue) + +
    +          Set default values for the parameter or an option
    + voidOption.setValue(java.lang.String dValue) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-frame.html b/website/dm_javadoc/compbio/metadata/package-frame.html new file mode 100644 index 0000000..f97ccf8 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-frame.html @@ -0,0 +1,93 @@ + + + + + + +compbio.metadata + + + + + + + + + + + +compbio.metadata + + + + +
    +Interfaces  + +
    +Argument
    + + + + + + +
    +Classes  + +
    +ChunkHolder +
    +Limit +
    +LimitsManager +
    +Option +
    +Parameter +
    +Preset +
    +PresetManager +
    +RunnerConfig +
    +ValueConstrain
    + + + + + + +
    +Enums  + +
    +JobStatus +
    +ValueConstrain.Type
    + + + + + + +
    +Exceptions  + +
    +JobExecutionException +
    +JobSubmissionException +
    +LimitExceededException +
    +ResultNotAvailableException +
    +UnsupportedRuntimeException +
    +WrongParameterException
    + + + + diff --git a/website/dm_javadoc/compbio/metadata/package-summary.html b/website/dm_javadoc/compbio/metadata/package-summary.html new file mode 100644 index 0000000..5a82c1e --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-summary.html @@ -0,0 +1,286 @@ + + + + + + +compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +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.
    LimitExceededExceptionThrown 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
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-tree.html b/website/dm_javadoc/compbio/metadata/package-tree.html new file mode 100644 index 0000000..c75cbfa --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-tree.html @@ -0,0 +1,178 @@ + + + + + + +compbio.metadata Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For Package compbio.metadata +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-use.html b/website/dm_javadoc/compbio/metadata/package-use.html new file mode 100644 index 0000000..2319b12 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-use.html @@ -0,0 +1,347 @@ + + + + + + +Uses of Package compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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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.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +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 + +
    +          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.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 + +
    +          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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/Jws2Client.html b/website/dm_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..3908c59 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,360 @@ + + + + + + +Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.client +
    +Class Jws2Client

    +
    +java.lang.Object
+  extended by compbio.ws.client.Jws2Client
+
    +
    +
    +
    public class Jws2Client
    extends java.lang.Object
    + + +

    +A command line client for JAva Bioinformatics Analysis Web Services +

    + +

    +

    +
    Version:
    +
    1.0
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> MsaWS<T>
    +    		connect(java.lang.String host, + Services service) + +
    +          Connects to a web service by the host and the service name
    +static java.lang.StringgetHost(java.lang.String[] cmd) + +
    +          Extracts host name from the command line
    +static java.lang.StringgetServiceName(java.lang.String[] cmd) + +
    +          Extracts service name from the command line
    +static voidmain(java.lang.String[] args) + +
    +          Starts command line client, if no parameter are supported print help.
    +static booleanvalidURL(java.lang.String urlstr) + +
    +          Attempt to construct the URL object from the string
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +validURL

    +
    +public static boolean validURL(java.lang.String urlstr)
    +
    +
    Attempt to construct the URL object from the string +

    +

    +
    Parameters:
    urlstr - +
    Returns:
    true if it succeed false otherwise
    +
    +
    +
    + +

    +getServiceName

    +
    +public static java.lang.String getServiceName(java.lang.String[] cmd)
    +
    +
    Extracts service name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    service name or null if it is not defined
    +
    +
    +
    + +

    +getHost

    +
    +public static java.lang.String getHost(java.lang.String[] cmd)
    +
    +
    Extracts host name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    host name or null if it is not defined
    +
    +
    +
    + +

    +connect

    +
    +public static <T> MsaWS<T> connect(java.lang.String host,
+                                   Services service)
+                        throws javax.xml.ws.WebServiceException
    +
    +
    Connects to a web service by the host and the service name +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    host -
    service - +
    Returns:
    MsaWS +
    Throws: +
    javax.xml.ws.WebServiceException
    +
    +
    +
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    Starts command line client, if no parameter are supported print help. Two + parameters are required for successfull 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!
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/dm_javadoc/compbio/ws/client/Services.html b/website/dm_javadoc/compbio/ws/client/Services.html new file mode 100644 index 0000000..4b844db --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Services.html @@ -0,0 +1,412 @@ + + + + + + +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
    + + + +
    + +

    + +compbio.ws.client +
    +Enum Services

    +
    +java.lang.Object
+  extended by java.lang.Enum<Services>
+      extended by compbio.ws.client.Services
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Services>
    +
    +
    +
    +
    public enum Services
    extends java.lang.Enum<Services>
    + + +

    +List of web services currently supported by JABAWS version 1 +

    + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    ClustalWS + +
    +           
    MafftWS + +
    +           
    MuscleWS + +
    +           
    ProbconsWS + +
    +           
    TcoffeeWS + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static ServicesgetService(java.lang.Class wsImplClass) + +
    +           
    +static ServicesgetService(java.lang.String servName) + +
    +           
    +static ServicesvalueOf(java.lang.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
    clone, compareTo, equals, finalize, 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
    +
    +
    +
    +
    +
    + +

    +TcoffeeWS

    +
    +public static final Services TcoffeeWS
    +
    +
    +
    +
    +
    + +

    +ProbconsWS

    +
    +public static final Services ProbconsWS
    +
    +
    +
    +
    + + + + + + + + +
    +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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    +
    + +

    +getService

    +
    +public static Services getService(java.lang.String servName)
    +
    +
    +
    +
    +
    +
    + +

    +getService

    +
    +public static Services getService(java.lang.Class wsImplClass)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/dm_javadoc/compbio/ws/client/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html new file mode 100644 index 0000000..546b1c9 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/WSTester.html @@ -0,0 +1,278 @@ + + + + + + +WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.client +
    +Class WSTester

    +
    +java.lang.Object
+  extended by compbio.ws.client.WSTester
+
    +
    +
    +
    public class WSTester
    extends java.lang.Object
    + + +

    +Class for testing web services +

    + +

    +

    +
    Version:
    +
    1.0 February 2010
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSTester() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> void
    +    		main(java.lang.String[] args) + +
    +          Test JWS2 web services
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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    +Constructor Detail
    + +

    +WSTester

    +
    +public WSTester()
    +
    +
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    +Method Detail
    + +

    +main

    +
    +public static <T> void main(java.lang.String[] args)
+                 throws java.io.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: +
    java.io.IOException
    +
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    +
    + + + + + + + + + +
    +Packages that use Services
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of Services in compbio.ws.client
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.client that return Services
    +static ServicesServices.getService(java.lang.Class wsImplClass) + +
    +           
    +static ServicesServices.getService(java.lang.String servName) + +
    +           
    +static ServicesServices.valueOf(java.lang.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 with parameters of type Services
    +static + + + + +
    +<T> MsaWS<T>
    +    		Jws2Client.connect(java.lang.String host, + Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

    +

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    +Jws2Client +
    +WSTester
    + + + + + + +
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    +Services
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    +Package compbio.ws.client +

    +A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + +
    +Class Summary
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    WSTesterClass for testing web services
    +  + +

    + + + + + + + + + +
    +Enum Summary
    ServicesList of web services currently supported by JABAWS version 1
    +  + +

    +

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

    + + + + + + + + +
    +Classes in compbio.ws.client used by compbio.ws.client
    Services + +
    +          List of web services currently supported by JABAWS version 1
    +  +

    +

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    +compbio.data.*
    + +

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    compbio.data.sequence.ClustalAlignmentUtil
    +public static final chargapchar45
    + +

    + +

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    +compbio.metadata.*
    + +

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    compbio.metadata.PresetManager<T>
    +public static final java.lang.StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
    + +

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    +A

    +
    +
    AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Valid Amino acids +
    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 +
    addPossibleValues(String...) - +Method in class compbio.metadata.Parameter +
      +
    align(List<FastaSequence>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with default settings. +
    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 +
      +
    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 +
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +
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    +L

    +
    +
    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 +
      +
    Limit(int, int, String, boolean) - +Constructor for class compbio.metadata.Limit +
      +
    LimitExceededException - Exception in compbio.metadata
    Thrown if the task larger in size that the limit that applies to the + calculation.
    LimitExceededException(String) - +Constructor for exception compbio.metadata.LimitExceededException +
      +
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - +Constructor for class compbio.metadata.LimitsManager +
      +
    LOCAL_ENGINE_LIMIT_PRESET - +Static variable in class compbio.metadata.PresetManager +
      +
    +
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    +M

    +
    +
    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 +
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    +
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    name - +Variable in class compbio.metadata.Option +
      +
    newLimitExceeded(Limit<?>, List<FastaSequence>) - +Static method in exception compbio.metadata.LimitExceededException +
      +
    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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    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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    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 +
      +
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - +Constructor for class compbio.metadata.Preset +
      +
    presetAlign(List<FastaSequence>, Preset<T>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with preset. +
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - +Constructor for class compbio.metadata.PresetManager +
      +
    Program - Enum in compbio.data.sequence
    The list of programmes that can produce alignments
    pullExecStatistics(String, long) - +Method in interface compbio.data.msa.MsaWS +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. +
    +
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    readClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Read Clustal formatted alignment. +
    readClustalFile(File) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
      +
    readFasta(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +
    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. +
    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 +
      +
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - +Constructor for class compbio.metadata.RunnerConfig +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 1
    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 +
      +
    setFurtherDetails(URL) - +Method in class compbio.metadata.Option +
      +
    setMax(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setMin(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setName(String) - +Method in class compbio.metadata.Option +
      +
    setName(String) - +Method in class compbio.metadata.Preset +
      +
    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<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 +
    setParameters(List<Parameter<T>>) - +Method in class compbio.metadata.RunnerConfig +
    Sets the list of parameters as internal list +
    setPossibleValues(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setPresets(List<Preset<T>>) - +Method in class compbio.metadata.PresetManager +
      +
    setPrmSeparator(String) - +Method in class compbio.metadata.RunnerConfig +
    Sets name value separator character +
    setRequired(boolean) - +Method in class compbio.metadata.Option +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.PresetManager +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.RunnerConfig +
    Set the name of a runner class +
    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 +
      +
    +
    + + + + + + + + + + + + + + + +
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    +
    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.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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    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. +
    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.sequence.Program +
    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.ws.client.Services +
    Returns the enum constant of this type with the specified name. +
    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.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.ws.client.Services +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    cancelJob(String) - +Method in interface compbio.data.msa.MsaWS +
    Stop running the job jobId but leave its output untouched +
    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 +
      +
    cleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all whitespace chars in the sequence string +
    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 +
      +
    compbio.data.msa - package compbio.data.msa
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.ws.client - package compbio.ws.client
    A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    connect(String, Services) - +Static method in class compbio.ws.client.Jws2Client +
    Connects to a web service by the host and the service name +
    copyAndValidateRConfig(RunnerConfig<?>) - +Method in class compbio.metadata.RunnerConfig +
      +
    countMatchesInSequence(String, String) - +Static method in class compbio.data.sequence.FastaSequence +
      +
    customAlign(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with options. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    WHITE_SPACE - +Static variable in class compbio.data.sequence.SequenceUtil +
    A whitespace character: [\t\n\x0B\f\r] +
    writeClustalAlignment(OutputStream, 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 +
      +
    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 +
      +
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester() - +Constructor for class compbio.ws.client.WSTester +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +
    deepCleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all special characters and digits as well as whitespace chars + from the sequence +
    defaultValue - +Variable in class compbio.metadata.Option +
      +
    description - +Variable in class compbio.metadata.Option +
      +
    DIGIT - +Static variable in class compbio.data.sequence.SequenceUtil +
    A digit +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    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.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 +
      +
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    +F

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    +
    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 +
    furtherDetails - +Variable in class compbio.metadata.Option +
      +
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    +
    +
    gapchar - +Static variable in class compbio.data.sequence.ClustalAlignmentUtil +
    Dash char to be used as gap char in the alignments +
    getActualNumberofSequences() - +Method in exception compbio.metadata.LimitExceededException +
      +
    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 +
    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 +
    getChunk() - +Method in class compbio.metadata.ChunkHolder +
      +
    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. +
    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 +
      +
    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 +
      +
    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 +
      +
    getHost(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts host name from the command line +
    getId() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of id +
    getJobStatus(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the status of the job. +
    getLength() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getLimit(String) - +Method in interface compbio.data.msa.MsaWS +
    Get a Limit for a preset. +
    getLimitByName(String) - +Method in class compbio.metadata.LimitsManager +
      +
    getLimits() - +Method in interface compbio.data.msa.MsaWS +
    List Limits supported by a web service. +
    getLimits() - +Method in class compbio.metadata.LimitsManager +
      +
    getMax() - +Method in class compbio.metadata.ValueConstrain +
      +
    getMetadata() - +Method in class compbio.data.sequence.Alignment +
      +
    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 +
      +
    getNextPosition() - +Method in class compbio.metadata.ChunkHolder +
      +
    getNumberOfSequencesAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    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.metadata.Preset +
      +
    getOptions() - +Method in class compbio.metadata.RunnerConfig +
    Returns the list of the Options supported by the executable of type T +
    getParameters() - +Method in class compbio.metadata.RunnerConfig +
    Returns the list of parameters supported executable of type T. +
    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.metadata.Limit +
      +
    getPresetByName(String) - +Method in class compbio.metadata.PresetManager +
      +
    getPresets() - +Method in interface compbio.data.msa.MsaWS +
    Get presets supported by a web service +
    getPresets() - +Method in class compbio.metadata.PresetManager +
      +
    getPrmSeparator() - +Method in class compbio.metadata.RunnerConfig +
      +
    getProgram() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    getResult(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the result of the job. +
    getRunnerClassName() - +Method in class compbio.metadata.PresetManager +
      +
    getRunnerClassName() - +Method in class compbio.metadata.RunnerConfig +
      +
    getRunnerOptions() - +Method in interface compbio.data.msa.MsaWS +
    Get options supported by a web service +
    getSeqNumber() - +Method in class compbio.metadata.Limit +
      +
    getSequence() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of sequence +
    getSequenceLenghtActual() - +Method in exception compbio.metadata.LimitExceededException +
      +
    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 +
      +
    getService(Class) - +Static method in enum compbio.ws.client.Services +
      +
    getServiceName(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts service name from the command line +
    getSize() - +Method in class compbio.data.sequence.Alignment +
      +
    getType() - +Method in class compbio.metadata.ValueConstrain +
      +
    getValidValue() - +Method in class compbio.metadata.Parameter +
      +
    +
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    +
    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.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 +
      +
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    isAmbiguosProtein(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Check whether the sequence confirms to amboguous protein sequence +
    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 limits the values defined by this Limit +
    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 +
      +
    isProteinSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isRequired - +Variable in class compbio.metadata.Option +
      +
    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 +
    isValidClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Please note this method closes the input stream provided as a parameter +
    +
    + + + + + + + + + + + + + + + +
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    +
    +
    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 +
      +
    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 +
      +
    Jws2Client - Class in compbio.ws.client
    A command line client for JAva Bioinformatics Analysis Web Services
    +
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    All Classes +

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    +Packages
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    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.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    + +

    + 

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    +Hierarchy For All Packages

    +
    +
    +
    Package Hierarchies:
    compbio.data.msa, compbio.data.sequence, compbio.metadata, compbio.ws.client
    +
    +

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    +Serialized Form

    +
    +
    + + + + + +
    +Package compbio.data.sequence
    + +

    + + + + + +
    +Class compbio.data.sequence.UnknownFileFormatException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: 196629543695636854L + +

    + + + + + +
    +Serialized Fields
    + +

    +file

    +
    +java.io.File file
    +
    +
    +
    +
    +
    + + + + + +
    +Package compbio.metadata
    + +

    + + + + + +
    +Class compbio.metadata.JobExecutionException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -5477751361755778769L + +

    + +

    + + + + + +
    +Class compbio.metadata.JobSubmissionException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: 607986894357895572L + +

    + +

    + + + + + +
    +Class compbio.metadata.LimitExceededException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: 15066952180013505L + +

    + + + + + +
    +Serialized Fields
    + +

    +numberOfSequencesAllowed

    +
    +int numberOfSequencesAllowed
    +
    +
    +
    +
    +
    +

    +actualNumberofSequences

    +
    +int actualNumberofSequences
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtAllowed

    +
    +int aSequenceLenghtAllowed
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtActual

    +
    +int aSequenceLenghtActual
    +
    +
    +
    +
    + +

    + + + + + +
    +Class compbio.metadata.ResultNotAvailableException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -5475613614578761L + +

    + +

    + + + + + +
    +Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: -86624836785110293L + +

    + +

    + + + + + +
    +Class compbio.metadata.WrongParameterException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -547775417557345769L + +

    + +

    +

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    + + + +
    + + + +
    +

    JABAWS Client

    + +

    The command line client is an executable Java program which can use JABAWS. It is good for scripting against JABA web services. If you prefer point-and-click interface - download the Graphical User Interface (GUI) client, the Jalview. If you intend to write you own client and need a template - download a command line client source package. For a help on generating GUI's for JABA web services you can consult Jalview source code.

    + +
      +
    • Command line client + +
      • +
    • GUI client + (Jalview) + +
      • +
    + +

    Please refer to Jalview help pages for a help on connecting to JABAWS instance. Help with a command line client is available from How To pages.

    +

    JABAWS Server

    + +

    The server is provided as a self-contained Web Application +Archive (WAR) containing all necessary binaries. WAR file can be deployed on any + web application server +supporting Servlet 2.4 specification i.e. Tomcat 6.0. Download this +if you intend to run JABAWS services locally.

    + +
      +
    • A Complete Server for all platforms: download +(45M)
      • + +
    • A Complete Server for Windows: download +(16M)
      • +
    + + +

    Please bear in mind that server for Windows supports only Muscle and Clustal web services! Please refer to the how to pages to find out why. If you want to run other web services on Windows choose Virtual Appliance package below.

    +

    A JABAWS Server Virtual Appliance

    +

    JABAWS virtual appliance is a complete installation of JABAWS software on TurnKey Linux. By using virtual appliance you can completely avoid JABAWS installation. The appliance comes fully configured to run JABAWS. All JABAWS clients, such as Jalview can be easily configured to use the appliance. You can run the appliance with freely available VMWare Player or Oracle VirtualBox. We have tested JABAWS appliance with VMWare Player on Windows and Linux, and VirtualBox on Windows, Linux and Mac. However, you are not limited to these virtualization systems and can use JABAWS appliance with any commercial alternative.

    +
      +
    • JABAWS Virtual Appliance: download (520M)
      • +
    +

    Please review the relevant manual and how to sections for the configuration settings.

    +

     

    +
    +
    Packages for experts
    + +
    +

    JABAWS server without alignment programs

    + +

    If you have all the programs or wish to download them +separately, then this package is for you.

    +
      +
    • Complete server without native executables: +download (14M)
      • +
    + +

    The complete source code

    + +

    We offer the code under Apache licence. The code archive contains the complete Eclipse JABAWS project, but Eclipse is not +necessary to build it. Please examine the Ant build file (build.xml) +to build and test JABAWS from sources.

    + +
      +
    • A complete Eclipse project package: download +(82M)
      • + +
    • JABAWS source only package: download (250K)
      • +
    + +
    +
    +
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    + + + + + + + diff --git a/website/full_javadoc/allclasses-frame.html b/website/full_javadoc/allclasses-frame.html new file mode 100644 index 0000000..16054f8 --- /dev/null +++ b/website/full_javadoc/allclasses-frame.html @@ -0,0 +1,309 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
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    +BlastAll +
    +BlastParameters +
    +BlastParser +
    +CancelJob +
    +CancelJobResponse +
    +ChunkHolder +
    +Cleaner +
    +ClustalAlignmentUtil +
    +ClustalW +
    +ClustalWS +
    +ClusterJobId +
    +ClusterNativeSpecExecutable +
    +ClusterSession +
    +ClusterUtil +
    +CommandBuilder +
    +ConfExecutable +
    +Configurator +
    +ConfiguredExecutable +
    +CustomAlign +
    +CustomAlignResponse +
    +DirectoryManager +
    +Disembl +
    +Environment +
    +EnvVariableProcessor +
    +Executable +
    +Executable.ExecProvider +
    +ExecutableWrapper +
    +FastaSequence +
    +FilePuller +
    +GetJobStatus +
    +GetJobStatusResponse +
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    +GetLimitsResponse +
    +GetPresets +
    +GetPresetsResponse +
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    +JnetAnnotation +
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    +JobExecutionException +
    +JobExecutionExceptionBean +
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    +JpredResult +
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    +Jws2Client.Services +
    +Limit +
    +LimitExceededException +
    +LimitExceededExceptionBean +
    +LimitsManager +
    +LoadBalancer +
    +LocalEngineUtil +
    +LocalExecutorService +
    +LocalRunner +
    +Mafft +
    +MafftWS +
    +Mcl +
    +MsaWS +
    +Muscle +
    +MuscleWS +
    +NetNglyc +
    +OB +
    +Option +
    +OptionCombinator +
    +Pairwise +
    +Parameter +
    +PathValidator +
    +PipedExecutable +
    +Preset +
    +PresetAlign +
    +PresetAlignResponse +
    +PresetManager +
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    +ProbconsWS +
    +Program +
    +ProgressGetter +
    +PropertyHelperManager +
    +PScore +
    +PSIBlast +
    +PsiBlast +
    +PulledFileCache +
    +PullExecStatistics +
    +PullExecStatisticsResponse +
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    +PullFileResponse +
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    +ResultNotAvailableExceptionBean +
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    +Runners +
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    +Util +
    +Util +
    +ValueConstrain +
    +ValueConstrain.Type +
    +WrongParameterException +
    +WrongParameterExceptionBean +
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    +_DrmaaExample +
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    +_SkeletalCommandBuilder +
    +_TrackingExecutor +
    +
    + + + diff --git a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html new file mode 100644 index 0000000..7afbc88 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html @@ -0,0 +1,418 @@ + + + + + + +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:
    java.io.Serializable, java.lang.Comparable<JnetAnnotation>
    +
    +
    +
    +
    public enum JnetAnnotation
    extends java.lang.Enum<JnetAnnotation>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    JNETCONF + +
    +           
    JNETHMM + +
    +           
    jnetpred + +
    +           
    JNETPROPE + +
    +           
    JNETPROPH + +
    +           
    JNETSOL0 + +
    +           
    JNETSOL25 + +
    +           
    JNETSOL5 + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static JnetAnnotationvalueOf(java.lang.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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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 new file mode 100644 index 0000000..d72000f --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html @@ -0,0 +1,418 @@ + + + + + + +JpredAnnotation + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + +

    + +compbio.data._structure +
    +Enum JpredAnnotation

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

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    JNETCONF + +
    +           
    JNETHMM + +
    +           
    jnetpred + +
    +           
    JNETPROPE + +
    +           
    JNETPROPH + +
    +           
    JNETSOL0 + +
    +           
    JNETSOL25 + +
    +           
    JNETSOL5 + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static JpredAnnotationvalueOf(java.lang.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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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 new file mode 100644 index 0000000..904c222 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/JpredResult.html @@ -0,0 +1,260 @@ + + + + + + +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 java.lang.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()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/_structure/class-use/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html new file mode 100644 index 0000000..db95c3b --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html @@ -0,0 +1,189 @@ + + + + + + +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(java.lang.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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    + + + diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html new file mode 100644 index 0000000..fcae915 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Class compbio.data._structure.JpredAnnotation + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.data._structure.JpredAnnotation

    +
    + + + + + + + + + +
    +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(java.lang.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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    + + + diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html new file mode 100644 index 0000000..8366955 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data._structure.JpredResult + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.data._structure.JpredResult

    +
    +No usage of compbio.data._structure.JpredResult +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/_structure/package-frame.html b/website/full_javadoc/compbio/data/_structure/package-frame.html new file mode 100644 index 0000000..aef6a7c --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/package-frame.html @@ -0,0 +1,45 @@ + + + + + + +compbio.data._structure + + + + + + + + + + + +compbio.data._structure + + + + +
    +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 new file mode 100644 index 0000000..9f34326 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/package-summary.html @@ -0,0 +1,203 @@ + + + + + + +compbio.data._structure + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +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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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/_structure/package-tree.html b/website/full_javadoc/compbio/data/_structure/package-tree.html new file mode 100644 index 0000000..defdc96 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/package-tree.html @@ -0,0 +1,163 @@ + + + + + + +compbio.data._structure Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Hierarchy For Package compbio.data._structure +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    +
      +
    • java.lang.Object +
    +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
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    + + + + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Package
    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/MsaWS.html b/website/full_javadoc/compbio/data/msa/MsaWS.html new file mode 100644 index 0000000..911f90d --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/MsaWS.html @@ -0,0 +1,567 @@ + + + + + + +MsaWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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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 Known Implementing Classes:
    ClustalWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
    +
    +
    +
    +
    public interface MsaWS<T>
    + + +

    +Multiple Sequence Alignment (MSA) Web Services Interface +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<T>getLimit(java.lang.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
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<T>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws UnsupportedRuntimeException,
+                              LimitExceededException,
+                              JobSubmissionException
    +
    +
    Align a list of sequences with default settings. + + 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. - This + exception 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. +
    java.security.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 +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                             java.util.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. - This + exception 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. +
    java.security.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 +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                             Preset<T> preset)
+                             throws UnsupportedRuntimeException,
+                                    LimitExceededException,
+                                    JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Align a list of sequences with preset. @see 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. - This + exception 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. +
    java.security.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 +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Return the result of the job. +

    +

    +
    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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException. +
    java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format
    +
    +
    +
    + +

    +cancelJob

    +
    +boolean cancelJob(java.lang.String jobId)
    +
    +
    Stop running job but leave its output untouched +

    +

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

    +getJobStatus

    +
    +JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Return the status of the job. @see JobStatus +

    +

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

    +pullExecStatistics

    +
    +ChunkHolder pullExecStatistics(java.lang.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 - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read +
    Throws: +
    java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format and also if the position value is negative
    +
    +
    +
    + +

    +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(java.lang.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. +

    +

    +
    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:
    LimitManager
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/MsaWS.html b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html new file mode 100644 index 0000000..30ccaec --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html @@ -0,0 +1,249 @@ + + + + + + +Uses of Interface compbio.data.msa.MsaWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Interface
    compbio.data.msa.MsaWS

    +
    + + + + + + + + + + + + + +
    +Packages that use MsaWS
    compbio.ws.client  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of MsaWS in compbio.ws.client
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.client that return MsaWS
    +static + + + + +
    +<T> MsaWS<T>
    +    		Jws2Client.connect(java.lang.String host, + Jws2Client.Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

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

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

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/Align.html new file mode 100644 index 0000000..b4181e3 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/Align.html @@ -0,0 +1,272 @@ + + + + + + +Align + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 Align

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Align() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<FastaSequence>getFastaSequences() + +
    +           
    + voidsetFastaSequences(java.util.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 java.util.List<FastaSequence> getFastaSequences()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setFastaSequences

    +
    +public void setFastaSequences(java.util.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/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html new file mode 100644 index 0000000..1a50071 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html @@ -0,0 +1,272 @@ + + + + + + +AlignResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 AlignResponse

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AlignResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetReturn() + +
    +           
    + voidsetReturn(java.lang.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 java.lang.String getReturn()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(java.lang.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 new file mode 100644 index 0000000..e858d81 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html @@ -0,0 +1,272 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CancelJob() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.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 java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.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 new file mode 100644 index 0000000..69785d5 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html @@ -0,0 +1,272 @@ + + + + + + +CancelJobResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 CancelJobResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.CancelJobResponse
+
    +
    +
    +
    public class CancelJobResponse
    extends java.lang.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 new file mode 100644 index 0000000..838e512 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html @@ -0,0 +1,311 @@ + + + + + + +CustomAlign + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 CustomAlign

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CustomAlign() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<FastaSequence>getFastaSequences() + +
    +           
    + java.util.List<Option>getOptions() + +
    +           
    + voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidsetOptions(java.util.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 java.util.List<FastaSequence> getFastaSequences()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setFastaSequences

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

    +getOptions

    +
    +public java.util.List<Option> getOptions()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setOptions

    +
    +public void setOptions(java.util.List<Option> options)
    +
    +
    +
    Parameters:
    options - the value for the options 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/CustomAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html new file mode 100644 index 0000000..a7d5cfe --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html @@ -0,0 +1,272 @@ + + + + + + +CustomAlignResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 CustomAlignResponse

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CustomAlignResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetReturn() + +
    +           
    + voidsetReturn(java.lang.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 java.lang.String getReturn()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(java.lang.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/GetJobStatus.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html new file mode 100644 index 0000000..e4f1719 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html @@ -0,0 +1,272 @@ + + + + + + +GetJobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetJobStatus

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetJobStatus() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.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 java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.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/GetJobStatusResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html new file mode 100644 index 0000000..401d145 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetJobStatusResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetJobStatusResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetJobStatusResponse
+
    +
    +
    +
    public class GetJobStatusResponse
    extends java.lang.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 
    +    		 + +
    + 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/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html new file mode 100644 index 0000000..3433200 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html @@ -0,0 +1,272 @@ + + + + + + +GetLimit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetLimit

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetLimit() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetPresetName() + +
    +           
    + voidsetPresetName(java.lang.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 java.lang.String getPresetName()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setPresetName

    +
    +public void setPresetName(java.lang.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   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html new file mode 100644 index 0000000..5def54c --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetLimitResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetLimitResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimitResponse
+
    +
    +
    +
    public class GetLimitResponse
    extends java.lang.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   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html new file mode 100644 index 0000000..aa83b59 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html @@ -0,0 +1,224 @@ + + + + + + +GetLimits + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetLimits

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimits
+
    +
    +
    +
    public class GetLimits
    extends java.lang.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 
    +    		 + +
    + 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/GetLimitsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html new file mode 100644 index 0000000..04d2e7a --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetLimitsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetLimitsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimitsResponse
+
    +
    +
    +
    public class GetLimitsResponse
    extends java.lang.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   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html new file mode 100644 index 0000000..a9ea45a --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html @@ -0,0 +1,224 @@ + + + + + + +GetPresets + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetPresets

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetPresets
+
    +
    +
    +
    public class GetPresets
    extends java.lang.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 
    +    		 + +
    + 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/GetPresetsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html new file mode 100644 index 0000000..f5f62bb --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html @@ -0,0 +1,272 @@ + + + + + + +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 java.lang.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   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html new file mode 100644 index 0000000..97f3af9 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html @@ -0,0 +1,272 @@ + + + + + + +GetProgress + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetProgress

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetProgress
+
    +
    +
    +
    public class GetProgress
    extends java.lang.Object
    + + +

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetProgress

    +
    +public GetProgress()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.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/GetProgressResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html new file mode 100644 index 0000000..0f30084 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetProgressResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetProgressResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetProgressResponse
+
    +
    +
    +
    public class GetProgressResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetProgressResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + bytegetReturn() + +
    +           
    + voidsetReturn(byte _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetProgressResponse

    +
    +public GetProgressResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public byte getReturn()
    +
    +
    + +
    Returns:
    returns byte
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(byte _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/GetResult.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html new file mode 100644 index 0000000..c4e3b36 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html @@ -0,0 +1,272 @@ + + + + + + +GetResult + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetResult

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetResult() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.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 java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.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/GetResultResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html new file mode 100644 index 0000000..e5da690 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetResultResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + 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 java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/GetRunnerOptions.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html new file mode 100644 index 0000000..e3125c6 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html @@ -0,0 +1,224 @@ + + + + + + +GetRunnerOptions + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetRunnerOptions

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetRunnerOptions
+
    +
    +
    +
    public class GetRunnerOptions
    extends java.lang.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()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/GetRunnerOptionsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html new file mode 100644 index 0000000..ddc4c44 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetRunnerOptionsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 GetRunnerOptionsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetRunnerOptionsResponse
+
    +
    +
    +
    public class GetRunnerOptionsResponse
    extends java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/JobExecutionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html new file mode 100644 index 0000000..90a42af --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +JobExecutionExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 JobExecutionExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.JobExecutionExceptionBean
+
    +
    +
    +
    public class JobExecutionExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +JobExecutionExceptionBean

    +
    +public JobExecutionExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message 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/JobSubmissionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html new file mode 100644 index 0000000..53f43dd --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +JobSubmissionExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 JobSubmissionExceptionBean

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

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    JobSubmissionExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.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 java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message 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/LimitExceededExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html new file mode 100644 index 0000000..301ea94 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html @@ -0,0 +1,434 @@ + + + + + + +LimitExceededExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 LimitExceededExceptionBean

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

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LimitExceededExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intgetActualNumberofSequences() + +
    +           
    + java.lang.StringgetMessage() + +
    +           
    + intgetNumberOfSequencesAllowed() + +
    +           
    + intgetSequenceLenghtActual() + +
    +           
    + intgetSequenceLenghtAllowed() + +
    +           
    + voidsetActualNumberofSequences(int actualNumberofSequences) + +
    +           
    + voidsetMessage(java.lang.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 java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/PresetAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html new file mode 100644 index 0000000..57cf5af --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html @@ -0,0 +1,311 @@ + + + + + + +PresetAlign + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 PresetAlign

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PresetAlign() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<FastaSequence>getFastaSequences() + +
    +           
    + PresetgetPreset() + +
    +           
    + voidsetFastaSequences(java.util.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 java.util.List<FastaSequence> getFastaSequences()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setFastaSequences

    +
    +public void setFastaSequences(java.util.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/PresetAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html new file mode 100644 index 0000000..318712e --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html @@ -0,0 +1,272 @@ + + + + + + +PresetAlignResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PresetAlignResponse

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

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +PresetAlignResponse

    +
    +public PresetAlignResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public java.lang.String getReturn()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(java.lang.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/PullExecStatistics.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html new file mode 100644 index 0000000..1ab6ead --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html @@ -0,0 +1,311 @@ + + + + + + +PullExecStatistics + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PullExecStatistics

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

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullExecStatistics

    +
    +public PullExecStatistics()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/PullExecStatisticsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html new file mode 100644 index 0000000..a5658d1 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html @@ -0,0 +1,272 @@ + + + + + + +PullExecStatisticsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 PullExecStatisticsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullExecStatisticsResponse
+
    +
    +
    +
    public class PullExecStatisticsResponse
    extends java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/PullFile.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html new file mode 100644 index 0000000..ff92d78 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html @@ -0,0 +1,311 @@ + + + + + + +PullFile + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PullFile

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullFile
+
    +
    +
    +
    public class PullFile
    extends java.lang.Object
    + + +

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullFile

    +
    +public PullFile()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/PullFileResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html new file mode 100644 index 0000000..966917b --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html @@ -0,0 +1,272 @@ + + + + + + +PullFileResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 PullFileResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullFileResponse
+
    +
    +
    +
    public class PullFileResponse
    extends java.lang.Object
    + + +

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullFileResponse

    +
    +public PullFileResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

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

    +setReturn

    +
    +public void setReturn(ChunkHolder _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/ResultNotAvailableExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html new file mode 100644 index 0000000..9f89492 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +ResultNotAvailableExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 ResultNotAvailableExceptionBean

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

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +ResultNotAvailableExceptionBean

    +
    +public ResultNotAvailableExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message 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/UnsupportedRuntimeExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html new file mode 100644 index 0000000..1660fdf --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +UnsupportedRuntimeExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 UnsupportedRuntimeExceptionBean

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

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    UnsupportedRuntimeExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.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 java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message 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/WrongParameterExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html new file mode 100644 index 0000000..ecf51ab --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +WrongParameterExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class WrongParameterExceptionBean

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

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WrongParameterExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.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 java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message 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/class-use/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html new file mode 100644 index 0000000..63a3520 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.Align + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.Align

    +
    +No usage of compbio.data.msa.jaxws.Align +

    +

    + + + + + + + + + + + + + + + +
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    compbio.data.msa.jaxws.AlignResponse

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

    +

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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJob.html new file mode 100644 index 0000000..2c0d93c --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJob.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.CancelJob + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.CancelJob

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

    +

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    compbio.data.msa.jaxws.CancelJobResponse

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

    +

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    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.CustomAlign

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

    +

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    +Uses of Class
    compbio.data.msa.jaxws.CustomAlignResponse

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

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetJobStatus

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

    +

    + + + + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetJobStatusResponse

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

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetLimit.html new file mode 100644 index 0000000..0fbfaa9 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetLimit.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.GetLimit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetLimit

    +
    +No usage of compbio.data.msa.jaxws.GetLimit +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetLimitResponse

    +
    +No usage of compbio.data.msa.jaxws.GetLimitResponse +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetLimits

    +
    +No usage of compbio.data.msa.jaxws.GetLimits +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetLimitsResponse

    +
    +No usage of compbio.data.msa.jaxws.GetLimitsResponse +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetPresets.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetPresets.html new file mode 100644 index 0000000..216ca63 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetPresets.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.GetPresets + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetPresets

    +
    +No usage of compbio.data.msa.jaxws.GetPresets +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetPresetsResponse

    +
    +No usage of compbio.data.msa.jaxws.GetPresetsResponse +

    +

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    +Uses of Class
    compbio.data.msa.jaxws.GetProgress

    +
    +No usage of compbio.data.msa.jaxws.GetProgress +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetProgressResponse

    +
    +No usage of compbio.data.msa.jaxws.GetProgressResponse +

    +

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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetResult.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetResult.html new file mode 100644 index 0000000..a8a8131 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetResult.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.GetResult + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.msa.jaxws.GetResult

    +
    +No usage of compbio.data.msa.jaxws.GetResult +

    +

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    +Uses of Class
    compbio.data.msa.jaxws.GetResultResponse

    +
    +No usage of compbio.data.msa.jaxws.GetResultResponse +

    +

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    +Uses of Class
    compbio.data.msa.jaxws.GetRunnerOptions

    +
    +No usage of compbio.data.msa.jaxws.GetRunnerOptions +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetRunnerOptionsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetRunnerOptionsResponse.html new file mode 100644 index 0000000..409fc9e --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/GetRunnerOptionsResponse.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.GetRunnerOptionsResponse + + + + + + + + + + + + +
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    +

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    +

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    +

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    +

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    +

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    +

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    compbio.data.msa.jaxws.PullFile

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    +

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    compbio.data.msa.jaxws.WrongParameterExceptionBean

    +
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    +

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    +Classes  + +
    +Align +
    +AlignResponse +
    +CancelJob +
    +CancelJobResponse +
    +CustomAlign +
    +CustomAlignResponse +
    +GetJobStatus +
    +GetJobStatusResponse +
    +GetLimit +
    +GetLimitResponse +
    +GetLimits +
    +GetLimitsResponse +
    +GetPresets +
    +GetPresetsResponse +
    +GetProgress +
    +GetProgressResponse +
    +GetResult +
    +GetResultResponse +
    +GetRunnerOptions +
    +GetRunnerOptionsResponse +
    +JobExecutionExceptionBean +
    +JobSubmissionExceptionBean +
    +LimitExceededExceptionBean +
    +PresetAlign +
    +PresetAlignResponse +
    +PullExecStatistics +
    +PullExecStatisticsResponse +
    +PullFile +
    +PullFileResponse +
    +ResultNotAvailableExceptionBean +
    +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 new file mode 100644 index 0000000..cf10084 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html @@ -0,0 +1,281 @@ + + + + + + +compbio.data.msa.jaxws + + + + + + + + + + + + +
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    +Package compbio.data.msa.jaxws +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    Align 
    AlignResponse 
    CancelJob 
    CancelJobResponse 
    CustomAlign 
    CustomAlignResponse 
    GetJobStatus 
    GetJobStatusResponse 
    GetLimit 
    GetLimitResponse 
    GetLimits 
    GetLimitsResponse 
    GetPresets 
    GetPresetsResponse 
    GetProgress 
    GetProgressResponse 
    GetResult 
    GetResultResponse 
    GetRunnerOptions 
    GetRunnerOptionsResponse 
    JobExecutionExceptionBeanThis class was generated by the JAX-WS RI.
    JobSubmissionExceptionBeanThis class was generated by the JAX-WS RI.
    LimitExceededExceptionBeanThis class was generated by the JAX-WS RI.
    PresetAlign 
    PresetAlignResponse 
    PullExecStatistics 
    PullExecStatisticsResponse 
    PullFile 
    PullFileResponse 
    ResultNotAvailableExceptionBeanThis class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBeanThis class was generated by the JAX-WS RI.
    WrongParameterExceptionBeanThis class was generated by the JAX-WS RI.
    +  + +

    +

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    +Hierarchy For Package compbio.data.msa.jaxws +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

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    compbio.data.msa.jaxws

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    +

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    +Interfaces  + +
    +MsaWS
    + + + + diff --git a/website/full_javadoc/compbio/data/msa/package-summary.html b/website/full_javadoc/compbio/data/msa/package-summary.html new file mode 100644 index 0000000..3cb53ac --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/package-summary.html @@ -0,0 +1,157 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + + +
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    +Package compbio.data.msa +

    + + + + + + + + + +
    +Interface Summary
    MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
    +  + +

    +

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    + + + diff --git a/website/full_javadoc/compbio/data/msa/package-tree.html b/website/full_javadoc/compbio/data/msa/package-tree.html new file mode 100644 index 0000000..5c3f09e --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/package-tree.html @@ -0,0 +1,151 @@ + + + + + + +compbio.data.msa Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.data.msa +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Interface Hierarchy +

    +
      +
    • compbio.data.msa.MsaWS<T>
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/package-use.html b/website/full_javadoc/compbio/data/msa/package-use.html new file mode 100644 index 0000000..1d034e0 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/package-use.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Package compbio.data.msa + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Package
    compbio.data.msa

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.data.msa
    compbio.ws.client  
    compbio.ws.server  
    +  +

    + + + + + + + + +
    +Classes in compbio.data.msa used by compbio.ws.client
    MsaWS + +
    +          Multiple Sequence Alignment (MSA) Web Services Interface
    +  +

    + + + + + + + + +
    +Classes in compbio.data.msa used by compbio.ws.server
    MsaWS + +
    +          Multiple Sequence Alignment (MSA) Web Services Interface
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/Alignment.html b/website/full_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..8cad073 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,381 @@ + + + + + + +Alignment + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 Alignment

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

    +Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. That is it does not guarantee that the neither the names of + sequences or the sequences themselves are unique. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    See Also:
    FastaSequence, +AlignmentMetadata
    +
    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +Alignment

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

    +Alignment

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

    +getSequences

    +
    +public java.util.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 java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

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

    +

    +
    Overrides:
    equals in class java.lang.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/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..6650404 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,329 @@ + + + + + + +AlignmentMetadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 AlignmentMetadata

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

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

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AlignmentMetadata(Program program, + char gapchar) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.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(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..c7fb25a --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,385 @@ + + + + + + +ClustalAlignmentUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 ClustalAlignmentUtil

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

    +Tools to read and write clustal formated files +

    + +

    +

    +
    Author:
    +
    Petr Troshin based on jimp class + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Field Summary
    +static chargapchar + +
    +          Dash char to be used as gap char in the alignments
    +  + + + + + + + + + + +
    +Constructor Summary
    ClustalAlignmentUtil() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleanisValidClustalFile(java.io.InputStream input) + +
    +           
    +static AlignmentreadClustalFile(java.io.File file) + +
    +           
    +static AlignmentreadClustalFile(java.io.InputStream instream) + +
    +          Read Clustal formatted alignment.
    +static voidwriteClustalAlignment(java.io.OutputStream outStream, + 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(java.io.InputStream instream)
+                                 throws java.io.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} +
    java.io.IOException +
    UnknownFileFormatException
    +
    +
    +
    + +

    +isValidClustalFile

    +
    +public static boolean isValidClustalFile(java.io.InputStream input)
    +
    +
    +
    Parameters:
    input - +
    Returns:
    true if the file is recognised as Clustal formatted alignment, + false otherwise
    +
    +
    +
    + +

    +writeClustalAlignment

    +
    +public static void writeClustalAlignment(java.io.OutputStream outStream,
+                                         Alignment alignment)
+                                  throws java.io.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:
    outStream -
    alignment - +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +readClustalFile

    +
    +public static Alignment readClustalFile(java.io.File file)
+                                 throws UnknownFileFormatException,
+                                        java.io.IOException
    +
    +
    + +
    Throws: +
    UnknownFileFormatException +
    java.io.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/data/sequence/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..07a1dcf --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,448 @@ + + + + + + +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 java.lang.Object
    + + +

    +A FASTA formatted sequence. Please note that this class does not make any + assumptions as to what sequence it store 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 +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +FastaSequence

    +
    +public FastaSequence(java.lang.String id,
+                     java.lang.String sequence)
    +
    +
    Upon construction the any whitespace characters are removed from the + sequence +

    +

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

    +getId

    +
    +public java.lang.String getId()
    +
    +
    Gets the value of id +

    +

    + +
    Returns:
    the value of id
    +
    +
    +
    + +

    +getSequence

    +
    +public java.lang.String getSequence()
    +
    +
    Gets the value of sequence +

    +

    + +
    Returns:
    the value of sequence
    +
    +
    +
    + +

    +countMatchesInSequence

    +
    +public static int countMatchesInSequence(java.lang.String theString,
+                                         java.lang.String theRegExp)
    +
    +
    +
    +
    +
    +
    + +

    +getFormattedFasta

    +
    +public java.lang.String getFormattedFasta()
    +
    +
    +
    +
    +
    +
    + +

    +getOnelineFasta

    +
    +public java.lang.String getOnelineFasta()
    +
    +
    + +
    Returns:
    one line name, next line sequence, no matter what the sequence + length is
    +
    +
    +
    + +

    +getFormatedSequence

    +
    +public java.lang.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 java.lang.String toString()
    +
    +
    Same as oneLineFasta +

    +

    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.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 new file mode 100644 index 0000000..4c68bca --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,388 @@ + + + + + + +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:
    java.io.Serializable, java.lang.Comparable<Program>
    +
    +
    +
    +
    public enum Program
    extends java.lang.Enum<Program>
    + + +

    +Programmes that can produce alignments +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    CLUSTAL + +
    +          ClustalW
    MAFFT + +
    +          Mafft
    MUSCLE + +
    +          Muscle
    Probcons + +
    +          Probcons
    Tcoffee + +
    +          Tcoffee
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ProgramvalueOf(java.lang.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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..a7bdf1a --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,624 @@ + + + + + + +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 java.lang.Object
    + + +

    +Utility class for operations on sequences +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Field Summary
    +static java.util.regex.PatternAA + +
    +          Valid Amino acids
    +static java.util.regex.PatternAMBIGUOUS_AA + +
    +          Same as AA pattern but with two additional letters - XU
    +static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE + +
    +          Ambiguous nucleotide
    +static java.util.regex.PatternDIGIT + +
    +          A digit
    +static java.util.regex.PatternNON_AA + +
    +          inversion of AA pattern
    +static java.util.regex.PatternNON_NUCLEOTIDE + +
    +          Non nucleotide
    +static java.util.regex.PatternNONWORD + +
    +          Non word
    +static java.util.regex.PatternNUCLEOTIDE + +
    +          Nucleotides a, t, g, c, u
    +static java.util.regex.PatternWHITE_SPACE + +
    +          A whitespace character: [\t\n\x0B\f\r]
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringcleanSequence(java.lang.String sequence) + +
    +          Removes all whitespace chars in the sequence string
    +static java.lang.StringdeepCleanSequence(java.lang.String sequence) + +
    +          Removes all special characters and digits as well as whitespace chars + from the sequence
    +static booleanisAmbiguosProtein(java.lang.String sequence) + +
    +          Check whether the sequence confirms to amboguous protein sequence
    +static booleanisNonAmbNucleotideSequence(java.lang.String sequence) + +
    +          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
    +static booleanisNucleotideSequence(FastaSequence s) + +
    +           
    +static booleanisProteinSequence(java.lang.String sequence) + +
    +           
    +static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) + +
    +          Reads fasta sequences from inStream into the list of FastaSequence + objects
    +static voidwriteFasta(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) + +
    +          Writes FastaSequence in the file, each sequence will take one line only
    +static voidwriteFasta(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) + +
    +          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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

    +WHITE_SPACE

    +
    +public static final java.util.regex.Pattern WHITE_SPACE
    +
    +
    A whitespace character: [\t\n\x0B\f\r] +

    +

    +
    +
    +
    + +

    +DIGIT

    +
    +public static final java.util.regex.Pattern DIGIT
    +
    +
    A digit +

    +

    +
    +
    +
    + +

    +NONWORD

    +
    +public static final java.util.regex.Pattern NONWORD
    +
    +
    Non word +

    +

    +
    +
    +
    + +

    +AA

    +
    +public static final java.util.regex.Pattern AA
    +
    +
    Valid Amino acids +

    +

    +
    +
    +
    + +

    +NON_AA

    +
    +public static final java.util.regex.Pattern NON_AA
    +
    +
    inversion of AA pattern +

    +

    +
    +
    +
    + +

    +AMBIGUOUS_AA

    +
    +public static final java.util.regex.Pattern AMBIGUOUS_AA
    +
    +
    Same as AA pattern but with two additional letters - XU +

    +

    +
    +
    +
    + +

    +NUCLEOTIDE

    +
    +public static final java.util.regex.Pattern NUCLEOTIDE
    +
    +
    Nucleotides a, t, g, c, u +

    +

    +
    +
    +
    + +

    +AMBIGUOUS_NUCLEOTIDE

    +
    +public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
    +
    +
    Ambiguous nucleotide +

    +

    +
    +
    +
    + +

    +NON_NUCLEOTIDE

    +
    +public static final java.util.regex.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(java.lang.String sequence)
    +
    +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +

    +

    +
    +
    +
    +
    + +

    +cleanSequence

    +
    +public static java.lang.String cleanSequence(java.lang.String sequence)
    +
    +
    Removes all whitespace chars in the sequence string +

    +

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

    +deepCleanSequence

    +
    +public static java.lang.String deepCleanSequence(java.lang.String sequence)
    +
    +
    Removes all special characters and digits as well as whitespace chars + from the sequence +

    +

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

    +isProteinSequence

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

    +isAmbiguosProtein

    +
    +public static boolean isAmbiguosProtein(java.lang.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(java.io.OutputStream outstream,
+                              java.util.List<FastaSequence> sequences,
+                              int width)
+                       throws java.io.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: +
    java.io.IOException
    +
    +
    +
    + +

    +readFasta

    +
    +public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
+                                               throws java.io.IOException
    +
    +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +

    +

    +
    Parameters:
    inStream - from +
    Returns:
    list of FastaSequence objects +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +writeFasta

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

    +

    +
    Parameters:
    os -
    sequences - +
    Throws: +
    java.io.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/data/sequence/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..d45a4ea --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,300 @@ + + + + + + +UnknownFileFormatException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 UnknownFileFormatException

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

    +

    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    UnknownFileFormatException() + +
    +           
    UnknownFileFormatException(java.io.File file, + java.lang.Throwable cause) + +
    +           
    UnknownFileFormatException(java.lang.String message) + +
    +           
    UnknownFileFormatException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    UnknownFileFormatException(java.lang.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(java.io.File file,
+                                  java.lang.Throwable cause)
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.lang.String message,
+                                  java.lang.Throwable cause)
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.lang.String message)
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.lang.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/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..af197d7 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,433 @@ + + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.data.sequence.Alignment

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Alignment
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.data.sequenceA 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.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(java.lang.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(java.io.File file) + +
    +           
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) + +
    +          Read Clustal formatted alignment.
    +  +

    + + + + + + + + + +
    Methods in compbio.data.sequence with parameters of type Alignment
    +static voidClustalAlignmentUtil.writeClustalAlignment(java.io.OutputStream outStream, + 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(java.lang.String workDirectory, + java.lang.String clustFile) + +
    +           
    +  +

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

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return Alignment
    + AlignmentTcoffee.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentClustalW.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentProbcons.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMuscle.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMafft.getResults(java.lang.String workDirectory) + +
    +           
    +  +

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

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return Alignment
    + AlignmentTcoffeeWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentProbconsWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMuscleWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMafftWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentClustalWS.getResult(java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html new file mode 100644 index 0000000..efa449b --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html @@ -0,0 +1,196 @@ + + + + + + +Uses of Class compbio.data.sequence.AlignmentMetadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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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 + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +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(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html new file mode 100644 index 0000000..6a07291 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.ClustalAlignmentUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.data.sequence.ClustalAlignmentUtil

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

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html new file mode 100644 index 0000000..cbc8cd7 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,718 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.data.sequence.FastaSequence

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use FastaSequence
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    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
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

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

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
    + java.util.List<FastaSequence>PresetAlign.getFastaSequences() + +
    +           
    + java.util.List<FastaSequence>CustomAlign.getFastaSequences() + +
    +           
    + java.util.List<FastaSequence>Align.getFastaSequences() + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
    + voidPresetAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidCustomAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    +  +

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

    + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that return types with arguments of type FastaSequence
    + java.util.List<FastaSequence>Alignment.getSequences() + +
    +           
    +static java.util.List<FastaSequence>SequenceUtil.readFasta(java.io.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(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) + +
    +          Writes FastaSequence in the file, each sequence will take one line only
    +static voidSequenceUtil.writeFasta(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) + +
    +          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
    +  +

    + + + + + + + + + + + +
    Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
    Alignment(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
    +           
    Alignment(java.util.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, + java.util.List<FastaSequence> dataSet) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		LoadBalancer.getEngine(Executable<V> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.metadata
    +  +

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

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

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

    + + + + + +
    +Uses of FastaSequence in compbio.runner
    +  +

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

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

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type FastaSequence
    + java.lang.StringTcoffeeWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringProbconsWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMuscleWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMafftWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringClustalWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +static voidWSUtil.validateFastaInput(java.util.List<FastaSequence> sequences) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Program.html b/website/full_javadoc/compbio/data/sequence/class-use/Program.html new file mode 100644 index 0000000..bfc36ba --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/Program.html @@ -0,0 +1,221 @@ + + + + + + +Uses of Class compbio.data.sequence.Program + + + + + + + + + + + + +
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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 + Classes in this package have no dependencies to other sources in the project. 
    +  +

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

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that return Program
    + ProgramAlignmentMetadata.getProgram() + +
    +           
    +static ProgramProgram.valueOf(java.lang.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(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
    +           
    AlignmentMetadata(Program program, + char gapchar) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html new file mode 100644 index 0000000..03ed214 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.SequenceUtil + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.sequence.SequenceUtil

    +
    +No usage of compbio.data.sequence.SequenceUtil +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html new file mode 100644 index 0000000..a24599c --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html @@ -0,0 +1,219 @@ + + + + + + +Uses of Class compbio.data.sequence.UnknownFileFormatException + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.sequence.UnknownFileFormatException

    +
    + + + + + + + + + + + + + +
    +Packages that use UnknownFileFormatException
    compbio.data.sequenceA 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 UnknownFileFormatException in compbio.data.sequence
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that throw UnknownFileFormatException
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) + +
    +           
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) + +
    +          Read Clustal formatted alignment.
    +  +

    + + + + + +
    +Uses of UnknownFileFormatException in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that throw UnknownFileFormatException
    +static AlignmentUtil.readClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-frame.html b/website/full_javadoc/compbio/data/sequence/package-frame.html new file mode 100644 index 0000000..a4e673c --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-frame.html @@ -0,0 +1,62 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + +compbio.data.sequence + + + + +
    +Classes  + +
    +Alignment +
    +AlignmentMetadata +
    +ClustalAlignmentUtil +
    +FastaSequence +
    +SequenceUtil
    + + + + + + +
    +Enums  + +
    +Program
    + + + + + + +
    +Exceptions  + +
    +UnknownFileFormatException
    + + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..04cec6a --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,223 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +

    +Package compbio.data.sequence +

    +A data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    AlignmentMultiple sequence alignment.
    AlignmentMetadataAlignment metadata e.g.
    ClustalAlignmentUtilTools to read and write clustal formated files
    FastaSequenceA FASTA formatted sequence.
    SequenceUtilUtility class for operations on sequences
    +  + +

    + + + + + + + + + +
    +Enum Summary
    ProgramProgrammes that can produce alignments
    +  + +

    + + + + + + + + + +
    +Exception Summary
    UnknownFileFormatException 
    +  + +

    +

    +Package compbio.data.sequence Description +

    + +

    +A 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 Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-tree.html b/website/full_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..fab7633 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,168 @@ + + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.data.sequence +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Package
    compbio.data.sequence

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.data.sequence
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    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.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.
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.data.msa.jaxws
    Alignment + +
    +          Multiple sequence alignment.
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.data.sequence
    Alignment + +
    +          Multiple sequence alignment.
    AlignmentMetadata + +
    +          Alignment metadata e.g.
    FastaSequence + +
    +          A FASTA formatted sequence.
    Program + +
    +          Programmes that can produce alignments
    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.
    UnknownFileFormatException + +
    +           
    +  +

    + + + + + + + + +
    +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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/AsyncExecutor.html b/website/full_javadoc/compbio/engine/AsyncExecutor.html new file mode 100644 index 0000000..b5f9af4 --- /dev/null +++ b/website/full_javadoc/compbio/engine/AsyncExecutor.html @@ -0,0 +1,344 @@ + + + + + + +AsyncExecutor + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +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(java.lang.String jobId) + +
    +          Stop running job.
    + booleancleanup(java.lang.String jobId) + +
    +          Remove all files and a job directory for a jobid.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Query the status of the job
    + ConfiguredExecutable<?>getResults(java.lang.String jobId) + +
    +          Retrieve the results of the job.
    + java.lang.StringgetWorkDirectory(java.lang.String jobId) + +
    +           
    + java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) + +
    +          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +submitJob

    +
    +java.lang.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(java.lang.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

    +
    +java.lang.String getWorkDirectory(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - unique job identifier +
    Returns:
    task working directory
    +
    +
    +
    + +

    +cleanup

    +
    +boolean cleanup(java.lang.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(java.lang.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(java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/Cleaner.html b/website/full_javadoc/compbio/engine/Cleaner.html new file mode 100644 index 0000000..f5a3e89 --- /dev/null +++ b/website/full_javadoc/compbio/engine/Cleaner.html @@ -0,0 +1,278 @@ + + + + + + +Cleaner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 Cleaner

    +
    +java.lang.Object
+  extended by compbio.engine.Cleaner
+
    +
    +
    +
    public class Cleaner
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Cleaner() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleandeleteAllFiles(java.lang.String directory) + +
    +           
    +static booleandeleteFiles(ConfiguredExecutable<?> exec) + +
    +          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()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +deleteFiles

    +
    +public static boolean deleteFiles(ConfiguredExecutable<?> exec)
    +
    +
    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:
    +
    +
    +
    + +

    +deleteAllFiles

    +
    +public static boolean deleteAllFiles(java.lang.String directory)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/ClusterJobId.html b/website/full_javadoc/compbio/engine/ClusterJobId.html new file mode 100644 index 0000000..cedced1 --- /dev/null +++ b/website/full_javadoc/compbio/engine/ClusterJobId.html @@ -0,0 +1,297 @@ + + + + + + +ClusterJobId + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 ClusterJobId

    +
    +java.lang.Object
+  extended by compbio.engine.ClusterJobId
+
    +
    +
    +
    @Immutable
+public class ClusterJobId
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ClusterJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetJobId() + +
    +           
    + inthashCode() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ClusterJobId

    +
    +public ClusterJobId(java.lang.String jobId)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.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/Configurator.html b/website/full_javadoc/compbio/engine/Configurator.html new file mode 100644 index 0000000..61bbed4 --- /dev/null +++ b/website/full_javadoc/compbio/engine/Configurator.html @@ -0,0 +1,538 @@ + + + + + + +Configurator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 Configurator

    +
    +java.lang.Object
+  extended by compbio.engine.Configurator
+
    +
    +
    +
    public class Configurator
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringCLUSTER_WORK_DIRECTORY + +
    +           
    +static booleanIS_CLUSTER_ENGINE_ENABLED + +
    +           
    +static booleanIS_LOCAL_ENGINE_ENABLED + +
    +           
    +static java.lang.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, + java.util.List<FastaSequence> dataSet) + +
    +           
    +static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static AsyncExecutorgetAsyncEngine(java.lang.String taskId) + +
    +           
    +static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static java.lang.StringgetWorkDirectory(java.lang.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 java.lang.String LOCAL_WORK_DIRECTORY
    +
    +
    +
    +
    +
    + +

    +CLUSTER_WORK_DIRECTORY

    +
    +public static final java.lang.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,
+                                                              java.util.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(java.lang.String taskId)
    +
    +
    +
    +
    +
    +
    + +

    +getSyncEngine

    +
    +public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable)
+                                  throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +public static java.lang.String getWorkDirectory(java.lang.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 new file mode 100644 index 0000000..5a017ae --- /dev/null +++ b/website/full_javadoc/compbio/engine/FilePuller.html @@ -0,0 +1,551 @@ + + + + + + +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:
    java.lang.Comparable<java.util.concurrent.Delayed>, java.util.concurrent.Delayed
    +
    +
    +
    +
    public class FilePuller
    extends java.lang.Object
    implements java.util.concurrent.Delayed
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intcompareTo(java.util.concurrent.Delayed o) + +
    +           
    + voiddisconnect() + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + longgetDelay(java.util.concurrent.TimeUnit unit) + +
    +           
    + java.lang.StringgetFile() + +
    +           
    + bytegetProgress() + +
    +           
    + inthashCode() + +
    +           
    + booleanhasMoreData() + +
    +           
    + voidinitPull() + +
    +           
    + booleanisFileCreated() + +
    +           
    +static FilePullernewFilePuller(java.lang.String file, + int chunkSize) + +
    +           
    +static FilePullernewProgressPuller(java.lang.String file) + +
    +          Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more.
    + ChunkHolderpull(long position) + +
    +           
    + java.lang.StringtoString() + +
    +           
    + voidwaitForFile(long maxWaitSeconds) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +newFilePuller

    +
    +public static FilePuller newFilePuller(java.lang.String file,
+                                       int chunkSize)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +newProgressPuller

    +
    +public static FilePuller newProgressPuller(java.lang.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:
    +
    +
    +
    + +

    +pull

    +
    +public ChunkHolder pull(long position)
+                 throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +initPull

    +
    +public void initPull()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getFile

    +
    +public java.lang.String getFile()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +isFileCreated

    +
    +public boolean isFileCreated()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +waitForFile

    +
    +public void waitForFile(long maxWaitSeconds)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +hasMoreData

    +
    +public boolean hasMoreData()
+                    throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +compareTo

    +
    +public int compareTo(java.util.concurrent.Delayed o)
    +
    +
    +
    Specified by:
    compareTo in interface java.lang.Comparable<java.util.concurrent.Delayed>
    +
    +
    +
    +
    +
    +
    + +

    +getDelay

    +
    +public long getDelay(java.util.concurrent.TimeUnit unit)
    +
    +
    +
    Specified by:
    getDelay in interface java.util.concurrent.Delayed
    +
    +
    +
    +
    +
    +
    + +

    +disconnect

    +
    +public void disconnect()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getProgress

    +
    +public byte getProgress()
+                 throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.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 new file mode 100644 index 0000000..dc4790d --- /dev/null +++ b/website/full_javadoc/compbio/engine/Job.html @@ -0,0 +1,403 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Job(java.lang.String taskId, + java.lang.String jobId, + ConfiguredExecutable<?> cexecutable) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    +static JobgetByJobId(java.lang.String jobId, + java.util.List<Job> jobs) + +
    +           
    +static JobgetByTaskId(java.lang.String taskId, + java.util.List<Job> jobs) + +
    +           
    + ConfiguredExecutable<?>getConfExecutable() + +
    +           
    + ClusterJobIdgetJobId() + +
    +           
    + java.lang.StringgetTaskId() + +
    +           
    + inthashCode() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Job

    +
    +public Job(java.lang.String taskId,
+           java.lang.String jobId,
+           ConfiguredExecutable<?> cexecutable)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public ClusterJobId getJobId()
    +
    +
    +
    +
    +
    +
    + +

    +getTaskId

    +
    +public java.lang.String getTaskId()
    +
    +
    +
    +
    +
    +
    + +

    +getConfExecutable

    +
    +public ConfiguredExecutable<?> getConfExecutable()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getByTaskId

    +
    +public static Job getByTaskId(java.lang.String taskId,
+                              java.util.List<Job> jobs)
    +
    +
    +
    +
    +
    +
    + +

    +getByJobId

    +
    +public static Job getByJobId(java.lang.String jobId,
+                             java.util.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 new file mode 100644 index 0000000..eb3b1d9 --- /dev/null +++ b/website/full_javadoc/compbio/engine/LoadBalancer.html @@ -0,0 +1,247 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + +
    +Method Summary
    +static Executable.ExecProvidergetEngine(Executable<?> executable) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		getEngine(Executable<V> executable, + java.util.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,
+                                                      java.util.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 new file mode 100644 index 0000000..93c4cd3 --- /dev/null +++ b/website/full_javadoc/compbio/engine/ProgressGetter.html @@ -0,0 +1,273 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ProgressGetter() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static bytegetProgress(java.lang.String progressFile) + +
    +           
    +static ChunkHolderpull(java.lang.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(java.lang.String file,
+                                     long position)
    +
    +
    +
    +
    +
    +
    + +

    +getProgress

    +
    +public static final byte getProgress(java.lang.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 new file mode 100644 index 0000000..0d11dcf --- /dev/null +++ b/website/full_javadoc/compbio/engine/PulledFileCache.html @@ -0,0 +1,275 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PulledFileCache() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static FilePullerget(java.lang.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(java.lang.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:
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 new file mode 100644 index 0000000..9a83cd7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/SubmissionManager.html @@ -0,0 +1,286 @@ + + + + + + +SubmissionManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + 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 java.lang.Object
    + + +

    +Submit jobs for execution +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static voidaddTask(ConfiguredExecutable<?> executable, + java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static java.util.concurrent.Future<ConfiguredExecutable<?>>getTask(java.lang.String taskId) + +
    +           
    +static voidremoveTask(ConfiguredExecutable<?> executable) + +
    +           
    +static voidremoveTask(java.lang.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,
+                           java.util.concurrent.Future<ConfiguredExecutable<?>> future)
    +
    +
    +
    +
    +
    +
    + +

    +getTask

    +
    +public static java.util.concurrent.Future<ConfiguredExecutable<?>> getTask(java.lang.String taskId)
    +
    +
    +
    +
    +
    +
    + +

    +removeTask

    +
    +public static void removeTask(ConfiguredExecutable<?> executable)
    +
    +
    +
    +
    +
    +
    + +

    +removeTask

    +
    +public static void removeTask(java.lang.String key)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/engine/SyncExecutor.html b/website/full_javadoc/compbio/engine/SyncExecutor.html new file mode 100644 index 0000000..ac2be71 --- /dev/null +++ b/website/full_javadoc/compbio/engine/SyncExecutor.html @@ -0,0 +1,337 @@ + + + + + + +SyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +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.
    + java.lang.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

    +
    +java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/engine/class-use/AsyncExecutor.html b/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html new file mode 100644 index 0000000..b28efa7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html @@ -0,0 +1,285 @@ + + + + + + +Uses of Interface compbio.engine.AsyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Interface
    compbio.engine.AsyncExecutor

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use AsyncExecutor
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    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(java.lang.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) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/Cleaner.html b/website/full_javadoc/compbio/engine/class-use/Cleaner.html new file mode 100644 index 0000000..2817a0e --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/Cleaner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.Cleaner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.Cleaner

    +
    +No usage of compbio.engine.Cleaner +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html b/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html new file mode 100644 index 0000000..b2ba6dc --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html @@ -0,0 +1,227 @@ + + + + + + +Uses of Class compbio.engine.ClusterJobId + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.engine.ClusterJobId

    +
    + + + + + + + + + + + + + +
    +Packages that use ClusterJobId
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +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(java.lang.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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/Configurator.html b/website/full_javadoc/compbio/engine/class-use/Configurator.html new file mode 100644 index 0000000..40b9770 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/Configurator.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.Configurator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.Configurator

    +
    +No usage of compbio.engine.Configurator +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/FilePuller.html b/website/full_javadoc/compbio/engine/class-use/FilePuller.html new file mode 100644 index 0000000..c27be52 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/FilePuller.html @@ -0,0 +1,214 @@ + + + + + + +Uses of Class compbio.engine.FilePuller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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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(java.lang.String fileName) + +
    +           
    +static FilePullerFilePuller.newFilePuller(java.lang.String file, + int chunkSize) + +
    +           
    +static FilePullerFilePuller.newProgressPuller(java.lang.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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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/Job.html b/website/full_javadoc/compbio/engine/class-use/Job.html new file mode 100644 index 0000000..def898e --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/Job.html @@ -0,0 +1,216 @@ + + + + + + +Uses of Class compbio.engine.Job + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.Job

    +
    + + + + + + + + + +
    +Packages that use Job
    compbio.engine  
    +  +

    + + + + + +
    +Uses of Job in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return Job
    +static JobJob.getByJobId(java.lang.String jobId, + java.util.List<Job> jobs) + +
    +           
    +static JobJob.getByTaskId(java.lang.String taskId, + java.util.List<Job> jobs) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.engine with type arguments of type Job
    +static JobJob.getByJobId(java.lang.String jobId, + java.util.List<Job> jobs) + +
    +           
    +static JobJob.getByTaskId(java.lang.String taskId, + java.util.List<Job> jobs) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html b/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html new file mode 100644 index 0000000..233f48a --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.LoadBalancer + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.LoadBalancer

    +
    +No usage of compbio.engine.LoadBalancer +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/ProgressGetter.html b/website/full_javadoc/compbio/engine/class-use/ProgressGetter.html new file mode 100644 index 0000000..7841509 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/ProgressGetter.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.ProgressGetter + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.ProgressGetter

    +
    +No usage of compbio.engine.ProgressGetter +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html b/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html new file mode 100644 index 0000000..2454b33 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.PulledFileCache + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.PulledFileCache

    +
    +No usage of compbio.engine.PulledFileCache +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html b/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html new file mode 100644 index 0000000..557e5c0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.SubmissionManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.SubmissionManager

    +
    +No usage of compbio.engine.SubmissionManager +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html b/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html new file mode 100644 index 0000000..5bb0963 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html @@ -0,0 +1,248 @@ + + + + + + +Uses of Interface compbio.engine.SyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Interface
    compbio.engine.SyncExecutor

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use SyncExecutor
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + +
    +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 + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html new file mode 100644 index 0000000..3eb5b72 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html @@ -0,0 +1,243 @@ + + + + + + +ClusterNativeSpecExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 ClusterNativeSpecExecutable<T>

    +
    +
    All Superinterfaces:
    Executable<T>
    +
    +
    +
    All Known Implementing Classes:
    Tcoffee
    +
    +
    +
    +
    public interface ClusterNativeSpecExecutable<T>
    extends Executable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetNativeSpecs() + +
    +           
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getNativeSpecs

    +
    +java.lang.String getNativeSpecs()
    +
    +
    +
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/engine/client/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/CommandBuilder.html new file mode 100644 index 0000000..a717442 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/CommandBuilder.html @@ -0,0 +1,582 @@ + + + + + + +CommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class CommandBuilder<T>

    +
    +java.lang.Object
+  extended by compbio.engine.client.CommandBuilder<T>
+
    +
    +
    +
    public class CommandBuilder<T>
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CommandBuilder(java.lang.String nameValueSeparator) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + voidaddParams(java.util.List<java.lang.String> params) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.util.List<java.lang.String>getCommands() + +
    +           
    + java.lang.StringgetCommandString() + +
    +           
    + java.lang.StringgetParamValue(java.lang.String paramName) + +
    +           
    + inthashCode() + +
    +           
    + booleanhasParam(java.lang.String paramName) + +
    +           
    +static + + + + +
    +<T> CommandBuilder<T>
    +    		newCommandBuilder(java.util.List<? extends Option<T>> arguments, + java.lang.String nameValueSeparator) + +
    +          This produces the same result as getCommands method.
    + booleanremoveParam(java.lang.String paramName) + +
    +           
    + booleansetFirst(java.lang.String param) + +
    +           
    + booleansetLast(java.lang.String paramName) + +
    +           
    + booleansetLast(java.lang.String paramName, + java.lang.String paramValue) + +
    +           
    + booleansetParam(java.lang.String param) + +
    +           
    + booleansetParam(java.lang.String paramName, + java.lang.String paramValue) + +
    +           
    + voidsetParams(java.util.List<java.lang.String> params) + +
    +           
    + intsize() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +CommandBuilder

    +
    +public CommandBuilder(java.lang.String nameValueSeparator)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +addParams

    +
    +public void addParams(java.util.List<java.lang.String> params)
    +
    +
    +
    +
    +
    +
    + +

    +setParams

    +
    +public void setParams(java.util.List<java.lang.String> params)
    +
    +
    +
    +
    +
    +
    + +

    +hasParam

    +
    +public boolean hasParam(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +setFirst

    +
    +public boolean setFirst(java.lang.String param)
    +
    +
    +
    +
    +
    +
    + +

    +setParam

    +
    +public boolean setParam(java.lang.String param)
    +
    +
    +
    +
    +
    +
    + +

    +setLast

    +
    +public boolean setLast(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +setLast

    +
    +public boolean setLast(java.lang.String paramName,
+                       java.lang.String paramValue)
    +
    +
    +
    +
    +
    +
    + +

    +getParamValue

    +
    +public java.lang.String getParamValue(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +removeParam

    +
    +public boolean removeParam(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +setParam

    +
    +public boolean setParam(java.lang.String paramName,
+                        java.lang.String paramValue)
    +
    +
    +
    +
    +
    +
    + +

    +getCommands

    +
    +public java.util.List<java.lang.String> getCommands()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandString

    +
    +public java.lang.String getCommandString()
    +
    +
    +
    +
    +
    +
    + +

    +newCommandBuilder

    +
    +public static <T> CommandBuilder<T> newCommandBuilder(java.util.List<? extends Option<T>> arguments,
+                                                      java.lang.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:
    +
    +
    +
    + +

    +size

    +
    +public int size()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.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 new file mode 100644 index 0000000..a6ea5cc --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ConfExecutable.html @@ -0,0 +1,1000 @@ + + + + + + +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 java.lang.Object
    implements ConfiguredExecutable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringCLUSTER_TASK_ID_PREFIX + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ConfExecutable(Executable<T> executable, + java.lang.String taskDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Executable<T>addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.util.Map<java.lang.String,java.lang.String>getEnvironment() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + Executable.ExecProvidergetExecProvider() + +
    +           
    + Executable<T>getExecutable() + +
    +           
    + java.lang.StringgetInput() + +
    +          Not all input paths are relative! Input path could be absolute!
    + Limit<T>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<T>getLimits() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<T>getParameters() + +
    +           
    + CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults() + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + RunConfigurationgetRunConfiguration() + +
    +           
    +static + + + + +
    +<V> LimitsManager<V>
    +    		getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) + +
    +          This method should be executed once and result of its execution reused.
    +static + + + + +
    +<V> RunnerConfig<V>
    +    		getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +static + + + + +
    +<V> PresetManager<V>
    +    		getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    + Executable.ExecProvidergetSupportedRuntimes() + +
    +           
    + java.lang.StringgetTaskId() + +
    +           
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>loadRunConfiguration(java.io.InputStream input) + +
    +           
    + ConfiguredExecutable<?>loadRunConfiguration(RunConfiguration rconf) + +
    +           
    +static ConfiguredExecutable<?>newConfExecutable(RunConfiguration rconf) + +
    +           
    + booleansaveRunConfiguration() + +
    +           
    + voidsetExecProvider(Executable.ExecProvider provider) + +
    +           
    + voidsetWorkDirectory(java.lang.String workDirectory) + +
    +           
    + java.lang.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 java.lang.String CLUSTER_TASK_ID_PREFIX
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ConfExecutable

    +
    +public ConfExecutable(Executable<T> executable,
+                      java.lang.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 java.lang.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(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<T> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getTaskId

    +
    +public java.lang.String getTaskId()
    +
    +
    +
    Specified by:
    getTaskId in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +setWorkDirectory

    +
    +public void setWorkDirectory(java.lang.String workDirectory)
    +
    +
    +
    Specified by:
    setWorkDirectory in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +public java.lang.String getWorkDirectory()
    +
    +
    +
    Specified by:
    getWorkDirectory in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public Executable<T> addParameters(java.util.List<java.lang.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 java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    Specified by:
    getCreatedFiles in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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(java.lang.String directory)
+             throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<T>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public static <V> RunnerConfig<V> getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
+                                        throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getRunnerPresets

    +
    +public static <V> PresetManager<V> getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)
+                                         throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getRunnerLimits

    +
    +public static <V> LimitsManager<V> getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz)
+                                        throws java.io.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:
    +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getEnvironment

    +
    +public java.util.Map<java.lang.String,java.lang.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 java.io.IOException
    +
    +
    +
    Specified by:
    saveRunConfiguration in interface ConfiguredExecutable<T>
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getRunConfiguration

    +
    +public RunConfiguration getRunConfiguration()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
+                                             throws java.io.IOException
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface ConfiguredExecutable<T>
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.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/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html new file mode 100644 index 0000000..1a59a09 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html @@ -0,0 +1,504 @@ + + + + + + +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
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.util.Map<java.lang.String,java.lang.String>getEnvironment() + +
    +           
    + Executable.ExecProvidergetExecProvider() + +
    +           
    + Executable<T>getExecutable() + +
    +           
    + CommandBuilder<T>getParameters() + +
    +           
    + + + + + +
    +<V> V
    +    		getResults() + +
    +           
    + Executable.ExecProvidergetSupportedRuntimes() + +
    +           
    + java.lang.StringgetTaskId() + +
    +           
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>loadRunConfiguration(java.io.InputStream input) + +
    +           
    + booleansaveRunConfiguration() + +
    +           
    + voidsetWorkDirectory(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getEnvironment

    +
    +java.util.Map<java.lang.String,java.lang.String> getEnvironment()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getTaskId

    +
    +java.lang.String getTaskId()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +java.lang.String getCommand(Executable.ExecProvider provider)
+                            throws JobSubmissionException
    +
    +
    +
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +getSupportedRuntimes

    +
    +Executable.ExecProvider getSupportedRuntimes()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +java.lang.String getWorkDirectory()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setWorkDirectory

    +
    +void setWorkDirectory(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +<V> V getResults()
+             throws ResultNotAvailableException
    +
    +
    +
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getExecutable

    +
    +Executable<T> getExecutable()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +CommandBuilder<T> getParameters()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +saveRunConfiguration

    +
    +boolean saveRunConfiguration()
+                             throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
+                                             throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.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 new file mode 100644 index 0000000..096638b --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html @@ -0,0 +1,294 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringPATH + +
    +          Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable
    +  + + + + + + + + + + +
    +Constructor Summary
    EnvVariableProcessor() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static java.util.Map<java.lang.String,java.lang.String>getEnvVariables(java.lang.String property, + java.lang.Class<?> clazz) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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

    +PATH

    +
    +public static final java.lang.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 java.util.Map<java.lang.String,java.lang.String> getEnvVariables(java.lang.String property,
+                                                                               java.lang.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 new file mode 100644 index 0000000..085b7fc --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html @@ -0,0 +1,341 @@ + + + + + + +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:
    java.io.Serializable, java.lang.Comparable<Executable.ExecProvider>
    +
    +
    +
    Enclosing interface:
    Executable<T>
    +
    +
    +
    +
    public static enum Executable.ExecProvider
    extends java.lang.Enum<Executable.ExecProvider>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    Any + +
    +           
    Cluster + +
    +           
    Local + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static Executable.ExecProvidervalueOf(java.lang.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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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 new file mode 100644 index 0000000..9f7254f --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/Executable.html @@ -0,0 +1,423 @@ + + + + + + +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:
    ClusterNativeSpecExecutable<T>, ConfiguredExecutable<T>, PipedExecutable<T>
    +
    +
    +
    All Known Implementing Classes:
    _SkeletalCommandBuilder, BlastAll, ClustalW, ConfExecutable, Disembl, Mafft, Mcl, Muscle, NetNglyc, OB, Probcons, PsiBlast, 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(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + Limit<T>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<T>getLimits() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +addParameters

    +
    +Executable<T> addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Adds parameter to the list of parameters for a native executable +

    +

    +
    Parameters:
    parameters - +
    Returns:
    this Executable
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +java.lang.String getInput()
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +java.lang.String getOutput()
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +java.lang.String getError()
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +<V> V getResults(java.lang.String directory)
+             throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +Limit<T> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +LimitsManager<T> getLimits()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 new file mode 100644 index 0000000..d83660e --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/PathValidator.html @@ -0,0 +1,362 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PathValidator() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleanisAbsolutePath(java.lang.String path) + +
    +          Whether a certain path is absolute or not is operation system dependent!
    +static booleanisValidDirectory(java.lang.String directory) + +
    +           
    +static booleanisValidExecutable(java.lang.String command) + +
    +           
    +static voidvalidateDirectory(java.lang.String workDirectory) + +
    +           
    +static voidvalidateExecutable(java.lang.String command) + +
    +           
    +static voidvalidatePathNames(java.util.List<java.lang.String> filenames, + java.lang.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(java.lang.String command)
    +
    +
    +
    +
    +
    +
    + +

    +validateExecutable

    +
    +public static void validateExecutable(java.lang.String command)
+                               throws java.lang.IllegalArgumentException
    +
    +
    + +
    Throws: +
    java.lang.IllegalArgumentException
    +
    +
    +
    + +

    +isValidDirectory

    +
    +public static boolean isValidDirectory(java.lang.String directory)
    +
    +
    +
    +
    +
    +
    + +

    +validatePathNames

    +
    +public static void validatePathNames(java.util.List<java.lang.String> filenames,
+                                     java.lang.String type)
+                              throws java.lang.IllegalArgumentException
    +
    +
    +
    Parameters:
    filenames -
    type - - merely a string to be added to error message to explain what + type of files are lacking +
    Throws: +
    java.lang.IllegalArgumentException
    +
    +
    +
    + +

    +isAbsolutePath

    +
    +public static boolean isAbsolutePath(java.lang.String path)
    +
    +
    Whether a certain path is absolute or not is operation system dependent! +

    +

    +
    Parameters:
    path - +
    Returns:
    +
    +
    +
    + +

    +validateDirectory

    +
    +public static void validateDirectory(java.lang.String workDirectory)
+                              throws java.lang.IllegalArgumentException
    +
    +
    + +
    Throws: +
    java.lang.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 new file mode 100644 index 0000000..e3e7f54 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/PipedExecutable.html @@ -0,0 +1,228 @@ + + + + + + +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, 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 +

    + +

    +

    +
    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, 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 new file mode 100644 index 0000000..56783a6 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/RunConfiguration.html @@ -0,0 +1,572 @@ + + + + + + +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 java.lang.Object
    + + +

    +Value class for persisting ConfExecutable instances +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringrconfigFile + +
    +           
    +  + + + + + + + + + + + + + +
    +Constructor Summary
    RunConfiguration() + +
    +           
    RunConfiguration(ConfExecutable<?> cexec) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<?>getParameters() + +
    +           
    + java.lang.StringgetRunnerClassName() + +
    +           
    + inthashCode() + +
    +           
    +static RunConfigurationload(java.io.InputStream input) + +
    +           
    + voidsetError(java.lang.String error) + +
    +           
    + voidsetInput(java.lang.String input) + +
    +           
    + voidsetOutput(java.lang.String output) + +
    +           
    + voidsetParameters(CommandBuilder<?> parameters) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +static booleanwrite(RunConfiguration rconf) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

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

    +rconfigFile

    +
    +public static final java.lang.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 java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +load

    +
    +public static RunConfiguration load(java.io.InputStream input)
+                             throws java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +setOutput

    +
    +public void setOutput(java.lang.String output)
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<?> getParameters()
    +
    +
    +
    +
    +
    +
    + +

    +setParameters

    +
    +public void setParameters(CommandBuilder<?> parameters)
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    +
    +
    +
    + +

    +setError

    +
    +public void setError(java.lang.String error)
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    +
    + +

    +setInput

    +
    +public void setInput(java.lang.String input)
    +
    +
    +
    +
    +
    +
    + +

    +getRunnerClassName

    +
    +public java.lang.String getRunnerClassName()
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.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 new file mode 100644 index 0000000..bc14f0c --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html @@ -0,0 +1,641 @@ + + + + + + +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:
    ClustalW, Mafft, Muscle, Probcons, PsiBlast, Tcoffee
    +
    +
    +
    +
    public abstract class SkeletalExecutable<T>
    extends java.lang.Object
    implements Executable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + + + + +
    +Constructor Summary
    SkeletalExecutable() + +
    +           
    SkeletalExecutable(java.lang.String parameterKeyValueDelimiter) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Executable<T>addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetClusterSettings() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
    +           
    +abstract  java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + inthashCode() + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + SkeletalExecutable<T>setError(java.lang.String errFile) + +
    +           
    + SkeletalExecutable<T>setInput(java.lang.String inFile) + +
    +           
    + SkeletalExecutable<T>setOutput(java.lang.String outFile) + +
    +           
    + Executable<T>setParameter(java.lang.String parameter) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    getLimit, getLimits, getResults
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +SkeletalExecutable

    +
    +public SkeletalExecutable()
    +
    +
    +
    + +

    +SkeletalExecutable

    +
    +public SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setInput

    +
    +public SkeletalExecutable<T> setInput(java.lang.String inFile)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setOutput

    +
    +public SkeletalExecutable<T> setOutput(java.lang.String outFile)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setError

    +
    +public SkeletalExecutable<T> setError(java.lang.String errFile)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public Executable<T> addParameters(java.util.List<java.lang.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(java.lang.String parameter)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.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 java.lang.String getInput()
    +
    +
    +
    Specified by:
    getInput in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getClusterSettings

    +
    +public java.lang.String getClusterSettings()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public abstract java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/Util.html b/website/full_javadoc/compbio/engine/client/Util.html new file mode 100644 index 0000000..5574f03 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/Util.html @@ -0,0 +1,505 @@ + + + + + + +Util + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class Util

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

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Util() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringconvertToAbsolute(java.lang.String relativePath) + +
    +           
    +static java.lang.StringgetCommand(Executable.ExecProvider provider, + java.lang.Class<?> clazz) + +
    +           
    +static java.lang.StringgetExecProperty(java.lang.String propertySpec, + java.lang.Class<?> clazz) + +
    +           
    +static java.lang.StringgetExecProperty(java.lang.String propertySpec, + Executable<?> exec) + +
    +           
    +static java.lang.StringgetFullPath(java.lang.String workDirectory, + java.lang.String fileName) + +
    +           
    +static Executable.ExecProvidergetSupportedRuntimes(java.lang.Class<?> clazz) + +
    +           
    +static booleanisMarked(java.lang.String workDirectory, + JobStatus marker) + +
    +           
    +static booleanisValidJobId(java.lang.String key) + +
    +           
    +static ConfiguredExecutable<?>loadExecutable(java.lang.String taskId) + +
    +           
    +static java.util.Map<java.lang.String,java.lang.String>mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified, + java.util.Map<java.lang.String,java.lang.String> variables) + +
    +           
    +static voidwriteFile(java.lang.String workDirectory, + java.lang.String fileAndEventName, + java.lang.String content, + boolean override) + +
    +           
    +static booleanwriteMarker(java.lang.String workDirectory, + JobStatus fileType) + +
    +           
    +static voidwriteStatFile(java.lang.String workDirectory, + java.lang.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(java.lang.String key)
    +
    +
    +
    +
    +
    +
    + +

    +writeStatFile

    +
    +public static void writeStatFile(java.lang.String workDirectory,
+                                 java.lang.String fileAndEventName)
    +
    +
    +
    +
    +
    +
    + +

    +writeFile

    +
    +public static void writeFile(java.lang.String workDirectory,
+                             java.lang.String fileAndEventName,
+                             java.lang.String content,
+                             boolean override)
    +
    +
    +
    +
    +
    +
    + +

    +writeMarker

    +
    +public static final boolean writeMarker(java.lang.String workDirectory,
+                                        JobStatus fileType)
    +
    +
    +
    +
    +
    +
    + +

    +isMarked

    +
    +public static boolean isMarked(java.lang.String workDirectory,
+                               JobStatus marker)
    +
    +
    +
    +
    +
    +
    + +

    +mergeEnvVariables

    +
    +public static java.util.Map<java.lang.String,java.lang.String> mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,
+                                                                                 java.util.Map<java.lang.String,java.lang.String> variables)
    +
    +
    +
    +
    +
    +
    + +

    +convertToAbsolute

    +
    +public static java.lang.String convertToAbsolute(java.lang.String relativePath)
    +
    +
    +
    +
    +
    +
    + +

    +getExecProperty

    +
    +public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               Executable<?> exec)
    +
    +
    +
    +
    +
    +
    + +

    +getExecProperty

    +
    +public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getFullPath

    +
    +public static java.lang.String getFullPath(java.lang.String workDirectory,
+                                           java.lang.String fileName)
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public static java.lang.String getCommand(Executable.ExecProvider provider,
+                                          java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getSupportedRuntimes

    +
    +public static Executable.ExecProvider getSupportedRuntimes(java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +loadExecutable

    +
    +public static ConfiguredExecutable<?> loadExecutable(java.lang.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/client/class-use/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html new file mode 100644 index 0000000..d57b7bd --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Interface compbio.engine.client.ClusterNativeSpecExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Interface
    compbio.engine.client.ClusterNativeSpecExecutable

    +
    + + + + + + + + + +
    +Packages that use ClusterNativeSpecExecutable
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    +  +

    + + + + + +
    +Uses of ClusterNativeSpecExecutable in compbio.runner.msa
    +  +

    + + + + + + + + + +
    Classes in compbio.runner.msa that implement ClusterNativeSpecExecutable
    + classTcoffee + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html new file mode 100644 index 0000000..663f217 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html @@ -0,0 +1,339 @@ + + + + + + +Uses of Class compbio.engine.client.CommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.client.CommandBuilder

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use CommandBuilder
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    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<T>ConfiguredExecutable.getParameters() + +
    +           
    + CommandBuilder<T>ConfExecutable.getParameters() + +
    +           
    + CommandBuilder<?>RunConfiguration.getParameters() + +
    +           
    + CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    +static + + + + +
    +<T> CommandBuilder<T>
    +    		CommandBuilder.newCommandBuilder(java.util.List<? extends Option<T>> arguments, + java.lang.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) + +
    +           
    +  +

    + + + + + +
    +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.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.msa that return CommandBuilder
    + CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html new file mode 100644 index 0000000..e5755d1 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html @@ -0,0 +1,178 @@ + + + + + + +Uses of Class compbio.engine.client.ConfExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.client.ConfExecutable

    +
    + + + + + + + + + +
    +Packages that use ConfExecutable
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    +  +

    + + + + + +
    +Uses of ConfExecutable in compbio.engine.client
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.client with parameters of type ConfExecutable
    RunConfiguration(ConfExecutable<?> cexec) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html new file mode 100644 index 0000000..85add53 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html @@ -0,0 +1,744 @@ + + + + + + +Uses of Interface compbio.engine.client.ConfiguredExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Interface
    compbio.engine.client.ConfiguredExecutable

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use ConfiguredExecutable
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    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, + java.util.List<FastaSequence> dataSet) + +
    +           
    + ConfiguredExecutable<?>Job.getConfExecutable() + +
    +           
    + ConfiguredExecutable<?>AsyncExecutor.getResults(java.lang.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 java.util.concurrent.Future<ConfiguredExecutable<?>>SubmissionManager.getTask(java.lang.String taskId) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine with parameters of type ConfiguredExecutable
    +static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, + java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static booleanCleaner.deleteFiles(ConfiguredExecutable<?> exec) + +
    +          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) + +
    +           
    + java.lang.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, + java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine with parameters of type ConfiguredExecutable
    Job(java.lang.String taskId, + java.lang.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(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>ConfiguredExecutable.loadRunConfiguration(java.io.InputStream input) + +
    +           
    + ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(java.io.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(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncJobRunner.getResults(java.lang.String jobId) + +
    +           
    + ConfiguredExecutable<?>JobRunner.waitForResult() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
    +static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) + +
    +           
    + java.lang.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(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncLocalRunner.getResults(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>LocalRunner.waitForResult() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.local with parameters of type ConfiguredExecutable
    +static booleanLocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable) + +
    +           
    + java.lang.StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable
    +static booleanLocalEngineUtil.cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String workDirectory) + +
    +           
    +static JobStatusLocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    +  +

    + + + + + + + + + + + +
    Constructors in compbio.engine.local with parameters of type ConfiguredExecutable
    ExecutableWrapper(ConfiguredExecutable<?> executable, + java.lang.String workDirectory) + +
    +           
    LocalRunner(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner with parameters of type ConfiguredExecutable
    +static voidUtil.writeInput(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.ws.server
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.ws.server with parameters of type ConfiguredExecutable
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html new file mode 100644 index 0000000..8647d6e --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.client.EnvVariableProcessor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.EnvVariableProcessor

    +
    +No usage of compbio.engine.client.EnvVariableProcessor +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/class-use/Executable.ExecProvider.html new file mode 100644 index 0000000..e8cae7f --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/Executable.ExecProvider.html @@ -0,0 +1,516 @@ + + + + + + +Uses of Class compbio.engine.client.Executable.ExecProvider + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.client.Executable.ExecProvider

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Executable.ExecProvider
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    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, + java.util.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(java.lang.Class<?> clazz) + +
    +           
    +static Executable.ExecProviderExecutable.ExecProvider.valueOf(java.lang.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
    + java.lang.StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringConfExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    +static java.lang.StringUtil.getCommand(Executable.ExecProvider provider, + java.lang.Class<?> clazz) + +
    +           
    + CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>Executable.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) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable.ExecProvider in compbio.runner._impl
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner._impl with parameters of type Executable.ExecProvider
    + java.lang.StringMcl.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringBlastAll.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringRPSBlast.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringRonn.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringPSIBlast.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringDisembl.getCommand(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<NetNglyc>NetNglyc.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) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/Executable.html b/website/full_javadoc/compbio/engine/client/class-use/Executable.html new file mode 100644 index 0000000..d3f24c0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/Executable.html @@ -0,0 +1,892 @@ + + + + + + +Uses of Interface compbio.engine.client.Executable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Interface
    compbio.engine.client.Executable

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Executable
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.confClasses commonly used by both engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    +  +

    + + + + + +
    +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, + java.util.List<FastaSequence> dataSet) + +
    +           
    +static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		LoadBalancer.getEngine(Executable<V> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + +
    Subinterfaces of Executable in compbio.engine.client
    + interfaceClusterNativeSpecExecutable<T> + +
    +           
    + 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>SkeletalExecutable.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    + Executable<T>Executable.addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + Executable<T>ConfExecutable.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    + Executable<T>ConfiguredExecutable.getExecutable() + +
    +           
    + Executable<T>ConfExecutable.getExecutable() + +
    +           
    + Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + Executable<T>SkeletalExecutable.setParameter(java.lang.String parameter) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that return types with arguments of type Executable
    +abstract  java.lang.Class<? extends Executable<?>>SkeletalExecutable.getType() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type Executable
    +static java.lang.StringUtil.getExecProperty(java.lang.String propertySpec, + Executable<?> exec) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.engine.client with type arguments of type Executable
    +static + + + + +
    +<V> LimitsManager<V>
    +    		ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) + +
    +          This method should be executed once and result of its execution reused.
    +static + + + + +
    +<V> RunnerConfig<V>
    +    		ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +static + + + + +
    +<V> PresetManager<V>
    +    		ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.client with parameters of type Executable
    ConfExecutable(Executable<T> executable, + java.lang.String taskDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.engine.conf
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.conf that return types with arguments of type Executable
    +static java.lang.Class<Executable<?>>DirectoryManager.getClass(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.runner
    +  +

    + + + + + + + + + +
    Classes in compbio.runner that implement Executable
    + class_SkeletalCommandBuilder + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return Executable
    + Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type Executable
    +static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    +static + + + + +
    +<T> LimitsManager<T>
    +    		Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) + +
    +          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +static + + + + +
    +<T> PresetManager<T>
    +    		Util.getPresets(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +static + + + + +
    +<T> RunnerConfig<T>
    +    		Util.getSupportedOptions(java.lang.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 + +
    +           
    + classDisembl + +
    +           
    + 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.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Classes in compbio.runner.msa that implement Executable
    + classClustalW + +
    +           
    + classMafft + +
    +           
    + classMuscle + +
    +           
    + classProbcons + +
    +           
    + classTcoffee + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Executable
    + java.lang.Class<? extends Executable<?>>Tcoffee.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>ClustalW.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>Probcons.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>Muscle.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>Mafft.getType() + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Classes in compbio.runner.psiblast that implement Executable
    + classPsiBlast + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that return types with arguments of type Executable
    + java.lang.Class<? extends Executable<?>>PsiBlast.getType() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html b/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html new file mode 100644 index 0000000..9d4b585 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.client.PathValidator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.PathValidator

    +
    +No usage of compbio.engine.client.PathValidator +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html new file mode 100644 index 0000000..2cb2e67 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html @@ -0,0 +1,241 @@ + + + + + + +Uses of Interface compbio.engine.client.PipedExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Interface
    compbio.engine.client.PipedExecutable

    +
    + + + + + + + + + + + + + +
    +Packages that use PipedExecutable
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    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.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Classes in compbio.runner.msa that implement PipedExecutable
    + classMafft + +
    +           
    + classProbcons + +
    +           
    + classTcoffee + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html new file mode 100644 index 0000000..656c2a0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html @@ -0,0 +1,294 @@ + + + + + + +Uses of Class compbio.engine.client.RunConfiguration + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.client.RunConfiguration

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use RunConfiguration
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    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(java.io.InputStream input) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type RunConfiguration
    + Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + Executable<?>Executable.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) + +
    +           
    +  +

    + + + + + +
    +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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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html new file mode 100644 index 0000000..30e7933 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html @@ -0,0 +1,286 @@ + + + + + + +Uses of Class compbio.engine.client.SkeletalExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.SkeletalExecutable

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use SkeletalExecutable
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    +  +

    + + + + + +
    +Uses of SkeletalExecutable in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return SkeletalExecutable
    + SkeletalExecutable<T>SkeletalExecutable.setError(java.lang.String errFile) + +
    +           
    + SkeletalExecutable<T>SkeletalExecutable.setInput(java.lang.String inFile) + +
    +           
    + SkeletalExecutable<T>SkeletalExecutable.setOutput(java.lang.String outFile) + +
    +           
    +  +

    + + + + + +
    +Uses of SkeletalExecutable in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Subclasses of SkeletalExecutable in compbio.runner.msa
    + classClustalW + +
    +           
    + classMafft + +
    +           
    + classMuscle + +
    +           
    + classProbcons + +
    +           
    + classTcoffee + +
    +           
    +  +

    + + + + + +
    +Uses of SkeletalExecutable in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Subclasses of SkeletalExecutable in compbio.runner.psiblast
    + classPsiBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/Util.html b/website/full_javadoc/compbio/engine/client/class-use/Util.html new file mode 100644 index 0000000..0e5ecf7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/Util.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.client.Util + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.Util

    +
    +No usage of compbio.engine.client.Util +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/package-frame.html b/website/full_javadoc/compbio/engine/client/package-frame.html new file mode 100644 index 0000000..32306b8 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-frame.html @@ -0,0 +1,72 @@ + + + + + + +compbio.engine.client + + + + + + + + + + + +compbio.engine.client + + + + +
    +Interfaces  + +
    +ClusterNativeSpecExecutable +
    +ConfiguredExecutable +
    +Executable +
    +PipedExecutable
    + + + + + + +
    +Classes  + +
    +CommandBuilder +
    +ConfExecutable +
    +EnvVariableProcessor +
    +PathValidator +
    +RunConfiguration +
    +SkeletalExecutable +
    +Util
    + + + + + + +
    +Enums  + +
    +Executable.ExecProvider
    + + + + diff --git a/website/full_javadoc/compbio/engine/client/package-summary.html b/website/full_javadoc/compbio/engine/client/package-summary.html new file mode 100644 index 0000000..8ce82d7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-summary.html @@ -0,0 +1,242 @@ + + + + + + +compbio.engine.client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.engine.client +

    +Classes and interfaces representing an input for engines. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Interface Summary
    ClusterNativeSpecExecutable<T> 
    ConfiguredExecutable<T> 
    Executable<T>Interface to a native executable.
    PipedExecutable<T>This is a marker interface to indicate that the output of the process must be + captured.
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    CommandBuilder<T> 
    ConfExecutable<T> 
    EnvVariableProcessor 
    PathValidator 
    RunConfigurationValue class for persisting ConfExecutable instances
    SkeletalExecutable<T> 
    Util 
    +  + +

    + + + + + + + + + +
    +Enum Summary
    Executable.ExecProvider 
    +  + +

    +

    +Package compbio.engine.client Description +

    + +

    +Classes and interfaces representing an input for engines. These classes are known to runners, + which form the next layer of the JABAWS hierarchy. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/package-tree.html b/website/full_javadoc/compbio/engine/client/package-tree.html new file mode 100644 index 0000000..ce4996a --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-tree.html @@ -0,0 +1,176 @@ + + + + + + +compbio.engine.client Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Hierarchy For Package compbio.engine.client +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/package-use.html b/website/full_javadoc/compbio/engine/client/package-use.html new file mode 100644 index 0000000..010d2bf --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-use.html @@ -0,0 +1,470 @@ + + + + + + +Uses of Package compbio.engine.client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Package
    compbio.engine.client

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.engine.client
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.confClasses commonly used by both engines. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    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 + +
    +           
    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.msa
    ClusterNativeSpecExecutable + +
    +           
    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.psiblast
    Executable + +
    +          Interface to a native executable.
    SkeletalExecutable + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.ws.server
    ConfiguredExecutable + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html new file mode 100644 index 0000000..779a787 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html @@ -0,0 +1,412 @@ + + + + + + +AsyncJobRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.drmaa +
    +Class AsyncJobRunner

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.AsyncJobRunner
+
    +
    +
    All Implemented Interfaces:
    AsyncExecutor
    +
    +
    +
    +
    public class AsyncJobRunner
    extends java.lang.Object
    implements AsyncExecutor
    + + +

    +Single cluster job runner class +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AsyncJobRunner() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job.
    + booleancleanup(java.lang.String jobId) + +
    +          Remove all files and a job directory for a jobid.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
    + ConfiguredExecutable<?>getResults(java.lang.String jobId) + +
    +          Retrieve the results of the job.
    + java.lang.StringgetWorkDirectory(java.lang.String jobId) + +
    +           
    + java.lang.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 java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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 java.lang.String getWorkDirectory(java.lang.String jobId)
    +
    +
    +
    Specified by:
    getWorkDirectory in interface AsyncExecutor
    +
    +
    +
    Parameters:
    jobId - unique job identifier +
    Returns:
    task working directory
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/cluster/drmaa/ClusterSession.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html new file mode 100644 index 0000000..51b0e22 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html @@ -0,0 +1,471 @@ + + + + + + +ClusterSession + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.drmaa +
    +Class ClusterSession

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.ClusterSession
+
    +
    +
    +
    public final class ClusterSession
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringJOBID + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + voidclose() + +
    +           
    +static ClusterJobIdgetClusterJobId(java.lang.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 java.lang.StringgetJobStatus(int status) + +
    +          Deprecated. 
    + ConfiguredExecutable<?>getResults(java.lang.String taskId) + +
    +           
    + org.ggf.drmaa.SessiongetSession() + +
    +           
    +static StatisticManagergetStatistics(org.ggf.drmaa.JobInfo status) + +
    +           
    + voidremoveJob(java.lang.String taskId) + +
    +           
    + org.ggf.drmaa.JobInfowaitForJob(java.lang.String taskId) + +
    +           
    + org.ggf.drmaa.JobInfowaitForJob(java.lang.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 java.lang.String JOBID
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getSession

    +
    +public org.ggf.drmaa.Session getSession()
    +
    +
    +
    +
    +
    +
    + +

    +close

    +
    +public void close()
    +
    +
    +
    +
    +
    +
    + +

    +removeJob

    +
    +public void removeJob(java.lang.String taskId)
    +
    +
    +
    +
    +
    +
    + +

    +waitForJob

    +
    +public org.ggf.drmaa.JobInfo waitForJob(java.lang.String taskId)
+                                 throws org.ggf.drmaa.DrmaaException,
+                                        java.io.IOException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException +
    java.io.IOException
    +
    +
    +
    + +

    +getClusterJobId

    +
    +public static ClusterJobId getClusterJobId(java.lang.String taskId)
+                                    throws java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +waitForJob

    +
    +public org.ggf.drmaa.JobInfo waitForJob(java.lang.String jobId,
+                                        long waitingTime)
+                                 throws org.ggf.drmaa.DrmaaException,
+                                        java.io.IOException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException +
    java.io.IOException
    +
    +
    +
    + +

    +getResults

    +
    +public ConfiguredExecutable<?> getResults(java.lang.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 java.lang.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:
    +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/cluster/drmaa/ClusterUtil.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html new file mode 100644 index 0000000..ad68763 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html @@ -0,0 +1,314 @@ + + + + + + +ClusterUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.drmaa +
    +Class ClusterUtil

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.ClusterUtil
+
    +
    +
    +
    public class ClusterUtil
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.text.NumberFormatCLUSTER_STAT_IN_SEC + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ClusterUtil() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleancancelJob(java.lang.String jobId, + ClusterSession csession) + +
    +           
    +static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, + java.lang.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 java.text.NumberFormat CLUSTER_STAT_IN_SEC
    +
    +
    +
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ClusterUtil

    +
    +public ClusterUtil()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +cancelJob

    +
    +public static final boolean cancelJob(java.lang.String jobId,
+                                      ClusterSession csession)
    +
    +
    +
    +
    +
    +
    + +

    +waitForResult

    +
    +public static final org.ggf.drmaa.JobInfo waitForResult(ClusterSession csession,
+                                                        java.lang.String jobId)
+                                                 throws JobExecutionException
    +
    +
    + +
    Throws: +
    JobExecutionException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/cluster/drmaa/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html new file mode 100644 index 0000000..da7c2e3 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html @@ -0,0 +1,487 @@ + + + + + + +JobRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.drmaa +
    +Class JobRunner

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.JobRunner
+
    +
    +
    All Implemented Interfaces:
    SyncExecutor
    +
    +
    +
    +
    public class JobRunner
    extends java.lang.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.
    + java.lang.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 java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/cluster/drmaa/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html new file mode 100644 index 0000000..da1ad93 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html @@ -0,0 +1,759 @@ + + + + + + +StatisticManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.drmaa +
    +Class StatisticManager

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.StatisticManager
+
    +
    +
    +
    public class StatisticManager
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    StatisticManager(org.ggf.drmaa.JobInfo status) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetAllStats() + +
    +           
    + java.lang.StringgetCalculationTime() + +
    +           
    + java.lang.StringgetCPUTimeStat() + +
    +           
    + java.lang.StringgetCPUUsageTime() + +
    +           
    + java.lang.StringgetDataTransfered() + +
    +           
    + java.lang.StringgetEndTime() + +
    +           
    + java.lang.StringgetExecutionStat() + +
    +           
    + java.lang.StringgetExitStatus() + +
    +           
    + java.lang.StringgetIOWait() + +
    +           
    + java.lang.StringgetJobId() + +
    +           
    + java.lang.StringgetJobPriority() + +
    +           
    + java.lang.StringgetMaxVMem() + +
    +           
    + java.lang.StringgetMemoryStat() + +
    +           
    + java.util.Map<java.lang.String,java.lang.String>getRawUsage() + +
    +           
    + java.lang.StringgetStartTime() + +
    +           
    + java.lang.StringgetSubmissionTime() + +
    +           
    + java.lang.StringgetTimeStat() + +
    +           
    + java.lang.StringgetUsedSysTime() + +
    +           
    + java.lang.StringgetUsedUserTime() + +
    +           
    + java.lang.StringgetVMem() + +
    +           
    + booleanhasDump() + +
    +           
    + booleanhasExited() + +
    +           
    + booleanhasSignaled() + +
    +           
    + java.lang.StringtermSignal() + +
    +           
    + java.lang.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 java.lang.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 java.lang.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 java.lang.String getSubmissionTime()
    +
    +
    +
    +
    +
    +
    + +

    +getVMem

    +
    +public java.lang.String getVMem()
    +
    +
    +
    +
    +
    +
    + +

    +getMaxVMem

    +
    +public java.lang.String getMaxVMem()
    +
    +
    +
    +
    +
    +
    + +

    +getUsedSysTime

    +
    +public java.lang.String getUsedSysTime()
    +
    +
    +
    +
    +
    +
    + +

    +getUsedUserTime

    +
    +public java.lang.String getUsedUserTime()
    +
    +
    +
    +
    +
    +
    + +

    +getCalculationTime

    +
    +public java.lang.String getCalculationTime()
    +
    +
    +
    +
    +
    +
    + +

    +getEndTime

    +
    +public java.lang.String getEndTime()
    +
    +
    +
    +
    +
    +
    + +

    +getStartTime

    +
    +public java.lang.String getStartTime()
    +
    +
    +
    +
    +
    +
    + +

    +getIOWait

    +
    +public java.lang.String getIOWait()
    +
    +
    +
    +
    +
    +
    + +

    +getCPUUsageTime

    +
    +public java.lang.String getCPUUsageTime()
    +
    +
    +
    +
    +
    +
    + +

    +getDataTransfered

    +
    +public java.lang.String getDataTransfered()
    +
    +
    +
    +
    +
    +
    + +

    +getJobPriority

    +
    +public java.lang.String getJobPriority()
    +
    +
    +
    +
    +
    +
    + +

    +getExitStatus

    +
    +public java.lang.String getExitStatus()
    +
    +
    +
    +
    +
    +
    + +

    +getAllStats

    +
    +public java.lang.String getAllStats()
+                             throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getExecutionStat

    +
    +public java.lang.String getExecutionStat()
+                                  throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getMemoryStat

    +
    +public java.lang.String getMemoryStat()
    +
    +
    +
    +
    +
    +
    + +

    +getCPUTimeStat

    +
    +public java.lang.String getCPUTimeStat()
    +
    +
    +
    +
    +
    +
    + +

    +getTimeStat

    +
    +public java.lang.String getTimeStat()
    +
    +
    +
    +
    +
    +
    + +

    +getRawUsage

    +
    +public java.util.Map<java.lang.String,java.lang.String> getRawUsage()
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.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/cluster/drmaa/_DrmaaExample.html b/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html new file mode 100644 index 0000000..158c30c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html @@ -0,0 +1,255 @@ + + + + + + +_DrmaaExample + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.drmaa +
    +Class _DrmaaExample

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa._DrmaaExample
+
    +
    +
    +
    public class _DrmaaExample
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _DrmaaExample() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_DrmaaExample

    +
    +public _DrmaaExample()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
+                 throws java.lang.Exception
    +
    +
    + +
    Throws: +
    java.lang.Exception
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html b/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html new file mode 100644 index 0000000..6aaaf54 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html @@ -0,0 +1,252 @@ + + + + + + +_JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class _JobStatus

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa._JobStatus
+
    +
    +
    +
    public class _JobStatus
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _JobStatus() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_JobStatus

    +
    +public _JobStatus()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/engine/cluster/drmaa/class-use/AsyncJobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html new file mode 100644 index 0000000..1c73aaf --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.AsyncJobRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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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 new file mode 100644 index 0000000..17e4869 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterSession.html @@ -0,0 +1,190 @@ + + + + + + +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.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +Uses of ClusterSession in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa with parameters of type ClusterSession
    +static booleanClusterUtil.cancelJob(java.lang.String jobId, + ClusterSession csession) + +
    +           
    +static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, + java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterUtil.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterUtil.html new file mode 100644 index 0000000..3db6abc --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/ClusterUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.ClusterUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.cluster.drmaa.ClusterUtil

    +
    +No usage of compbio.engine.cluster.drmaa.ClusterUtil +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/JobRunner.html new file mode 100644 index 0000000..4f09e88 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/JobRunner.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.JobRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.engine.cluster.drmaa.JobRunner

    +
    + + + + + + + + + +
    +Packages that use JobRunner
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +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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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/StatisticManager.html new file mode 100644 index 0000000..fc796c4 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/StatisticManager.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.StatisticManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.cluster.drmaa.StatisticManager

    +
    + + + + + + + + + +
    +Packages that use StatisticManager
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +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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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/_DrmaaExample.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/_DrmaaExample.html new file mode 100644 index 0000000..87d0ccd --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/_DrmaaExample.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa._DrmaaExample + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.cluster.drmaa._DrmaaExample

    +
    +No usage of compbio.engine.cluster.drmaa._DrmaaExample +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/_JobStatus.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/_JobStatus.html new file mode 100644 index 0000000..01b4c89 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/_JobStatus.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa._JobStatus + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.cluster.drmaa._JobStatus

    +
    +No usage of compbio.engine.cluster.drmaa._JobStatus +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-frame.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-frame.html new file mode 100644 index 0000000..bdbf88c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/package-frame.html @@ -0,0 +1,44 @@ + + + + + + +compbio.engine.cluster.drmaa + + + + + + + + + + + +compbio.engine.cluster.drmaa + + + + +
    +Classes  + +
    +_DrmaaExample +
    +_JobStatus +
    +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 new file mode 100644 index 0000000..a995ad5 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html @@ -0,0 +1,203 @@ + + + + + + +compbio.engine.cluster.drmaa + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.engine.cluster.drmaa +

    +An cluster engine classes responsible for execution of Executables on the clusters. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _DrmaaExample 
    _JobStatus 
    AsyncJobRunnerSingle cluster job runner class
    ClusterSession 
    ClusterUtil 
    JobRunnerSingle cluster job runner class
    StatisticManager 
    +  + +

    +

    +Package compbio.engine.cluster.drmaa Description +

    + +

    +An cluster engine classes responsible for execution of Executables on the clusters. + Implementation uses DRMAA library. + Classes in this package depend on the data model classes. + They form a second layer of Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-tree.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-tree.html new file mode 100644 index 0000000..e51bdff --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/package-tree.html @@ -0,0 +1,155 @@ + + + + + + +compbio.engine.cluster.drmaa Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.engine.cluster.drmaa +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.engine.cluster.drmaa

    +
    + + + + + + + + + +
    +Packages that use compbio.engine.cluster.drmaa
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + + + + + + + + + + +
    +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 new file mode 100644 index 0000000..613a3c0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html @@ -0,0 +1,517 @@ + + + + + + +_Queue + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + 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:
    java.io.Serializable, java.lang.Comparable<_Queue>
    +
    +
    +
    +
    public enum _Queue
    extends java.lang.Enum<_Queue>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    BIGINT + +
    +           
    BIGMEM + +
    +           
    BIT64 + +
    +           
    DEVEL + +
    +          Order of the constraint reflect the priority of the queue
    PRIBIT64 + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intgetMemoryLimit() + +
    +          return max memory limit in Mb
    +static _QueuegetQueue(int maxMemory, + int timeLimitInHours) + +
    +           
    + _QueuegetQueue(java.lang.String queueName) + +
    +           
    +static _QueuegetQueueByMemoryRequirements(int maxMemory) + +
    +           
    + intgetTimeLimit() + +
    +          0 - unlimited
    + booleanhasTimeLimit() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +static _QueuevalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static _Queue[]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, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +DEVEL

    +
    +public static final _Queue DEVEL
    +
    +
    Order of the constraint reflect the priority of the queue +

    +

    +
    +
    +
    + +

    +PRIBIT64

    +
    +public static final _Queue PRIBIT64
    +
    +
    +
    +
    +
    + +

    +BIT64

    +
    +public static final _Queue BIT64
    +
    +
    +
    +
    +
    + +

    +BIGINT

    +
    +public static final _Queue BIGINT
    +
    +
    +
    +
    +
    + +

    +BIGMEM

    +
    +public static final _Queue BIGMEM
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static _Queue[] 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 (_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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Enum<_Queue>
    +
    +
    +
    +
    +
    +
    + +

    +getTimeLimit

    +
    +public int getTimeLimit()
    +
    +
    0 - unlimited +

    +

    + +
    Returns:
    max runtime in hours
    +
    +
    +
    + +

    +hasTimeLimit

    +
    +public boolean hasTimeLimit()
    +
    +
    + +
    Returns:
    true if the queue has time limit, false overwise
    +
    +
    +
    + +

    +getMemoryLimit

    +
    +public int getMemoryLimit()
    +
    +
    return max memory limit in Mb +

    +

    + +
    Returns:
    +
    +
    +
    + +

    +getQueueByMemoryRequirements

    +
    +public static _Queue getQueueByMemoryRequirements(int maxMemory)
    +
    +
    +
    +
    +
    +
    + +

    +getQueue

    +
    +public static _Queue getQueue(int maxMemory,
+                              int timeLimitInHours)
    +
    +
    +
    +
    +
    +
    + +

    +getQueue

    +
    +public _Queue getQueue(java.lang.String queueName)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/cluster/dundee/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html new file mode 100644 index 0000000..f951552 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html @@ -0,0 +1,281 @@ + + + + + + +_QueueConstraints + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.cluster.dundee +
    +Class _QueueConstraints

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.dundee._QueueConstraints
+
    +
    +
    +
    public final class _QueueConstraints
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Field Summary
    +static intFIRST_MEMORY_LIMIT + +
    +           
    +static intLONG_TIME_LIMIT + +
    +           
    +static intMAX_MEMORY_LIMIT + +
    +           
    +static intSHORT_TIME_LIMIT + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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

    +SHORT_TIME_LIMIT

    +
    +public static final int SHORT_TIME_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +LONG_TIME_LIMIT

    +
    +public static final int LONG_TIME_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +FIRST_MEMORY_LIMIT

    +
    +public static final int FIRST_MEMORY_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +MAX_MEMORY_LIMIT

    +
    +public static final int MAX_MEMORY_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/cluster/dundee/class-use/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html new file mode 100644 index 0000000..d5b990c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html @@ -0,0 +1,243 @@ + + + + + + +Uses of Class compbio.engine.cluster.dundee._Queue + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +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) + +
    +           
    + _Queue_Queue.getQueue(java.lang.String queueName) + +
    +           
    +static _Queue_Queue.getQueueByMemoryRequirements(int maxMemory) + +
    +           
    +static _Queue_Queue.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static _Queue[]_Queue.values() + +
    +          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() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html new file mode 100644 index 0000000..233b459 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.dundee._QueueConstraints + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.cluster.dundee._QueueConstraints

    +
    +No usage of compbio.engine.cluster.dundee._QueueConstraints +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-frame.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-frame.html new file mode 100644 index 0000000..80f27d5 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-frame.html @@ -0,0 +1,43 @@ + + + + + + +compbio.engine.cluster.dundee + + + + + + + + + + + +compbio.engine.cluster.dundee + + + + +
    +Classes  + +
    +_QueueConstraints
    + + + + + + +
    +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 new file mode 100644 index 0000000..5cbb529 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html @@ -0,0 +1,171 @@ + + + + + + +compbio.engine.cluster.dundee + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.engine.cluster.dundee +

    + + + + + + + + + +
    +Class Summary
    _QueueConstraints 
    +  + +

    + + + + + + + + + +
    +Enum Summary
    _Queue 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-tree.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-tree.html new file mode 100644 index 0000000..189d945 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-tree.html @@ -0,0 +1,163 @@ + + + + + + +compbio.engine.cluster.dundee Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For Package compbio.engine.cluster.dundee +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) +
          +
        • compbio.engine.cluster.dundee._Queue
        +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html new file mode 100644 index 0000000..998ba3c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Package compbio.engine.cluster.dundee + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +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 + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.cluster.dundee used by compbio.runner
    _Queue + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/DirectoryManager.html new file mode 100644 index 0000000..f4e425b --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/DirectoryManager.html @@ -0,0 +1,307 @@ + + + + + + +DirectoryManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.conf +
    +Class DirectoryManager

    +
    +java.lang.Object
+  extended by compbio.engine.conf.DirectoryManager
+
    +
    +
    +
    public class DirectoryManager
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringDELIM + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    DirectoryManager() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.Class<Executable<?>>getClass(java.lang.String taskId) + +
    +           
    +static java.lang.StringgetTaskDirectory(java.lang.Class<?> clazz) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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

    +DELIM

    +
    +public static final java.lang.String DELIM
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +DirectoryManager

    +
    +public DirectoryManager()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTaskDirectory

    +
    +public static java.lang.String getTaskDirectory(java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getClass

    +
    +public static java.lang.Class<Executable<?>> getClass(java.lang.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/conf/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html new file mode 100644 index 0000000..d4816f8 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html @@ -0,0 +1,332 @@ + + + + + + +PropertyHelperManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.conf +
    +Class PropertyHelperManager

    +
    +java.lang.Object
+  extended by compbio.engine.conf.PropertyHelperManager
+
    +
    +
    +
    public final class PropertyHelperManager
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringconfDir + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    PropertyHelperManager() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.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 java.lang.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:
    +
    +
    +
    + +

    +getLocalPath

    +
    +public static java.lang.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:
    +
    Throws: +
    javax.naming.ConfigurationException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/conf/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html new file mode 100644 index 0000000..6457ed8 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html @@ -0,0 +1,507 @@ + + + + + + +RunnerConfigMarshaller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.conf +
    +Class RunnerConfigMarshaller<T>

    +
    +java.lang.Object
+  extended by compbio.engine.conf.RunnerConfigMarshaller<T>
+
    +
    +
    +
    public class RunnerConfigMarshaller<T>
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    RunnerConfigMarshaller(java.lang.Class<?> rootClass) + +
    +           
    RunnerConfigMarshaller(java.lang.Class<?> rootClass, + java.lang.Class<?>... classes) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static javax.xml.validation.SchemagetSchema(java.lang.String schemafile) + +
    +           
    +static javax.xml.validation.ValidatorgetValidator(javax.xml.validation.Schema schema) + +
    +           
    +static javax.xml.validation.ValidatorgetValidator(java.lang.String schemafile) + +
    +           
    + + + + + +
    +<V> V
    +    		read(java.io.InputStream instream, + java.lang.Class<V> resultElemType) + +
    +           
    + + + + + +
    +<V> V
    +    		read(java.io.InputStream instream, + java.lang.Class<V> resultElemType, + java.lang.Class<?>... classes) + +
    +           
    + + + + + +
    +<V> V
    +    		readAndValidate(java.io.InputStream document, + java.lang.Class<V> resultElemType) + +
    +           
    +static booleanvalidate(javax.xml.validation.Validator validator, + java.lang.String document) + +
    +           
    + voidwrite(java.lang.Object xmlRootElement, + java.io.OutputStream out) + +
    +           
    + voidwriteAndValidate(java.lang.Object xmlRootElement, + java.lang.String schemafile, + java.io.OutputStream out) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +RunnerConfigMarshaller

    +
    +public RunnerConfigMarshaller(java.lang.Class<?> rootClass)
+                       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    +
    + +

    +RunnerConfigMarshaller

    +
    +public RunnerConfigMarshaller(java.lang.Class<?> rootClass,
+                              java.lang.Class<?>... classes)
+                       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    + + + + + + + + +
    +Method Detail
    + +

    +write

    +
    +public void write(java.lang.Object xmlRootElement,
+                  java.io.OutputStream out)
+           throws javax.xml.bind.JAXBException,
+                  java.io.IOException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException +
    java.io.IOException
    +
    +
    +
    + +

    +writeAndValidate

    +
    +public void writeAndValidate(java.lang.Object xmlRootElement,
+                             java.lang.String schemafile,
+                             java.io.OutputStream out)
+                      throws javax.xml.bind.JAXBException,
+                             java.io.IOException,
+                             org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException +
    java.io.IOException +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +getSchema

    +
    +public static javax.xml.validation.Schema getSchema(java.lang.String schemafile)
+                                             throws org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +getValidator

    +
    +public static javax.xml.validation.Validator getValidator(java.lang.String schemafile)
+                                                   throws org.xml.sax.SAXException
    +
    +
    + +
    Returns:
    +
    Throws: +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +getValidator

    +
    +public static javax.xml.validation.Validator getValidator(javax.xml.validation.Schema schema)
+                                                   throws org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +validate

    +
    +public static boolean validate(javax.xml.validation.Validator validator,
+                               java.lang.String document)
+                        throws java.io.IOException,
+                               org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    java.io.IOException +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +readAndValidate

    +
    +public <V> V readAndValidate(java.io.InputStream document,
+                             java.lang.Class<V> resultElemType)
+                  throws javax.xml.bind.JAXBException,
+                         java.io.IOException,
+                         org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException +
    java.io.IOException +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +read

    +
    +public <V> V read(java.io.InputStream instream,
+                  java.lang.Class<V> resultElemType)
+       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    +
    +
    + +

    +read

    +
    +public <V> V read(java.io.InputStream instream,
+                  java.lang.Class<V> resultElemType,
+                  java.lang.Class<?>... classes)
+       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/_Key.html b/website/full_javadoc/compbio/engine/conf/_Key.html new file mode 100644 index 0000000..68d1965 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/_Key.html @@ -0,0 +1,354 @@ + + + + + + +_Key + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
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    + + + +
    + +

    + +compbio.engine.conf +
    +Class _Key

    +
    +java.lang.Object
+  extended by compbio.engine.conf._Key
+
    +
    +
    +
    public final class _Key
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringDELIM + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    _Key(java.lang.Class<?> clazz) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + inthashCode() + +
    +           
    +static _Keyparse(java.lang.String key) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

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

    +DELIM

    +
    +public static final java.lang.String DELIM
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +_Key

    +
    +public _Key(java.lang.Class<?> clazz)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +parse

    +
    +public static _Key parse(java.lang.String key)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html new file mode 100644 index 0000000..8152d4c --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.conf.DirectoryManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.conf.DirectoryManager

    +
    +No usage of compbio.engine.conf.DirectoryManager +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html new file mode 100644 index 0000000..e8d0067 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.conf.PropertyHelperManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
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    +
    +No usage of compbio.engine.conf.PropertyHelperManager +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html new file mode 100644 index 0000000..deeac1c --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.conf.RunnerConfigMarshaller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.conf.RunnerConfigMarshaller

    +
    +No usage of compbio.engine.conf.RunnerConfigMarshaller +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/_Key.html b/website/full_javadoc/compbio/engine/conf/class-use/_Key.html new file mode 100644 index 0000000..223d824 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/_Key.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.engine.conf._Key + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.conf._Key

    +
    + + + + + + + + + +
    +Packages that use _Key
    compbio.engine.confClasses commonly used by both engines. 
    +  +

    + + + + + +
    +Uses of _Key in compbio.engine.conf
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.conf that return _Key
    +static _Key_Key.parse(java.lang.String key) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-frame.html b/website/full_javadoc/compbio/engine/conf/package-frame.html new file mode 100644 index 0000000..29f4ef3 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-frame.html @@ -0,0 +1,38 @@ + + + + + + +compbio.engine.conf + + + + + + + + + + + +compbio.engine.conf + + + + +
    +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 new file mode 100644 index 0000000..7dc8a3b --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-summary.html @@ -0,0 +1,188 @@ + + + + + + +compbio.engine.conf + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.engine.conf +

    +Classes commonly used by both engines. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _Key 
    DirectoryManager 
    PropertyHelperManager 
    RunnerConfigMarshaller<T> 
    +  + +

    +

    +Package compbio.engine.conf Description +

    + +

    +Classes commonly used by both engines. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-tree.html b/website/full_javadoc/compbio/engine/conf/package-tree.html new file mode 100644 index 0000000..460b1b5 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-tree.html @@ -0,0 +1,153 @@ + + + + + + +compbio.engine.conf Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.engine.conf +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-use.html b/website/full_javadoc/compbio/engine/conf/package-use.html new file mode 100644 index 0000000..46402ba --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-use.html @@ -0,0 +1,170 @@ + + + + + + +Uses of Package compbio.engine.conf + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.engine.conf

    +
    + + + + + + + + + +
    +Packages that use compbio.engine.conf
    compbio.engine.confClasses commonly used by both engines. 
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.conf used by compbio.engine.conf
    _Key + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html new file mode 100644 index 0000000..4e4459d --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html @@ -0,0 +1,402 @@ + + + + + + +AsyncLocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class AsyncLocalRunner

    +
    +java.lang.Object
+  extended by compbio.engine.local.AsyncLocalRunner
+
    +
    +
    All Implemented Interfaces:
    AsyncExecutor
    +
    +
    +
    +
    public final class AsyncLocalRunner
    extends java.lang.Object
    implements AsyncExecutor
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AsyncLocalRunner() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job.
    + booleancleanup(java.lang.String jobId) + +
    +          Remove all files and a job directory for a jobid.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Query the status of the job
    + ConfiguredExecutable<?>getResults(java.lang.String taskId) + +
    +          Retrieve the results of the job.
    + java.lang.StringgetWorkDirectory(java.lang.String jobId) + +
    +           
    + java.lang.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 java.lang.String getWorkDirectory(java.lang.String jobId)
    +
    +
    +
    Specified by:
    getWorkDirectory in interface AsyncExecutor
    +
    +
    +
    Parameters:
    jobId - unique job identifier +
    Returns:
    task working directory
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.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(java.lang.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 java.lang.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(java.lang.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:
    +
    +
    +
    + +

    +getResults

    +
    +public ConfiguredExecutable<?> getResults(java.lang.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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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html b/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html new file mode 100644 index 0000000..421469f --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html @@ -0,0 +1,331 @@ + + + + + + +ExecutableWrapper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class ExecutableWrapper

    +
    +java.lang.Object
+  extended by compbio.engine.local.ExecutableWrapper
+
    +
    +
    All Implemented Interfaces:
    java.util.concurrent.Callable<ConfiguredExecutable<?>>
    +
    +
    +
    +
    @Immutable
+public final class ExecutableWrapper
    extends java.lang.Object
    implements java.util.concurrent.Callable<ConfiguredExecutable<?>>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringPROC_ERR_FILE + +
    +           
    +static java.lang.StringPROC_OUT_FILE + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ExecutableWrapper(ConfiguredExecutable<?> executable, + java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    + ConfiguredExecutable<?>call() + +
    +          It is vital that output and error streams are captured immediately for + this call() to succeed.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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

    +PROC_OUT_FILE

    +
    +public static final java.lang.String PROC_OUT_FILE
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +PROC_ERR_FILE

    +
    +public static final java.lang.String PROC_ERR_FILE
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ExecutableWrapper

    +
    +public ExecutableWrapper(ConfiguredExecutable<?> executable,
+                         java.lang.String workDirectory)
+                  throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    + + + + + + + + +
    +Method Detail
    + +

    +call

    +
    +public ConfiguredExecutable<?> call()
+                             throws java.io.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 java.util.concurrent.Callable<ConfiguredExecutable<?>>
    +
    +
    + +
    Throws: +
    java.io.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/local/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html new file mode 100644 index 0000000..a4edf4a --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html @@ -0,0 +1,335 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LocalEngineUtil() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleancancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String workDirectory) + +
    +           
    +static booleancleanup(ConfiguredExecutable<?> confExecutable) + +
    +           
    +static JobStatusgetJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static JobStatusgetRecordedJobStatus(java.lang.String jobId) + +
    +           
    +static ConfiguredExecutable<?>getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.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(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
+                                java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getJobStatus

    +
    +public static JobStatus getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future)
    +
    +
    +
    +
    +
    +
    + +

    +getRecordedJobStatus

    +
    +public static JobStatus getRecordedJobStatus(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +cleanup

    +
    +public static boolean cleanup(ConfiguredExecutable<?> confExecutable)
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public static ConfiguredExecutable<?> getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
+                                                 java.lang.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 new file mode 100644 index 0000000..9cf5fd7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html @@ -0,0 +1,310 @@ + + + + + + +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:
    java.util.concurrent.Executor, java.util.concurrent.ExecutorService
    +
    +
    +
    +
    public final class LocalExecutorService
    extends java.util.concurrent.ThreadPoolExecutor
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor
    java.util.concurrent.ThreadPoolExecutor.AbortPolicy, java.util.concurrent.ThreadPoolExecutor.CallerRunsPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardOldestPolicy, java.util.concurrent.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:
    +
    +
    +
    + +

    +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 +

    +

    +
    +
    +
    +
    + +

    +canAcceptMoreWork

    +
    +public boolean canAcceptMoreWork()
    +
    +
    If the Executor queue is empty +

    +

    + +
    Returns:
    true is not all threads are busy, false overwise
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/LocalRunner.html b/website/full_javadoc/compbio/engine/local/LocalRunner.html new file mode 100644 index 0000000..b64d9db --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/LocalRunner.html @@ -0,0 +1,398 @@ + + + + + + +LocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 LocalRunner

    +
    +java.lang.Object
+  extended by compbio.engine.local.LocalRunner
+
    +
    +
    All Implemented Interfaces:
    SyncExecutor
    +
    +
    +
    +
    public final class LocalRunner
    extends java.lang.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.
    + java.lang.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 java.lang.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: +
    java.util.concurrent.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/StreamGobbler.html new file mode 100644 index 0000000..4ddf4c6 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/StreamGobbler.html @@ -0,0 +1,226 @@ + + + + + + +StreamGobbler + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 StreamGobbler

    +
    +java.lang.Object
+  extended by compbio.engine.local.StreamGobbler
+
    +
    +
    All Implemented Interfaces:
    java.lang.Runnable
    +
    +
    +
    +
    @ThreadSafe
+public class StreamGobbler
    extends java.lang.Object
    implements java.lang.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 java.lang.Runnable
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/_TrackingExecutor.html b/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html new file mode 100644 index 0000000..e10952d --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html @@ -0,0 +1,427 @@ + + + + + + +_TrackingExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 _TrackingExecutor

    +
    +java.lang.Object
+  extended by java.util.concurrent.AbstractExecutorService
+      extended by compbio.engine.local._TrackingExecutor
+
    +
    +
    All Implemented Interfaces:
    java.util.concurrent.Executor, java.util.concurrent.ExecutorService
    +
    +
    +
    +
    public class _TrackingExecutor
    extends java.util.concurrent.AbstractExecutorService
    + + +

    +This executor extends standard Java ExecutorService by adding the method to + obtain all Runnables which were running and did not complete upon executor + termination. For this to work properly Runnables must propagate an + Interruption exceptions, not swallow them, which a good Runnable should do + anyway. + + TODO it may be better to persists task from different place +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _TrackingExecutor(java.util.concurrent.ExecutorService executor) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanawaitTermination(long timeout, + java.util.concurrent.TimeUnit unit) + +
    +           
    + voidexecute(java.lang.Runnable runnable) + +
    +           
    + java.util.ListgetCancelledTasks() + +
    +           
    + booleanisShutdown() + +
    +           
    + booleanisTerminated() + +
    +           
    + voidshutdown() + +
    +           
    + java.util.List<java.lang.Runnable>shutdownNow() + +
    +           
    + + + + + +
    +<T> java.util.concurrent.Future<T>
    +    		submit(java.util.concurrent.Callable<T> task) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.util.concurrent.AbstractExecutorService
    invokeAll, invokeAll, invokeAny, invokeAny, submit, submit
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_TrackingExecutor

    +
    +public _TrackingExecutor(java.util.concurrent.ExecutorService executor)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getCancelledTasks

    +
    +public java.util.List getCancelledTasks()
    +
    +
    +
    +
    +
    +
    + +

    +execute

    +
    +public void execute(java.lang.Runnable runnable)
    +
    +
    +
    +
    +
    +
    + +

    +submit

    +
    +public <T> java.util.concurrent.Future<T> submit(java.util.concurrent.Callable<T> task)
    +
    +
    +
    Specified by:
    submit in interface java.util.concurrent.ExecutorService
    Overrides:
    submit in class java.util.concurrent.AbstractExecutorService
    +
    +
    +
    +
    +
    +
    + +

    +awaitTermination

    +
    +public boolean awaitTermination(long timeout,
+                                java.util.concurrent.TimeUnit unit)
+                         throws java.lang.InterruptedException
    +
    +
    + +
    Throws: +
    java.lang.InterruptedException
    +
    +
    +
    + +

    +isShutdown

    +
    +public boolean isShutdown()
    +
    +
    +
    +
    +
    +
    + +

    +isTerminated

    +
    +public boolean isTerminated()
    +
    +
    +
    +
    +
    +
    + +

    +shutdown

    +
    +public void shutdown()
    +
    +
    +
    +
    +
    +
    + +

    +shutdownNow

    +
    +public java.util.List<java.lang.Runnable> shutdownNow()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/class-use/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html new file mode 100644 index 0000000..a5689d9 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local.AsyncLocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.local.AsyncLocalRunner

    +
    +No usage of compbio.engine.local.AsyncLocalRunner +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +Uses of Class
    compbio.engine.local.LocalExecutorService

    +
    + + + + + + + + + +
    +Packages that use LocalExecutorService
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + +
    +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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    +

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    +

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    compbio.engine.local._TrackingExecutor

    +
    +No usage of compbio.engine.local._TrackingExecutor +

    +

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    +Classes  + +
    +_TrackingExecutor +
    +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 new file mode 100644 index 0000000..b9dc15d --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/package-summary.html @@ -0,0 +1,207 @@ + + + + + + +compbio.engine.local + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Package compbio.engine.local +

    +An local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _TrackingExecutorThis executor extends standard Java ExecutorService by adding the method to + obtain all Runnables which were running and did not complete upon executor + termination.
    AsyncLocalRunner 
    ExecutableWrapper 
    LocalEngineUtil 
    LocalExecutorService 
    LocalRunner 
    StreamGobbler 
    +  + +

    +

    +Package compbio.engine.local Description +

    + +

    +An local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). + Implementation uses Java 6 Executor framework to execute native programmes in parallel in different threads. + Classes in this package depend on the data model classes. + They form a second layer of Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.engine.local +

    +
    +
    +
    Package Hierarchies:
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    +
    +

    +Class Hierarchy +

    + +
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    + + + + + + + + + + + + + + + +
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    +Uses of Package
    compbio.engine.local

    +
    + + + + + + + + + +
    +Packages that use compbio.engine.local
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.local used by compbio.engine.local
    LocalExecutorService + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Interfaces  + +
    +AsyncExecutor +
    +SyncExecutor
    + + + + + + +
    +Classes  + +
    +Cleaner +
    +ClusterJobId +
    +Configurator +
    +FilePuller +
    +Job +
    +LoadBalancer +
    +ProgressGetter +
    +PulledFileCache +
    +SubmissionManager
    + + + + diff --git a/website/full_javadoc/compbio/engine/package-summary.html b/website/full_javadoc/compbio/engine/package-summary.html new file mode 100644 index 0000000..da7acf2 --- /dev/null +++ b/website/full_javadoc/compbio/engine/package-summary.html @@ -0,0 +1,208 @@ + + + + + + +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
    Cleaner 
    ClusterJobId 
    Configurator 
    FilePuller 
    Job 
    LoadBalancer 
    ProgressGetter 
    PulledFileCache 
    SubmissionManagerSubmit jobs for execution
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.engine +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +
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    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.engine

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.engine
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    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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    + + + diff --git a/website/full_javadoc/compbio/metadata/Argument.html b/website/full_javadoc/compbio/metadata/Argument.html new file mode 100644 index 0000000..656cb78 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Argument.html @@ -0,0 +1,327 @@ + + + + + + +Argument + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +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
    + java.lang.StringgetDefaultValue() + +
    +           
    + java.lang.StringgetDescription() + +
    +           
    + java.net.URLgetFurtherDetails() + +
    +           
    + java.lang.StringgetName() + +
    +           
    + java.util.List<java.lang.String>getPossibleValues() + +
    +           
    + voidsetValue(java.lang.String defaultValue) + +
    +          Set default values for the parameter or an option
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getFurtherDetails

    +
    +java.net.URL getFurtherDetails()
    +
    +
    +
    +
    +
    +
    + +

    +getDefaultValue

    +
    +java.lang.String getDefaultValue()
    +
    +
    +
    +
    +
    +
    + +

    +getDescription

    +
    +java.lang.String getDescription()
    +
    +
    +
    +
    +
    +
    + +

    +getName

    +
    +java.lang.String getName()
    +
    +
    +
    +
    +
    +
    + +

    +getPossibleValues

    +
    +java.util.List<java.lang.String> getPossibleValues()
    +
    +
    + +
    Returns:
    List of values allowed for an Argument
    +
    +
    +
    + +

    +setValue

    +
    +void setValue(java.lang.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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/ChunkHolder.html b/website/full_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..9b66ead --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,350 @@ + + + + + + +ChunkHolder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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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 java.lang.Object
    + + +

    +Represents a chunk of string data together with the position in a file from + where corresponding to of the data. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ChunkHolder(java.lang.String chunk, + long position) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetChunk() + +
    +           
    + longgetNextPosition() + +
    +           
    + inthashCode() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ChunkHolder

    +
    +public ChunkHolder(java.lang.String chunk,
+                   long position)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getChunk

    +
    +public java.lang.String getChunk()
    +
    +
    +
    +
    +
    +
    + +

    +getNextPosition

    +
    +public long getNextPosition()
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.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/JobExecutionException.html b/website/full_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..6e1b992 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,279 @@ + + + + + + +JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 JobExecutionException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobExecutionException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class JobExecutionException
    extends java.lang.Exception
    + + +

    +JobExecutionException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides DrmaaException +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    JobExecutionException(java.lang.String message) + +
    +           
    JobExecutionException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    JobExecutionException(java.lang.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(java.lang.String message)
    +
    +
    +
    + +

    +JobExecutionException

    +
    +public JobExecutionException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +JobExecutionException

    +
    +public JobExecutionException(java.lang.String message,
+                             java.lang.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/JobStatus.html b/website/full_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..7d716e8 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,465 @@ + + + + + + +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:
    java.io.Serializable, java.lang.Comparable<JobStatus>
    +
    +
    +
    +
    public enum JobStatus
    extends java.lang.Enum<JobStatus>
    + + +

    +The status of the job. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +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(java.lang.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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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 new file mode 100644 index 0000000..c290dba --- /dev/null +++ b/website/full_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,283 @@ + + + + + + +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
    + + + +
    + +

    + +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:
    java.io.Serializable
    +
    +
    +
    Direct Known Subclasses:
    LimitExceededException, UnsupportedRuntimeException
    +
    +
    +
    +
    public class JobSubmissionException
    extends java.lang.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(java.lang.String message) + +
    +           
    JobSubmissionException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    JobSubmissionException(java.lang.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(java.lang.String message)
    +
    +
    +
    + +

    +JobSubmissionException

    +
    +public JobSubmissionException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +JobSubmissionException

    +
    +public JobSubmissionException(java.lang.String message,
+                              java.lang.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 new file mode 100644 index 0000000..f2f4095 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,459 @@ + + + + + + +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 java.lang.Object
    + + +

    +A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date January 2010
    +
    See Also:
    LimitsManager
    +
    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    Limit(int seqNumber, + int seqLength, + java.lang.String preset) + +
    +           
    Limit(int seqNumber, + int seqLength, + java.lang.String preset, + boolean isDefault) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + intgetAvgSeqLength() + +
    +           
    +static intgetAvgSequenceLength(java.util.List<FastaSequence> data) + +
    +          Calculates an average sequence length of the dataset
    + java.lang.StringgetPreset() + +
    +           
    + intgetSeqNumber() + +
    +           
    + inthashCode() + +
    +           
    + booleanisDefault() + +
    +           
    + booleanisExceeded(java.util.List<FastaSequence> data) + +
    +          Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Limit

    +
    +public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset)
    +
    +
    +
    + +

    +Limit

    +
    +public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset,
+             boolean isDefault)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getPreset

    +
    +public java.lang.String getPreset()
    +
    +
    +
    +
    +
    +
    + +

    +getAvgSeqLength

    +
    +public int getAvgSeqLength()
    +
    +
    +
    +
    +
    +
    + +

    +getSeqNumber

    +
    +public int getSeqNumber()
    +
    +
    +
    +
    +
    +
    + +

    +isDefault

    +
    +public boolean isDefault()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +isExceeded

    +
    +public boolean isExceeded(java.util.List<FastaSequence> data)
    +
    +
    Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit +

    +

    +
    Parameters:
    data - +
    Returns:
    true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise.
    +
    +
    +
    + +

    +getAvgSequenceLength

    +
    +public static int getAvgSequenceLength(java.util.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 new file mode 100644 index 0000000..910baa8 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,357 @@ + + + + + + +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:
    java.io.Serializable
    +
    +
    +
    +
    public class LimitExceededException
    extends JobSubmissionException
    + + +

    +Thrown if the task larger in size that the limit that applies to the + calculation. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    See Also:
    Limit, +Serialized Form
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LimitExceededException(java.lang.String message) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intgetActualNumberofSequences() + +
    +           
    + intgetNumberOfSequencesAllowed() + +
    +           
    + intgetSequenceLenghtActual() + +
    +           
    + intgetSequenceLenghtAllowed() + +
    +           
    +static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, + java.util.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(java.lang.String message)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +newLimitExceeded

    +
    +public static LimitExceededException newLimitExceeded(Limit<?> limit,
+                                                      java.util.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 new file mode 100644 index 0000000..88195c6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,363 @@ + + + + + + +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 java.lang.Object
    + + +

    +A collection of Limits +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date January 2010
    +
    See Also:
    Limit
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LimitsManager() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Limit<T>getDefaultLimit() + +
    +           
    + Limit<T>getLimitByName(java.lang.String presetName) + +
    +           
    + java.util.List<Limit<T>>getLimits() + +
    +           
    + java.lang.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 java.util.List<Limit<T>> getLimits()
    +
    +
    + +
    Returns:
    all limits defined for an executable T
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getLimitByName

    +
    +public Limit<T> getLimitByName(java.lang.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 javax.xml.bind.ValidationException
    +
    +
    Validate Limits +

    +

    +
    Parameters:
    presets - +
    Throws: +
    javax.xml.bind.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 new file mode 100644 index 0000000..1bb99d9 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Option.html @@ -0,0 +1,714 @@ + + + + + + +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 java.lang.Object
    implements Argument<T>
    + + +

    +Command line option/flag or multiple exclusive options with no value. Example + -protein, -dna, -auto +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Option(java.lang.String name, + java.lang.String description) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) + +
    +          Adds an option to the optionName list
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetDefaultValue() + +
    +          A default value of the option.
    + java.lang.StringgetDescription() + +
    +          A long description of the Option
    + java.net.URLgetFurtherDetails() + +
    +          The URL where further details about the option can be found
    + java.lang.StringgetName() + +
    +          Human readable name of the option
    + java.util.List<java.lang.String>getOptionNames() + +
    +           
    + java.util.List<java.lang.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(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidsetDescription(java.lang.String description) + +
    +           
    + voidsetFurtherDetails(java.net.URL furtherDetails) + +
    +           
    + voidsetName(java.lang.String name) + +
    +           
    + voidsetOptionNames(java.util.Set<java.lang.String> optionNames) + +
    +           
    + voidsetRequired(boolean isRequired) + +
    +           
    + voidsetValue(java.lang.String dValue) + +
    +          Set default values for the parameter or an option
    + java.lang.StringtoCommand(java.lang.String nameValueSeparator) + +
    +          Convert the option to the command string.
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Option

    +
    +public Option(java.lang.String name,
+              java.lang.String description)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getName

    +
    +public java.lang.String getName()
    +
    +
    Human readable name of the option +

    +

    +
    Specified by:
    getName in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setName

    +
    +public void setName(java.lang.String name)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getDescription

    +
    +public java.lang.String getDescription()
    +
    +
    A long description of the Option +

    +

    +
    Specified by:
    getDescription in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setDescription

    +
    +public void setDescription(java.lang.String description)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getFurtherDetails

    +
    +public java.net.URL getFurtherDetails()
    +
    +
    The URL where further details about the option can be found +

    +

    +
    Specified by:
    getFurtherDetails in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setFurtherDetails

    +
    +public void setFurtherDetails(java.net.URL furtherDetails)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getDefaultValue

    +
    +public java.lang.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(java.lang.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 java.util.List<java.lang.String> getOptionNames()
    +
    +
    +
    +
    +
    + +
    Returns:
    List of option names
    +
    +
    +
    + +

    +setOptionNames

    +
    +public void setOptionNames(java.util.Set<java.lang.String> optionNames)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addOptionNames

    +
    +public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
    +
    +
    Adds an option to the optionName list +

    +

    +
    +
    +
    +
    Parameters:
    value - +
    Returns:
    modified optionName list
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toCommand

    +
    +public java.lang.String toCommand(java.lang.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(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getPossibleValues

    +
    +public java.util.List<java.lang.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(java.lang.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 new file mode 100644 index 0000000..45505e0 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,572 @@ + + + + + + +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 option supported by the web service e.g. + seqType=protein. Where seqType is a optionName and protein is one of + possibleValues +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date November 2009
    +
    See Also:
    Option, +Argument
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Parameter(java.lang.String name, + java.lang.String description) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) + +
    +          Adds an option to the optionName list
    + java.util.Set<java.lang.String>addPossibleValues(java.lang.String... value) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetOptionName() + +
    +           
    + java.util.List<java.lang.String>getPossibleValues() + +
    +          List is more convenient to work with
    + ValueConstraingetValidValue() + +
    +           
    + inthashCode() + +
    +           
    + voidsetDefaultValue(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidsetOptionName(java.lang.String optionName) + +
    +           
    + voidsetOptionNames(java.util.Set<java.lang.String> optionName) + +
    +           
    + voidsetPossibleValues(java.util.Set<java.lang.String> possibleValues) + +
    +           
    + voidsetValidValue(ValueConstrain validValue) + +
    +           
    + java.lang.StringtoCommand(java.lang.String nameValueSeparator) + +
    +          Convert the option to the command string.
    + java.lang.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(java.lang.String name,
+                 java.lang.String description)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getValidValue

    +
    +public ValueConstrain getValidValue()
    +
    +
    +
    +
    +
    +
    + +

    +setValidValue

    +
    +public void setValidValue(ValueConstrain validValue)
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +toCommand

    +
    +public java.lang.String toCommand(java.lang.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(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +getPossibleValues

    +
    +public java.util.List<java.lang.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(java.util.Set<java.lang.String> possibleValues)
    +
    +
    +
    +
    +
    +
    + +

    +addPossibleValues

    +
    +public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +setOptionNames

    +
    +public void setOptionNames(java.util.Set<java.lang.String> optionName)
    +
    +
    +
    Overrides:
    setOptionNames in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +addOptionNames

    +
    +public java.util.Set<java.lang.String> addOptionNames(java.lang.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 java.lang.String getOptionName()
    +
    +
    +
    +
    +
    +
    + +

    +setOptionName

    +
    +public void setOptionName(java.lang.String optionName)
    +
    +
    +
    +
    +
    +
    + +

    +setDefaultValue

    +
    +public void setDefaultValue(java.lang.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 new file mode 100644 index 0000000..2995b06 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,455 @@ + + + + + + +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 java.lang.Object
    + + +

    +Collection of Options and Parameters with their values +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    See Also:
    Option, +Parameter
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Preset() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + java.lang.StringgetDescription() + +
    +           
    + java.lang.StringgetName() + +
    +           
    + java.util.List<java.lang.String>getOptions() + +
    +           
    + inthashCode() + +
    +           
    + voidsetDescription(java.lang.String description) + +
    +           
    + voidsetName(java.lang.String name) + +
    +           
    + voidsetOptions(java.util.List<java.lang.String> option) + +
    +           
    + java.lang.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(java.util.List<java.lang.String> option)
    +
    +
    +
    +
    +
    +
    + +

    +setName

    +
    +public void setName(java.lang.String name)
    +
    +
    +
    +
    +
    +
    + +

    +setDescription

    +
    +public void setDescription(java.lang.String description)
    +
    +
    +
    +
    +
    +
    + +

    +getOptions

    +
    +public java.util.List<java.lang.String> getOptions()
    +
    +
    + +
    Returns:
    a List of Options as a String
    +
    +
    +
    + +

    +getName

    +
    +public java.lang.String getName()
    +
    +
    + +
    Returns:
    - name of the Preset
    +
    +
    +
    + +

    +getDescription

    +
    +public java.lang.String getDescription()
    +
    +
    + +
    Returns:
    - a long description of the Preset
    +
    +
    +
    + +

    +getArguments

    +
    +public java.util.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 java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.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 new file mode 100644 index 0000000..17b792a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,428 @@ + + + + + + +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 java.lang.Object
    + + +

    +Collection of presets and methods to manipulate them @see Preset +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringLOCAL_ENGINE_LIMIT_PRESET + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    PresetManager() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Preset<T>getPresetByName(java.lang.String presetName) + +
    +           
    + java.util.List<Preset<T>>getPresets() + +
    +           
    + java.lang.StringgetRunnerClassName() + +
    +           
    + voidsetPresets(java.util.List<Preset<T>> presets) + +
    +           
    + voidsetRunnerClassName(java.lang.String runnerClassName) + +
    +           
    + java.lang.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 java.lang.String LOCAL_ENGINE_LIMIT_PRESET
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +PresetManager

    +
    +public PresetManager()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getPresets

    +
    +public java.util.List<Preset<T>> getPresets()
    +
    +
    +
    +
    +
    +
    + +

    +setPresets

    +
    +public void setPresets(java.util.List<Preset<T>> presets)
    +
    +
    +
    +
    +
    +
    + +

    +getRunnerClassName

    +
    +public java.lang.String getRunnerClassName()
    +
    +
    + +
    Returns:
    fully qualified class name of type T
    +
    +
    +
    + +

    +setRunnerClassName

    +
    +public void setRunnerClassName(java.lang.String runnerClassName)
    +
    +
    +
    +
    +
    +
    + +

    +getPresetByName

    +
    +public Preset<T> getPresetByName(java.lang.String presetName)
    +
    +
    +
    Parameters:
    presetName - +
    Returns:
    preset by its name, null if no preset found
    +
    +
    +
    + +

    +validate

    +
    +public void validate(RunnerConfig<T> options)
+              throws javax.xml.bind.ValidationException
    +
    +
    Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly! +

    +

    + +
    Throws: +
    javax.xml.bind.ValidationException - if preset is found to be invalid.
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.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 new file mode 100644 index 0000000..c0d8b57 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,280 @@ + + + + + + +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:
    java.io.Serializable
    +
    +
    +
    +
    public class ResultNotAvailableException
    extends java.lang.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(java.lang.String message) + +
    +           
    ResultNotAvailableException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    ResultNotAvailableException(java.lang.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(java.lang.String message)
    +
    +
    +
    + +

    +ResultNotAvailableException

    +
    +public ResultNotAvailableException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +ResultNotAvailableException

    +
    +public ResultNotAvailableException(java.lang.String message,
+                                   java.lang.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 new file mode 100644 index 0000000..7f59fd8 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,640 @@ + + + + + + +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 java.lang.Object
    + + +

    +The list of Parameters and Options supported by executable. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    RunnerConfig() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + voidaddOption(Option<T> option) + +
    +           
    + voidaddParameter(Parameter<T> param) + +
    +           
    + RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + Option<T>getArgument(java.lang.String name) + +
    +          Returns the argument by its name if found, NULL otherwise
    + Option<T>getArgumentByOptionName(java.lang.String optionName) + +
    +          Returns the argument by option name, NULL if the argument is not found
    + java.util.List<Option<T>>getArguments() + +
    +           
    + java.util.List<Option<T>>getOptions() + +
    +           
    + java.util.List<Parameter<T>>getParameters() + +
    +           
    + java.lang.StringgetPrmSeparator() + +
    +           
    + java.lang.StringgetRunnerClassName() + +
    +           
    + booleanremoveArgument(java.lang.String name) + +
    +          Removes the argument Argument if found.
    + booleanremoveArgumentByOptionName(java.lang.String optionName) + +
    +          Removes the argument
    + voidsetOptions(java.util.List<Option<T>> parameters) + +
    +           
    + voidsetParameters(java.util.List<Parameter<T>> parameters) + +
    +           
    + voidsetPrmSeparator(java.lang.String prmSeparator) + +
    +           
    + voidsetRunnerClassName(java.lang.String runnerClassName) + +
    +           
    + java.lang.StringtoString() + +
    +           
    + voidvalidate() + +
    +          Validate the arguments
    +  + + + + + + + +
    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 java.util.List<Option<T>> getOptions()
    +
    +
    + +
    Returns:
    list of Option supported by type T
    +
    +
    +
    + +

    +addParameter

    +
    +public void addParameter(Parameter<T> param)
    +
    +
    +
    +
    +
    +
    + +

    +addOption

    +
    +public void addOption(Option<T> option)
    +
    +
    +
    +
    +
    +
    + +

    +getArguments

    +
    +public java.util.List<Option<T>> getArguments()
    +
    +
    + +
    Returns:
    list of Option and Parameter supported by type T
    +
    +
    +
    + +

    +getPrmSeparator

    +
    +public java.lang.String getPrmSeparator()
    +
    +
    + +
    Returns:
    name value separator character
    +
    +
    +
    + +

    +setPrmSeparator

    +
    +public void setPrmSeparator(java.lang.String prmSeparator)
    +
    +
    +
    +
    +
    +
    + +

    +setOptions

    +
    +public void setOptions(java.util.List<Option<T>> parameters)
    +
    +
    +
    +
    +
    +
    + +

    +getRunnerClassName

    +
    +public java.lang.String getRunnerClassName()
    +
    +
    + +
    Returns:
    fully qualified class name for type T
    +
    +
    +
    + +

    +setRunnerClassName

    +
    +public void setRunnerClassName(java.lang.String runnerClassName)
    +
    +
    +
    +
    +
    +
    + +

    +setParameters

    +
    +public void setParameters(java.util.List<Parameter<T>> parameters)
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public java.util.List<Parameter<T>> getParameters()
    +
    +
    + +
    Returns:
    List of Parameter supported by type T.
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getArgument

    +
    +public Option<T> getArgument(java.lang.String name)
    +
    +
    Returns the argument by its name if found, NULL otherwise +

    +

    +
    Parameters:
    name - +
    Returns:
    Argument
    +
    +
    +
    + +

    +removeArgument

    +
    +public boolean removeArgument(java.lang.String name)
    +
    +
    Removes the argument Argument if found. +

    +

    +
    Parameters:
    name - of the argument +
    Returns:
    true if argument was removed, false otherwise
    +
    +
    +
    + +

    +getArgumentByOptionName

    +
    +public Option<T> getArgumentByOptionName(java.lang.String optionName)
    +
    +
    Returns the argument by option name, NULL if the argument is not found +

    +

    +
    Parameters:
    optionName - - the name of the option +
    Returns:
    Option
    +
    +
    +
    + +

    +removeArgumentByOptionName

    +
    +public boolean removeArgumentByOptionName(java.lang.String optionName)
    +
    +
    Removes the argument +

    +

    +
    Parameters:
    optionName - +
    Returns:
    true if argument with optionName exists and was removed, false + otherwise
    +
    +
    +
    + +

    +validate

    +
    +public void validate()
+              throws javax.xml.bind.ValidationException
    +
    +
    Validate the arguments +

    +

    + +
    Throws: +
    javax.xml.bind.ValidationException - if any of the arguments found invalid which is when +
    +
  • Parameter value outside ValueConstrain boundary
    • +
  • Parameter name is not listed in possible values
    • +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..b7d4950 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,265 @@ + + + + + + +UnsupportedRuntimeException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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:
    java.io.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(java.lang.String message) + +
    +           
    UnsupportedRuntimeException(java.lang.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(java.lang.String message)
    +
    +
    +
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(java.lang.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/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..62a7160 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,325 @@ + + + + + + +ValueConstrain.Type + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 ValueConstrain.Type

    +
    +java.lang.Object
+  extended by java.lang.Enum<ValueConstrain.Type>
+      extended by compbio.metadata.ValueConstrain.Type
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<ValueConstrain.Type>
    +
    +
    +
    Enclosing class:
    ValueConstrain
    +
    +
    +
    +
    public static enum ValueConstrain.Type
    extends java.lang.Enum<ValueConstrain.Type>
    + + +

    +

    + +

    + + + + + + + + + + + + + +
    +Enum Constant Summary
    Float + +
    +           
    Integer + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ValueConstrain.TypevalueOf(java.lang.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(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.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/ValueConstrain.html b/website/full_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..0d924f6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,440 @@ + + + + + + +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
    + + + +
    + +

    + +compbio.metadata +
    +Class ValueConstrain

    +
    +java.lang.Object
+  extended by compbio.metadata.ValueConstrain
+
    +
    +
    +
    public class ValueConstrain
    extends java.lang.Object
    + + +

    +The type and the lower and upper boundaries for numerical value. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date November 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classValueConstrain.Type + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ValueConstrain() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.NumbergetMax() + +
    +           
    + java.lang.NumbergetMin() + +
    +           
    + ValueConstrain.TypegetType() + +
    +           
    + inthashCode() + +
    +           
    + voidsetMax(java.lang.String max) + +
    +           
    + voidsetMin(java.lang.String min) + +
    +           
    + voidsetType(ValueConstrain.Type type) + +
    +           
    + java.lang.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 java.lang.Number getMax()
    +
    +
    +
    +
    +
    +
    + +

    +setMax

    +
    +public void setMax(java.lang.String max)
    +
    +
    +
    +
    +
    +
    + +

    +getMin

    +
    +public java.lang.Number getMin()
    +
    +
    +
    +
    +
    +
    + +

    +setMin

    +
    +public void setMin(java.lang.String min)
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.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/WrongParameterException.html b/website/full_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..9d95892 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,294 @@ + + + + + + +WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 WrongParameterException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.WrongParameterException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class WrongParameterException
    extends java.lang.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. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    WrongParameterException(Option<?> option) + +
    +           
    WrongParameterException(java.lang.String message) + +
    +           
    WrongParameterException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    WrongParameterException(java.lang.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(java.lang.String message)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.String message,
+                               java.lang.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 new file mode 100644 index 0000000..11f5c1a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Argument.html @@ -0,0 +1,189 @@ + + + + + + +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 option supported by the web service e.g.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html new file mode 100644 index 0000000..30abc70 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html @@ -0,0 +1,356 @@ + + + + + + +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.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return ChunkHolder
    + ChunkHolderMsaWS.pullExecStatistics(java.lang.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
    + ChunkHolderPullFileResponse.getReturn() + +
    +           
    + ChunkHolderPullExecStatisticsResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type ChunkHolder
    + voidPullFileResponse.setReturn(ChunkHolder _return) + +
    +           
    + voidPullExecStatisticsResponse.setReturn(ChunkHolder _return) + +
    +           
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return ChunkHolder
    + ChunkHolderFilePuller.pull(long position) + +
    +           
    +static ChunkHolderProgressGetter.pull(java.lang.String file, + long position) + +
    +           
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return ChunkHolder
    + ChunkHolderTcoffeeWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderProbconsWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderMuscleWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderMafftWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderClustalWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    +static ChunkHolderWSUtil.pullFile(java.lang.String jobId, + long position) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html new file mode 100644 index 0000000..2efb5f4 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html @@ -0,0 +1,257 @@ + + + + + + +Uses of Class compbio.metadata.JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobExecutionException

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use JobExecutionException
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + +
    +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, + java.lang.String jobId) + +
    +           
    +  +

    + + + + + +
    +Uses of JobExecutionException in compbio.engine.local
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.local that throw JobExecutionException
    + ConfiguredExecutable<?>LocalRunner.waitForResult() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/JobStatus.html b/website/full_javadoc/compbio/metadata/class-use/JobStatus.html new file mode 100644 index 0000000..227a5b0 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/JobStatus.html @@ -0,0 +1,501 @@ + + + + + + +Uses of Class compbio.metadata.JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobStatus

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use JobStatus
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    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
    + JobStatusMsaWS.getJobStatus(java.lang.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(java.lang.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(java.lang.String workDirectory, + JobStatus marker) + +
    +           
    +static booleanUtil.writeMarker(java.lang.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(java.lang.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(java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    + JobStatusAsyncLocalRunner.getJobStatus(java.lang.String jobId) + +
    +           
    +static JobStatusLocalEngineUtil.getRecordedJobStatus(java.lang.String jobId) + +
    +           
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return JobStatus
    +static JobStatusJobStatus.valueOf(java.lang.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
    +static JobStatusWSUtil.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusTcoffeeWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusProbconsWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusMuscleWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusMafftWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusClustalWS.getJobStatus(java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html new file mode 100644 index 0000000..1e1329f --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html @@ -0,0 +1,651 @@ + + + + + + +Uses of Class compbio.metadata.JobSubmissionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.JobSubmissionException

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use JobSubmissionException
    compbio.data.msa  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    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 JobSubmissionException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw JobSubmissionException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +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, + java.util.List<FastaSequence> dataSet) + +
    +           
    + voidSyncExecutor.executeJob() + +
    +          Execute the job
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    + java.lang.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
    + java.lang.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) + +
    +           
    + java.lang.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() + +
    +           
    + java.lang.StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.local that throw JobSubmissionException
    ExecutableWrapper(ConfiguredExecutable<?> executable, + java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Subclasses of JobSubmissionException in compbio.metadata
    + classLimitExceededException + +
    +          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.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that throw JobSubmissionException
    + java.lang.StringTcoffeeWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringProbconsWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMuscleWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMafftWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringClustalWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Limit.html b/website/full_javadoc/compbio/metadata/class-use/Limit.html new file mode 100644 index 0000000..fa7eced --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Limit.html @@ -0,0 +1,570 @@ + + + + + + +Uses of Class compbio.metadata.Limit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.Limit

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Limit
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    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.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Limit in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return Limit
    + Limit<T>MsaWS.getLimit(java.lang.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(java.lang.String presetName) + +
    +           
    + Limit<T>ConfExecutable.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Limit
    + Limit<T>LimitsManager.getDefaultLimit() + +
    +           
    + Limit<T>LimitsManager.getLimitByName(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Limit
    + java.util.List<Limit<T>>LimitsManager.getLimits() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Limit
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return Limit
    + Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Limit
    + Limit<NetNglyc>NetNglyc.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return Limit
    + Limit<Tcoffee>Tcoffee.getLimit(java.lang.String presetName) + +
    +           
    + Limit<ClustalW>ClustalW.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Probcons>Probcons.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Muscle>Muscle.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Mafft>Mafft.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that return Limit
    + Limit<PsiBlast>PsiBlast.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return Limit
    + Limit<Tcoffee>TcoffeeWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Probcons>ProbconsWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Muscle>MuscleWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Mafft>MafftWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<ClustalW>ClustalWS.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.server with parameters of type Limit
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html b/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html new file mode 100644 index 0000000..22163d6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html @@ -0,0 +1,270 @@ + + + + + + +Uses of Class compbio.metadata.LimitExceededException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    +

    +Uses of Class
    compbio.metadata.LimitExceededException

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use LimitExceededException
    compbio.data.msa  
    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
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return LimitExceededException
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.ws.server
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.server that throw LimitExceededException
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html new file mode 100644 index 0000000..1bbf5d5 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html @@ -0,0 +1,502 @@ + + + + + + +Uses of Class compbio.metadata.LimitsManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    +

    +Uses of Class
    compbio.metadata.LimitsManager

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use LimitsManager
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return LimitsManager
    + LimitsManager<T>MsaWS.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>ConfExecutable.getLimits() + +
    +           
    +static + + + + +
    +<V> LimitsManager<V>
    +    		ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<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() + +
    +           
    +static + + + + +
    +<T> LimitsManager<T>
    +    		Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) + +
    +          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return LimitsManager
    + LimitsManager<NetNglyc>NetNglyc.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return LimitsManager
    + LimitsManager<Tcoffee>Tcoffee.getLimits() + +
    +           
    + LimitsManager<ClustalW>ClustalW.getLimits() + +
    +           
    + LimitsManager<Probcons>Probcons.getLimits() + +
    +           
    + LimitsManager<Muscle>Muscle.getLimits() + +
    +           
    + LimitsManager<Mafft>Mafft.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that return LimitsManager
    + LimitsManager<PsiBlast>PsiBlast.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return LimitsManager
    + LimitsManager<Tcoffee>TcoffeeWS.getLimits() + +
    +           
    + LimitsManager<Probcons>ProbconsWS.getLimits() + +
    +           
    + LimitsManager<Muscle>MuscleWS.getLimits() + +
    +           
    + LimitsManager<Mafft>MafftWS.getLimits() + +
    +           
    + LimitsManager<ClustalW>ClustalWS.getLimits() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Option.html b/website/full_javadoc/compbio/metadata/class-use/Option.html new file mode 100644 index 0000000..1defb5a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Option.html @@ -0,0 +1,539 @@ + + + + + + +Uses of Class compbio.metadata.Option + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.Option

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Option
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    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
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    +  +

    + + + + + +
    +Uses of Option in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return types with arguments of type Option
    + java.util.List<Option>CustomAlign.getOptions() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.data.msa.jaxws with type arguments of type Option
    + voidCustomAlign.setOptions(java.util.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(java.util.List<? extends Option<T>> arguments, + java.lang.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 option supported by the web service e.g.
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Option
    + Option<T>RunnerConfig.getArgument(java.lang.String name) + +
    +          Returns the argument by its name if found, NULL otherwise
    + Option<T>RunnerConfig.getArgumentByOptionName(java.lang.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
    + java.util.List<Option<T>>RunnerConfig.getArguments() + +
    +           
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + java.util.List<Option<T>>RunnerConfig.getOptions() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Option
    + voidRunnerConfig.addOption(Option<T> option) + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Option
    + voidRunnerConfig.setOptions(java.util.List<Option<T>> parameters) + +
    +           
    +  +

    + + + + + + + + +
    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
    + java.util.List<Option<?>>OptionCombinator.getAllOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type Option
    + java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments) + +
    +           
    +static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    + java.util.List<java.lang.String>OptionCombinator.optionsToCommandString(java.util.List<Option<?>> options) + +
    +           
    +  +

    + + + + + +
    +Uses of Option in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type Option
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    +static + + + + +
    +<T> java.util.List<java.lang.String>
    +    		WSUtil.getCommands(java.util.List<Option<T>> options, + java.lang.String keyValueSeparator) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Parameter.html b/website/full_javadoc/compbio/metadata/class-use/Parameter.html new file mode 100644 index 0000000..8038618 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Parameter.html @@ -0,0 +1,284 @@ + + + + + + +Uses of Class compbio.metadata.Parameter + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.Parameter

    +
    + + + + + + + + + + + + + +
    +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
    + java.util.List<Parameter<T>>RunnerConfig.getParameters() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Parameter
    + voidRunnerConfig.addParameter(Parameter<T> param) + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Parameter
    + voidRunnerConfig.setParameters(java.util.List<Parameter<T>> parameters) + +
    +           
    +  +

    + + + + + +
    +Uses of Parameter in compbio.runner
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner that return types with arguments of type Parameter
    + java.util.Map<Parameter<?>,java.lang.String>OptionCombinator.getAllConstrainedParametersWithBorderValues(boolean minValue) + +
    +           
    + java.util.Map<Parameter<?>,java.lang.String>OptionCombinator.getAllConstrainedParametersWithRandomValues() + +
    +           
    + java.util.List<Parameter<?>>OptionCombinator.getAllParameters() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type Parameter
    + java.util.List<java.lang.String>OptionCombinator.parametersToCommandString(java.util.List<Parameter<?>> orderedList, + java.util.Map<Parameter<?>,java.lang.String> prmValue) + +
    +           
    + java.util.List<java.lang.String>OptionCombinator.parametersToCommandString(java.util.List<Parameter<?>> orderedList, + java.util.Map<Parameter<?>,java.lang.String> prmValue) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Preset.html b/website/full_javadoc/compbio/metadata/class-use/Preset.html new file mode 100644 index 0000000..e8f8abe --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Preset.html @@ -0,0 +1,354 @@ + + + + + + +Uses of Class compbio.metadata.Preset + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.Preset

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Preset
    compbio.data.msa  
    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
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of Preset in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return Preset
    + PresetPresetAlign.getPreset() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type Preset
    + voidPresetAlign.setPreset(Preset preset) + +
    +           
    +  +

    + + + + + +
    +Uses of Preset in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return Preset
    + Preset<T>PresetManager.getPresetByName(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Preset
    + java.util.List<Preset<T>>PresetManager.getPresets() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Preset
    + voidPresetManager.setPresets(java.util.List<Preset<T>> presets) + +
    +           
    +  +

    + + + + + +
    +Uses of Preset in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server with parameters of type Preset
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/PresetManager.html b/website/full_javadoc/compbio/metadata/class-use/PresetManager.html new file mode 100644 index 0000000..c6c458a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/PresetManager.html @@ -0,0 +1,388 @@ + + + + + + +Uses of Class compbio.metadata.PresetManager + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.PresetManager

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use PresetManager
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    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>MsaWS.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(java.lang.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(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return PresetManager
    + PresetManager<Tcoffee>TcoffeeWS.getPresets() + +
    +           
    + PresetManager<Probcons>ProbconsWS.getPresets() + +
    +           
    + PresetManager<Muscle>MuscleWS.getPresets() + +
    +           
    + PresetManager<Mafft>MafftWS.getPresets() + +
    +           
    + PresetManager<ClustalW>ClustalWS.getPresets() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html new file mode 100644 index 0000000..2be5ac6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html @@ -0,0 +1,532 @@ + + + + + + +Uses of Class compbio.metadata.ResultNotAvailableException + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.ResultNotAvailableException

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use ResultNotAvailableException
    compbio.data.msa  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that throw ResultNotAvailableException
    + AlignmentMsaWS.getResult(java.lang.String jobId) + +
    +          Return the result of the job.
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine
    +  +

    + + + + + + + + + +
    Methods in compbio.engine that throw ResultNotAvailableException
    + ConfiguredExecutable<?>AsyncExecutor.getResults(java.lang.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(java.lang.String directory) + +
    +           
    + + + + + +
    +<V> V
    +    		ConfExecutable.getResults(java.lang.String directory) + +
    +           
    +static ConfiguredExecutable<?>Util.loadExecutable(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that throw ResultNotAvailableException
    + ConfiguredExecutable<?>ClusterSession.getResults(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncJobRunner.getResults(java.lang.String jobId) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine.local
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.local that throw ResultNotAvailableException
    +static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncLocalRunner.getResults(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that throw ResultNotAvailableException
    + AlignmentTcoffee.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentClustalW.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentProbcons.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMuscle.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMafft.getResults(java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that throw ResultNotAvailableException
    + + + + + +
    +<V> V
    +    		PsiBlast.getResults(java.lang.String directory) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that throw ResultNotAvailableException
    + AlignmentTcoffeeWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentProbconsWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMuscleWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMafftWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentClustalWS.getResult(java.lang.String jobId) + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.RunnerConfig

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use RunnerConfig
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    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>MsaWS.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(java.lang.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) + +
    +           
    + java.util.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(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner with parameters of type RunnerConfig
    +static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.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<Tcoffee>TcoffeeWS.getRunnerOptions() + +
    +           
    + RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() + +
    +           
    + RunnerConfig<Muscle>MuscleWS.getRunnerOptions() + +
    +           
    + RunnerConfig<Mafft>MafftWS.getRunnerOptions() + +
    +           
    + RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.UnsupportedRuntimeException

    +
    + + + + + + + + + + + + + +
    +Packages that use UnsupportedRuntimeException
    compbio.data.msa  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.engine.client
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that throw UnsupportedRuntimeException
    + java.lang.StringConfExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html new file mode 100644 index 0000000..41624ef --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html @@ -0,0 +1,214 @@ + + + + + + +Uses of Class compbio.metadata.ValueConstrain.Type + + + + + + + + + + + + +
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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(java.lang.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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    +Uses of Class
    compbio.metadata.ValueConstrain

    +
    + + + + + + + + + +
    +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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    +Uses of Class
    compbio.metadata.WrongParameterException

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use WrongParameterException
    compbio.data.msa  
    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
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that throw WrongParameterException
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidParameter.setDefaultValue(java.lang.String defaultVal) + +
    +           
    + voidOption.setDefaultValue(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidArgument.setValue(java.lang.String defaultValue) + +
    +          Set default values for the parameter or an option
    + voidOption.setValue(java.lang.String dValue) + +
    +           
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that throw WrongParameterException
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/package-frame.html b/website/full_javadoc/compbio/metadata/package-frame.html new file mode 100644 index 0000000..1739396 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/package-frame.html @@ -0,0 +1,93 @@ + + + + + + +compbio.metadata + + + + + + + + + + + +compbio.metadata + + + + +
    +Interfaces  + +
    +Argument
    + + + + + + +
    +Classes  + +
    +ChunkHolder +
    +Limit +
    +LimitsManager +
    +Option +
    +Parameter +
    +Preset +
    +PresetManager +
    +RunnerConfig +
    +ValueConstrain
    + + + + + + +
    +Enums  + +
    +JobStatus +
    +ValueConstrain.Type
    + + + + + + +
    +Exceptions  + +
    +JobExecutionException +
    +JobSubmissionException +
    +LimitExceededException +
    +ResultNotAvailableException +
    +UnsupportedRuntimeException +
    +WrongParameterException
    + + + + diff --git a/website/full_javadoc/compbio/metadata/package-summary.html b/website/full_javadoc/compbio/metadata/package-summary.html new file mode 100644 index 0000000..5f5b66b --- /dev/null +++ b/website/full_javadoc/compbio/metadata/package-summary.html @@ -0,0 +1,286 @@ + + + + + + +compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
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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 string data together with the position in a file from + where corresponding to of the data.
    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 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.
    LimitExceededExceptionThrown 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 Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
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    + + + diff --git a/website/full_javadoc/compbio/metadata/package-tree.html b/website/full_javadoc/compbio/metadata/package-tree.html new file mode 100644 index 0000000..3d95bb3 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/package-tree.html @@ -0,0 +1,178 @@ + + + + + + +compbio.metadata Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.metadata +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
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    +Uses of Package
    compbio.metadata

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.metadata
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    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.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder + +
    +          Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    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 + +
    +          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 string data together with the position in a file from + where corresponding to of the data.
    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 string data together with the position in a file from + where corresponding to of the data.
    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 + +
    +          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 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
    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 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.msa
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.runner.psiblast
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    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 string data together with the position in a file from + where corresponding to of the data.
    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 + +
    +          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.
    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.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html b/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html new file mode 100644 index 0000000..f15b429 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html @@ -0,0 +1,259 @@ + + + + + + +BlastParser + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.pipeline._jpred +
    +Class BlastParser

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.BlastParser
+
    +
    +
    +
    public class BlastParser
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    BlastParser() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +          args[0] is assumed to be the name of a Blast output file
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +BlastParser

    +
    +public BlastParser()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
+                 throws java.io.FileNotFoundException,
+                        javax.xml.stream.XMLStreamException
    +
    +
    args[0] is assumed to be the name of a Blast output file +

    +

    + +
    Throws: +
    javax.xml.stream.XMLStreamException +
    java.io.FileNotFoundException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/pipeline/_jpred/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html new file mode 100644 index 0000000..8669156 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html @@ -0,0 +1,277 @@ + + + + + + +Jpred4 + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.pipeline._jpred +
    +Class Jpred4

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.Jpred4
+
    +
    +
    +
    public class Jpred4
    extends java.lang.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
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Jpred4() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    + voidrunPsiBlast() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Jpred4

    +
    +public Jpred4()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +runPsiBlast

    +
    +public void runPsiBlast()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/pipeline/_jpred/PScore.html b/website/full_javadoc/compbio/pipeline/_jpred/PScore.html new file mode 100644 index 0000000..668b60b --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/PScore.html @@ -0,0 +1,299 @@ + + + + + + +PScore + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.pipeline._jpred +
    +Class PScore

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.PScore
+
    +
    +
    +
    public class PScore
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PScore() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + inthashCode() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PScore

    +
    +public PScore()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.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/pipeline/_jpred/Pairwise.html b/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html new file mode 100644 index 0000000..3200264 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html @@ -0,0 +1,257 @@ + + + + + + +Pairwise + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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.pipeline._jpred +
    +Class Pairwise

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.Pairwise
+
    +
    +
    +
    public class Pairwise
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Pairwise(java.util.List<FastaSequence> sequences) + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Pairwise

    +
    +public Pairwise(java.util.List<FastaSequence> sequences)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static final void main(java.lang.String[] args)
+                       throws java.io.FileNotFoundException,
+                              java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.FileNotFoundException +
    java.io.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/pipeline/_jpred/class-use/BlastParser.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html new file mode 100644 index 0000000..5380574 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.BlastParser + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.BlastParser

    +
    +No usage of compbio.pipeline._jpred.BlastParser +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html new file mode 100644 index 0000000..e70f570 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.Jpred4 + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.Jpred4

    +
    +No usage of compbio.pipeline._jpred.Jpred4 +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html new file mode 100644 index 0000000..26263db --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.PScore + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.PScore

    +
    +No usage of compbio.pipeline._jpred.PScore +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html new file mode 100644 index 0000000..754a87e --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.Pairwise + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.Pairwise

    +
    +No usage of compbio.pipeline._jpred.Pairwise +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html b/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html new file mode 100644 index 0000000..f22d288 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html @@ -0,0 +1,38 @@ + + + + + + +compbio.pipeline._jpred + + + + + + + + + + + +compbio.pipeline._jpred + + + + +
    +Classes  + +
    +BlastParser +
    +Jpred4 +
    +Pairwise +
    +PScore
    + + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html new file mode 100644 index 0000000..06bf2f8 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html @@ -0,0 +1,179 @@ + + + + + + +compbio.pipeline._jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.pipeline._jpred +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    BlastParser 
    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 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html b/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html new file mode 100644 index 0000000..e907ee7 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html @@ -0,0 +1,153 @@ + + + + + + +compbio.pipeline._jpred Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For Package compbio.pipeline._jpred +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-use.html b/website/full_javadoc/compbio/pipeline/_jpred/package-use.html new file mode 100644 index 0000000..90ca61e --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-use.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Package compbio.pipeline._jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Package
    compbio.pipeline._jpred

    +
    +No usage of compbio.pipeline._jpred +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/OptionCombinator.html b/website/full_javadoc/compbio/runner/OptionCombinator.html new file mode 100644 index 0000000..69a5662 --- /dev/null +++ b/website/full_javadoc/compbio/runner/OptionCombinator.html @@ -0,0 +1,421 @@ + + + + + + +OptionCombinator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 OptionCombinator

    +
    +java.lang.Object
+  extended by compbio.runner.OptionCombinator
+
    +
    +
    +
    @Immutable
+public final class OptionCombinator
    extends java.lang.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
    + java.util.List<java.lang.String>argumentsToCommandString(java.util.List<? extends Option<?>> arguments) + +
    +           
    +static java.util.List<java.lang.String>argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    + java.util.Map<Parameter<?>,java.lang.String>getAllConstrainedParametersWithBorderValues(boolean minValue) + +
    +           
    + java.util.Map<Parameter<?>,java.lang.String>getAllConstrainedParametersWithRandomValues() + +
    +           
    + java.util.List<Option<?>>getAllOptions() + +
    +           
    + java.util.List<Parameter<?>>getAllParameters() + +
    +           
    + java.util.List<java.lang.String>getOptionsAtRandom() + +
    +           
    + java.util.List<java.lang.String>optionsToCommandString(java.util.List<Option<?>> options) + +
    +           
    + java.util.List<java.lang.String>parametersToCommandString(java.util.List<Parameter<?>> orderedList, + java.util.Map<Parameter<?>,java.lang.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 java.util.List<java.lang.String> optionsToCommandString(java.util.List<Option<?>> options)
    +
    +
    +
    +
    +
    +
    + +

    +getOptionsAtRandom

    +
    +public java.util.List<java.lang.String> getOptionsAtRandom()
    +
    +
    +
    +
    +
    +
    + +

    +getAllOptions

    +
    +public java.util.List<Option<?>> getAllOptions()
    +
    +
    +
    +
    +
    +
    + +

    +getAllParameters

    +
    +public java.util.List<Parameter<?>> getAllParameters()
    +
    +
    +
    +
    +
    +
    + +

    +argumentsToCommandString

    +
    +public java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments)
    +
    +
    +
    +
    +
    +
    + +

    +argumentsToCommandString

    +
    +public static java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments,
+                                                                        RunnerConfig<? extends Executable<?>> rconfig)
    +
    +
    +
    +
    +
    +
    + +

    +parametersToCommandString

    +
    +public java.util.List<java.lang.String> parametersToCommandString(java.util.List<Parameter<?>> orderedList,
+                                                                  java.util.Map<Parameter<?>,java.lang.String> prmValue)
    +
    +
    +
    +
    +
    +
    + +

    +getAllConstrainedParametersWithBorderValues

    +
    +public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithBorderValues(boolean minValue)
    +
    +
    +
    +
    +
    +
    + +

    +getAllConstrainedParametersWithRandomValues

    +
    +public java.util.Map<Parameter<?>,java.lang.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 new file mode 100644 index 0000000..d09afc7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/Util.html @@ -0,0 +1,409 @@ + + + + + + +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 java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringSPACE + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Util() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> LimitsManager<T>
    +    		getLimits(java.lang.Class<? extends Executable<T>> clazz) + +
    +          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +static + + + + +
    +<T> PresetManager<T>
    +    		getPresets(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +static + + + + +
    +<T> RunnerConfig<T>
    +    		getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +static AlignmentreadClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) + +
    +           
    +static voidwriteInput(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

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

    +SPACE

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

    +Util

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

    +getLimits

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

    +

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

    +getSupportedOptions

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

    +getPresets

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

    +readClustalFile

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

    +writeInput

    +
    +public static void writeInput(java.util.List<FastaSequence> sequences,
+                              ConfiguredExecutable<?> exec)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 new file mode 100644 index 0000000..05a5ca7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html @@ -0,0 +1,347 @@ + + + + + + +_NativeSpecHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 _NativeSpecHelper

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

    +

    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    _NativeSpecHelper(int requiredMemory) + +
    +           
    _NativeSpecHelper(int requiredMemory, + int maxCalculationTime) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + _QueuegetApproprieteQueue() + +
    +           
    + java.lang.StringgetNativeSpec() + +
    +           
    + java.lang.StringgetQueue() + +
    +           
    + voidsetQueue(java.lang.String queue) + +
    +           
    + voidsetRequiredMemory(int memory) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_NativeSpecHelper

    +
    +public _NativeSpecHelper(int requiredMemory)
    +
    +
    +
    + +

    +_NativeSpecHelper

    +
    +public _NativeSpecHelper(int requiredMemory,
+                         int maxCalculationTime)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setRequiredMemory

    +
    +public void setRequiredMemory(int memory)
    +
    +
    +
    +
    +
    +
    + +

    +setQueue

    +
    +public void setQueue(java.lang.String queue)
    +
    +
    +
    +
    +
    +
    + +

    +getQueue

    +
    +public java.lang.String getQueue()
    +
    +
    +
    +
    +
    +
    + +

    +getNativeSpec

    +
    +public java.lang.String getNativeSpec()
+                               throws java.net.UnknownServiceException
    +
    +
    + +
    Throws: +
    java.net.UnknownServiceException
    +
    +
    +
    + +

    +getApproprieteQueue

    +
    +public _Queue getApproprieteQueue()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html new file mode 100644 index 0000000..ff0efa8 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html @@ -0,0 +1,586 @@ + + + + + + +_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, Disembl, Mcl, OB, PSIBlast, Ronn, RPSBlast
    +
    +
    +
    +
    public abstract class _SkeletalCommandBuilder
    extends java.lang.Object
    implements Executable<_SkeletalCommandBuilder>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    _SkeletalCommandBuilder() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + _SkeletalCommandBuilderaddParameter(java.lang.String parameter) + +
    +           
    + _SkeletalCommandBuilderaddParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + _SkeletalCommandBuilderaddParameters(java.lang.String[] parameters) + +
    +           
    + java.lang.StringgetEmail() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + Limit<_SkeletalCommandBuilder>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<_SkeletalCommandBuilder>getLimits() + +
    +           
    + java.lang.StringgetName() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<_SkeletalCommandBuilder>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + _SkeletalCommandBuildersetEmail(java.lang.String email) + +
    +           
    + _SkeletalCommandBuildersetName(java.lang.String name) + +
    +           
    +  + + + + + + + +
    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()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setEmail

    +
    +public _SkeletalCommandBuilder setEmail(java.lang.String email)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setName

    +
    +public _SkeletalCommandBuilder setName(java.lang.String name)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getName

    +
    +public java.lang.String getName()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getEmail

    +
    +public java.lang.String getEmail()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public _SkeletalCommandBuilder addParameters(java.lang.String[] parameters)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public _SkeletalCommandBuilder addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    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)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +addParameter

    +
    +public _SkeletalCommandBuilder addParameter(java.lang.String parameter)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
    +
    +
    +
    Specified by:
    getResults in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<_SkeletalCommandBuilder> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<_SkeletalCommandBuilder> getLimits()
    +
    +
    +
    Specified by:
    getLimits 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 new file mode 100644 index 0000000..2faddc5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/BlastAll.html @@ -0,0 +1,360 @@ + + + + + + +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(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + booleanremoveOutput(java.lang.String outfile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +removeOutput

    +
    +public boolean removeOutput(java.lang.String outfile)
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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 new file mode 100644 index 0000000..0dfb3cf --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html @@ -0,0 +1,200 @@ + + + + + + +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 java.lang.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/Disembl.html b/website/full_javadoc/compbio/runner/_impl/Disembl.html new file mode 100644 index 0000000..9c5d600 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Disembl.html @@ -0,0 +1,379 @@ + + + + + + +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._impl +
    +Class Disembl

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.Disembl
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class Disembl
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    Disembl(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.util.List<java.lang.String>getTestArgs() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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
    + +

    +Disembl

    +
    +public Disembl(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTestArgs

    +
    +public static java.util.List<java.lang.String> getTestArgs()
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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/Environment.html b/website/full_javadoc/compbio/runner/_impl/Environment.html new file mode 100644 index 0000000..bc7399c --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Environment.html @@ -0,0 +1,265 @@ + + + + + + +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 java.lang.Object
    + + +

    +This is utility class to encapsulate environmental variables like directory paths +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringgetBlastBinDir() + +
    +           
    +static java.lang.StringgetBlastDatabasesDir() + +
    +           
    +static java.lang.StringgetRPSBlastDatabasesDir() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getBlastBinDir

    +
    +public static java.lang.String getBlastBinDir()
    +
    +
    +
    +
    +
    +
    + +

    +getBlastDatabasesDir

    +
    +public static final java.lang.String getBlastDatabasesDir()
    +
    +
    +
    +
    +
    +
    + +

    +getRPSBlastDatabasesDir

    +
    +public static final java.lang.String getRPSBlastDatabasesDir()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/Mcl.html b/website/full_javadoc/compbio/runner/_impl/Mcl.html new file mode 100644 index 0000000..c5c546f --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Mcl.html @@ -0,0 +1,379 @@ + + + + + + +Mcl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +static java.util.List<java.lang.String>getTestParams() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTestParams

    +
    +public static java.util.List<java.lang.String> getTestParams()
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html new file mode 100644 index 0000000..418085d --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html @@ -0,0 +1,552 @@ + + + + + + +NetNglyc + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 NetNglyc

    +
    +java.lang.Object
+  extended by compbio.runner._impl.NetNglyc
+
    +
    +
    All Implemented Interfaces:
    Executable<NetNglyc>
    +
    +
    +
    +
    public class NetNglyc
    extends java.lang.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(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + Limit<NetNglyc>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<NetNglyc>getLimits() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<NetNglyc>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    +static java.util.List<java.lang.String>getTestArgs() + +
    +           
    +static java.lang.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 java.util.List<java.lang.String> getTestArgs()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public NetNglyc addParameters(java.util.List<java.lang.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 java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    Specified by:
    getCreatedFiles in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    Specified by:
    getInput in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
    +
    +
    +
    Specified by:
    getResults in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<NetNglyc> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<NetNglyc> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/OB.html b/website/full_javadoc/compbio/runner/_impl/OB.html new file mode 100644 index 0000000..55d1730 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/OB.html @@ -0,0 +1,382 @@ + + + + + + +OB + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + java.util.List<java.lang.String>getTestArgs() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getTestArgs

    +
    +public java.util.List<java.lang.String> getTestArgs()
    +
    +
    +
    +
    +
    +
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html new file mode 100644 index 0000000..b14bdb4 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html @@ -0,0 +1,360 @@ + + + + + + +PSIBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + booleanremoveOutput(java.lang.String outfile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +removeOutput

    +
    +public boolean removeOutput(java.lang.String outfile)
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html new file mode 100644 index 0000000..64cecfd --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html @@ -0,0 +1,360 @@ + + + + + + +RPSBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    +static java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public static java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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/Ronn.html b/website/full_javadoc/compbio/runner/_impl/Ronn.html new file mode 100644 index 0000000..d5f9998 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Ronn.html @@ -0,0 +1,360 @@ + + + + + + +Ronn + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, 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(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.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/Runners.html b/website/full_javadoc/compbio/runner/_impl/Runners.html new file mode 100644 index 0000000..3a3978d --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Runners.html @@ -0,0 +1,371 @@ + + + + + + +Runners + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 Runners

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

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static BlastAllgetBlastAllRunnable(java.lang.String workDirectory) + +
    +           
    +static DisemblgetDisemblRunnable(java.lang.String workDirectory) + +
    +           
    +static MclgetMclRunnable(java.lang.String workDirectory) + +
    +           
    +static NetNglycgetNetNglycRunnable(java.lang.String workDirectory) + +
    +           
    +static OBgetOBRunnable(java.lang.String workDirectory) + +
    +           
    +static PSIBlastgetPSIBlastRunnable(java.lang.String workDirectory) + +
    +           
    +static RonngetRonnRunnable(java.lang.String workDirectory) + +
    +           
    +static RPSBlastgetRPSBlastRunnable(java.lang.String workDirectory) + +
    +           
    +static compbio.runner._impl.Tmhmm2getTmhmm2Runnable(java.lang.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(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getOBRunnable

    +
    +public static OB getOBRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getDisemblRunnable

    +
    +public static Disembl getDisemblRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getNetNglycRunnable

    +
    +public static NetNglyc getNetNglycRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getRonnRunnable

    +
    +public static Ronn getRonnRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getTmhmm2Runnable

    +
    +public static compbio.runner._impl.Tmhmm2 getTmhmm2Runnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getRPSBlastRunnable

    +
    +public static RPSBlast getRPSBlastRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getBlastAllRunnable

    +
    +public static BlastAll getBlastAllRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getPSIBlastRunnable

    +
    +public static PSIBlast getPSIBlastRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/class-use/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html new file mode 100644 index 0000000..6389cd6 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.BlastAll + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.BlastAll

    +
    + + + + + + + + + +
    +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(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html new file mode 100644 index 0000000..8ebcce6 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._impl.BlastParameters + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.BlastParameters

    +
    +No usage of compbio.runner._impl.BlastParameters +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html new file mode 100644 index 0000000..005572a --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.Disembl + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.Disembl

    +
    + + + + + + + + + +
    +Packages that use Disembl
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of Disembl in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Disembl
    +static DisemblRunners.getDisemblRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html b/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html new file mode 100644 index 0000000..243aeae --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._impl.Environment + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.Environment

    +
    +No usage of compbio.runner._impl.Environment +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html new file mode 100644 index 0000000..d08bb98 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.Mcl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
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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(java.lang.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 new file mode 100644 index 0000000..ecd9ab5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html @@ -0,0 +1,220 @@ + + + + + + +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(java.util.List<java.lang.String> parameters) + +
    +           
    +static NetNglycRunners.getNetNglycRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner._impl that return types with arguments of type NetNglyc
    + Limit<NetNglyc>NetNglyc.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<NetNglyc>NetNglyc.getLimits() + +
    +           
    + CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/OB.html b/website/full_javadoc/compbio/runner/_impl/class-use/OB.html new file mode 100644 index 0000000..ce2519a --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/OB.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.OB + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.OB

    +
    + + + + + + + + + +
    +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(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html new file mode 100644 index 0000000..8bc9956 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.PSIBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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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(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html new file mode 100644 index 0000000..a1f52e3 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.RPSBlast + + + + + + + + + + + + +
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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(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html b/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html new file mode 100644 index 0000000..cc6975e --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.Ronn + + + + + + + + + + + + +
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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(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html b/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html new file mode 100644 index 0000000..af87076 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._impl.Runners + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.Runners

    +
    +No usage of compbio.runner._impl.Runners +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-frame.html b/website/full_javadoc/compbio/runner/_impl/package-frame.html new file mode 100644 index 0000000..55be9ff --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-frame.html @@ -0,0 +1,52 @@ + + + + + + +compbio.runner._impl + + + + + + + + + + + +compbio.runner._impl + + + + +
    +Classes  + +
    +BlastAll +
    +BlastParameters +
    +Disembl +
    +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 new file mode 100644 index 0000000..c985bf0 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-summary.html @@ -0,0 +1,197 @@ + + + + + + +compbio.runner._impl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.runner._impl +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    BlastAll 
    BlastParametersUtility class for common Blast parameters
    Disembl 
    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 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-tree.html b/website/full_javadoc/compbio/runner/_impl/package-tree.html new file mode 100644 index 0000000..3f894d8 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-tree.html @@ -0,0 +1,157 @@ + + + + + + +compbio.runner._impl Class Hierarchy + + + + + + + + + + + + +
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    +
    +

    +Hierarchy For Package compbio.runner._impl +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-use.html b/website/full_javadoc/compbio/runner/_impl/package-use.html new file mode 100644 index 0000000..5ada742 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-use.html @@ -0,0 +1,212 @@ + + + + + + +Uses of Package compbio.runner._impl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Package
    compbio.runner._impl

    +
    + + + + + + + + + +
    +Packages that use compbio.runner._impl
    compbio.runner._impl  
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.runner._impl used by compbio.runner._impl
    BlastAll + +
    +           
    Disembl + +
    +           
    Mcl + +
    +           
    NetNglyc + +
    +           
    OB + +
    +          TODO this needs fixing! Executable does not work
    PSIBlast + +
    +           
    Ronn + +
    +           
    RPSBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/_Jpred.html b/website/full_javadoc/compbio/runner/_jpred/_Jpred.html new file mode 100644 index 0000000..4eee1a7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/_Jpred.html @@ -0,0 +1,224 @@ + + + + + + +_Jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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._jpred +
    +Class _Jpred

    +
    +java.lang.Object
+  extended by compbio.runner._jpred._Jpred
+
    +
    +
    +
    public class _Jpred
    extends java.lang.Object
    + + +

    +

    + +

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

    + + + + + + + + +
    +Constructor Detail
    + +

    +_Jpred

    +
    +public _Jpred()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/runner/_jpred/class-use/_Jpred.html b/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html new file mode 100644 index 0000000..fd98536 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._jpred._Jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +    		 + +
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    +Uses of Class
    compbio.runner._jpred._Jpred

    +
    +No usage of compbio.runner._jpred._Jpred +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-frame.html b/website/full_javadoc/compbio/runner/_jpred/package-frame.html new file mode 100644 index 0000000..2640f34 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-frame.html @@ -0,0 +1,32 @@ + + + + + + +compbio.runner._jpred + + + + + + + + + + + +compbio.runner._jpred + + + + +
    +Classes  + +
    +_Jpred
    + + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-summary.html b/website/full_javadoc/compbio/runner/_jpred/package-summary.html new file mode 100644 index 0000000..f375d9f --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-summary.html @@ -0,0 +1,157 @@ + + + + + + +compbio.runner._jpred + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +

    +Package compbio.runner._jpred +

    + + + + + + + + + +
    +Class Summary
    _Jpred 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-tree.html b/website/full_javadoc/compbio/runner/_jpred/package-tree.html new file mode 100644 index 0000000..e9e4095 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-tree.html @@ -0,0 +1,153 @@ + + + + + + +compbio.runner._jpred Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.runner._jpred +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    +
      +
    • java.lang.Object
        +
      • compbio.runner._jpred._Jpred
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-use.html b/website/full_javadoc/compbio/runner/_jpred/package-use.html new file mode 100644 index 0000000..dd3eac5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-use.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Package compbio.runner._jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.runner._jpred

    +
    +No usage of compbio.runner._jpred +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html b/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html new file mode 100644 index 0000000..82f1f31 --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner.OptionCombinator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner.OptionCombinator

    +
    +No usage of compbio.runner.OptionCombinator +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/Util.html b/website/full_javadoc/compbio/runner/class-use/Util.html new file mode 100644 index 0000000..7d1eef5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/Util.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner.Util + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.runner.Util

    +
    +No usage of compbio.runner.Util +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html new file mode 100644 index 0000000..cbcc70d --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._NativeSpecHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._NativeSpecHelper

    +
    +No usage of compbio.runner._NativeSpecHelper +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html new file mode 100644 index 0000000..46aa6c4 --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html @@ -0,0 +1,321 @@ + + + + + + +Uses of Class compbio.runner._SkeletalCommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.runner._SkeletalCommandBuilder

    +
    + + + + + + + + + + + + + +
    +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(java.lang.String parameter) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(java.lang.String[] parameters) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.setEmail(java.lang.String email) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.setName(java.lang.String name) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner that return types with arguments of type _SkeletalCommandBuilder
    + Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() + +
    +           
    + CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of _SkeletalCommandBuilder in compbio.runner._impl
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Subclasses of _SkeletalCommandBuilder in compbio.runner._impl
    + classBlastAll + +
    +           
    + classDisembl + +
    +           
    + classMcl + +
    +           
    + classOB + +
    +          TODO this needs fixing! Executable does not work
    + classPSIBlast + +
    +           
    + classRonn + +
    +           
    + classRPSBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html new file mode 100644 index 0000000..e2cbdb5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/ClustalW.html @@ -0,0 +1,473 @@ + + + + + + +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 java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ClustalW() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<ClustalW>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<ClustalW>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    +static java.lang.StringgetStatFile() + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + ClustalWsetInput(java.lang.String inFile) + +
    +           
    + ClustalWsetOutput(java.lang.String outFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, 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 java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ClustalW

    +
    +public ClustalW()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setOutput

    +
    +public ClustalW setOutput(java.lang.String outFile)
    +
    +
    +
    Overrides:
    setOutput in class SkeletalExecutable<ClustalW>
    +
    +
    +
    +
    +
    +
    + +

    +setInput

    +
    +public ClustalW setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<ClustalW>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.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 java.lang.String getStatFile()
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<ClustalW> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<ClustalW> getLimits()
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<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
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html new file mode 100644 index 0000000..0a6d12c --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Mafft.html @@ -0,0 +1,448 @@ + + + + + + +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>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Mafft() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + MafftaddParameters(java.util.List<java.lang.String> parameters) + +
    +          Mafft input must always be the last parameter!
    + Limit<Mafft>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Mafft>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + MafftsetInput(java.lang.String inFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    equals, getClusterSettings, getCreatedFiles, getError, getInput, 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
    getCreatedFiles, getError, getInput, getOutput, getParameters, loadRunConfiguration
    +  +

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

    +KEY_VALUE_SEPARATOR

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

    +Mafft

    +
    +public Mafft()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<Mafft>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +setInput

    +
    +public Mafft setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Mafft>
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public Mafft addParameters(java.util.List<java.lang.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
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Mafft> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<Mafft>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Mafft> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<Mafft>
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<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
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Muscle.html b/website/full_javadoc/compbio/runner/msa/Muscle.html new file mode 100644 index 0000000..479eb57 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Muscle.html @@ -0,0 +1,481 @@ + + + + + + +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 java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Muscle() + +
    +          Default options are + + -clwstrict - write output in clustal format
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<Muscle>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Muscle>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    +static java.lang.StringgetStatFile() + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + MusclesetInput(java.lang.String inFile) + +
    +           
    + MusclesetOutput(java.lang.String outFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, 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 java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Muscle

    +
    +public Muscle()
    +
    +
    Default options are + + -clwstrict - write output in clustal format +

    +

    +
    Parameters:
    workDirectory -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setOutput

    +
    +public Muscle setOutput(java.lang.String outFile)
    +
    +
    +
    Overrides:
    setOutput in class SkeletalExecutable<Muscle>
    +
    +
    +
    +
    +
    +
    + +

    +setInput

    +
    +public Muscle setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Muscle>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.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 java.lang.String getStatFile()
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Muscle> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Muscle> getLimits()
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<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
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Probcons.html b/website/full_javadoc/compbio/runner/msa/Probcons.html new file mode 100644 index 0000000..74a2d6a --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Probcons.html @@ -0,0 +1,452 @@ + + + + + + +Probcons + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 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 java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Probcons() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<Probcons>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Probcons>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + ProbconssetInput(java.lang.String inFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, 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, getError, getInput, getOutput, getParameters, loadRunConfiguration
    +  +

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

    +KEY_VALUE_SEPARATOR

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

    +Probcons

    +
    +public Probcons()
    +
    +
    +
    Parameters:
    workDirectory -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<Probcons>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.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(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Probcons>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Probcons> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<Probcons>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Probcons> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<Probcons>
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<Probcons>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 new file mode 100644 index 0000000..b35bcc1 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Tcoffee.html @@ -0,0 +1,542 @@ + + + + + + +Tcoffee + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 Tcoffee

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

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Tcoffee() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static intgetClusterCpuNum() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<Tcoffee>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Tcoffee>getLimits() + +
    +           
    + java.lang.StringgetNativeSpecs() + +
    +           
    + CommandBuilder<Tcoffee>getParameters(Executable.ExecProvider provider) + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + TcoffeesetInput(java.lang.String inFile) + +
    +           
    + voidsetNCore(int ncoreNumber) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, 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, getError, getInput, getOutput, loadRunConfiguration
    +  +

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

    +KEY_VALUE_SEPARATOR

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

    +Tcoffee

    +
    +public Tcoffee()
    +
    +
    +
    Parameters:
    workDirectory -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setInput

    +
    +public Tcoffee setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<Tcoffee>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.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>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Tcoffee> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Tcoffee> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getNativeSpecs

    +
    +public java.lang.String getNativeSpecs()
    +
    +
    +
    Specified by:
    getNativeSpecs in interface ClusterNativeSpecExecutable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getClusterCpuNum

    +
    +public static int getClusterCpuNum()
    +
    +
    +
    +
    +
    + +
    Returns:
    number of cpus to use on the cluster or 0 if the value is + undefined
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<Tcoffee>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/class-use/ClustalW.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html new file mode 100644 index 0000000..5d5eecf --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html @@ -0,0 +1,291 @@ + + + + + + +Uses of Class compbio.runner.msa.ClustalW + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +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(java.lang.String inFile) + +
    +           
    + ClustalWClustalW.setOutput(java.lang.String outFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type ClustalW
    + Limit<ClustalW>ClustalW.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<ClustalW>ClustalW.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of ClustalW in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type ClustalW
    + Limit<ClustalW>ClustalWS.getLimit(java.lang.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
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html new file mode 100644 index 0000000..65e6512 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html @@ -0,0 +1,291 @@ + + + + + + +Uses of Class compbio.runner.msa.Mafft + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +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(java.util.List<java.lang.String> parameters) + +
    +          Mafft input must always be the last parameter!
    + MafftMafft.setInput(java.lang.String inFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Mafft
    + Limit<Mafft>Mafft.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Mafft>Mafft.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of Mafft in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Mafft
    + Limit<Mafft>MafftWS.getLimit(java.lang.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
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.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 new file mode 100644 index 0000000..2621067 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html @@ -0,0 +1,291 @@ + + + + + + +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(java.lang.String inFile) + +
    +           
    + MuscleMuscle.setOutput(java.lang.String outFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Muscle
    + Limit<Muscle>Muscle.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Muscle>Muscle.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of Muscle in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Muscle
    + Limit<Muscle>MuscleWS.getLimit(java.lang.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
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.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 new file mode 100644 index 0000000..3ffa0e0 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html @@ -0,0 +1,283 @@ + + + + + + +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(java.lang.String inFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Probcons
    + Limit<Probcons>Probcons.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Probcons>Probcons.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of Probcons in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Probcons
    + Limit<Probcons>ProbconsWS.getLimit(java.lang.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
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.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 new file mode 100644 index 0000000..243fcd9 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html @@ -0,0 +1,291 @@ + + + + + + +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(java.lang.String inFile) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Tcoffee
    + Limit<Tcoffee>Tcoffee.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Tcoffee>Tcoffee.getLimits() + +
    +           
    + CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of Tcoffee in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Tcoffee
    + Limit<Tcoffee>TcoffeeWS.getLimit(java.lang.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
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    +Classes  + +
    +ClustalW +
    +Mafft +
    +Muscle +
    +Probcons +
    +Tcoffee
    + + + + diff --git a/website/full_javadoc/compbio/runner/msa/package-summary.html b/website/full_javadoc/compbio/runner/msa/package-summary.html new file mode 100644 index 0000000..82e1c12 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/package-summary.html @@ -0,0 +1,192 @@ + + + + + + +compbio.runner.msa + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +

    +Package compbio.runner.msa +

    +Wrappers for native executables for multiple sequence alignment (msa) +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    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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    + + + diff --git a/website/full_javadoc/compbio/runner/msa/package-tree.html b/website/full_javadoc/compbio/runner/msa/package-tree.html new file mode 100644 index 0000000..d790016 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/package-tree.html @@ -0,0 +1,159 @@ + + + + + + +compbio.runner.msa Class Hierarchy + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.runner.msa +

    +
    +
    +
    Package Hierarchies:
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    +
    +

    +Class Hierarchy +

    + +
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    +Uses of Package
    compbio.runner.msa

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.runner.msa
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.runner.msa used by compbio.runner.msa
    ClustalW + +
    +           
    Mafft + +
    +           
    Muscle + +
    +           
    Probcons + +
    +           
    Tcoffee + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.runner.msa used by compbio.ws.server
    ClustalW + +
    +           
    Mafft + +
    +           
    Muscle + +
    +           
    Probcons + +
    +           
    Tcoffee + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/package-frame.html b/website/full_javadoc/compbio/runner/package-frame.html new file mode 100644 index 0000000..6fd25a9 --- /dev/null +++ b/website/full_javadoc/compbio/runner/package-frame.html @@ -0,0 +1,38 @@ + + + + + + +compbio.runner + + + + + + + + + + + +compbio.runner + + + + +
    +Classes  + +
    +_NativeSpecHelper +
    +_SkeletalCommandBuilder +
    +OptionCombinator +
    +Util
    + + + + diff --git a/website/full_javadoc/compbio/runner/package-summary.html b/website/full_javadoc/compbio/runner/package-summary.html new file mode 100644 index 0000000..e5f3a22 --- /dev/null +++ b/website/full_javadoc/compbio/runner/package-summary.html @@ -0,0 +1,188 @@ + + + + + + +compbio.runner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +

    +Package compbio.runner +

    +Utilities commonly used by all runners. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _NativeSpecHelper 
    _SkeletalCommandBuilder 
    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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    + + + diff --git a/website/full_javadoc/compbio/runner/package-tree.html b/website/full_javadoc/compbio/runner/package-tree.html new file mode 100644 index 0000000..05b744b --- /dev/null +++ b/website/full_javadoc/compbio/runner/package-tree.html @@ -0,0 +1,154 @@ + + + + + + +compbio.runner Class Hierarchy + + + + + + + + + + + + +
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    + + + + + + + + + + + + +
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    +    		 + +
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    +Hierarchy For Package compbio.runner +

    +
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    +
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    +
    +

    +Class Hierarchy +

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    +Uses of Package
    compbio.runner

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.runner
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    +  +

    + + + + + + + + +
    +Classes in compbio.runner used by compbio.runner
    _SkeletalCommandBuilder + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.runner used by compbio.runner._impl
    _SkeletalCommandBuilder + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html b/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html new file mode 100644 index 0000000..072dda7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html @@ -0,0 +1,354 @@ + + + + + + +PsiBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.psiblast +
    +Class PsiBlast

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<PsiBlast>
+      extended by compbio.runner.psiblast.PsiBlast
+
    +
    +
    All Implemented Interfaces:
    Executable<PsiBlast>
    +
    +
    +
    +
    public class PsiBlast
    extends SkeletalExecutable<PsiBlast>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    PsiBlast() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Limit<PsiBlast>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<PsiBlast>getLimits() + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getCreatedFiles, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setInput, setOutput, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PsiBlast

    +
    +public PsiBlast()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
+             throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<PsiBlast> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<PsiBlast> getLimits()
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<PsiBlast>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
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    +Uses of Class
    compbio.runner.psiblast.PsiBlast

    +
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    +Packages that use PsiBlast
    compbio.runner.psiblast  
    +  +

    + + + + + +
    +Uses of PsiBlast in compbio.runner.psiblast
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.psiblast that return types with arguments of type PsiBlast
    + Limit<PsiBlast>PsiBlast.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<PsiBlast>PsiBlast.getLimits() + +
    +           
    +  +

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    PsiBlast 
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    compbio.runner.psiblast  
    +  +

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    +Classes in compbio.runner.psiblast used by compbio.runner.psiblast
    PsiBlast + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html new file mode 100644 index 0000000..35584df --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html @@ -0,0 +1,377 @@ + + + + + + +Jws2Client.Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Enum Jws2Client.Services

    +
    +java.lang.Object
+  extended by java.lang.Enum<Jws2Client.Services>
+      extended by compbio.ws.client.Jws2Client.Services
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Jws2Client.Services>
    +
    +
    +
    Enclosing class:
    Jws2Client
    +
    +
    +
    +
    public static enum Jws2Client.Services
    extends java.lang.Enum<Jws2Client.Services>
    + + +

    +List of web services currently supported by JWS2 +

    + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    ClustalWS + +
    +           
    MafftWS + +
    +           
    MuscleWS + +
    +           
    ProbconsWS + +
    +           
    TcoffeeWS + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static Jws2Client.ServicesvalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Jws2Client.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 Jws2Client.Services MafftWS
    +
    +
    +
    +
    +
    + +

    +MuscleWS

    +
    +public static final Jws2Client.Services MuscleWS
    +
    +
    +
    +
    +
    + +

    +ClustalWS

    +
    +public static final Jws2Client.Services ClustalWS
    +
    +
    +
    +
    +
    + +

    +TcoffeeWS

    +
    +public static final Jws2Client.Services TcoffeeWS
    +
    +
    +
    +
    +
    + +

    +ProbconsWS

    +
    +public static final Jws2Client.Services ProbconsWS
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static Jws2Client.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 (Jws2Client.Services c : Jws2Client.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 Jws2Client.Services valueOf(java.lang.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: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.html b/website/full_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..97c55bf --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,375 @@ + + + + + + +Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class Jws2Client

    +
    +java.lang.Object
+  extended by compbio.ws.client.Jws2Client
+
    +
    +
    +
    public class Jws2Client
    extends java.lang.Object
    + + +

    +A command line client for Jalview Web Services version 2 +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classJws2Client.Services + +
    +          List of web services currently supported by JWS2
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> MsaWS<T>
    +    		connect(java.lang.String host, + Jws2Client.Services service) + +
    +          Connects to a web service by the host and the service name
    +static java.lang.StringgetHost(java.lang.String[] cmd) + +
    +          Extracts host name from the command line
    +static java.lang.StringgetServiceName(java.lang.String[] cmd) + +
    +          Extracts service name from the command line
    +static voidmain(java.lang.String[] args) + +
    +          Starts command line client, if no parameter are supported print help.
    +static booleanvalidURL(java.lang.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(java.lang.String urlstr)
    +
    +
    Attempt to construct the URL object from the string +

    +

    +
    Parameters:
    urlstr - +
    Returns:
    true if it succeed false otherwise
    +
    +
    +
    + +

    +getServiceName

    +
    +public static java.lang.String getServiceName(java.lang.String[] cmd)
    +
    +
    Extracts service name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    service name or null if it is not defined
    +
    +
    +
    + +

    +getHost

    +
    +public static java.lang.String getHost(java.lang.String[] cmd)
    +
    +
    Extracts host name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    host name or null if it is not defined
    +
    +
    +
    + +

    +connect

    +
    +public static <T> MsaWS<T> connect(java.lang.String host,
+                                   Jws2Client.Services service)
+                        throws javax.xml.ws.WebServiceException
    +
    +
    Connects to a web service by the host and the service name +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    host -
    service - +
    Returns:
    MsaWS +
    Throws: +
    javax.xml.ws.WebServiceException
    +
    +
    +
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    Starts command line client, if no parameter are supported print help. Two + parameters are required for successfull 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!
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/client/SimpleWSClient.html b/website/full_javadoc/compbio/ws/client/SimpleWSClient.html new file mode 100644 index 0000000..724fc81 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/SimpleWSClient.html @@ -0,0 +1,263 @@ + + + + + + +SimpleWSClient + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class SimpleWSClient

    +
    +java.lang.Object
+  extended by compbio.ws.client.SimpleWSClient
+
    +
    +
    +
    public class SimpleWSClient
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    SimpleWSClient() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +SimpleWSClient

    +
    +public SimpleWSClient()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
+                 throws java.io.FileNotFoundException,
+                        java.io.IOException,
+                        JobSubmissionException,
+                        java.lang.InterruptedException,
+                        WrongParameterException
    +
    +
    + +
    Throws: +
    java.io.FileNotFoundException +
    java.io.IOException +
    JobSubmissionException +
    java.lang.InterruptedException +
    WrongParameterException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/client/WSTester.html b/website/full_javadoc/compbio/ws/client/WSTester.html new file mode 100644 index 0000000..f138ed2 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/WSTester.html @@ -0,0 +1,275 @@ + + + + + + +WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class WSTester

    +
    +java.lang.Object
+  extended by compbio.ws.client.WSTester
+
    +
    +
    +
    public class WSTester
    extends java.lang.Object
    + + +

    +Class for testing web services +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSTester() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> void
    +    		main(java.lang.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()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static <T> void main(java.lang.String[] args)
    +
    +
    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
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/client/class-use/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html new file mode 100644 index 0000000..7e5b0d6 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html @@ -0,0 +1,213 @@ + + + + + + +Uses of Class compbio.ws.client.Jws2Client.Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.Jws2Client.Services

    +
    + + + + + + + + + +
    +Packages that use Jws2Client.Services
    compbio.ws.client  
    +  +

    + + + + + +
    +Uses of Jws2Client.Services in compbio.ws.client
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.ws.client that return Jws2Client.Services
    +static Jws2Client.ServicesJws2Client.Services.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Jws2Client.Services[]Jws2Client.Services.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.client with parameters of type Jws2Client.Services
    +static + + + + +
    +<T> MsaWS<T>
    +    		Jws2Client.connect(java.lang.String host, + Jws2Client.Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +Classes  + +
    +Jws2Client +
    +WSTester
    + + + + + + +
    +Enums  + +
    +Jws2Client.Services
    + + + + diff --git a/website/full_javadoc/compbio/ws/client/package-summary.html b/website/full_javadoc/compbio/ws/client/package-summary.html new file mode 100644 index 0000000..bd6a63a --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/package-summary.html @@ -0,0 +1,175 @@ + + + + + + +compbio.ws.client + + + + + + + + + + + + +
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    +

    +Package compbio.ws.client +

    + + + + + + + + + + + + + +
    +Class Summary
    Jws2ClientA command line client for Jalview Web Services version 2
    WSTesterClass for testing web services
    +  + +

    + + + + + + + + + +
    +Enum Summary
    Jws2Client.ServicesList of web services currently supported by JWS2
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.ws.client +

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    Package Hierarchies:
    All Packages
    +
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    +Class Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
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    +Uses of Package
    compbio.ws.client

    +
    + + + + + + + + + +
    +Packages that use compbio.ws.client
    compbio.ws.client  
    +  +

    + + + + + + + + +
    +Classes in compbio.ws.client used by compbio.ws.client
    Jws2Client.Services + +
    +          List of web services currently supported by JWS2
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/ClustalWS.html b/website/full_javadoc/compbio/ws/server/ClustalWS.html new file mode 100644 index 0000000..09d7072 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/ClustalWS.html @@ -0,0 +1,599 @@ + + + + + + +ClustalWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class ClustalWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.ClustalWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<ClustalW>
    +
    +
    +
    +
    public class ClustalWS
    extends java.lang.Object
    implements MsaWS<ClustalW>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ClustalWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<ClustalW>getLimit(java.lang.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(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<ClustalW>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.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 java.lang.String align(java.util.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 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 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. JWS2 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
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<ClustalW> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see 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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    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: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<ClustalW> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<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: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<ClustalW> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    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 MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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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/MafftWS.html b/website/full_javadoc/compbio/ws/server/MafftWS.html new file mode 100644 index 0000000..d419846 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/MafftWS.html @@ -0,0 +1,599 @@ + + + + + + +MafftWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 MafftWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.MafftWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<Mafft>
    +
    +
    +
    +
    public class MafftWS
    extends java.lang.Object
    implements MsaWS<Mafft>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    MafftWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Mafft>getLimit(java.lang.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(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Mafft>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.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 java.lang.String align(java.util.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 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 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. JWS2 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
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Mafft> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see 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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Mafft> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<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: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    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 MsaWS<Mafft>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Mafft> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Mafft> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<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 new file mode 100644 index 0000000..0d9ec95 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/MuscleWS.html @@ -0,0 +1,599 @@ + + + + + + +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:
    MsaWS<Muscle>
    +
    +
    +
    +
    public class MuscleWS
    extends java.lang.Object
    implements MsaWS<Muscle>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    MuscleWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Muscle>getLimit(java.lang.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(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Muscle>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.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 java.lang.String align(java.util.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 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 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. JWS2 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
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Muscle> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see 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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Muscle> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<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: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    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 MsaWS<Muscle>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Muscle> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Muscle> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<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 new file mode 100644 index 0000000..a97b8eb --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/ProbconsWS.html @@ -0,0 +1,599 @@ + + + + + + +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:
    MsaWS<Probcons>
    +
    +
    +
    +
    public class ProbconsWS
    extends java.lang.Object
    implements MsaWS<Probcons>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ProbconsWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Probcons>getLimit(java.lang.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(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Probcons>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.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 java.lang.String align(java.util.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 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 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. JWS2 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
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Probcons> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see 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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Probcons> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<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: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    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 MsaWS<Probcons>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Probcons> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Probcons> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<Probcons>
    +
    +
    + +
    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/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html new file mode 100644 index 0000000..e4fd0ac --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html @@ -0,0 +1,263 @@ + + + + + + +SimpleWSPublisher + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 SimpleWSPublisher

    +
    +java.lang.Object
+  extended by compbio.ws.server.SimpleWSPublisher
+
    +
    +
    +
    public class SimpleWSPublisher
    extends java.lang.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(java.lang.Object exec, + java.lang.String context) + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +SimpleWSPublisher

    +
    +public SimpleWSPublisher(java.lang.Object exec,
+                         java.lang.String context)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html new file mode 100644 index 0000000..bc9ed89 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html @@ -0,0 +1,599 @@ + + + + + + +TcoffeeWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 TcoffeeWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.TcoffeeWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<Tcoffee>
    +
    +
    +
    +
    public class TcoffeeWS
    extends java.lang.Object
    implements MsaWS<Tcoffee>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    TcoffeeWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Tcoffee>getLimit(java.lang.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(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Tcoffee>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.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 java.lang.String align(java.util.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 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 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. JWS2 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
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Tcoffee> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see 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: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 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. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Tcoffee> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<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: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    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 MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Tcoffee> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Tcoffee> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<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 new file mode 100644 index 0000000..cb07ea7 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/WSUtil.html @@ -0,0 +1,510 @@ + + + + + + +WSUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    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 WSUtil

    +
    +java.lang.Object
+  extended by compbio.ws.server.WSUtil
+
    +
    +
    +
    public final class WSUtil
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSUtil() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> java.lang.String
    +    		align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +static booleancancelJob(java.lang.String jobId) + +
    +           
    +static + + + + +
    +<T> java.util.List<java.lang.String>
    +    		getCommands(java.util.List<Option<T>> options, + java.lang.String keyValueSeparator) + +
    +           
    +static AsyncExecutorgetEngine(ConfiguredExecutable<?> confClustal) + +
    +           
    +static JobStatusgetJobStatus(java.lang.String jobId) + +
    +           
    +static bytegetProgress(java.lang.String jobId) + +
    +           
    +static java.lang.StringgetRemoteAddress(javax.xml.ws.WebServiceContext wsContext) + +
    +           
    +static voidlog(org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String activity) + +
    +           
    +static voidlog(org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String jobId, + java.lang.String activity) + +
    +           
    +static ChunkHolderpullFile(java.lang.String jobId, + long position) + +
    +           
    +static voidvalidateFastaInput(java.util.List<FastaSequence> sequences) + +
    +           
    +static voidvalidateJobId(java.lang.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
    + +

    +log

    +
    +public static void log(org.apache.log4j.Logger statLog,
+                       javax.xml.ws.WebServiceContext wsContext,
+                       java.lang.String activity)
    +
    +
    +
    +
    +
    +
    + +

    +validateJobId

    +
    +public static final void validateJobId(java.lang.String jobId)
+                                throws java.security.InvalidParameterException
    +
    +
    + +
    Throws: +
    java.security.InvalidParameterException
    +
    +
    +
    + +

    +validateFastaInput

    +
    +public static final void validateFastaInput(java.util.List<FastaSequence> sequences)
+                                     throws java.security.InvalidParameterException
    +
    +
    + +
    Throws: +
    java.security.InvalidParameterException
    +
    +
    +
    + +

    +log

    +
    +public static void log(org.apache.log4j.Logger statLog,
+                       javax.xml.ws.WebServiceContext wsContext,
+                       java.lang.String jobId,
+                       java.lang.String activity)
    +
    +
    +
    +
    +
    +
    + +

    +getJobStatus

    +
    +public static JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +pullFile

    +
    +public static ChunkHolder pullFile(java.lang.String jobId,
+                                   long position)
    +
    +
    +
    +
    +
    +
    + +

    +getProgress

    +
    +public static byte getProgress(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +getEngine

    +
    +public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal)
    +
    +
    +
    +
    +
    +
    + +

    +cancelJob

    +
    +public static boolean cancelJob(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +getRemoteAddress

    +
    +public static java.lang.String getRemoteAddress(javax.xml.ws.WebServiceContext wsContext)
    +
    +
    +
    +
    +
    +
    + +

    +align

    +
    +public static <T> java.lang.String align(java.util.List<FastaSequence> sequences,
+                                         ConfiguredExecutable<T> confExec,
+                                         org.apache.log4j.Logger statLog,
+                                         javax.xml.ws.WebServiceContext wsContext,
+                                         java.lang.String callingMethod,
+                                         Limit<T> limit)
+                              throws LimitExceededException,
+                                     JobSubmissionException
    +
    +
    + +
    Throws: +
    LimitExceededException +
    JobSubmissionException
    +
    +
    +
    + +

    +getCommands

    +
    +public static final <T> java.util.List<java.lang.String> getCommands(java.util.List<Option<T>> options,
+                                                                     java.lang.String keyValueSeparator)
    +
    +
    +
    +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html b/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html new file mode 100644 index 0000000..b33dc12 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.ClustalWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.ws.server.ClustalWS

    +
    +No usage of compbio.ws.server.ClustalWS +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html b/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html new file mode 100644 index 0000000..5b7bfba --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.MafftWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.ws.server.MafftWS

    +
    +No usage of compbio.ws.server.MafftWS +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/MuscleWS.html b/website/full_javadoc/compbio/ws/server/class-use/MuscleWS.html new file mode 100644 index 0000000..9628b96 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/MuscleWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.MuscleWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.ws.server.MuscleWS

    +
    +No usage of compbio.ws.server.MuscleWS +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/class-use/ProbconsWS.html new file mode 100644 index 0000000..67df8c7 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/ProbconsWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.ProbconsWS + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.ws.server.ProbconsWS

    +
    +No usage of compbio.ws.server.ProbconsWS +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/class-use/SimpleWSPublisher.html new file mode 100644 index 0000000..32b96ee --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/SimpleWSPublisher.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.SimpleWSPublisher + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.ws.server.SimpleWSPublisher

    +
    +No usage of compbio.ws.server.SimpleWSPublisher +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/class-use/TcoffeeWS.html new file mode 100644 index 0000000..76756d7 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/TcoffeeWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.TcoffeeWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.ws.server.TcoffeeWS

    +
    +No usage of compbio.ws.server.TcoffeeWS +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/WSUtil.html b/website/full_javadoc/compbio/ws/server/class-use/WSUtil.html new file mode 100644 index 0000000..d4457fd --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/WSUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.WSUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.ws.server.WSUtil

    +
    +No usage of compbio.ws.server.WSUtil +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/package-frame.html b/website/full_javadoc/compbio/ws/server/package-frame.html new file mode 100644 index 0000000..cdb7eee --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/package-frame.html @@ -0,0 +1,44 @@ + + + + + + +compbio.ws.server + + + + + + + + + + + +compbio.ws.server + + + + +
    +Classes  + +
    +ClustalWS +
    +MafftWS +
    +MuscleWS +
    +ProbconsWS +
    +SimpleWSPublisher +
    +TcoffeeWS +
    +WSUtil
    + + + + diff --git a/website/full_javadoc/compbio/ws/server/package-summary.html b/website/full_javadoc/compbio/ws/server/package-summary.html new file mode 100644 index 0000000..4937713 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/package-summary.html @@ -0,0 +1,181 @@ + + + + + + +compbio.ws.server + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +

    +Package compbio.ws.server +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    ClustalWS 
    MafftWS 
    MuscleWS 
    ProbconsWS 
    SimpleWSPublisherThis class publish a web service.
    TcoffeeWS 
    WSUtil 
    +  + +

    +

    +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/package-tree.html b/website/full_javadoc/compbio/ws/server/package-tree.html new file mode 100644 index 0000000..709f0cf --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/package-tree.html @@ -0,0 +1,158 @@ + + + + + + +compbio.ws.server Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.ws.server +

    +
    +
    +
    Package Hierarchies:
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    +
    +

    +Class Hierarchy +

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    + + + diff --git a/website/full_javadoc/compbio/ws/server/package-use.html b/website/full_javadoc/compbio/ws/server/package-use.html new file mode 100644 index 0000000..9249a6d --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/package-use.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Package compbio.ws.server + + + + + + + + + + + + +
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    +Uses of Package
    compbio.ws.server

    +
    +No usage of compbio.ws.server +

    +

    + + + + + + + + + + + + + + + +
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    +Constant Field Values

    +
    +
    +Contents + + + + + + +
    +compbio.data.*
    + +

    + + + + + + + + + + + + +
    compbio.data.sequence.ClustalAlignmentUtil
    +public static final chargapchar45
    + +

    + +

    + + + + + +
    +compbio.engine.*
    + +

    + + + + + + + + + + + + +
    compbio.engine.client.ConfExecutable<T>
    +public static final java.lang.StringCLUSTER_TASK_ID_PREFIX"@"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.client.EnvVariableProcessor
    +public static final java.lang.StringPATH"PATH"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.client.RunConfiguration
    +public static final java.lang.StringrconfigFile"RunnerConfig.xml"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.cluster.drmaa.ClusterSession
    +public static final java.lang.StringJOBID"JOBID"
    + +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    compbio.engine.cluster.dundee._QueueConstraints
    +public static final intFIRST_MEMORY_LIMIT14000
    +public static final intLONG_TIME_LIMIT24
    +public static final intMAX_MEMORY_LIMIT30000
    +public static final intSHORT_TIME_LIMIT8
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.conf._Key
    +public static final java.lang.StringDELIM"#"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.conf.DirectoryManager
    +public static final java.lang.StringDELIM"#"
    + +

    + +

    + + + + + + + + + + + + + + + + + +
    compbio.engine.local.ExecutableWrapper
    +public static final java.lang.StringPROC_ERR_FILE"procError.txt"
    +public static final java.lang.StringPROC_OUT_FILE"procOutput.txt"
    + +

    + +

    + + + + + +
    +compbio.metadata.*
    + +

    + + + + + + + + + + + + +
    compbio.metadata.PresetManager<T>
    +public static final java.lang.StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
    + +

    + +

    + + + + + +
    +compbio.runner.*
    + +

    + + + + + + + + + + + + +
    compbio.runner.Util
    +public static final java.lang.StringSPACE" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.ClustalW
    +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Mafft
    +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Muscle
    +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Probcons
    +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Tcoffee
    +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
    + +

    + +

    +

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    +Deprecated API

    +
    +
    +Contents + + + + + + + + + +
    +Deprecated Methods
    compbio.engine.cluster.drmaa.ClusterSession.getJobStatus(int) +
    +           
    +  +

    +

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    +How This API Document Is Organized

    +
    +This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.

    +Overview

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    +The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.

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      +
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      +

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      +

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    +Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.
    +

    +Tree (Class Hierarchy)

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    +
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    +Deprecated API

    +
    +The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.
    +

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    +
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    +The Constant Field Values page lists the static final fields and their values. +

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    +A

    +
    +
    AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Valid Amino acids +
    addOption(Option<T>) - +Method in class compbio.metadata.RunnerConfig +
      +
    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 +
      +
    addParameter(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    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 +
      +
    addParameters(List<String>) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    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.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, WebServiceContext, 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 +
    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 +
      +
    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 +
      +
    awaitTermination(long, TimeUnit) - +Method in class compbio.engine.local._TrackingExecutor +
      +
    +
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    +
    +
    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 +
      +
    JobExecutionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobExecutionExceptionBean() - +Constructor for class compbio.data.msa.jaxws.JobExecutionExceptionBean +
      +
    JOBID - +Static variable in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    JobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    JobRunner(ConfiguredExecutable<?>) - +Constructor for class compbio.engine.cluster.drmaa.JobRunner +
      +
    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 +
      +
    Jws2Client - Class in compbio.ws.client
    A command line client for Jalview Web Services version 2
    Jws2Client.Services - Enum in compbio.ws.client
    List of web services currently supported by JWS2
    +
    + + + + + + + + + + + + + + + +
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    +
    +
    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 +
      +
    Limit(int, int, String, boolean) - +Constructor for class compbio.metadata.Limit +
      +
    LimitExceededException - Exception in compbio.metadata
    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
     
    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 +
      +
    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(Logger, WebServiceContext, String) - +Static method in class compbio.ws.server.WSUtil +
      +
    log(Logger, WebServiceContext, String, String) - +Static method in class compbio.ws.server.WSUtil +
      +
    LONG_TIME_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +M

    +
    +
    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.engine.cluster.drmaa._DrmaaExample +
      +
    main(String[]) - +Static method in class compbio.engine.cluster.drmaa._JobStatus +
      +
    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.Pairwise +
      +
    main(String[]) - +Static method in class compbio.runner._impl.OB +
      +
    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 +
      +
    MAX_MEMORY_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    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 +
      +
    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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    + + + + + + + + + + + + + + + +
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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 +
      +
    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. +
    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 +
      +
    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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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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 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 +
      +
    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<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 +
      +
    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
    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 +
      +
    PsiBlast - Class in compbio.runner.psiblast
     
    PsiBlast() - +Constructor for class compbio.runner.psiblast.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.MsaWS +
    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.ClustalWS +
      +
    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 - Class in compbio.data.msa.jaxws
     
    PullFile() - +Constructor for class compbio.data.msa.jaxws.PullFile +
      +
    pullFile(String, long) - +Static method in class compbio.ws.server.WSUtil +
      +
    PullFileResponse - Class in compbio.data.msa.jaxws
     
    PullFileResponse() - +Constructor for class compbio.data.msa.jaxws.PullFileResponse +
      +
    put(FilePuller) - +Static method in class compbio.engine.PulledFileCache +
    This method allows duplicates to be added. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +R

    +
    +
    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 +
      +
    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 +
      +
    readFasta(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +
    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 +
    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 +
      +
    removeTask(ConfiguredExecutable<?>) - +Static method in class compbio.engine.SubmissionManager +
      +
    removeTask(String) - +Static method in class compbio.engine.SubmissionManager +
      +
    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 +
      +
    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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +S

    +
    +
    saveRunConfiguration() - +Method in class compbio.engine.client.ConfExecutable +
      +
    saveRunConfiguration() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    setActualNumberofSequences(int) - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    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 +
      +
    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.CustomAlign +
      +
    setFastaSequences(List<FastaSequence>) - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    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.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.GetJobStatus +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.GetProgress +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.GetResult +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    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.JobExecutionExceptionBean +
      +
    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 +
      +
    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<String>) - +Method in class compbio.metadata.Preset +
      +
    setOptions(List<Option<T>>) - +Method in class compbio.metadata.RunnerConfig +
      +
    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.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 +
      +
    setParams(List<String>) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setPosition(long) - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    setPosition(long) - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    setPossibleValues(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setPreset(Preset) - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    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 +
      +
    setQueue(String) - +Method in class compbio.runner._NativeSpecHelper +
      +
    setRequired(boolean) - +Method in class compbio.metadata.Option +
      +
    setRequiredMemory(int) - +Method in class compbio.runner._NativeSpecHelper +
      +
    setReturn(String) - +Method in class compbio.data.msa.jaxws.AlignResponse +
      +
    setReturn(boolean) - +Method in class compbio.data.msa.jaxws.CancelJobResponse +
      +
    setReturn(String) - +Method in class compbio.data.msa.jaxws.CustomAlignResponse +
      +
    setReturn(JobStatus) - +Method in class compbio.data.msa.jaxws.GetJobStatusResponse +
      +
    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(byte) - +Method in class compbio.data.msa.jaxws.GetProgressResponse +
      +
    setReturn(Alignment) - +Method in class compbio.data.msa.jaxws.GetResultResponse +
      +
    setReturn(RunnerConfig) - +Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse +
      +
    setReturn(String) - +Method in class compbio.data.msa.jaxws.PresetAlignResponse +
      +
    setReturn(ChunkHolder) - +Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse +
      +
    setReturn(ChunkHolder) - +Method in class compbio.data.msa.jaxws.PullFileResponse +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.PresetManager +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.RunnerConfig +
      +
    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 +
      +
    SHORT_TIME_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    shutdown() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    shutDown() - +Static method in class compbio.engine.local.LocalExecutorService +
    This stops all executing processes via interruption. +
    shutdownNow() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    SimpleWSPublisher - Class in compbio.ws.server
    This class publish a web service.
    SimpleWSPublisher(Object, String) - +Constructor for class compbio.ws.server.SimpleWSPublisher +
      +
    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 +
      +
    SPACE - +Static variable in class compbio.runner.Util +
      +
    StatisticManager - Class in compbio.engine.cluster.drmaa
     
    StatisticManager(JobInfo) - +Constructor for class compbio.engine.cluster.drmaa.StatisticManager +
      +
    StreamGobbler - Class in compbio.engine.local
     
    SubmissionManager - Class in compbio.engine
    Submit jobs for execution
    submit(Callable<T>) - +Method in class compbio.engine.local._TrackingExecutor +
      +
    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 +
      +
    SyncExecutor - Interface in compbio.engine
    Synchronous executor, is an engine to run the Executable synchronously.
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/index-files/index-19.html b/website/full_javadoc/index-files/index-19.html new file mode 100644 index 0000000..134ddda --- /dev/null +++ b/website/full_javadoc/index-files/index-19.html @@ -0,0 +1,220 @@ + + + + + + +T-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +T

    +
    +
    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 +
      +
    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.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 +
      +
    toString() - +Method in class compbio.engine.conf._Key +
      +
    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.PScore +
      +
    +
    + + + + + + + + + + + + + + + +
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    BlastAll - Class in compbio.runner._impl
     
    BlastAll(String) - +Constructor for class compbio.runner._impl.BlastAll +
      +
    BlastParameters - Class in compbio.runner._impl
    Utility class for common Blast parameters
    BlastParser - Class in compbio.pipeline._jpred
     
    BlastParser() - +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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    +V

    +
    +
    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 arguments +
    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.Program +
    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 +
    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.ws.client.Jws2Client.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.Program +
    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 +
    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.ws.client.Jws2Client.Services +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +W

    +
    +
    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(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(OutputStream, 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 +
    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 +
      +
    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() - +Constructor for class compbio.ws.client.WSTester +
      +
    WSUtil - Class in compbio.ws.server
     
    WSUtil() - +Constructor for class compbio.ws.server.WSUtil +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +
    _DrmaaExample - Class in compbio.engine.cluster.drmaa
     
    _DrmaaExample() - +Constructor for class compbio.engine.cluster.drmaa._DrmaaExample +
      +
    _JobStatus - Class in compbio.engine.cluster.drmaa
     
    _JobStatus() - +Constructor for class compbio.engine.cluster.drmaa._JobStatus +
      +
    _Jpred - Class in compbio.runner._jpred
     
    _Jpred() - +Constructor for class compbio.runner._jpred._Jpred +
      +
    _Key - Class in compbio.engine.conf
     
    _Key(Class<?>) - +Constructor for class compbio.engine.conf._Key +
      +
    _NativeSpecHelper - Class in compbio.runner
     
    _NativeSpecHelper(int) - +Constructor for class compbio.runner._NativeSpecHelper +
      +
    _NativeSpecHelper(int, int) - +Constructor for class compbio.runner._NativeSpecHelper +
      +
    _Queue - Enum in compbio.engine.cluster.dundee
     
    _QueueConstraints - Class in compbio.engine.cluster.dundee
     
    _SkeletalCommandBuilder - Class in compbio.runner
     
    _SkeletalCommandBuilder() - +Constructor for class compbio.runner._SkeletalCommandBuilder +
      +
    _TrackingExecutor - Class in compbio.engine.local
    This executor extends standard Java ExecutorService by adding the method to + obtain all Runnables which were running and did not complete upon executor + termination.
    _TrackingExecutor(ExecutorService) - +Constructor for class compbio.engine.local._TrackingExecutor +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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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.MsaWS +
    Stop running job 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.ClustalWS +
      +
    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 +
      +
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    ChunkHolder(String, long) - +Constructor for class compbio.metadata.ChunkHolder +
      +
    Cleaner - Class in compbio.engine
     
    Cleaner() - +Constructor for class compbio.engine.Cleaner +
      +
    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.engine.cluster.drmaa.ClusterSession +
      +
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - +Constructor for class compbio.data.sequence.ClustalAlignmentUtil +
      +
    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 +
      +
    ClusterNativeSpecExecutable<T> - Interface in compbio.engine.client
     
    ClusterSession - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil() - +Constructor for class compbio.engine.cluster.drmaa.ClusterUtil +
      +
    CommandBuilder<T> - Class in compbio.engine.client
     
    CommandBuilder(String) - +Constructor for class compbio.engine.client.CommandBuilder +
      +
    compareTo(Delayed) - +Method in class compbio.engine.FilePuller +
      +
    compbio.data._structure - package compbio.data._structure
     
    compbio.data.msa - package compbio.data.msa
     
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
     
    compbio.pipeline._jpred - package compbio.pipeline._jpred
     
    compbio.runner._jpred - package compbio.runner._jpred
     
    compbio.runner.psiblast - package compbio.runner.psiblast
     
    compbio.ws.client - package compbio.ws.client
     
    compbio.ws.server - package compbio.ws.server
     
    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(String, Jws2Client.Services) - +Static method in class compbio.ws.client.Jws2Client +
    Connects to a web service by the host and the service name +
    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<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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +D

    +
    +
    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 +
    deleteAllFiles(String) - +Static method in class compbio.engine.Cleaner +
      +
    deleteFiles(ConfiguredExecutable<?>) - +Static method in class compbio.engine.Cleaner +
    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 +
      +
    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._impl
     
    Disembl(String) - +Constructor for class compbio.runner._impl.Disembl +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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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.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 +
      +
    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.PScore +
      +
    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 +
      +
    execute(Runnable) - +Method in class compbio.engine.local._TrackingExecutor +
      +
    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 +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    +F

    +
    +
    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
     
    FIRST_MEMORY_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +G

    +
    +
    gapchar - +Static variable in class compbio.data.sequence.ClustalAlignmentUtil +
    Dash char to be used as gap char in the alignments +
    get(String) - +Static method in class compbio.engine.PulledFileCache +
      +
    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 +
      +
    getAllStats() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getApproprieteQueue() - +Method in class compbio.runner._NativeSpecHelper +
      +
    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 +
      +
    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 +
      +
    getCancelledTasks() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    getChunk() - +Method in class compbio.metadata.ChunkHolder +
      +
    getClass(String) - +Static method in class compbio.engine.conf.DirectoryManager +
      +
    getClusterCpuNum() - +Static method in class compbio.runner.msa.Tcoffee +
      +
    getClusterJobId(String) - +Static method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    getClusterSettings() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    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.Disembl +
      +
    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.Disembl +
      +
    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 +
      +
    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.Disembl +
      +
    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.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 +
      +
    getDisemblRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getEmail() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    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 +
      +
    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 +
      +
    getFastaSequences() - +Method in class compbio.data.msa.jaxws.Align +
      +
    getFastaSequences() - +Method in class compbio.data.msa.jaxws.CustomAlign +
      +
    getFastaSequences() - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    getFile() - +Method in class compbio.engine.FilePuller +
      +
    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 +
      +
    getHost(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts host name from the command line +
    getId() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of id +
    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.Disembl +
      +
    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 +
      +
    getInstance(ConfiguredExecutable<?>) - +Static method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    getIOWait() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.CancelJob +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.GetJobStatus +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.GetProgress +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.GetResult +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    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 +
    getJobPriority() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    GetJobStatus - Class in compbio.data.msa.jaxws
     
    GetJobStatus() - +Constructor for class compbio.data.msa.jaxws.GetJobStatus +
      +
    getJobStatus(String) - +Method in interface compbio.data.msa.MsaWS +
    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.ClustalWS +
      +
    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 +
      +
    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.MsaWS +
    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.runner._impl.NetNglyc +
      +
    getLimit(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getLimit(String) - +Method in class compbio.runner.msa.ClustalW +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Mafft +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Muscle +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Probcons +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Tcoffee +
      +
    getLimit(String) - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getLimit(String) - +Method in class compbio.ws.server.ClustalWS +
      +
    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.MsaWS +
    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.metadata.LimitsManager +
      +
    getLimits() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getLimits() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getLimits() - +Method in class compbio.runner.msa.ClustalW +
      +
    getLimits() - +Method in class compbio.runner.msa.Mafft +
      +
    getLimits() - +Method in class compbio.runner.msa.Muscle +
      +
    getLimits() - +Method in class compbio.runner.msa.Probcons +
      +
    getLimits() - +Method in class compbio.runner.msa.Tcoffee +
      +
    getLimits() - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getLimits(Class<? extends Executable<T>>) - +Static method in class compbio.runner.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.ws.server.ClustalWS +
      +
    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 +
      +
    getLocalPath() - +Static method in class compbio.engine.conf.PropertyHelperManager +
    Method return the absolute path to the project root directory. +
    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 +
    return max memory limit in Mb +
    getMemoryStat() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.JobExecutionExceptionBean +
      +
    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 +
      +
    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 +
      +
    getNativeSpec() - +Method in class compbio.runner._NativeSpecHelper +
      +
    getNativeSpecs() - +Method in interface compbio.engine.client.ClusterNativeSpecExecutable +
      +
    getNativeSpecs() - +Method in class compbio.runner.msa.Tcoffee +
      +
    getNetNglycRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getNextPosition() - +Method in class compbio.metadata.ChunkHolder +
      +
    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.metadata.Preset +
      +
    getOptions() - +Method in class compbio.metadata.RunnerConfig +
      +
    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 +
      +
    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 +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.runner._impl.NetNglyc +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    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 +
      +
    getPosition() - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    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.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.MsaWS +
    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.ClustalWS +
      +
    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 - Class in compbio.data.msa.jaxws
     
    GetProgress() - +Constructor for class compbio.data.msa.jaxws.GetProgress +
      +
    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 +
      +
    GetProgressResponse - Class in compbio.data.msa.jaxws
     
    GetProgressResponse() - +Constructor for class compbio.data.msa.jaxws.GetProgressResponse +
      +
    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 +
      +
    getQueue(String) - +Method in enum compbio.engine.cluster.dundee._Queue +
      +
    getQueue() - +Method in class compbio.runner._NativeSpecHelper +
      +
    getQueueByMemoryRequirements(int) - +Static method in enum compbio.engine.cluster.dundee._Queue +
      +
    getRawUsage() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getRecordedJobStatus(String) - +Static method in class compbio.engine.local.LocalEngineUtil +
      +
    getRemoteAddress(WebServiceContext) - +Static method in class compbio.ws.server.WSUtil +
      +
    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.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 +
      +
    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 +
      +
    getResults(String) - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.AlignResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.CustomAlignResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetJobStatusResponse +
      +
    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.GetProgressResponse +
      +
    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.PresetAlignResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.PullFileResponse +
      +
    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 +
      +
    getRunnerClassName() - +Method in class compbio.engine.client.RunConfiguration +
      +
    getRunnerClassName() - +Method in class compbio.metadata.PresetManager +
      +
    getRunnerClassName() - +Method in class compbio.metadata.RunnerConfig +
      +
    getRunnerLimits(Class<? extends Executable<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.MsaWS +
    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.ClustalWS +
      +
    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 +
      +
    getSchema(String) - +Static method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    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 +
      +
    getServiceName(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts service name from the command line +
    getSession() - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    getSize() - +Method in class compbio.data.sequence.Alignment +
      +
    getStartTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    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 +
      +
    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 +
      +
    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.Disembl +
      +
    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.Disembl +
      +
    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 +
    0 - unlimited +
    getTimeStat() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getTmhmm2Runnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getType() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getType() - +Method in class compbio.metadata.ValueConstrain +
      +
    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 +
      +
    getType() - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    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 +
      +
    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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
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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.AlignmentMetadata +
      +
    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 +
      +
    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.PScore +
      +
    hasMoreData() - +Method in class compbio.engine.FilePuller +
      +
    hasParam(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    hasSignaled() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    hasTimeLimit() - +Method in enum compbio.engine.cluster.dundee._Queue +
      +
    +
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    +
    +
    initPull() - +Method in class compbio.engine.FilePuller +
      +
    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 +
    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 limits the values defined by this Limit +
    isFileCreated() - +Method in class compbio.engine.FilePuller +
      +
    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 +
      +
    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 +
      +
    isShutdown() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    isTerminated() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    isValidClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
      +
    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 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +compbio.engine.cluster.drmaa +
    +compbio.engine.cluster.dundee +
    +compbio.engine.conf +
    +compbio.engine.local +
    +compbio.metadata +
    +compbio.pipeline._jpred +
    +compbio.runner +
    +compbio.runner._impl +
    +compbio.runner._jpred +
    +compbio.runner.msa +
    +compbio.runner.psiblast +
    +compbio.ws.client +
    +compbio.ws.server +
    +

    + +

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    +Packages
    compbio.data._structure 
    compbio.data.msa 
    compbio.data.msa.jaxws 
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    compbio.engine 
    compbio.engine.clientClasses and interfaces representing an input for engines.
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters.
    compbio.engine.cluster.dundee 
    compbio.engine.confClasses commonly used by both engines.
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes).
    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.msaWrappers for native executables for multiple sequence alignment (msa)
    compbio.runner.psiblast 
    compbio.ws.client 
    compbio.ws.server 
    + +

    + 

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    +Hierarchy For All Packages

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    +
    Package Hierarchies:
    compbio.data._structure, compbio.data.msa, compbio.data.msa.jaxws, compbio.data.sequence, compbio.engine, compbio.engine.client, compbio.engine.cluster.drmaa, compbio.engine.cluster.dundee, compbio.engine.conf, compbio.engine.local, compbio.metadata, compbio.pipeline._jpred, compbio.runner, compbio.runner._impl, compbio.runner._jpred, compbio.runner.msa, compbio.runner.psiblast, compbio.ws.client, compbio.ws.server
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    +Serialized Form

    +
    +
    + + + + + +
    +Package compbio.data.sequence
    + +

    + + + + + +
    +Class compbio.data.sequence.UnknownFileFormatException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: 196629543695636854L + +

    + + + + + +
    +Serialized Fields
    + +

    +file

    +
    +java.io.File file
    +
    +
    +
    +
    +
    + + + + + +
    +Package compbio.metadata
    + +

    + + + + + +
    +Class compbio.metadata.JobExecutionException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -5477751361755778769L + +

    + +

    + + + + + +
    +Class compbio.metadata.JobSubmissionException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: 607986894357895572L + +

    + +

    + + + + + +
    +Class compbio.metadata.LimitExceededException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: 15066952180013505L + +

    + + + + + +
    +Serialized Fields
    + +

    +numberOfSequencesAllowed

    +
    +int numberOfSequencesAllowed
    +
    +
    +
    +
    +
    +

    +actualNumberofSequences

    +
    +int actualNumberofSequences
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtAllowed

    +
    +int aSequenceLenghtAllowed
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtActual

    +
    +int aSequenceLenghtActual
    +
    +
    +
    +
    + +

    + + + + + +
    +Class compbio.metadata.ResultNotAvailableException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -5475613614578761L + +

    + +

    + + + + + +
    +Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: -86624836785110293L + +

    + +

    + + + + + +
    +Class compbio.metadata.WrongParameterException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -547775417557345769L + +

    + +

    +

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    + +
    + + +
    + + + +

    JABAWS How To

    +

    Table of Content

    +

    About

    + +

    Installation

    + +

    Configuration

    + +

    Using JABAWS in your program (examples in java)

    + +

    JABAWS on Apache-Tomcat

    + + +

    JABAWS on VM (Virtual Machine)

    + + +

    About

    +

    What is JABAWS?

    +

    JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for multiple sequence alignment. For simplicity we referrer to them as JABAWS. It is a successor of Jalview Web Services. JABAWS makes it easy to access well-known multiple sequence alignment programs from JalView. However, the scope of JABAWS is not limited to multiple sequence alignment programs. Future versions of JABAWS will incorporate protein disorder prediction, BLAST, PSIBLAST and HMMER database searches and many other tools. For the list of currently supported programs see below

    +

    Why JABAWS?

    +

    JABA Web Services has a number of distinct features that are not + found in other bioinformatics web services systems. In particular, + JABAWS:

    +
      +
    1. Provides uniform remote access to a number of popular command line + tools.
      + JABAWS enable you to access your favorite research tools anywhere, at any time. For instance, all multiple sequence + alignment services can be accessed with a single command line + interface, simplifying their invocation. At the same time most of the + command line options for each program are supported, so you have + nearly the same level of control as if you were running them on the + command line yourself.
      2. +
    2. Enables web based or stand-alone applications, like Jalview, to + access a variety of bioinformatics analysis methods.
      + The JABAWS client library makes it very easy to + connect to one or more instances of JABAWS, so if one server is off + line, all you need to know is the URL of another server that will + do the job for you. + Moreover you are not limited to JABAWS own client as JABAWS are WS-I basic + profile v. 1.1 compatible, which means that clients + can be created for them in almost any programming + language.
      3. +
    3. Can be easily deployed as a server on a variety of platforms, + with command line tools run on the same machine or on a + cluster.This allow you keeping your private data safe.
      + You don't need to send your data to the + Internet anymore. Simply download and install JABAWS on a trusted machine in your + lab or institute, and use its web address instead of the public + JABAWS services. No data will leave your lab any longer! The JABAWS server can run programs on a single machine or on a + cluster, and are easy to install. + If your server is going to be heavily used, then it is better to configure JABAWS to access your + cluster, which is straightforward. + JABAWS + integrates with a number of cluster job management systems (e.g. + GridEngine, PBS, LSF, Condor). It also intelligently manages + task scheduling depending on their size, eliminating the scalability + issues and let you focus on your research.
      4. +
    4. Support custom parameters, unlike other web services
      + JABAWS includes a comprehensive parameter model and validation + mechanism, allowing you to specify additional options and + arguments. Want to use PAM200 substitution matrix, set the number + of iterations, or sequence clustering method? No problem - JABAWS + lets you do that. You are no longer limited to defaults!
      5. +
    +

    Installation

    +

    How to deploy JABAWS?

    +

    Download JABAWS Web Application Archive (war file). Deploy it on any Servlet 2.4 compatible container. We have tested deployment on Apache-Tomcat version 6. On windows servers just drop a JABAWS war file into the web application directory. On Linux unpack the war file into web application directory , cd to <webapplicationpath>/binaries/src directory and run setexecflag.sh script to set an executable flag for binaries. Start Tomcat. That is it. This should give you working JABAWS stack with tasks executed locally on the server. If you have cluster you may want to enable JABAWS to submit jobs to the cluster. To find out more about this and to find out about other configuration options read the manual.

    +

    I deployed JABAWS, how to make sure it is working?

    +

    First of all make sure that tomcat server is started successfully. If this was the case, then you should see JABAWS home page when you navigate to your tomcat JABAWS context path e.g. http://myhost.compbio.ac.uk:8080/jabawsIf you see it, then it is time to make sure that web services are working too. Assuming that you have unpacked/deployed JABAWS from the server war file, you should be able to navigate to the test program which can be found in <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type: java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path>

    +

    For example to test all JABAWS web services on host myhost.compbio.ac.uk type:

    +

    java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws

    +

    You can choose a particular web server using -s option like this java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=ClustalWS This command line assumes that java executable is in your path and jabaws-client.jar is located in the current directory.

    +

    An example of the report testing tool produces for operating web service looks like this:

    +

    Connecting to service MuscleWS on http://myhost.compbio.ac.uk:8080/jabaws ... OK
    + Testing alignment with default parameters:
    + Queering job status...OK
    + Retrieving results...OK
    + Testing alignment with presets:
    + Aligning with preset 'Protein alignment(Fastest speed)'... OK
    + Aligning with preset 'Nucleotide alignment(Fastest speed)'... OK
    + Aligning with preset 'Huge alignments (speed-oriented)'... OK
    + Queering presets...OK
    + Queering Parameters...OK
    + Queering Limits...OK
    + Queering Local Engine Limits...OK
    + Check is completed service MuscleWS IS WORKING    An example of the response of a web service which is deployed but is not operating is below:

    +

    Connecting to service ProbconsWS on http://localhost:8080/ws ... OK
    + Testing alignment with default parameters:FAILED
    + Service ProbconsWS IS NOT FUNCTIONAL    If the web server did not respond the message looks like following: Connecting to service TcoffeeWS on http://localhost:8080/ws ... FAILED

    +

    Which Alignment programs are supported?

    +

    JABAWS provide access to the following programs

    +     +

    I do not use windows and I am having troubles compiling binaries. Where can I get the pre compiled binaries for my system?

    + +

    We would however recommend to compile the binaries for your system whenever possible. This is likely to give you a significant performance gain.

    +

    Configuration

    +

    Can I use a different version of the alignment program with JABAWS?

    +

    JABAWS supplied with binaries and source code of the executables which version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions JABAWS executable supported. This could be the case with more recent executable. If the options supported by your chosen executable is different when the standard JABAWS executable, than you need to edit ExecutableNameParamaters.xml  configuration file.

    +

    Is there a documentation for client library methods?

    +

    Yes there is. Javadoc is available for all methods of the library and data structures.

    +

    I want to use JABAWS. Which JABAWS distribution should I choose?

    +

    There are two main packages you could use

    +
      +
    1. A client package - for anyone who wants to use JABAWS from your own code, without Jalview.
      2. +
    2. Web Services package (there are a few platform specific variants of this one) - for anyone who wants to run they own copy of JABA Web Services.
      3. +
    3. Virtual Appliance - for anyone who wants to run JABAWS locally, but work on Windows or have configuration problems.
      4. +
    +

    A client only package (1) contains the code sufficient to connect to a third party version of JABAWS and use it. This is the package for anyone who wants to connect to and to use JABAWS from their own software. The package also includes a command line client tool. Read more about how to use command line client below. +JABAWS are fully WS-I compliant, so one could use any language to access them. However, a client package offer additional convenience methods, which is not available otherwise. For example methods to read Clustal formatted sequence alignment files and convert them to the List of FastaSequence objects, which JABAWS will be happy to consume. The trade off is that the client package is written in java, which may not be the language of your choice.

    +

    Web Services package (2) contains JABAWS web services. There are versions for Unix/Linux and Windows operation systems. JABAWS will work on any operation system which has web application server like Tomcat, and GNU compatible C/C++ compiler. This includes Mac. If you are interested in running JABAWS on Mac you would need to recompile binaries JABAWS depends on, in particular these executables. You can configure JalView to use your version of JABAWS, or a any combinations of publicly available instance of JABAWS with your local.

    +

    Finally, you can download core JABAWS package, which contains the code for executing programs locally or on the variety of clusters. This is likely to be of interest for developers only.

    +

    Virtual Appliance package (3) contains TurnKey Linux with JABAWS installed. You can use this package as long as you can run a virtual appliance on your computer. You can find out more about JABAWS virtual appliance in the relevant manual and how to sections.

    +

    Can I program against JABAWS?

    +

    Yes. The simplest way to do it is to download a client package, and use it to access JABAWS. This package contains value object which you could alternatively generate with wsimport in java, or similar tool in other languages. It offers some additional manually developed methods which further simplify working with JABAWS. For more information please refer to the data model javadoc. However should you wish to generate the code using wsimport tool you will be able to do so. As JABAWS are WS-I basic profile compliant, they can be accessed in a standard way as any other web service.

    +

    Is there a command line client to JABAWS?

    +

    Yes, it comes as a part of client package which you are welcome to download.

    +

    The command client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

    +Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS] +-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
    +-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS] +

    +
    +ACTIONS:
    +-i=<inputFile> - 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=<presetName> - name of the preset to use
    +-o=<outputFile> - full path to the file where to write an alignment
    +-f=<parameterInputFile> - 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!     +

    Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console.

    +

    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta

    +

    Content of input.fasta file is show below (please note sequences has been trimmed for clarity)>Foobar
    + MTADGPRELLQLRAAVRHRPQDFVAWL
    + >Bar
    + MGDTTAGEMAVQRGLALHQ
    + QRHAEAAVLLQQASDAAPE
    + >Foofriend
    + MTADGPRELLQLRAAV

    +

    Align as in above example, but write output alignment in a file out.clustal, using parameters defined in prm.in file

    +

    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in

    +

    The content of the prm.in file is shown below --nofft
    + --noscore
    + --fastaparttree
    + --retree=10
    + --op=2.2

    +

    The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but the setting controlling output are not. This is due to the fact the output have to be handled by JABAWS, so must remain within its control. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equal sign. This format is constant no matter which JABAWS web service is used.
    + java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters

    +

    Can I use a JABAWS command line client to connect and use JABAWS web services in Dundee and my local lab?

    +

    Yes, just point it to the host you want to use by changing the value of -h key. For example you used -h=http://myhost.compbio.ac.uk:8080/jabaws server, now you want to use another server to -h=http://mylabserver.myuni.edu. This comes handy if you want to align many sequence or do not want to sent some of your data to the internet.

    +

    Sometimes users sent very large number of sequences to JABAWS server, so that it becomes unresponsive. Can I limit the number of sequences users can submit to my server.

    +

    Yes, JABAWS can be configured to reject the requests based the number of sequences as well as the number of sequence and they average length per single align request. Look at the Restricting JABAWS section for further details.

    +

    My cluster is quite busy so the waiting times in the task queue is significant. At the same time I have powerful server with many cores. Can I use the server for small tasks and send really big ones to the cluster?

    +

    Yes, you can. For this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. In JABAWS the size of the task can be defined as a number of sequences and an average sequence length. Edit "# LocalEngineExecutionLimit #" preset in <ServiceName>Limits.xml file accordingly.

    +

    Can I run my own JABAWS if I do not have a cluster?

    +

    Yes, JABAWS can be run on a single server. Obviously the capacity will be limited, but may be sufficient for a small lab. Installed on a single server, JABAWS executes tasks in parallel, so the more cores the server has the more requests it will be able to handle.

    +

    My cluster uses LSF/PBS/SGE etc can I run JABAWS on my cluster?

    +

    JABAWS uses DRMAA v. 1.0 library to send and manage jobs on the cluster. DRMAA supports many different cluster job management systems. Namely Sun Grid Engine, Condor, PBS, GridWay, Globus 2/4, PBSPro, LSF. For up to date information please consult DRMAA web site. We found that DRMAA implementation differ from platform to platform and were trying to use only the basic functions. We have only tested JABAWS on Sun Grid Engine v 6.2. Please let use know if you have any experience of running JABAWS on other platforms.

    +

    My cluster does not have shared disk space can I run JABAWS?

    +

    No, not on the cluster. At the moment to operate on the cluster JABAWS require a disk space each cluster nodes have access to. However, you could still run JABAWS on a single server.

    +

    I installed JABAWS in my lab. I would like to define different limits for public and lab users

    +

    Currently only one set of limits is supported per a web service. If you need to provide different quality of service for different group of users it is best to make a second JABAWS installation on a different server (could be on the same server but in the different context) and define different limits on a second server. So the lab users could use one server, and public another.

    +

    I tried aligning 5000 sequences using Jalview on my laptop. It crashed. Why JalView allowed me to do that?

    +

    Jalview uses the same code for local task execution as JABAWS. Currently JABAWS machinery supports limits on web services level only. If you execute the task locally or make direct submission to the cluster no limits are applied.

    +

    Can I run many JABAWS instances on the same server?

    +

    Yes. JABAWS is supplied as one Web Application Archive which can be dealt with as any other web applications. Make two different contexts on your application server and unpack JABAWS in both of them. For example if your server name is http://www.align.ac.uk, and the context names are public and private. Than one group of users could be given a URL http://www.align.ac.uk/public and another http://www.align.ac.uk/private. These contexts will be served by two independent JABAWS instances, and could be configured differently. If you keep local engine enabled, make sure you reduce the number of threads local engine is allowed to use to avoid overloading the server. Alternatively two completely separate web application server instances (e.g. Apache-Tomcat) could be used. This will give you a better resilience and more flexibility in memory settings.

    +

    I deployed JABAWS on windows why not all alignment programs work?

    +

    JABAWS are platform independent, and thus can be deployed on any operation system which supports java. However, the executables which do the calculations are platform specific. JABAWS uses different versions of executables for different platforms under the hood. However, if executable is not available for a particular platform, then this service will not function.

    +

    If I install JABAWS on windows which web services will work?

    +

    From all supported only Clustal and Muscle will work. This is due to the fact that only these two executables supports windows natively.

    +

    There are versions of Mafft and Tcoffee for windows, so why you do not support them?

    +

    Indeed Mafft and Tcoffee can be executed on windows platform but only in the Linux environment provided by Cygwin. They setup is very complicated and performance will suffer in such an environment. We do not support such a configuration and unlikely to support it in the future. JABAWS are best installed on Unix like environment after this is done they can be accessed from any operation system.

    +

    What operation system JABAWS can run on?

    +

    JABAWS can be run on any operation system that support java. However, its best to be run on unix like operation system as all the programs JABAWS uses are available for unix platform, and only a few are available on windows. Currently only Clustal and Muscle are available for windows platform.

    +

    What happens if the number of requests to my JABAWS installation is greater the the server can process?

    +

    That depends on your configuration. If only cluster submission is enabled, than tasks will be sent to the cluster and you will experience a longer wait as a result of a task queuing. It is common, that the number of tasks that web server can send to the cluster is unlimited, but the number of tasks that can be run in parallel is controlled, hence the queue. +
    +If only local execution is enabled, the number of tasks that can be executed in parallel are limited to the number of threads, which is equal to the number of cores available on the server by default, but can be defined declaratively too. The tasks that cannot be executed immediately will be waiting in the queue. You can expect a greater execution time. If both local and cluster submission is enabled, then when the task cannot be immediately executed locally it gets sent to the cluster.

    + + +

    I would like to keep and eye on who is using JABAWS services on my server.

    +

    Enable Tomcat log valve. To do this uncomment the following section of <tomcat_root>/conf/server.xml configuration file.

    +

    <Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
    +prefix="localhost_access_log." suffix=".txt" pattern="common" resolveHosts="false"/>

    +

    The following information will be logged:

    + + + + + + + + + + + + + + + +
    Remote IPDateMethod server_URL protocol HTTP status Response size in bytes
    10.31.11.159[10/Feb/2010:16:51:32 +0000]"POST /jws2/MafftWS HTTP/1.1"2002067
    +

    Which can be processed in various programs for log analysis , such as WebAlizer, Analog, AWStats.

    +

    I would like to know how much of the CPU time has been consumed and which tasks were the longest.

    +

    JABAWS stores cluster task ids for all tasks which were run on the cluster. Using cluster ids the detailed statistics can be extracted from cluster accounting system. Due to the fact that each cluster supported by JABAWS have different accounting system it was not possible to provide ready to use statistics.
    +For the local execution the starting and finishing time in nano seconds can be found in STARTED and FINISHED files respectively. In time we will provide the tools to extract execution time statistics, so keep the content of your working directory ready!

    +

    I noticed that jobsout, conf and binaries directories are not placed in WEB-INF directory are they not accessible to anyone?

    +

    Access to these directories is prohibited to any unauthorized users by means of security constrain defined in web application descriptor file. There is a special user role called admin who can access these directories. This comes handy if you would like to keep an eye on any of the task outputs stored in jobsout, or would like to view the configuration files. To access these directories add admin user into your application server. The way you do it will depends on where you would like the user passwords to come from and you web application server. If you use Tomcat, than the simplest way is to use Tomcat Memory Realm which is linked to a plain text configuration file. To define the user in Tomcat server add an entry in conf/tomcat-user.xml file. <role rolename="admin"/>
    +<user username="admin" password="your password here " roles="admin"/>

    +

    Once this is done make sure the servlet that returns the web application directory listings is enabled. Look in the <tomcatroot>/conf/web.xml file for the following <param-name>listings</param-name>
    +<param-value>true</param-value>

    +

    The whole section that defined default listing servlet is below

    +

    <servlet>
    +<servlet-name>default</servlet-name>
    +<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
    + <init-param>
    + <param-name>debug</param-name>
    + <param-value>0</param-value>
    +</init-param>
    +<init-param>
    +<param-name>listings</param-name>
    +<param-value>true</param-value>
    +</init-param>
    +<load-on-startup>1</load-on-startup>
    +</servlet>
    +

    +These listings are read only by default. +

    Sometimes something goes wrong with JABAWS, but I cannot figure out why. Can you help?

    +

    JABAWS logs all errors to the stdout and in the file called activity.log if logging is enabled. Stdout is usually recorded in web server log files. Have a look there and you may find the reason for the problems. If it is still unclear what went wrong try increasing the logging level. Setting the logging level to TRACE or DEBUG will give you a lot of insights in what goes on behind the scene. We would need this log if you need us to help you, or if you would like to report the bug. To change the log level, replace ERROR keyword in ACTIVITY logger to TRACE.

    +

    Using JABAWS in your program

    +

    Connecting to JABAWS

    +

    For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.

    +

    Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

    +

    import java.net.URL;
    + import javax.xml.namespace.QName;
    + import javax.xml.ws.Service;
    + ...............
    + 1) String qualifiedName = "http://msa.data.compbio/01/01/2010/";
    + 2) URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");
    + 3) QName qname = new QName(, "ClustalWS");
    +4) Service serv = Service.create(url, qname);
    +5) MsaWS msaws = serv.getPort(new QName(qualifiedName, "ClustalWSPort"), +MsaWS.class);

    +

    Line 1 makes a qualified name for JABA web services.
    + Line 2 + constructs the URL to the web services WSDL.
    +Line 3 makes a qualified name instance for Clustal JABA web service.
    +Line 4 creates a service instance.
    +Line 5 makes a connection to the server.

    +

    A more generic connection method would look like this

    +

    import java.net.URL;
    +import javax.xml.namespace.QName;
    +import javax.xml.ws.Service;
    +import compbio.ws.client.Services
    +.............. +
    +String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";
    +String host = "http://www.compbio.dundee.ac.uk/jabaws";
    +// In real life the service name can come from args
    +Services clustal = Services.ClustalWS;
    +URL url = new URL(host + "/" + clustal.toString() + "?wsdl");
    +QName qname = new QName(qualifiedServiceName, clustal.toString());
    +Service serv = Service.create(url, qname);
    +MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal
    ++ "Port"), MsaWS.class);

    +

    Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS interface. The full documentation of MsaWS functions is available from the javadoc.

    +

    Valid JABAWS service names and WSDL files

    +
      +
    • ClustalWS (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl)
      • +
    • MuscleWS (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl)
      • +
    • MafftWS (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl)
      • +
    • TcoffeeWS (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl)
      • +
    • ProbconsWS (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl)
      • +
    +

    Aligning sequences

    +

    Given that msaws is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows:

    +

    1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
    + 2) String jobId = msaws.align(fastalist); +
    + 3) Alignment alignment = msaws.getResult(jobId);

    +

    Line one loads FASTA sequence from the file
    + Line two submits them to web service represented by msaws proxy
    + Line three retrieves the alignment from a web service. This line will block the execution until the result is available. Use this with caution. In general, you should make sure that the calculation has been completed before attempting retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. While this may be ok with your local server, our public server (www.compbio.dundee.ac.uk/jabaws) will not let you hold the connection for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check the status of the calculation.
    +Methods and classes mentioned in the excerpt are available from the JABAWS client library.

    +

    Checking the status of the calculation

    +

    You may have noticed that there was no pause between submitting the job and retrieving of the results. This is because getResult(jobId) method block the processing until the calculation is completed. However, taking into account that the connection holds server resources, our public server (www.compbio.dundee.ac.uk/jabaws) is configured to reset the connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the calculation has been completed before accessing the results. You can do it like this:

    +

    while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
    +     Thread.sleep(2000); // wait two seconds, then recheck the status +
    + }

    +

    Aligning with presets

    +

    1) PresetManager presetman = msaws.getPresets();
    + 2) Preset preset = presetman.getPresetByName(presetName);
    + 3) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
    + 4) String jobId = msaws.presetAlign(fastalist, preset);
    + 5) Alignment alignment = msaws.getResult(jobId);

    +

    Line one obtains the lists of presets supported by a web service.
    + Line two return a particular Preset + by its name
    + Lines three to five are doing the same job as in the first aligning sequences example.

    +

    Aligning with custom parameters

    +

    1) RunnerConfig options = msaws.getRunnerOptions();
    + 2) Argument matrix = options.getArgument("MATRIX");
    + 3) matrix.setValue("PAM300");
    + 4) Argument gapopenpenalty = options.getArgument("GAPOPEN");
    + 5) gapopenpenalty.setValue("20");
    + 6) List<Argument> arguments = new ArrayList<Argument>(); +
    + 7) arguments.add(matrix); + arguments.add(gapopenpenalty);
    + 8) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
    + 9) String jobId = msaws.customAlign(fastalist, arguments);
    + 10) Alignment alignment = msaws.getResult(jobId);

    +

    Line one obtains the RunnerConfig object that holds information on supported parameters and their values
    + Line two retrieve a particular parameter from the holder by its name
    + Lines three sets a value to this parameter which will be used in the calculation.
    + Line four and five do the same but for another parameter
    + Line 6 makes a List to hold the parameters
    + Line seven puts the parameters into that list
    + Line eight + and ten is the same as in previous examples
    + Line nine submit an alignment request with the sequences and the parameters
    + The names of all the parameters supported by a web service e.g. "PAM300" can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the javadoc.

    +

    Writing alignments to a file

    +

    There is a utility method in the client library that does exactly that.

    +

    Alignment alignment = align(...)
    + FileOutputStream outStream = new FileOutputStream(file);
    + ClustalAlignmentUtil.writeClustalAlignment(outStream, align);

    +

    A complete client example

    +

    Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a nicely colorized PDF version of this example. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

    +
    +import java.io.ByteArrayInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URL;
+import java.util.List;
+
+import javax.xml.namespace.QName;
+import javax.xml.ws.Service;
+
+import compbio.data.msa.MsaWS;
+import compbio.data.sequence.Alignment;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.SequenceUtil;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.UnsupportedRuntimeException;
+import compbio.metadata.WrongParameterException;
+
+public class Example {
+
+	/*
+	 * Input sequences for alignment
+	 */
+	static final String input = ">Foo\r\n"
+			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR"
+			+ "VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ"
+			+ "LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL"
+			+ "APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA"
+			+ "STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD"
+			+ "YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN"
+			+ "PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD"
+			+ "LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS"
+			+ "DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n"
+			+ "\r\n"
+			+ ">Bar\r\n"
+			+ "MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH"
+			+ "QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA"
+			+ "HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG"
+			+ "IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL"
+			+ "RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL"
+			+ "SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC"
+			+ "PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV"
+			+ "FEMDGFADDFGALLQALARRHGWLGI\r\n"
+			+ "\r\n"
+			+ ">Friends\r\n"
+			+ "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV"
+			+ "RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG"
+			+ "VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL"
+			+ "TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD"
+			+ "LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF"
+			+ "QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA"
+			+ "DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP"
+			+ "GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI";
+
+	public static void main(String[] args) throws UnsupportedRuntimeException,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException, FileNotFoundException, IOException,
+			ResultNotAvailableException, InterruptedException {
+
+		String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";
+
+		/* Make a URL pointing to web service WSDL */
+		URL url = new URL(
+				"http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");
+
+		/*
+		 * If you are making a client that connects to different web services
+		 * you can use something like this:
+		 */
+		// URL url = new URL(host + "/" + Services.ClustalWS.toString() +
+		// "?wsdl");
+
+		QName qname = new QName(qualifiedServiceName, "ClustalWS");
+		Service serv = Service.create(url, qname);
+		/*
+		 * Multiple sequence alignment interface for Clustal web service
+		 * instance
+		 */
+		MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, "ClustalWS"
+				+ "Port"), MsaWS.class);
+
+		/* Get the list of available presets */
+		PresetManager presetman = msaws.getPresets();
+
+		/* Get the Preset object by preset name */
+		Preset preset = presetman
+				.getPresetByName("Disable gap weighting (Speed-oriented)");
+
+		/*
+		 * Load sequences in FASTA format from the file You can use something
+		 * like new FileInputStream() to load sequence from the file
+		 */
+		List fastalist = SequenceUtil
+				.readFasta(new ByteArrayInputStream(input.getBytes()));
+
+		/*
+		 * Submit loaded sequences for an alignment using preset. The job
+		 * identifier is returned by this method, you can retrieve the results
+		 * with it sometime later.
+		 */
+		String jobId = msaws.presetAlign(fastalist, preset);
+
+		/* This method will block for the duration of the calculation */
+		Alignment alignment = msaws.getResult(jobId);
+
+		/*
+		 * This is a better way of obtaining results, it does not involve
+		 * holding the connection open for the duration of the calculation,
+		 * Besides, as the University of Dundee public server will reset the
+		 * connection after 10 minutes of idling, this is the only way to obtain
+		 * the results of long running task from our public server.
+		 */
+		// while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
+		// Thread.sleep(1000); // wait a second, then recheck the status
+		// }
+
+		/* Output the alignment to standard out */
+		System.out.println(alignment);
+
+		// Alternatively, you can record retrieved alignment into the file in
+		// ClustalW format
+
+		// ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(
+		// "output.al"), alignment);
+
+	}
+}
+
    +For a more detailed description of all available types and their functions please refer to the data model javadoc. +

    Building web services artifacts

    +

    JABAWS are the standard JAX-WS SOAP web services, which are WS-I basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as it provides a handful of useful methods in addition to plain data types.

    +

    wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl

    +

    JABAWS on Apache-Tomcat

    +

    I dropped jaba.war file into web application directory but nothing happened. What do I do next?

    +
      +
    • Make sure tomcat have sufficient access rights to read your war file.
      • +
    • Restart the tomcat, sometimes it will not since that the new war file is added without restart
      • +
    • If tomcat still refuses to unpack the war file, unpack it manually into web application folder. Set executable flag for native executables (alignment programs) as described here. Restart tomcat.
      • +
    +

    I removed the JABAWS war file after it was deployed from the webapps directory and my JABAWS web application folder disappear. Where it has gone to?

    +

    If you used tomcat automated deployment for JABAWS, which is when you just drop a war file in to webapps directory than, if the war file is removed, tomcat will automatically undeploy your application. So do not remove the war file if you intend to keep JABAWS running.

    +

    I want to make sure that tomcat will not undeploy/delete JABAWS directory from the server. What should I do?

    +

    Use an explicit application descriptor. It could come in different flavors, the one I prefer if to drop a context descriptor file into <tomcatRoot>conf/Catalina/localhost directory. Name your context file the same as your application folder e.g. if you JABAWS resides in webappl/jaba folder, then call the context file jaba.xml. Below is an example of content this file might have.

    +

    <?xml version="1.0" encoding="UTF-8"?>
    + <Context antiResourceLocking="false" privileged="true" />

    +

    This should be sufficient to prevent tomcat from removing your JABAWS deployment folder. For more information about tomcat deployer read this documentation on the tomcat web site.

    + +

    JABAWS on VM (Virtual Machine)

    +

    I cannot open VM using VirtualBox due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception. Can you help?

    +

    VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such problem, please make sure you have configured JABAWS VM with 1 CPU and disabled VT-X extensions. Alternatively you can enable virtualization extensions ion from the BIOS of your computer. Unfortunately, we cannot give you exact instructions on how to do this, as this would depend on your computer BIOS manufacturer. For MACs it may not be possible at all.

    +

    VMWare Player - Failed to query source for information. I cannot open OVF file using VMware player. Why is this?

    +

    At a time of writing, the latest version of VMware Player 3.1.2 support only a legacy OVF version 0.9. Whereas OVF packaged with JABAWS VM is version 1.0. Please use VMX - VMware specific configuration file with all VMware products.

    +

    I want to connect to the Internet from my VM. Can I do that?

    + +

    By default JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use Bridged network. In such case you would have to configure the VM IP address manually (unless of cause your network have a DHCP server to do that).

    +
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+ + + + + diff --git a/website/manual.html b/website/manual.html new file mode 100644 index 0000000..5941807 --- /dev/null +++ b/website/manual.html @@ -0,0 +1,663 @@ + + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) +manual + + + + + +
    + + +
    + + + +
    +

    JABAWS Manual

    + +

    Table of content

    +

    +

    JABAWS Virtual Appliance

    + + +

    JABAWS Installation

    + +

    Configuring JABAWS

    + +

    For Developers

    + +

    JABA Web Services Internals

    + +

    JABAWS Virtual Appliance

    +

    When to use virtual appliance

    +

    The appliance best suits for individual users who want to use JABA web services locally, without Internet connection, want to keep their data private and uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users but they can always deploy a war distribution instead.
    +To run the appliance you would need to have relatively powerful computer. The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M.

    +

    VirtualBox appliance configuration

    +

    VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operation systems. Use VitualBox "Import Appliance" option to import JABAWS. Please bear in mind that to benefit from multiple CPU support under VirtualBox software you need to enable hardware virtualization extensions, such as Intel Virtualization VT-x or AMD-V support in the BIOS of your computer. Unfortunately, we were unable to find a reliable way to do it on Mac, so some Macs running VirtualBox will be limited to one CPU only, irrespective of the number of CPUs of the host machine.

    +

    We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the VERR_VMX_MSR_LOCKED_OR_DISABLED exception if you computer does not support the extensions or their support is disabled. Just deselect the checkboxes shown on the screen shot below to solve the problem.

    +

    VirtualBox JABAWS VM configuration screen shot displaying virtualization settings.

    +

    VT-x extension on VirtualBox

    +

    VMware Player appliance configuration

    +

    Free VMware Player can be used to run JABAWS services from Windows and Linux host operation system, there is no support for Mac in time of writing. However, VMware Fusion, a commercial VMware product, offer virtual machine support for Mac computers too.

    +

    To run JABAWS server on VMware player, unpack JABAWS VM into one of the folders on your local hard drive. Open VMware Player, and click "Open Virtual Machine" and point the Player to the location of the JABAWS, choose JABAWS.vmx file to open an appliance.

    +

    When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all.

    +

    JABAWS Appliance details

    +

    By default, JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory let your VM deal with larger tasks, e.g. work with large alignments.

    +

    The VMware Player screen shot below displays JABAWS VM CPU settings.

    +

    vmware cpu settings

    +

    JABAWS appliance configuration:

    +

    VMware info
    + - Date of creation: 8 October 2010
    + - CPUs : 1
    + - RAM : 512 MB
    + - Networking : Host only (the VM has no access to the outside network, nothing from outside network can access the VM)
    + - Hard disk : 20 GB (expanding)
    + - VMware tools : Installed

    +

    OS info
    + - OS : TurnKey Linux, based on Ubuntu 8.0.4 JEOS (Just-Enough-Operation-System)
    + - Installation : Oracle Java 6, Tomcat 6, JABAWS v. 1.0
    + - Hostname : tomcat
    + - Patches : till date of creation
    + - IPv4 address : dhcp
    + - IPv6 address : auto
    + - DNS name : none
    + - Name server : dhcp
    + - Route : dhcp
    + - Keyboard : US_intl

    +

    Login credentials
    + - Root password: jabaws

    +

    Services

    +
      +
    • Default virtual console Alt+F7
      • +
    • Tomcat web server.
      + Access: http://VM_IP
      • +
    • JABAWS URL: http://VM_IP/jabaws
      • +
    • Web Shell
      + Access: https://VM_IP:12320/
      • +
    • Webmean
      + Access: https://VM_IP:12321/
      • +
    • SSH/SFTP
      + Access: root@VM_IP
      • +
    +

    Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. Under VirtualBox host only networking, first VM may have 192.168.56.101 IP address.

    +

    Configuring Jalview to work with your JABAWS VM

    +

    After you booted JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview help pages.

    +

    JABAWS welcome screen

    +

    If you click on Advanced Menu, you will see the configuration console, similar to the one below.

    +

    JABAWS welcome screen

    +

    If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.

    +

    JABAWS Installation

    +

    System Requirements

    + +

    JABAWS requires a Java web application server compliant with +version 2.4 of the Java Servlet specification, and a Java 6 runtime +environment. We recommend using an official Oracle Java 6 runtime +environment, and Apache-Tomcat web application server version 6, but other versions may work as well.

    + + +

    Installing the JABAWS WAR file

    + +

    JABAWS is distributed as a web application archive (WAR). To +deploy JABAWS in Apache-Tomcat - simply drop the war file into the +webapps directory of a running +Tomcat, and it will do the rest. For any other web application +server, please follow your server's specific deployment procedure +for 'WAR' files. If you are installing on a windows machine, then +at this point your JABAWS installation will already be up and +running, and you can try its services out using the JABAWS test client, but +installations on other operating systems will require a final step +to ensure JABAWS can locate and execute the binary programs it +needs.

    + +

    Preparing executables for use with JABAWS

    + +

    JABAWS's web services use command line programs to do +the actual analysis, so it must have access to programs +which can be executed on your platform. The native executables +bundled with JABAWS for Windows (32-bit) and Linux (i386) should be +OK for those systems. However, the source code for these +programs is also provided so you can recompile for your own +architecture and exploit any optimizations that your system can +provide. Alternately, if you have already got binaries on your +system, then you can simply change the paths in JABAWS's +configuration files so these are used instead.

    + +

    Using the pre-compiled i386 binaries on Linux

    + +

    Before the binaries that are bundled with JABAWS can be used, +they must first be made executable using the provided 'setexecflag.sh' script:

    + +
      +
    1. cd to <webapplicationpath>/binaries/src
      2. + +
    2. run sh setexecflag.sh
      3. + +
    3. Make sure binaries supplied work under your OS.
      + For this run each binary, without any command line options or +input files. If you see an error message complaining about missing +libraries or other problems, then you probably need to recompile the binaries. with
      4. + +
    4. Restart the Tomcat.
      5. +
    + +That's it! JABAWS should work at this point. Try it out using theJABAWS test client. If not, +read on... or have a look at deploying on Tomcat tips.
    + Note: You may want to enable logging, see +below for instructions on how to do that.
    + + +

    Recompiling the bundled +programs for your system

    + +

    If you have a fully equipped build environment on your +(POSIX-like) system, then you should be able to recompile the +programs from the source distributions which are included +in the JABAWS war file. A script called 'compilebin.sh' is provided +to automate this task.

    + +
      +
    1. In a terminal window, change the working directory to binaries/src
      2. + +
    2. execute the compilebin.sh +script,
      + either use: chmod +x compilebin.sh; +compilebin.sh > compilebin.out;
      + or: sh compilebin.sh > +compilebin.out
      3. + +
    3. Now run sh setexecflag.sh
      + If any of the binaries was not recompiled, then a 'file not found' +error will be raised.
      4. + +
    4. Finally, restart your tomcat (or servlet container), and use +the JABAWS test client to +check that JABAWS can use the new binaries.
      5. +
    + +

    If you couldn't compile everthing, then it may be that your system does +not have all the tools required for compiling the programs. At the very +least check that you have gcc, g++ and make installed in your +system. If not install these packages and repeat the compilation +steps again. You should also review the compilebin.sh output - +which was redirected to compilebin.out, and any errors output to +the terminal. Finally, try obtaining the pre +compiled binaries for your OS.

    + +

    Reuse the binaries that are +already in your system

    + +

    If you would like to use the binaries you already have then you +just need to let JABAWS know there they are. To do this, edit: +conf/Executable.properties +

    When specifying paths to executables that already exist on your system, make sure you provide an absolute path, or one relative to the JABAWS directory inside webapps. For example, the default path for clustalw is defined +aslocal.clustalw.bin=binaries/src/clustalw/src/clustalw2 +Alternatively, instead of changing Executable.properties you could also replace +the executables bundled with JABAWS with the ones that you have, or make symlinks to them. +Then the default configuration will work for you. More information +about the +Executable.properties file is given below.

    + +

    Obtaining alignment +programs for your operation system from elsewhere

    + +

    You could search for pre-packaged compiled executable in your +system package repository or alternately, download pre-compiled +binaries from each alignment program's home page. Then, either +replace the executables supplied with the downloaded ones, or +modify the paths in executable.properties as described above.

    + +

    Configuring JABAWS

    +

    There are three parts of the system you can configure. The local +and cluster engines, and the paths to individual executables for +each engine. These settings are stored in configuration files +within the web application directory (for an overview, then take a +look at the war file content table).

    + +

    Default JABA Web Services Configuration

    + +

    Initially, JABAWS is configured with only the local engine +enabled, with job output written to directory called "jobsout" +within the web application itself. This means that JABAWS will work +out of the box, but may not be suitable for serving a whole lab or +instute.

    + +

    Local Engine Configuration

    + +

    The Local execution engine configuration is defined in the +properties file conf/Engine.local.properties. The supported +configuration settings are:
    + engine.local.enable=true - # +enable or disable local engine, valid values true | false
    + local.tmp.directory=D:\\clusterengine\\testoutput +- a directory to use for temporary files storage, optional, +defaults to java temporary directory
    + engine.local.thread.number=4 - +Number of threads for tasks execution (valid values between 1 and +2x cpu. Where x is a number of cores available in the system). +Optional defaults to the number of cores for core number <=4 and +number of cores-1 for greater core numbers.

    + +

    If you are planning to heavily use the local engine (which you +have to if you do not have a cluster) it is a good idea to increase +the amount of memory available for the web application server. If +you are using Apache-Tomcat, then you can define its memory +settings in the JAVA_OPTS environment variable. To specify which +JVM to use for Apache-Tomcat, put the full path to the JRE +installation in the JAVA_HOME environment variable (We would +recommend using Sun Java Virtual Machine (JVM) in preference to +Open JDK). Below is an example of code which can be added to <tomcat_dir>/bin/setenv.sh script +to define which JVM to use and a memory settings for Tomcat server. +Tomcat server startup script (catalina.sh) will execute setenv.sh on each server start +automatically.
    + export +JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/
    + export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"

    + +

    Cluster Engine Configuration

    + +

    Supported configuration settings:
    + engine.cluster.enable=true - # +enable or disable local engine true | false, defaults to +false
    + cluster.tmp.directory=/homes/clustengine/testoutput- +a directory to use for temporary files storage. The value must be +an absolute path to the temporary directory. Required. The value +must be different from what is defined for local engine. This +directory must be accessible from all cluster nodes.
    + For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH +environment variables have to be defined. They tell the cluster +engine where to find DRMAA libraries. These variables +should be defined when the web application server starts up, e.g.

    + +

    SGE_ROOT=/gridware/sge
    + LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64

    + +

    Finally, do not forget to configure executables for the cluster +execution, they may be the same as for the local execution but may +be different. Please refer to the executable configuration section +for further details.

    + +

    Executable Configuration

    + +

    All the executable programs +are configured in conf/Executable.properties file. Each executable +is configured with a number of options. They are: local.X.bin.windows=<path to executable under windows +system, optional>
    + local.X.bin=<path to the executable under non-windows system, +optional>
    + cluster.X.bin=<path to the executable on the cluster, all +cluster nodes must see it, optional>
    + X.bin.env=<semicolon separated list of environment variables +for executable, use hash symbol as name value separator, +optional>
    + X.--aamatrix.path=<path to the directory containing +substitution matrices, optional>
    + X.presets.file=<path to the preset configuration file, optional +>
    + X.parameters.file=<path to the parameters configuration file, +optional>
    + X.limits.file=<path to the limits configuration file, +optional>
    + X.cluster.settings=<list of the cluster specific options, +optional>

    + +

    Where X is a short executable wrapper class name.

    + +

    Default JABAWS configuration includes path to local executables +to be run by the local engine only, all cluster related settings +are commened out, but they are there for you as example. Cluster +engine is disabled by default. To configure executable for cluster +execution uncomment the X.cluster settings and change them +appropriately.

    +

    By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.
    + After you have completed the editing your configuration may look like + this:local.mafft.bin.windows=
    + local.mafft.bin=binaries/mafft
    + cluster.mafft.bin=/homes/cengine/mafft
    + mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;
    + mafft.--aamatrix.path=binaries/matrices
    + mafft.presets.file=conf/settings/MafftPresets.xml
    + mafft.parameters.file=conf/settings/MafftParameters.xml
    + mafft.limits.file=conf/settings/MafftLimits.xml
    + mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l + h_vmem=6000M -l ram=6000M

    +

    Please not that relative paths must only be specified for the +files that reside inside web application directory, all other paths +must be supplied as absolute!

    + +

    Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly +specify the absolute path to anything +normally evaluated from an environment variable at execution time.

    + +

    If you are using JABAWS to submit jobs to the cluster (with +cluster engine enabled), executables must be available from all +cluster nodes the task can be sent to, also paths to the +executables on the cluster e.g. cluster.<exec_name>.bin must be +absolute.

    + +

    Executables can be located anywhere in your system, they do not +have to reside on the server as long as the web application server +can access and execute them.

    + +

    Cluster settings are treated as a black box, the system will +just pass whatever is specified in this line directly to the +cluster submission library. This is how DRMAA itself treats this +settings. More exactly DRMAA JobTemplate.setNativeSpecification() +function will be called.

    + +

    Defining Environment Variables for +Executables

    + +

    Environment variables can be defined in property x.bin.env Where x is +one of five executables supported by JABAWS. Several environment +variables can be specified in the same line. For example.
    + mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;

    + +

    The example above defines two environment variables with names +MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft +and /bin/fasta34 respectively. Semicolon is used as a separator +between different environment variables whereas hash is used as a +separator for name and value of the variable.

    + +

    Configure JABAWS to Work +with Mafft

    + +

    If you use default configuration you do not need to read any +further. The default configuration will work for you without any +changes, however, if you want to install Mafft yourself then there +is a couple of more steps to do.

    + +

    Mafft executable needs to know the location of other files +supplied with Mafft. In addition some Mafft functions depends on +the fasta executable, which is not supplied with Mafft, but is a +separate package. Mafft needs to know the location of fasta34 +executable.

    + +

    To let Mafft know where the other files from its package are +change the value of MAFFT-BINARIES environment variables. To let +Mafft know where is the fasta34 executable set the value of +FASTA_4_MAFFT environment variable to point to a location of +fasta34 program. The latter can be added to the PATH variable +instead. If you are using executables supplied with JABAWS, the +path to Mafft binaries would be like <relative path to web application +directory>/binaries/src/mafft/binaries and the path to +fasta34 binary would be <relative path +to web application +directory>/binaries/src/fasta34/fasta34. You can specify +the location of Mafft binaries as well as fasta34 program elsewhere +by providing an absolute path to them. All these settings are +defined in conf/Executable.properties file.

    + +

    For Developers

    +

    Web service functions description

    +

    All JABA multiple sequence alignment web services comply to the same interface, thus the function described below are available from all the services.

    +

    Functions for initiating the alignment String id = align(List<FastaSequence> list)
    + String id = customAlign(List<FastaSequence> sequenceList, List<Option> optionList)
    + String id = presetAlign(List<FastaSequence> sequenceList, Preset preset)

    +

    Functions pertaining to job monitoring and control
    + JobStatus status = getJobStatus(String id)
    + Alignment al = getResult(String id)
    + boolean cancelled = cancelJob(String id)
    + ChunkHolder chunk = pullExecStatistics(String id, long marker)

    +

    Functions relating to service features discovery
    + RunnerConfig rc = getRunnerOptions()
    + Limit limit = getLimit(String name)
    + LimitsManager lm = getLimits()
    + PresetManager pm = getPresets()

    +

    Please refer to a data model javadoc for a detailed description of each methods.

    +

    Structure of the template command line client

    + + + + + + + + + + + + + + + + + + + + + +
    PackagesClasses and Interfaces
    compbio.data.msa MsaWS the interface for all multiple sequence alignment web services
    compbio.data.sequenceJABAWS data types
    compbio.metadataJABAWS meta data types
    compbio.ws.clientJABAWS command line client
    +

    Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.
    + Please refer to a data model javadoc for a detailed description of each class and its methods.

    +

    JABA Web Services Internals

    +

    Testing JABA Web Services

    +

    You can use a command line client (part of the client only +package) to test you JABAWS installation as described here. If you downloaded a JABAWS +server package, you can use <your_jaba_context_name>/WEB-INF/lib/jaba-client.jar +to test JABAWS installation as described in how-to. If you downloaded the source +code, then you could run a number of test suits defined in the +build.xml ant build file.

    + +

    JABAWS Log Files

    + +

    JABAWS can be configured to log what it is doing. This comes +handy if you would like to see who is using your web services or +need to chase some problems. JABAWS uses log4j to do the logging, +the example of log4j configuration is bundled with JABAWS war file. +You will find it in the /WEB-INF/classes/log4j.properties file. All the +lines in this file are commented out. The reason why the logging is +disabled by default it simple, log4j have to know the exact +location where the log files should be stored. This is not known up +until the deployment time. To enable the logging you need to +definelogDir property in the log4j.properties and uncomment section of +the file which corresponds to your need. More information is given +in the log4j.properties file +itself. Restart the tomcat or the JABAWS web application to apply +the settings.

    + +

    After you have done this, assuming that you did not change the +log4j.properties file yourself, you should see the application log +file called activity.log. The +amount of information logged can be adjusted using different +logging levels, it is reduced in the following order of log levels +TRACE, DEBUG, INFO, WARN, ERROR, FATAL.

    + +

    If you would like to know who is using your services, you might +want to enable tomcat access +logging.

    + +

    JABAWS War File Content

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    DirectoryContent description
    conf/contains configuration files such as Executable.properties, +Engine.local.properties, Engine.cluster.properties
    conf/settingsContains individual executable description files. In particular +XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the +name of the executable
    jobsout/Contains directories generated when running an individual executable. E.g. input and output files and some other task +related data. (optional)
    binaries/Directory contains native executables - programs, +windows binaries (optional)
    binaries/srcContains source of native executables and Linux i386 +binaries.
    binaries/matricesSubstitution matrices
    WEB-INFWeb application descriptor
    WEB-INF/libWeb application libraries
    WEB-INF/classeslog4j.properties - log configuration file (optional)
    Help Pages
    /help pages, index.html is the starting page
    dm_javadocjavadoc for JABAWS client (the link is available from How To +pages)
    prog_docsdocumentation for programmes that JABAWS uses
    imagesimages referenced by html pages
    + +

     

    +
    + + + +
    + + +
    + + + + + + + + diff --git a/website/print.css b/website/print.css new file mode 100644 index 0000000..daec545 --- /dev/null +++ b/website/print.css @@ -0,0 +1,183 @@ + +#banner { background:none !important; color:#000000 !important; text-align:center; } + +#panel { display:none !important } + +#content { margin:0.5em; border-bottom:solid 1px #6994af; } + +#page { margin: 0.5em; } + +#wrapper { background:none; } + +ul { + list-style-type: circle; +} + +#panel a:link, a:visited { + text-decoration: none; + display:block; + line-height: 1em; + padding:10px; + color:#000000; + text-decoration:none; + } + +#panel a:hover { + background-color: transparent; + text-decoration: underline; + } + + +strong { + font-weight:bold; + color:#003366; +} + +pre { + font-family:Arial, Helvetica, sans-serif; +} + +p { + line-height: 1.4em; +} + +.hightlight { +font-style:italic; +font-family:"Courier New", Courier, monospace; +} + +.code { + font-size-adjust:0.4; + color:black; + background-color:#F5F5F5; + font-family:"Courier New",Courier,monospace; + font-style:normal; + margin:1em 0; + padding: 0.5em; + border: 1px dashed black; +} + + +.box { + font-size-adjust:0.5; + color:black; + background-color:#F5F5F5; + font-family:Arial, Helvetica, sans-serif; + font-style:normal; + margin:1em 0; + padding: 0.5em; + border: 1px solid black; + display:block; +} + +.u { text-decoration: underline; } +.headeru { text-shadow: black 0.05em 0.05em 0.01em ;} + +/* Table styles */ +table { + border-collapse: collapse; + border: 1px solid #666; + margin: 20px 0 20px 0; + width: 100%; +} +th, td { + margin: 2px 4px 2px 4px; + padding: 0 5px; + text-align: left; + vertical-align: top; + border: 1px solid #666; +} + +table caption { + font: 1.5em Georgia, "Times New Roman", Times, serif; + padding: 1em; + background-color: #9c9; +} + +.mainheader { + font: 1.5em Georgia, "Times New Roman", Times, serif; + background-color: #9c9; + text-align:center; + line-height:1em; +} + +tr { + background-color: #eee; +} + +tr:nth-child(odd) { + background-color: #ccc; +} + + +span.directory { +background: transparent url(images/dir.gif) no-repeat scroll left center; +color:#666666; +font-family:"Courier New",Courier,monospace; +font-style:normal; +padding:0 0 0 15px; +} + +.attention { +color:#993333; +} + +.source { + border:1px solid #858789; + display:block; + margin:26px 0; + overflow:visible; +} + +/* OPEN state styles */ +.source .body { + background:#F5F5F5 none repeat scroll right 0; + color:#434546; + padding:7px 15px; +/* white-space:pre-wrap; */ + word-wrap:break-word; +} + +.source .header { + background:#E9EAEC url(images/minus.png) no-repeat scroll 98% center; + color:#3B3D3F; + cursor:pointer; + font-weight:bold; + height:30px; + line-height:30px; + padding:0 0 0 15px; +} + +/* CLOSED state styles */ +.source .body.collapsed { + display:block !important; +} + +.source .header.collapsed { + background:#E9EAEC url(images/plus.png) no-repeat scroll 98% center; + padding:0 15px 0 15px; +} + +#copyright { text-align:right; + color:#999999; + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:smaller; + line-height:1em; + } + +.body .code { + margin:0; + padding:0; + border:0; + font-family:"Courier New",Courier,monospace; + font-style:normal; +} + +body { + font-family:Arial, Helvetica, sans-serif; + font-size: 9pt; + background-color: white; + line-height: 2em; +} + +h3 {border-bottom: 1px solid grey; margin-top: 2em; } \ No newline at end of file diff --git a/website/prog_docs/clustalw.txt b/website/prog_docs/clustalw.txt new file mode 100644 index 0000000..fd50671 --- /dev/null +++ b/website/prog_docs/clustalw.txt @@ -0,0 +1,720 @@ + + + + CLUSTAL 2.0.12 Multiple Sequence Alignments + + + + +>> HELP NEW << NEW FEATURES/OPTIONS + +==UPGMA== + The UPGMA algorithm has been added to allow faster tree construction. The user now + has the choice of using Neighbour Joining or UPGMA. The default is still NJ, but the + user can change this by setting the clustering parameter. + + -CLUSTERING= :NJ or UPGMA + +==ITERATION== + + A remove first iteration scheme has been added. This can be used to improve the final + alignment or improve the alignment at each stage of the progressive alignment. During the + iteration step each sequence is removed in turn and realigned. If the resulting alignment + is better than the previous alignment it is kept. This process is repeated until the score + converges (the score is not improved) or until the maximum number of iterations is + reached. The user can iterate at each step of the progressive alignment by setting the + iteration parameter to TREE or just on the final alignment by seting the iteration + parameter to ALIGNMENT. The default is no iteration. The maximum number of iterations can + be set using the numiter parameter. The default number of iterations is 3. + + -ITERATION= :NONE or TREE or ALIGNMENT + + -NUMITER=n :Maximum number of iterations to perform + +==HELP== + + -FULLHELP :Print out the complete help content + +==MISC== + + -MAXSEQLEN=n :Maximum allowed sequence length + + -QUIET :Reduce console output to minimum + + -STATS=file :Log some alignents statistics to file + + +>> HELP 1 << General help for CLUSTAL W (2.0.12) + +Clustal W is a general purpose multiple alignment program for DNA or proteins. + +SEQUENCE INPUT: all sequences must be in 1 file, one after another. +7 formats are automatically recognised: NBRF-PIR, EMBL-SWISSPROT, +Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file. +All non-alphabetic characters (spaces, digits, punctuation marks) are ignored +except "-" which is used to indicate a GAP ("." in MSF-RSF). + +To do a MULTIPLE ALIGNMENT on a set of sequences, use item 1 from this menu to +INPUT them; go to menu item 2 to do the multiple alignment. + +PROFILE ALIGNMENTS (menu item 3) are used to align 2 alignments. Use this to +add a new sequence to an old alignment, or to use secondary structure to guide +the alignment process. GAPS in the old alignments are indicated using the "-" +character. PROFILES can be input in ANY of the allowed formats; just +use "-" (or "." for MSF-RSF) for each gap position. + +PHYLOGENETIC TREES (menu item 4) can be calculated from old alignments (read in +with "-" characters to indicate gaps) OR after a multiple alignment while the +alignment is still in memory. + + +The program tries to automatically recognise the different file formats used +and to guess whether the sequences are amino acid or nucleotide. This is not +always foolproof. + +FASTA and NBRF-PIR formats are recognised by having a ">" as the first +character in the file. + +EMBL-Swiss Prot formats are recognised by the letters +ID at the start of the file (the token for the entry name field). + +CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file. + +GCG-MSF format is recognised by one of the following: + - the word PileUp at the start of the file. + - the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT + at the start of the file. + - the word MSF on the first line of the line, and the characters .. + at the end of this line. + +GCG-RSF format is recognised by the word !!RICH_SEQUENCE at the beginning of +the file. + + +If 85% or more of the characters in the sequence are from A,C,G,T,U or N, the +sequence will be assumed to be nucleotide. This works in 97.3% of cases +but watch out! + + +>> HELP 2 << Help for multiple alignments + +If you have already loaded sequences, use menu item 1 to do the complete +multiple alignment. You will be prompted for 2 output files: 1 for the +alignment itself; another to store a dendrogram that describes the similarity +of the sequences to each other. + +Multiple alignments are carried out in 3 stages (automatically done from menu +item 1 ...Do complete multiple alignments now): + +1) all sequences are compared to each other (pairwise alignments); + +2) a dendrogram (like a phylogenetic tree) is constructed, describing the +approximate groupings of the sequences by similarity (stored in a file). + +3) the final multiple alignment is carried out, using the dendrogram as a guide. + + +PAIRWISE ALIGNMENT parameters control the speed-sensitivity of the initial +alignments. + +MULTIPLE ALIGNMENT parameters control the gaps in the final multiple alignments. + + +RESET GAPS (menu item 7) will remove any new gaps introduced into the sequences +during multiple alignment if you wish to change the parameters and try again. +This only takes effect just before you do a second multiple alignment. You +can make phylogenetic trees after alignment whether or not this is ON. +If you turn this OFF, the new gaps are kept even if you do a second multiple +alignment. This allows you to iterate the alignment gradually. Sometimes, the +alignment is improved by a second or third pass. + +SCREEN DISPLAY (menu item 8) can be used to send the output alignments to the +screen as well as to the output file. + +You can skip the first stages (pairwise alignments; dendrogram) by using an +old dendrogram file (menu item 3); or you can just produce the dendrogram +with no final multiple alignment (menu item 2). + + +OUTPUT FORMAT: Menu item 9 (format options) allows you to choose from 6 +different alignment formats (CLUSTAL, GCG, NBRF-PIR, PHYLIP, GDE, NEXUS, and FASTA). + + + +>> HELP 3 << Help for pairwise alignment parameters + +A distance is calculated between every pair of sequences and these are used to +construct the dendrogram which guides the final multiple alignment. The scores +are calculated from separate pairwise alignments. These can be calculated using +2 methods: dynamic programming (slow but accurate) or by the method of Wilbur +and Lipman (extremely fast but approximate). + +You can choose between the 2 alignment methods using menu option 8. The +slow-accurate method is fine for short sequences but will be VERY SLOW for +many (e.g. >100) long (e.g. >1000 residue) sequences. + +SLOW-ACCURATE alignment parameters: + These parameters do not have any affect on the speed of the alignments. +They are used to give initial alignments which are then rescored to give percent +identity scores. These % scores are the ones which are displayed on the +screen. The scores are converted to distances for the trees. + +1) Gap Open Penalty: the penalty for opening a gap in the alignment. +2) Gap extension penalty: the penalty for extending a gap by 1 residue. +3) Protein weight matrix: the scoring table which describes the similarity + of each amino acid to each other. +4) DNA weight matrix: the scores assigned to matches and mismatches + (including IUB ambiguity codes). + + +FAST-APPROXIMATE alignment parameters: + +These similarity scores are calculated from fast, approximate, global align- +ments, which are controlled by 4 parameters. 2 techniques are used to make +these alignments very fast: 1) only exactly matching fragments (k-tuples) are +considered; 2) only the 'best' diagonals (the ones with most k-tuple matches) +are used. + +K-TUPLE SIZE: This is the size of exactly matching fragment that is used. +INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity. +For longer sequences (e.g. >1000 residues) you may need to increase the default. + +GAP PENALTY: This is a penalty for each gap in the fast alignments. It has +little affect on the speed or sensitivity except for extreme values. + +TOP DIAGONALS: The number of k-tuple matches on each diagonal (in an imaginary +dot-matrix plot) is calculated. Only the best ones (with most matches) are +used in the alignment. This parameter specifies how many. Decrease for speed; +increase for sensitivity. + +WINDOW SIZE: This is the number of diagonals around each of the 'best' +diagonals that will be used. Decrease for speed; increase for sensitivity. + + +>> HELP 4 << Help for multiple alignment parameters + +These parameters control the final multiple alignment. This is the core of the +program and the details are complicated. To fully understand the use of the +parameters and the scoring system, you will have to refer to the documentation. + +Each step in the final multiple alignment consists of aligning two alignments +or sequences. This is done progressively, following the branching order in +the GUIDE TREE. The basic parameters to control this are two gap penalties and +the scores for various identical-non-indentical residues. + +1) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the +cost of opening up every new gap and the cost of every item in a gap. +Increasing the gap opening penalty will make gaps less frequent. Increasing +the gap extension penalty will make gaps shorter. Terminal gaps are not +penalised. + +3) The DELAY DIVERGENT SEQUENCES switch delays the alignment of the most +distantly related sequences until after the most closely related sequences have +been aligned. The setting shows the percent identity level required to delay +the addition of a sequence; sequences that are less identical than this level +to any other sequences will be aligned later. + + + +4) The TRANSITION WEIGHT gives transitions (A <--> G or C <--> T +i.e. purine-purine or pyrimidine-pyrimidine substitutions) a weight between 0 +and 1; a weight of zero means that the transitions are scored as mismatches, +while a weight of 1 gives the transitions the match score. For distantly related +DNA sequences, the weight should be near to zero; for closely related sequences +it can be useful to assign a higher score. + + +5) PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of +weight matrices. The default for proteins in version 1.8 is the PAM series +derived by Gonnet and colleagues. Note, a series is used! The actual matrix +that is used depends on how similar the sequences to be aligned at this +alignment step are. Different matrices work differently at each evolutionary +distance. + +6) DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series) +can be selected. The default is the matrix used by BESTFIT for comparison of +nucleic acid sequences. + +Further help is offered in the weight matrix menu. + + +7) In the weight matrices, you can use negative as well as positive values if +you wish, although the matrix will be automatically adjusted to all positive +scores, unless the NEGATIVE MATRIX option is selected. + +8) PROTEIN GAP PARAMETERS displays a menu allowing you to set some Gap Penalty +options which are only used in protein alignments. + + +>> HELP A << Help for protein gap parameters. + +1) RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce +or increase the gap opening penalties at each position in the alignment or +sequence. See the documentation for details. As an example, positions that +are rich in glycine are more likely to have an adjacent gap than positions that +are rich in valine. + +2) 3) HYDROPHILIC GAP PENALTIES are used to increase the chances of a gap within +a run (5 or more residues) of hydrophilic amino acids; these are likely to +be loop or random coil regions where gaps are more common. The residues that +are "considered" to be hydrophilic are set by menu item 3. + +4) GAP SEPARATION DISTANCE tries to decrease the chances of gaps being too +close to each other. Gaps that are less than this distance apart are penalised +more than other gaps. This does not prevent close gaps; it makes them less +frequent, promoting a block-like appearance of the alignment. + +5) END GAP SEPARATION treats end gaps just like internal gaps for the purposes +of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above). +If you turn this off, end gaps will be ignored for this purpose. This is +useful when you wish to align fragments where the end gaps are not biologically +meaningful. + + +>> HELP 5 << Help for output format options. + +Six output formats are offered. You can choose any (or all 6 if you wish). + +CLUSTAL format output is a self explanatory alignment format. It shows the +sequences aligned in blocks. It can be read in again at a later date to +(for example) calculate a phylogenetic tree or add a new sequence with a +profile alignment. + +GCG output can be used by any of the GCG programs that can work on multiple +alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG +.msf format files (multiple sequence file); new in version 7 of GCG. + +PHYLIP format output can be used for input to the PHYLIP package of Joe +Felsenstein. This is an extremely widely used package for doing every +imaginable form of phylogenetic analysis (MUCH more than the the modest intro- +duction offered by this program). + +NBRF-PIR: this is the same as the standard PIR format with ONE ADDITION. Gap +characters "-" are used to indicate the positions of gaps in the multiple +alignment. These files can be re-used as input in any part of clustal that +allows sequences (or alignments or profiles) to be read in. + +GDE: this is the flat file format used by the GDE package of Steven Smith. + +NEXUS: the format used by several phylogeny programs, including PAUP and +MacClade. + +GDE OUTPUT CASE: sequences in GDE format may be written in either upper or +lower case. + +CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the +alignment lines in clustalw format. + +OUTPUT ORDER is used to control the order of the sequences in the output +alignments. By default, the order corresponds to the order in which the +sequences were aligned (from the guide tree-dendrogram), thus automatically +grouping closely related sequences. This switch can be used to set the order +to the same as the input file. + +PARAMETER OUTPUT: This option allows you to save all your parameter settings +in a parameter file. This file can be used subsequently to rerun Clustal W +using the same parameters. + + +>> HELP 6 << Help for profile and structure alignments + +By PROFILE ALIGNMENT, we mean alignment using existing alignments. Profile +alignments allow you to store alignments of your favourite sequences and add +new sequences to them in small bunches at a time. A profile is simply an +alignment of one or more sequences (e.g. an alignment output file from CLUSTAL +W). Each input can be a single sequence. One or both sets of input sequences +may include secondary structure assignments or gap penalty masks to guide the +alignment. + +The profiles can be in any of the allowed input formats with "-" characters +used to specify gaps (except for MSF-RSF where "." is used). + +You have to specify the 2 profiles by choosing menu items 1 and 2 and giving +2 file names. Then Menu item 3 will align the 2 profiles to each other. +Secondary structure masks in either profile can be used to guide the alignment. + +Menu item 4 will take the sequences in the second profile and align them to +the first profile, 1 at a time. This is useful to add some new sequences to +an existing alignment, or to align a set of sequences to a known structure. +In this case, the second profile would not be pre-aligned. + + +The alignment parameters can be set using menu items 5, 6 and 7. These are +EXACTLY the same parameters as used by the general, automatic multiple +alignment procedure. The general multiple alignment procedure is simply a +series of profile alignments. Carrying out a series of profile alignments on +larger and larger groups of sequences, allows you to manually build up a +complete alignment, if necessary editing intermediate alignments. + +SECONDARY STRUCTURE OPTIONS. Menu Option 0 allows you to set 2D structure +parameters. If a solved structure is available, it can be used to guide the +alignment by raising gap penalties within secondary structure elements, so +that gaps will preferentially be inserted into unstructured surface loops. +Alternatively, a user-specified gap penalty mask can be supplied directly. + +A gap penalty mask is a series of numbers between 1 and 9, one per position in +the alignment. Each number specifies how much the gap opening penalty is to be +raised at that position (raised by multiplying the basic gap opening penalty +by the number) i.e. a mask figure of 1 at a position means no change +in gap opening penalty; a figure of 4 means that the gap opening penalty is +four times greater at that position, making gaps 4 times harder to open. + +The format for gap penalty masks and secondary structure masks is explained +in the help under option 0 (secondary structure options). + + +>> HELP B << Help for secondary structure - gap penalty masks + +The use of secondary structure-based penalties has been shown to improve the +accuracy of multiple alignment. Therefore CLUSTAL W now allows gap penalty +masks to be supplied with the input sequences. The masks work by raising gap +penalties in specified regions (typically secondary structure elements) so that +gaps are preferentially opened in the less well conserved regions (typically +surface loops). + +Options 1 and 2 control whether the input secondary structure information or +gap penalty masks will be used. + +Option 3 controls whether the secondary structure and gap penalty masks should +be included in the output alignment. + +Options 4 and 5 provide the value for raising the gap penalty at core Alpha +Helical (A) and Beta Strand (B) residues. In CLUSTAL format, capital residues +denote the A and B core structure notation. The basic gap penalties are +multiplied by the amount specified. + +Option 6 provides the value for the gap penalty in Loops. By default this +penalty is not raised. In CLUSTAL format, loops are specified by "." in the +secondary structure notation. + +Option 7 provides the value for setting the gap penalty at the ends of +secondary structures. Ends of secondary structures are observed to grow +and-or shrink in related structures. Therefore by default these are given +intermediate values, lower than the core penalties. All secondary structure +read in as lower case in CLUSTAL format gets the reduced terminal penalty. + +Options 8 and 9 specify the range of structure termini for the intermediate +penalties. In the alignment output, these are indicated as lower case. +For Alpha Helices, by default, the range spans the end helical turn. For +Beta Strands, the default range spans the end residue and the adjacent loop +residue, since sequence conservation often extends beyond the actual H-bonded +Beta Strand. + +CLUSTAL W can read the masks from SWISS-PROT, CLUSTAL or GDE format input +files. For many 3-D protein structures, secondary structure information is +recorded in the feature tables of SWISS-PROT database entries. You should +always check that the assignments are correct - some are quite inaccurate. +CLUSTAL W looks for SWISS-PROT HELIX and STRAND assignments e.g. + +FT HELIX 100 115 +FT STRAND 118 119 + +The structure and penalty masks can also be read from CLUSTAL alignment format +as comment lines beginning "!SS_" or "!GM_" e.g. + +!SS_HBA_HUMA ..aaaAAAAAAAAAAaaa.aaaAAAAAAAAAAaaaaaaAaaa.........aaaAAAAAA +!GM_HBA_HUMA 112224444444444222122244444444442222224222111111111222444444 +HBA_HUMA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK + +Note that the mask itself is a set of numbers between 1 and 9 each of which is +assigned to the residue(s) in the same column below. + +In GDE flat file format, the masks are specified as text and the names must +begin with "SS_ or "GM_. + +Either a structure or penalty mask or both may be used. If both are included in +an alignment, the user will be asked which is to be used. + + +>> HELP C << Help for secondary structure - gap penalty mask output options + +The options in this menu let you choose whether or not to include the masks +in the CLUSTAL W output alignments. Showing both is useful for understanding +how the masks work. The secondary structure information is itself very useful +in judging the alignment quality and in seeing how residue conservation +patterns vary with secondary structure. + + +>> HELP 7 << Help for phylogenetic trees + +1) Before calculating a tree, you must have an ALIGNMENT in memory. This can be +input in any format or you should have just carried out a full multiple +alignment and the alignment is still in memory. + + +*************** Remember YOU MUST ALIGN THE SEQUENCES FIRST!!!! *************** + + +The methods used are NJ (Neighbour Joining) and UPGMA. First +you calculate distances (percent divergence) between all pairs of sequence from +a multiple alignment; second you apply the NJ or UPGMA method to the distance matrix. + +2) EXCLUDE POSITIONS WITH GAPS? With this option, any alignment positions where +ANY of the sequences have a gap will be ignored. This means that 'like' will be +compared to 'like' in all distances, which is highly desirable. It also +automatically throws away the most ambiguous parts of the alignment, which are +concentrated around gaps (usually). The disadvantage is that you may throw away +much of the data if there are many gaps (which is why it is difficult for us to +make it the default). + + + +3) CORRECT FOR MULTIPLE SUBSTITUTIONS? For small divergence (say <10%) this +option makes no difference. For greater divergence, it corrects for the fact +that observed distances underestimate actual evolutionary distances. This is +because, as sequences diverge, more than one substitution will happen at many +sites. However, you only see one difference when you look at the present day +sequences. Therefore, this option has the effect of stretching branch lengths +in trees (especially long branches). The corrections used here (for DNA or +proteins) are both due to Motoo Kimura. See the documentation for details. + +Where possible, this option should be used. However, for VERY divergent +sequences, the distances cannot be reliably corrected. You will be warned if +this happens. Even if none of the distances in a data set exceed the reliable +threshold, if you bootstrap the data, some of the bootstrap distances may +randomly exceed the safe limit. + +4) To calculate a tree, use option 4 (DRAW TREE NOW). This gives an UNROOTED +tree and all branch lengths. The root of the tree can only be inferred by +using an outgroup (a sequence that you are certain branches at the outside +of the tree .... certain on biological grounds) OR if you assume a degree +of constancy in the 'molecular clock', you can place the root in the 'middle' +of the tree (roughly equidistant from all tips). + +5) TOGGLE PHYLIP BOOTSTRAP POSITIONS +By default, the bootstrap values are correctly placed on the tree branches of +the phylip format output tree. The toggle allows them to be placed on the +nodes, which is incorrect, but some display packages (e.g. TreeTool, TreeView +and Phylowin) only support node labelling but not branch labelling. Care +should be taken to note which branches and labels go together. + +6) OUTPUT FORMATS: four different formats are allowed. None of these displays +the tree visually. Useful display programs accepting PHYLIP format include +NJplot (from Manolo Gouy and supplied with Clustal W), TreeView (Mac-PC), and +PHYLIP itself - OR get the PHYLIP package and use the tree drawing facilities +there. (Get the PHYLIP package anyway if you are interested in trees). The +NEXUS format can be read into PAUP or MacClade. + + +>> HELP 8 << Help for choosing a weight matrix + +For protein alignments, you use a weight matrix to determine the similarity of +non-identical amino acids. For example, Tyr aligned with Phe is usually judged +to be 'better' than Tyr aligned with Pro. + +There are three 'in-built' series of weight matrices offered. Each consists of +several matrices which work differently at different evolutionary distances. To +see the exact details, read the documentation. Crudely, we store several +matrices in memory, spanning the full range of amino acid distance (from almost +identical sequences to highly divergent ones). For very similar sequences, it +is best to use a strict weight matrix which only gives a high score to +identities and the most favoured conservative substitutions. For more divergent +sequences, it is appropriate to use "softer" matrices which give a high score +to many other frequent substitutions. + +1) BLOSUM (Henikoff). These matrices appear to be the best available for +carrying out database similarity (homology searches). The matrices used are: +Blosum 80, 62, 45 and 30. (BLOSUM was the default in earlier Clustal W +versions) + +2) PAM (Dayhoff). These have been extremely widely used since the late '70s. +We use the PAM 20, 60, 120 and 350 matrices. + +3) GONNET. These matrices were derived using almost the same procedure as the +Dayhoff one (above) but are much more up to date and are based on a far larger +data set. They appear to be more sensitive than the Dayhoff series. We use the +GONNET 80, 120, 160, 250 and 350 matrices. This series is the default for +Clustal W version 1.8. + +We also supply an identity matrix which gives a score of 1.0 to two identical +amino acids and a score of zero otherwise. This matrix is not very useful. +Alternatively, you can read in your own (just one matrix, not a series). + +A new matrix can be read from a file on disk, if the filename consists only +of lower case characters. The values in the new weight matrix must be integers +and the scores should be similarities. You can use negative as well as positive +values if you wish, although the matrix will be automatically adjusted to all +positive scores. + + + +For DNA, a single matrix (not a series) is used. Two hard-coded matrices are +available: + + +1) IUB. This is the default scoring matrix used by BESTFIT for the comparison +of nucleic acid sequences. X's and N's are treated as matches to any IUB +ambiguity symbol. All matches score 1.9; all mismatches for IUB symbols score 0. + + +2) CLUSTALW(1.6). The previous system used by Clustal W, in which matches score +1.0 and mismatches score 0. All matches for IUB symbols also score 0. + +INPUT FORMAT The format used for a new matrix is the same as the BLAST program. +Any lines beginning with a # character are assumed to be comments. The first +non-comment line should contain a list of amino acids in any order, using the +1 letter code, followed by a * character. This should be followed by a square +matrix of integer scores, with one row and one column for each amino acid. The +last row and column of the matrix (corresponding to the * character) contain +the minimum score over the whole matrix. + + +>> HELP 9 << Help for command line parameters + + DATA (sequences) + +-INFILE=file.ext :input sequences. +-PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment). + + + VERBS (do things) + +-OPTIONS :list the command line parameters +-HELP or -CHECK :outline the command line params. +-FULLHELP :output full help content. +-ALIGN :do full multiple alignment. +-TREE :calculate NJ tree. +-PIM :output percent identity matrix (while calculating the tree) +-BOOTSTRAP(=n) :bootstrap a NJ tree (n= number of bootstraps; def. = 1000). +-CONVERT :output the input sequences in a different file format. + + + PARAMETERS (set things) + +***General settings:**** +-INTERACTIVE :read command line, then enter normal interactive menus +-QUICKTREE :use FAST algorithm for the alignment guide tree +-TYPE= :PROTEIN or DNA sequences +-NEGATIVE :protein alignment with negative values in matrix +-OUTFILE= :sequence alignment file name +-OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS +-OUTORDER= :INPUT or ALIGNED +-CASE :LOWER or UPPER (for GDE output only) +-SEQNOS= :OFF or ON (for Clustal output only) +-SEQNO_RANGE=:OFF or ON (NEW: for all output formats) +-RANGE=m,n :sequence range to write starting m to m+n +-MAXSEQLEN=n :maximum allowed input sequence length +-QUIET :Reduce console output to minimum +-STATS= :Log some alignents statistics to file + +***Fast Pairwise Alignments:*** +-KTUPLE=n :word size +-TOPDIAGS=n :number of best diags. +-WINDOW=n :window around best diags. +-PAIRGAP=n :gap penalty +-SCORE :PERCENT or ABSOLUTE + + +***Slow Pairwise Alignments:*** +-PWMATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename +-PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename +-PWGAPOPEN=f :gap opening penalty +-PWGAPEXT=f :gap opening penalty + + +***Multiple Alignments:*** +-NEWTREE= :file for new guide tree +-USETREE= :file for old guide tree +-MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename +-DNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename +-GAPOPEN=f :gap opening penalty +-GAPEXT=f :gap extension penalty +-ENDGAPS :no end gap separation pen. +-GAPDIST=n :gap separation pen. range +-NOPGAP :residue-specific gaps off +-NOHGAP :hydrophilic gaps off +-HGAPRESIDUES= :list hydrophilic res. +-MAXDIV=n :% ident. for delay +-TYPE= :PROTEIN or DNA +-TRANSWEIGHT=f :transitions weighting +-ITERATION= :NONE or TREE or ALIGNMENT +-NUMITER=n :maximum number of iterations to perform +-NOWEIGHTS :disable sequence weighting + + +***Profile Alignments:*** +-PROFILE :Merge two alignments by profile alignment +-NEWTREE1= :file for new guide tree for profile1 +-NEWTREE2= :file for new guide tree for profile2 +-USETREE1= :file for old guide tree for profile1 +-USETREE2= :file for old guide tree for profile2 + + +***Sequence to Profile Alignments:*** +-SEQUENCES :Sequentially add profile2 sequences to profile1 alignment +-NEWTREE= :file for new guide tree +-USETREE= :file for old guide tree + + +***Structure Alignments:*** +-NOSECSTR1 :do not use secondary structure-gap penalty mask for profile 1 +-NOSECSTR2 :do not use secondary structure-gap penalty mask for profile 2 +-SECSTROUT=STRUCTURE or MASK or BOTH or NONE :output in alignment file +-HELIXGAP=n :gap penalty for helix core residues +-STRANDGAP=n :gap penalty for strand core residues +-LOOPGAP=n :gap penalty for loop regions +-TERMINALGAP=n :gap penalty for structure termini +-HELIXENDIN=n :number of residues inside helix to be treated as terminal +-HELIXENDOUT=n :number of residues outside helix to be treated as terminal +-STRANDENDIN=n :number of residues inside strand to be treated as terminal +-STRANDENDOUT=n:number of residues outside strand to be treated as terminal + + +***Trees:*** +-OUTPUTTREE=nj OR phylip OR dist OR nexus +-SEED=n :seed number for bootstraps. +-KIMURA :use Kimura's correction. +-TOSSGAPS :ignore positions with gaps. +-BOOTLABELS=node OR branch :position of bootstrap values in tree display +-CLUSTERING= :NJ or UPGMA + + +>> HELP 0 << Help for tree output format options + +Four output formats are offered: 1) Clustal, 2) Phylip, 3) Just the distances +4) Nexus + +None of these formats displays the results graphically. Many packages can +display trees in the the PHYLIP format 2) below. It can also be imported into +the PHYLIP programs RETREE, DRAWTREE and DRAWGRAM for graphical display. +NEXUS format trees can be read by PAUP and MacClade. + +1) Clustal format output. +This format is verbose and lists all of the distances between the sequences and +the number of alignment positions used for each. The tree is described at the +end of the file. It lists the sequences that are joined at each alignment step +and the branch lengths. After two sequences are joined, it is referred to later +as a NODE. The number of a NODE is the number of the lowest sequence in that +NODE. + +2) Phylip format output. +This format is the New Hampshire format, used by many phylogenetic analysis +packages. It consists of a series of nested parentheses, describing the +branching order, with the sequence names and branch lengths. It can be used by +the RETREE, DRAWGRAM and DRAWTREE programs of the PHYLIP package to see the +trees graphically. This is the same format used during multiple alignment for +the guide trees. + +Use this format with NJplot (Manolo Gouy), supplied with Clustal W. Some other +packages that can read and display New Hampshire format are TreeView (Mac/PC), +TreeTool (UNIX), and Phylowin. + +3) The distances only. +This format just outputs a matrix of all the pairwise distances in a format +that can be used by the Phylip package. It used to be useful when one could not +produce distances from protein sequences in the Phylip package but is now +redundant (Protdist of Phylip 3.5 now does this). + +4) NEXUS FORMAT TREE. This format is used by several popular phylogeny programs, +including PAUP and MacClade. The format is described fully in: +Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. +NEXUS: an extensible file format for systematic information. +Systematic Biology 46:590-621. + +5) TOGGLE PHYLIP BOOTSTRAP POSITIONS +By default, the bootstrap values are placed on the nodes of the phylip format +output tree. This is inaccurate as the bootstrap values should be associated +with the tree branches and not the nodes. However, this format can be read and +displayed by TreeTool, TreeView and Phylowin. An option is available to +correctly place the bootstrap values on the branches with which they are +associated. diff --git a/website/prog_docs/mafft.html b/website/prog_docs/mafft.html new file mode 100644 index 0000000..3848d71 --- /dev/null +++ b/website/prog_docs/mafft.html @@ -0,0 +1,721 @@ + +Manpage of MAFFT + + +

    MAFFT

    +Section: Mafft Manual (1)
    Updated: 2007-06-09
    Index +Return to Main Contents
    + + + + + +  +

    NAME

    + +
    +mafft - Multiple alignment program for amino acid or nucleotide sequences +
    + +  +

    SYNOPSIS

    + +
    +
    +
    +mafft [options] input [> output] +
    +linsi input [> output] +
    +ginsi input [> output] +
    +einsi input [> output] +
    +fftnsi input [> output] +
    +fftns input [> output] +
    +nwns input [> output] +
    +nwnsi input [> output] +
    +mafft-profile group1 group2 [> output] +
    +

    +input, group1 and group2 must be in FASTA format. +

    +
    + +  +

    DESCRIPTION

    + +
    +MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods. +
    +  +

    Accuracy-oriented methods:

    + +

    +

    +*L-INS-i (probably most accurate; recommended for <200 sequences; +iterative refinement method incorporating local pairwise alignment +information): +
    +
    +mafft --localpair --maxiterate 1000 input [> output] +
    +linsi input [> output] +
    +
    + +

    +

    *G-INS-i (suitable for sequences +of similar lengths; recommended for <200 sequences; iterative +refinement method incorporating global pairwise alignment information): +
    +
    +mafft --globalpair --maxiterate 1000 input [> output] +
    +ginsi input [> output] +
    +
    + +

    +

    +*E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): +
    +
    +mafft --ep 0 --genafpair --maxiterate 1000 input [> output] +
    +einsi input [> output] +
    +

    +

    For E-INS-i, the +--ep +0 +option is recommended to allow large gaps. +
    +
    + +  +

    Speed-oriented methods:

    + +

    +

    +*FFT-NS-i (iterative refinement method; two cycles only): +
    +
    +mafft --retree 2 --maxiterate 2 input [> output] +
    +fftnsi input [> output] +
    +
    + +

    +

    +*FFT-NS-i (iterative refinement method; max. 1000 iterations): +
    +
    +mafft --retree 2 --maxiterate 1000 input [> output] +
    +
    + +

    +

    +*FFT-NS-2 (fast; progressive method): +
    +
    +mafft --retree 2 --maxiterate 0 input [> output] +
    +fftns input [> output] +
    +
    + +

    +

    +*FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree): +
    +
    +mafft --retree 1 --maxiterate 0 input [> output] +
    +
    + +

    +

    +*NW-NS-i (iterative refinement method without FFT approximation; two cycles only): +
    +
    +mafft --retree 2 --maxiterate 2 --nofft input [> output] +
    +nwnsi input [> output] +
    +
    + +

    +

    +*NW-NS-2 (fast; progressive method without the FFT approximation): +
    +
    +mafft --retree 2 --maxiterate 0 --nofft input [> output] +
    +nwns input [> output] +
    +
    + +

    +

    +*NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): +
    +
    +mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] +
    +
    + +  +

    Group-to-group alignments

    + +
    +
    +
    +mafft-profile group1 group2 [> output] +

    +

    or: +

    +mafft --maxiterate 1000 --seed group1 --seed group2 /dev/null [> output] +

    + + + +
    +  +

    OPTIONS

    + +  +

    Algorithm

    + +
    +

    + +--auto +

    +Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data +size. Default: off (always FFT-NS-2) +
    + +

    + +--6merpair +

    +Distance is calculated based on the number of shared 6mers. Default: on +
    + +

    + +--globalpair +

    +All pairwise alignments are computed with the Needleman-Wunsch +algorithm. More accurate but slower +than --6merpair. Suitable for a set of +globally alignable sequences. Applicable to +up to ~200 sequences. A combination with --maxiterate 1000 is recommended (G-INS-i). Default: off (6mer distance is used) +
    + +

    + +--localpair +

    +All pairwise alignments are computed with the Smith-Waterman +algorithm. More accurate but slower +than --6merpair. Suitable for a set of +locally alignable sequences. Applicable to +up to ~200 sequences. A combination with --maxiterate 1000 is recommended (L-INS-i). Default: off (6mer distance is used) +
    + +

    + +--genafpair +

    +All pairwise alignments are computed with a local +algorithm with the generalized affine gap cost +(Altschul 1998). More accurate but slower +than --6merpair. Suitable when large internal gaps +are expected. Applicable to +up to ~200 sequences. A combination with --maxiterate 1000 is recommended (E-INS-i). Default: off (6mer distance is used) +
    + + + + + + + +

    + +--fastapair +

    +All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). +FASTA is required. Default: off (6mer distance is used) +
    + + + + + + + +

    + +--weighti number +

    +Weighting factor for the consistency term calculated from pairwise alignments. Valid when +either of --blobalpair, --localpair, --genafpair, --fastapair or +--blastpair is selected. Default: 2.7 +
    + +

    + +--retree number +

    +Guide tree is built number times in the +progressive stage. Valid with 6mer distance. Default: 2 +
    + +

    + +--maxiterate number +

    +number cycles of iterative refinement are performed. Default: 0 +
    + +

    + +--fft +

    +Use FFT approximation in group-to-group alignment. Default: on +
    + +

    + +--nofft +

    +Do not use FFT approximation in group-to-group alignment. Default: off +
    + +

    + +--noscore +

    +Alignment score is not checked in the iterative refinement stage. Default: off (score is checked) +
    + +

    + +--memsave +

    +Use the Myers-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt). +
    + +

    + +--parttree +

    +Use a fast tree-building method (PartTree, Katoh and Toh 2007) with +the 6mer distance. Recommended for a large number (> ~10,000) +of sequences are input. Default: off +
    + +

    + +--dpparttree +

    +The PartTree algorithm is used with distances based on DP. Slightly +more accurate and slower than --parttree. Recommended for a large +number (> ~10,000) of sequences are input. Default: off +
    + +

    + +--fastaparttree +

    The PartTree algorithm is used +with distances based on FASTA. Slightly more accurate and slower than +--parttree. Recommended for a large number (> ~10,000) of sequences +are input. FASTA is required. Default: off +
    + +

    + +--partsize number +

    +The number of partitions in the PartTree algorithm. Default: 50 +
    + +

    + +--groupsize number +

    +Do not make alignment larger than number sequences. Valid only with the --*parttree options. Default: the number of input sequences +
    + +
    + +  +

    Parameter

    + +
    +

    + +--op number +

    +Gap opening penalty at group-to-group alignment. Default: 1.53 +
    + +

    + +--ep number +

    +Offset value, which works like gap extension penalty, for +group-to-group alignment. Deafult: 0.123 +
    + +

    + +--lop number +

    +Gap opening penalty at local pairwise +alignment. Valid when +the --localpair or --genafpair option is selected. Default: -2.00 +
    + +

    + +--lep number +

    +Offset value at local pairwise alignment. Valid when +the --localpair or --genafpair option is selected. Default: 0.1 +
    + +

    + +--lexp number +

    +Gap extension penalty at local pairwise alignment. Valid when +the --localpair or --genafpair option is selected. Default: -0.1 +
    + +

    + +--LOP number +

    +Gap opening penalty to skip the alignment. Valid when the +--genafpair option is selected. Default: -6.00 +
    + +

    + +--LEXP number +

    +Gap extension penalty to skip the alignment. Valid when the +--genafpair option is selected. Default: 0.00 +
    + +

    + +--bl number +

    +BLOSUM number matrix (Henikoff and Henikoff 1992) is used. number=30, 45, 62 or 80. Default: 62 +
    + +

    + +--jtt number +

    +JTT PAM number (Jones et al. 1992) matrix is used. number>0. Default: BLOSUM62 +
    + +

    + +--tm number +

    +Transmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62 +
    + +

    + +--aamatrix matrixfile +

    +Use a user-defined AA scoring matrix. The format of matrixfile is +the same to that of BLAST. Ignored when nucleotide sequences are input. Default: BLOSUM62 +
    + +

    + +--fmodel +

    +Incorporate the AA/nuc composition information into +the scoring matrix. Deafult: off +
    + +
    + +  +

    Output

    + +
    +

    + +--clustalout +

    +Output format: clustal format. Default: off (fasta format) +
    + +

    + +--inputorder +

    +Output order: same as input. Default: on +
    + +

    + +--reorder +

    +Output order: aligned. Default: off (inputorder) +
    + +

    + +--treeout +

    +Guide tree is output to the input.tree file. Default: off +
    + +

    + +--quiet +

    +Do not report progress. Default: off +
    + +
    + +  +

    Input

    + +
    +

    + +--nuc +

    +Assume the sequences are nucleotide. Deafult: auto +
    + +

    + +--amino +

    +Assume the sequences are amino acid. Deafult: auto +
    + +

    + +--seed alignment1 [--seed alignment2 --seed alignment3 ...] +

    +Seed alignments given in alignment_n (fasta format) are aligned with +sequences in input. The alignment within every seed is preserved. +
    + +
    + +  +

    FILES

    + +
    +

    + +Mafft stores the input sequences and other files in a temporary directory, which by default is located in +/tmp. +

    + +  +

    ENVIONMENT

    + +
    +

    + +MAFFT_BINARIES +

    +Indicates the location of the binary files used by mafft. By default, they are searched in +/usr/local/lib/mafft, but on Debian systems, they are searched in +/usr/lib/mafft. +
    + +

    + +FASTA_4_MAFFT +

    +This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH. +
    + +
    + +  +

    SEE ALSO

    + +
    +

    + +

    +mafft-homologs(1) +

    + +  +

    REFERENCES

    + +
    +
    +  +

    In English

    + +

    +

    *Katoh and Toh (Bioinformatics +23:372-374, 2007) PartTree: an algorithm to build an approximate tree +from a large number of unaligned sequences (describes the PartTree +algorithm). +
    + +

    +

    *Katoh, Kuma, Toh and Miyata +(Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in +accuracy of multiple sequence alignment (describes [ancestral versions +of] the G-INS-i, L-INS-i and E-INS-i strategies) +
    + +

    +

    *Katoh, Misawa, Kuma and Miyata +(Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid +multiple sequence alignment based on fast Fourier transform (describes +the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) +
    + +  +

    In Japanese

    + +

    +

    +*Katoh and Misawa (Seibutsubutsuri 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation +
    + +

    +

    +*Katoh and Kuma (Kagaku to Seibutsu 44:102-108, 2006) Jissen-teki Multiple Alignment +
    + + +  +

    AUTHORS

    + +
    +

    + +Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp> +

    +

    +
    +Wrote Mafft. +
    +

    + +Charles Plessy <charles-debian-nospam_at_plessy.org> +

    +

    +
    +Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template. +
    +
    + +  +

    COPYRIGHT

    + +
    +Copyright © 2002-2007 Kazutaka Katoh (mafft) +
    + +Copyright © 2007 Charles Plessy (this manpage) +
    + +

    + +Mafft and its manpage are offered under the following conditions: +

    Redistribution and use in source and binary forms, with or +without modification, are permitted provided that the following +conditions are met: +

    +

    + 1.Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +
    + +

    +

    2.Redistributions in binary +form must reproduce the above copyright notice, this list of conditions +and the following disclaimer in the documentation and/or other +materials provided with the distribution. +
    + +

    +

    3.The name of the author may +not be used to endorse or promote products derived from this software +without specific prior written permission. +
    + +

    THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR +IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, +INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) +HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, +STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING +IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. +
    + +

    + +

    + +

    + 

    Index

    +
    +
    NAME
    +
    SYNOPSIS
    +
    DESCRIPTION
    +
    +
    Accuracy-oriented methods:
    +
    Speed-oriented methods:
    +
    Group-to-group alignments
    +
    +
    OPTIONS
    +
    +
    Algorithm
    +
    Parameter
    +
    Output
    +
    Input
    +
    +
    FILES
    +
    ENVIONMENT
    +
    SEE ALSO
    +
    REFERENCES
    +
    +
    In English
    +
    In Japanese
    +
    +
    AUTHORS
    +
    COPYRIGHT
    +
    +
    +This document was created by +man2html, +using the manual pages.
    +Time: 02:26:04 GMT, August 14, 2007 + \ No newline at end of file diff --git a/website/prog_docs/muscle.html b/website/prog_docs/muscle.html new file mode 100644 index 0000000..36055f8 --- /dev/null +++ b/website/prog_docs/muscle.html @@ -0,0 +1,4171 @@ + + + + + + + + +MUSCLE User Guide + + + + + + + +
    + +

     

    + +

     

    + +

     

    + +

     

    + +

    MUSCLE User Guide

    + +

                                                                                                                                                                                

    + +

     

    + +

     

    + +

     

    + +

     

    + +

     

    + +

     

    + +

    Multiple sequence comparison +by log-expectation

    + +

    by Robert C. Edgar

    + +

     

    + +

    Version 3.6

    + +

    September 2005

    + +

     

    + +

     

    + +

    http://www.drive5.com/muscle

    + +

    email: muscle (at) drive5.com

    + +

     

    + +

    MUSCLE is updated regularly. +Send me an e-mail if you would like to be notified of new releases.

    + +

     

    + +

     

    + +

    Citation:

    + +

     

    + +

    Edgar, +Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and +high throughput, Nucleic Acids Research 32(5), 1792-97.

    + +

     

    + +

    For a complete +description of the algorithm, see also:

    + +

     

    + +

    Edgar, Robert C (2004), MUSCLE: a multiple sequence alignment method +with reduced time and space complexity. BMC Bioinformatics, 5(1):113.
    +    Table of Contents

    + +

    1 +Introduction. 3

    + +

    2 +Quick Start 3

    + +

    2.1 +Installation. 3

    + +

    2.2 +Making an alignment 3

    + +

    2.3 +Large alignments. 3

    + +

    2.4 +Faster speed. 4

    + +

    2.5 +Huge alignments. 4

    + +

    2.6 +Accuracy: caveat emptor 4

    + +

    2.7 +Pipelining. 4

    + +

    2.8 +Refining an existing alignment 4

    + +

    2.9 +Using a pre-computed guide tree. 4

    + +

    2.10 +Profile-profile alignment 5

    + +

    2.11 +Adding sequences to an existing alignment 5

    + +

    2.12 +Sequence clustering. 5

    + +

    2.13 +Specifying a substitution matrix. 6

    + +

    2.14 +Refining a long alignment 6

    + +

    3 +File Formats. 6

    + +

    3.1 +Input files. 6

    + +

    3.1.1 +Amino acid sequences. 6

    + +

    3.1.2 +Nucleotide sequences. 6

    + +

    3.1.3 +Determining sequence type. 7

    + +

    3.2 +Output files. 7

    + +

    3.2.1 +Sequence grouping. 7

    + +

    3.3 +CLUSTALW format 7

    + +

    3.4 +MSF format 7

    + +

    3.5 +HTML format 8

    + +

    3.6 +Phylip format 8

    + +

    4 +Using MUSCLE. 8

    + +

    4.1 +How the algorithm works. 8

    + +

    4.2 +Command-line options. 9

    + +

    4.3 +The maxiters option. 9

    + +

    4.4 +The maxtrees option. 10

    + +

    4.5 +The maxhours option. 10

    + +

    4.6 +The maxmb option. 10

    + +

    4.7 +The profile scoring function. 10

    + +

    4.8 +Diagonal optimization. 10

    + +

    4.9 +Anchor optimization. 11

    + +

    4.10 +Log file. 11

    + +

    4.11 +Progress messages. 11

    + +

    4.12 +Running out of memory. 12

    + +

    4.13 +Troubleshooting. 12

    + +

    4.14 +Technical support 12

    + +

    5 +Command Line Reference. 13

    + +

     

    + +
    +     + +

    1 Introduction

    + +

    MUSCLE is a program for creating multiple alignments of +amino acid or nucleotide sequences. A range of options is provided that give +you the choice of optimizing accuracy, speed, or some compromise between the +two. Default parameters are those that give the best average accuracy in our +tests. Using versions current at the time of writing, my tests show that MUSCLE +can achieve both better average accuracy and better speed than CLUSTALW or T‑Coffee, +depending on the chosen options. Many command line options are provided to vary +the internals of the algorithm; some of these will primarily be of interest to +algorithm developers who wish to better understand which features of the algorithm +are important in different circumstances.

    + +

    2 Quick Start

    + +

    The MUSCLE algorithm is delivered as a command-line program +called muscle. If you are running under Linux or Unix +you will be working at a shell prompt. If you are running under Windows, you should +be in a command window (nostalgically known to us older people as a DOS prompt). +If you don't know how to use command-line programs, you should get help from a +local guru.

    + +

    2.1 Installation

    + +

    Copy the muscle binary file to a directory that is +accessible from your computer. That's it—there are no configuration files, +libraries, environment variables or other settings to worry about. If you are +using Windows, then the binary file is named muscle.exe. From now on muscle +should be understood to mean "muscle if you are using Linux or Unix, muscle.exe if you are using Windows".

    + +

    2.2 Making +an alignment

    + +

    Make a FASTA file containing some sequences. (If you are not +familiar with FASTA format, it is described in detail later in this Guide.) For +now, just to make things fast, limit the number of sequence in the file to no +more than 50 and the sequence length to be no more than 500. Call the input +file seqs.fa. (An example file named seqs.fa is distributed with the standard MUSCLE +package). Make sure the directory containing the muscle binary is in +your path. (If it isn't, you can run it by typing the full path name, and the +following example command lines must be changed accordingly). Now type:

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa

    + +

     

    + +

    You should see some progress messages. If muscle completes +successfully, it will create a file seqs.afa +containing the alignment. By default, output is created in "aligned +FASTA" format (hence the .afa extension). +This is just like regular FASTA except that gaps are added in order to align +the sequences. This is a nice format for computers but not very readable for +people, so to look at the alignment you will want an alignment viewer such as Belvu, or a script that converts FASTA to a more readable format. +You can also use the –clw command-line option +to request output in CLUSTALW format, which is easier to understand for people. +If muscle gives an error message and you don't know how to fix it, +please read the Troubleshooting section.

    + +

     

    + +

    The default settings are designed to give the best accuracy, +so this may be all you need to know.

    + +

    2.3 Large +alignments

    + +

    If you have a large number of sequences (a few thousand), or +they are very long, then the default settings of may be too slow for practical +use. A good compromise between speed and accuracy is to run just the first two +iterations of the algorithm. On average, this gives accuracy comparable to +T-Coffee and speeds much faster than CLUSTALW. This is done by the option –maxiters +2, as in the following example.

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -maxiters 2

    + +

    2.4 Faster +speed

    + +

    The –diags option enables +an optimization for speed by finding common words (6-mers in a compressed amino +acid alphabet) between the two sequences as seeds for diagonals. This is +related to optimizations in programs such as BLAST and FASTA: you get faster speed, +but sometimes lower average accuracy. For large numbers of closely related +sequences, this option works very well.

    + +

     

    + +

    If you want the fastest possible speed, then the following +example shows the applicable options for proteins.

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags -sv +-distance1 kbit20_3

    + +

     

    + +

    For nucleotides, use:

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags

    + +

     

    + +

    At the time of writing, muscle with these options is faster +than any other multiple sequence alignment program +that I have tested. The alignments are not bad, especially when the sequences +are closely related. However, as you might expect, this blazing speed comes at +the cost of the lowest average accuracy of the options that muscle +provides.

    + +

    2.5 Huge +alignments

    + +

    If you have a very large number of sequences (several +thousand), or they are very long, then the kbit20_3 option may cause +problems because it needs a relatively large amount of memory. Better is to use +the default distance measure, which is roughly 2× or 3× slower but needs less +memory, like this:

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv

    + +

    2.6 Accuracy: +caveat emptor

    + +

    Why do I keep using the clumsy phrase "average +accuracy" instead of just saying "accuracy"? That's because the +quality of alignments produced by MUSCLE varies, as do those produced other programs +such as CLUSTALW and T-Coffee. The state of the art leaves plenty of room for +improvement. Sometimes the fastest speed options to muscle give +alignments that are better than T-Coffee, though the reverse will more often be +the case. With challenging sets of sequences, it is a good idea to make several +different alignments using different muscle options and to try other programs +too. Regions where different alignments agree are more believable than regions +where they disagree.

    + +

    2.7 Pipelining

    + +

    Input can be taken from standard input, and output can be +written to standard output. This is the default, so our first example would +also work like this:

    + +

     

    + +

    muscle < seqs.fa > seqs.afa

    + +

    2.8 Refining +an existing alignment

    + +

    You can ask muscle to try to improve an existing +alignment by using the –refine option. The input file must then be a +FASTA file containing an alignment. All sequences must be of equal length, gaps +can be specified using dots "." or dashes "–". For example:

    + +

     

    + +

    muscle -in seqs.afa -out refined.afa -refine

    + +

    2.9 Using +a pre-computed guide tree

    + +

    The –usetree option allows +you to provide your own guide tree. For example,

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -usetree mytree.phy

    + +

     

    + +

    The tree must by in Newick format, +as used by the Phylip package (hence the .phy extension). The Newick +format is described here:

    + +

     

    + +

            http://evolution.genetics.washington.edu/phylip/newicktree.html

    + +

     

    + +

    WARNING. Do not use this +option just because you believe that you have an accurate evolutionary tree for +your sequences. The best guide tree for multiple alignment +is not in general the correct evolutionary tree. This can be understood +by the following argument. Alignment accuracy decreases with lower sequence +identity. It follows that given a set of profiles, the +two that can be aligned most accurately will tend to be the pair with the +highest identity, i.e. at the shortest evolutionary distance. This is exactly +the pair selected by the nearest-neighbor criterion which MUSCLE uses by +default. When mutation rates are variable, the evolutionary neighbor may +not be the nearest neighbor. This explains why a nearest-neighbor tree +may be superior to the true evolutionary tree for guiding a progressive alignment.

    + +

     

    + +

    You will get a warning if you use the –usetree +option. To disable the warning, use ­–usetree_nowarn +instead,

    + +

    e.g.:

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -usetree_nowarn mytree.phy

    + +

    2.10 Profile-profile +alignment

    + +

    A fundamental step in the MUSCLE algorithm is aligning two +multiple sequence alignments. This operation is sometimes called +"profile-profile alignment". If you have two existing alignments of +related sequences you can use the –profile option of MUSCLE to align +those two sequences. Typical usage is:

    + +

     

    + +

    muscle -profile -in1 one.afa -in2 two.afa -out both.afa

    + +

     

    + +

    The alignments in one.afa +and two.afa, which must be in aligned FASTA +format, are aligned to each other, keeping input columns intact and inserting +columns of gaps where needed. Output is stored in both.afa.

    + +

     

    + +

    MUSCLE does not compute a similarity measure or measure of +statistical significance (such as an E-value), so this option is not useful for +discriminating homologs from unrelated sequences. For this task, I recommend Sadreyev & Grishin's COMPASS +program.

    + +

    2.11 Adding +sequences to an existing alignment

    + +

    To add a sequence to an existing alignment that you wish to +keep intact, use profile-profile alignment with the new sequence as a profile. +For example, if you have an existing alignment existing_aln.afa +and want to add a new sequence in new_seq.fa, +use the following commands:

    + +

     

    + +

    muscle -profile -in1 existing_aln.afa -in2 new_seq.fa -out +combined.afa

    + +

     

    + +

    If you have more than one new sequences, +you can align them first then add them, for example:

    + +

     

    + +

    muscle -in new_seqs.fa -out new_seqs.afa

    + +

    muscle -profile -in1 existing_aln.afa -in2 new_seqs.fa -out +combined.afas

    + +

    2.12 Sequence +clustering

    + +

    The first stage in MUSCLE is a fast clustering algorithm. +This may be of use in other applications. Typical usage is:

    + +

     

    + +

    muscle -cluster -in seqs.fa -tree1 tree.phy -maxiters 1

    + +

     

    + +

    The sequences will be clustered, and a tree written to tree.phy. Options –weight1, –distance1, +–cluster1 and –root1 can be applied if desired. Note that by +default, UPGMA clustering is used. You can use

    + +

     –neighborjoining if you prefer, but note that this is +substantially slower than UPGMA for large numbers of sequences, and is also +slightly less accurate. See discussion of –usetree +above.

    + +

    2.13 Specifying +a substitution matrix

    + +

    You can specify your own substitution matrix by using the -matrix +option. This reads a protein substitution matrix in NCBI or WU-BLAST format. +The alphabet is assumed to be amino acid, and sum-of-pairs scoring is used. The +­-gapopen, -gapextend +and -center parameters should be specified; normally you will specify a +zero value for the center. Note that gap penalties MUST be negative. The +environment variable MUSCLE_MXPATH can be used to specify a path where the +matrices are stored. For example,

    + +

     

    + +

    muscle -in seqs.fa -out seqs.afa -matrix blosum62 -gapopen -12.0

    + +

        -gapextend -1.0 -center 0.0

    + +

     

    + +

    You can hack a nucleotide matrix by pretending that AGCT are +amino acids and making a 20x20 matrix out of the original 4x4 matrix. Let me +know if this isn't clear, I can help you through it.

    + +

    2.14 Refining +a long alignment

    + +

    A long alignment can be refined using the –refinew option, which is primarily designed for +refining whole-genome nucleotide alignments. Usage is:

    + +

     

    + +

    muscle -in input.afa -out output.afa

    + +

     

    + +

    MUSCLE divides the input alignment into non-overlapping +windows and re-aligns each window from scratch, i.e. all gap characters are +discarded. The –refinewindow option may be +used to change the window length, which is 200 columns +by default.

    + +

    3 File Formats

    + +

    MUSCLE uses FASTA format for both input and output. For +output only, it also offers CLUSTALW, MSF, HTML, Phylip +sequential and Phylip interleaved formats. See the +following command-line options: ‑clw, ‑clwstrict, –msf, +–html, –phys, –phyi, ‑clwout, ‑clwstrictout, +–msfout, –htmlout, +–physout and –phyiout.

    + +

     

    + +

    3.1 Input +files

    + +

    Input files must be in FASTA format. These are plain text +files (word processing files such as Word documents are not understood!). Unix, Windows and DOS text files are supported (end-of-line +may be NL or CR NL). There is no explicit limit on the length of a sequence, +however if you are running a 32-bit version of muscle then the maximum +will be very roughly 10,000 letters due to maximum addressable size of tables +required in memory. Each sequence starts with an annotation line, which is +recognized by having a greater-than symbol ">" as its first +character. There is no limit on the length of an annotation line (this is new +as of version 3.5), and there is no requirement that the annotation be unique. The +sequence itself follows on one or more subsequent lines, and is terminated +either by the next annotation line or by the end of the file.

    + +

    3.1.1 Amino acid sequences

    + +

    The standard single-letter amino acid alphabet is used. Upper +and lower case is allowed, the case is not significant. The special characters +X, B, Z and U are understood. X means "unknown amino acid", B is D or +N, Z is E or Q. U is understood to be the 21st amino acid Selenocysteine. +White space (spaces, tabs and the end-of-line characters CR and NL) is allowed +inside sequence data. Dots "." and dashes "–" in sequences +are allowed and are discarded unless the input is expected to be aligned (e.g. +for the –refine option).

    + +

    3.1.2 Nucleotide sequences

    + +

    The usual letters A, G, C, T and U stand for nucleotides. +The letters T and U are equivalent as far as MUSCLE is concerned. N is the +wildcard meaning "unknown nucleotide". R means A or G, Y means C or +T/U. Other wildcards, such as those used by RFAM, are not understood in this +version and will be replaced by Ns. If you would like support for other DNA / +RNA alphabets, please let me know.

    + +

    3.1.3 Determining sequence type

    + +

    By default, MUSCLE looks at the first 100 letters in the +input sequence data (excluding gaps). If 95% or more of those letters are valid +nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as +amino acids. This method almost always guesses correctly, but you can make sure +by specifying the sequence type on the command line. This is done using the –seqtype option, which can take the following values:

    + +

     

    + +

            –­seqtype protein                          Amino acid

    + +

            –seqtype nucleo                          Nucleotide

    + +

            –seqtype auto                               Automatic +detection (default).

    + +

    3.2 Output +files

    + +

    By default, output is also written in FASTA format. All +letters are upper-case and gaps are represented by dashes "–". Output +is written to the following destination(s):

    + +

     

    + +

            If no other +output option is given, then standard output.

    + +

            If -out <filename> +is given, to the specified file.

    + +

            For all of the -xxxout options +(e.g. -fastaout, -clwout), +to the specified files.

    + +

    3.2.1 Sequence grouping

    + +

    By default, MUSCLE re-arranges sequences so that similar +sequences are adjacent in the output file. (This is done by ordering sequences +according to a prefix traversal of the guide tree). This makes the alignment +easier to evaluate by eye. If you want to the sequences to be output in the +same order as the input file, you can use the –stable option.

    + +

    3.2.2 Output to multiple file +formats

    + +

    You can request output to more than one file format by using +the -xxxout options. For example, to get both +FASTA and CLUSTALW formats:

    + +

     

    + +

    muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln

    + +

    3.3 CLUSTALW +format

    + +

    You can request CLUSTALW output by using the –clw option. This should be compatible with CLUSTALW, +with the exception of the program name in the file header. You can ask MUSCLE +to impersonate CLUSTALW by writing "CLUSTAL W (1.81)" as the program +name by using –clwstrict or ‑clwstrictout. Note that MUSCLE allows duplicate +sequence labels, while CLUSTALW forbids duplicates. If you use the –stable +option of muscle, then the order of the input sequences is preserved and +sequences can be unambiguously identified even if the labels differ. If you +have problems parsing MUSCLE output with scripts designed for CLUSTALW, please +let me know and I'll do my best to provide a fix.

    + +

    3.4 MSF +format

    + +

    MSF format, as used in the GCG package, is requested by +using the –msf option. As with CLUSTALW +format, this is easier for people to read than FASTA. As of MUSCLE 3.52, the +MSF format has been tweaked to be more compatible with GCG. The following +differences remain.

    + +

     

    + +

    (a) MUSCLE truncates at the first white space or after 63 +characters, which ever comes first. The GCG package apparently truncates after +10 characters. If this is a problem for you, please let me know and I'll add an +option to truncate after 10 in a future version.

    + +

     

    + +

    (b) MUSCLE allows duplicate sequence labels, while GCG +forbids duplicates. If you use the –stable option of muscle, then +the order of the input sequences is preserved and sequences can be +unambiguously identified even if the labels differ.

    + +

     

    + +

    Thanks to Eric Martel for help with improving GCG +compatibility.

    + +

    3.5 HTML +format

    + +

    I've added an experimental feature starting in version 3.4. To +get a Web page as output, use the –html option. The alignment is colored +using a color scheme from Eric Sonnhammer's Belvu editor, which is my personal favorite. A drawback of +this option is that the Web page typically contains a very large number of HTML +tags, which can be slow to display in the Internet Explorer browser. The +Netscape browser works much better. If you have any ideas about good ways to +make Web pages, please let me know.

    + +

    3.6 Phylip format

    + +

    The Phylip package supports two +different multiple sequence alignment file formats, called sequential and +interleaved respectively.

    + +

    4 Using MUSCLE

    + +

    In this section we give more details of the MUSCLE algorithm +and the more important options offered by the muscle implementation.

    + +

    4.1 How +the algorithm works

    + +

    I won't give a complete description of the MUSCLE algorithm +here—for that, you will have to read the papers. (See citations on title page +above). But hopefully a summary will help explain what some of the command-line +options do and how they might be useful in your work.

    + +

     

    + +

    The first step is to calculate a tree. In CLUSTALW, this is +done as follows. Each pair of input sequences is aligned, and used to compute +the pair-wise identity of the pair. Identities are converted to a measure of +distance. Finally, the distance matrix is converted to a tree using a +clustering method (CLUSTALW uses neighbor-joining). If you have 1,000 +sequences, there are (1,000 ´ 999)/2 = 499,500 pairs, so aligning every pair can take +a while. MUSCLE uses a much faster, but somewhat more approximate, method to +compute distances: it counts the number of short sub-sequences (known as k-mers, k-tuples or words) +that two sequences have in common, without constructing an alignment. This is +typically around 3,000 times faster that CLUSTALW's +method, but the trees will generally be less accurate. We call this step "k-mer clustering".

    + +

     

    + +

    The second step is to use the tree to construct what is +known as a progressive alignment. At each node of the binary tree, a pair-wise +alignment is constructed, progressing from the leaves towards the root. The +first alignment will be made from two sequences. Later alignments will be one +of the three following types: sequence-sequence, profile-sequence or +profile-profile, where "profile" means the multiple alignment of the sequences under a given internal node of +the tree. This is very similar to what CLUSTALW does once it has built a tree.

    + +

     

    + +

    Now we have a multiple +alignment, which has been built very quickly compared with conventional +methods, mainly because of the distance calculation using k-mers rather than alignments. The quality of this alignment +is typically pretty good—it will often tie or beat a T-Coffee alignment on our +tests. However, on average, we find that it can be improved by proceeding +through the following steps.

    + +

     

    + +

    From the multiple alignment, we can now compute the pair-wise identities of +each pair of sequences. This gives us a new distance matrix, from which we +estimate a new tree. We compare the old and new trees, and re-align subgroups +where needed to produce a progressive multiple alignment from the new tree. If +the two trees are identical, there is nothing to do; if there are no subtrees +that agree (very unusual), then the whole progressive alignment procedure must +be repeated from scratch. Typically we find that the tree is pretty stable near +the leaves, but some re-alignments are needed closer the root. This procedure +(compute pair-wise identities, estimate new tree, compare trees, re-align) is +iterated until the tree stabilizes or until a specified maximum number of +iterations has been done. We call this process "tree refinement", +although it also tends to improve the alignment.

    + +

     

    + +

    We now keep the tree fixed +and move to a new procedure which is designed to improve the multiple +alignment. The set of sequences is divided into two subsets (i.e., we make a +bipartition on the set of sequences). A profile is constructed for each of the +two subsets based on the current multiple alignment. +These two profiles are then re-aligned to each other using the same pair-wise +alignment algorithm as used in the progressive stage. If this improves an +"objective score" that measures the quality of the alignment, then +the new multiple alignment is kept, otherwise it is +discarded. By default, the objective score is the classic sum-of-pairs score +that takes the (sequence weighted) average of the pair-wise alignment score of +every pair of sequences in the alignment. Bipartitions are chosen by deleting +an edge in the guide tree, each of the two resulting subtrees defines a subset +of sequences. This procedure is called "tree dependent refinement". One iteration of tree dependent refinement tries +bipartitions produced by deleting every edge of the tree in depth order moving +from the leaves towards the center of the tree. Iterations continue until +convergence or up to a specified maximum.

    + +

     

    + +

    For convenience, the major +steps in MUSCLE are described as "iterations", though the first three +iterations all do quite different things and may take very different lengths of +time to complete. The tree-dependent refinement iterations 3, 4 ... are true +iterations and will take similar lengths of time.

    + +

     

    + + + + + + + + + + + + + + + + + + +
    +

    Iteration

    +     		+

    Actions

    +
    +

    1

    +     		+

    Distance matrix by k-mer clustering, estimate tree, progressive alignment + according to this tree.

    +

     

    +
    +

    2

    +     		+

    Distance matrix by + pair-wise identities from current multiple alignment, estimate tree, + progressive alignment according to new tree, repeat until convergence or specified + maximum number of times.

    +

     

    +
    +

    3, 4 ...

    +     		+

    Tree-dependent refinement. One iteration visits every edge in the tree one time.

    +
    + +

    4.2 Command-line +options

    + +

    There are two types of command-line options: value options +and flag options. Value options are followed by the value of the given +parameter, for example –in <filename>; flag options just stand for +themselves, such as –msf. All options are a +dash (not two dashes!) followed by a long name; there are no single-letter +equivalents. Value options must be separated from their values by white space +in the command line. Thus, muscle does not follow Unix, +Linux or Posix standards, for which we apologize. The +order in which options are given is irrelevant unless two options contradict, +in which case the right-most option silently wins.

    + +

    4.3 The +maxiters option

    + +

    You can control the number of iterations that MUSCLE does by +specifying the –maxiters option. If you specify 1, 2 or 3, then this is +exactly the number of iterations that will be performed. If the value is +greater than 3, then muscle will continue up to the maximum you specify +or until convergence is reached, which ever happens sooner. The default is 16. +If you have a large number of sequences, refinement may be rather slow.

    + +

    4.4 The +maxtrees option

    + +

    This option controls the maximum number of new trees to +create in iteration 2. Our experience suggests that a point of diminishing +returns is typically reached after the first tree, so the default value is 1. +If a larger value is given, the process will repeat until convergence or until +this number of trees has been created, which ever comes first.

    + +

    4.5 The +maxhours option

    + +

    If you have a large alignment, muscle may take a long +time to complete. It is sometimes convenient to say "I want the best +alignment I can get in 24 hours" rather than specifying a set of options +that will take an unknown length of time. This is done by using –maxhours, which specifies a floating-point number of +hours. If this time is exceeded, muscle will write out current alignment +and stop. For example,

    + +

     

    + +

    muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0

    + +

     

    + +

    Note that the actual time may exceed the specified limit by +a few minutes while muscle finishes up on a step. It is also possible +for no alignment to be produced if the time limit is too small.

    + +

    4.6 The +maxmb option

    + +

    If the amount of memory needed by MUSCLE exceeds available +physical RAM, then the operating system will probably begin paging (i.e., +swapping memory to and from hard disk), causing MUSCLE to run very slowly. This +is especially problematic when MUSCLE is used for batch processing, where one or +two very large alignments can cause a batch to effectively hang. Starting in +version 3.52, MUSCLE attempts to limit the amount of memory used. If the limit +is exceeded, MUSCLE quits, saving the best alignment so far produced (if any). +MUSCLE attempts to determine the amount of physical RAM by making an +appropriate operating system call. Under Linux and Windows, this works well. On +other systems, particularly other flavors of Unix, +MUSCLE doesn't know how to query the system and assumes that there is 500 Mb of +RAM. To override this default, you can specify the maximum number of megabytes +to allocate by using the –maxmb option, for +example to set a limit of 1.5 Gb:

    + +

     

    + +

    muscle -in huge.fa -out huge.afa -maxhours 1.0 -maxmb 1500

    + +

     

    + +

    This feature has been hacked on top of code that wasn't +really designed for it. So it doesn't always work perfectly, but is better than +nothing. The ideal solution would be to implement linear space dynamic +programming code (e.g., the Myers-Miller algorithm) for situations where memory +is tight. One day I might do this if there is sufficient interest. If you are +interested in contributing the code, e.g. for a class project, please let me +know, I'll be glad to provide support.

    + +

    4.7 The +profile scoring function

    + +

    Three different protein profile scoring functions are +supported, the log-expectation score (–le option) and a sum of pairs +score using either the PAM200 matrix (–sp) or the VTML240 matrix (–sv). The log-expectation score is the default as it +gives better results on our tests, but is typically somewhere between two or +three times slower than the sum-of-pairs score. For nucleotides, –spn is currently the only option (which is of course +the default for nucleotide data, so you don't need to specify this option).

    + +

    4.8 Diagonal +optimization

    + +

    Creating a pair-wise alignment by dynamic programming +requires computing an L1 ´ L2 +matrix, where L1 and L2 are the sequence +lengths. A trick used in algorithms such as BLAST is to reduce the size of this +matrix by using fast methods to find "diagonals", i.e. short regions +of high similarity between the two sequences. This speeds up the algorithm at +the expense of some reduction in accuracy. MUSCLE uses a technique called k-mer extension to find diagonals. It is disabled by default +because of the slight reduction in average accuracy and can be turned on by +specifying the –diags option. To enable +diagonal optimization in the first iteration, use –diags1, to enable +diagonal optimization in the second iteration, use –diags2. These are +provided separately because it would be a reasonable strategy to enable +diagonals in the first iteration but not the second (because the main goal of +the first iteration is to construct a multiple alignment quickly in order to +improve the distance matrix, which is not very sensitive to alignment quality; +whereas the goal of the second iteration is to make the best possible +progressive alignment).

    + +

    4.9 Anchor +optimization

    + +

    Tree-dependent refinement (iterations 3, 4 ... ) can be speeded up by dividing the alignment vertically +into blocks. Block boundaries are found by identifying high-scoring columns +(e.g., a perfectly conserved column of Cs or Ws would be a candidate). Each +vertical block is then refined independently before reassembling the complete +alignment, which is faster because of the L2 factor in +dynamic programming (e.g., suppose the alignment is split into two vertical +blocks, then 2 ´ +0.52 = 0.5, so the dynamic programming time is roughly halved). The +–noanchors option is used to disable this +feature. This option has no effect if –maxiters 1 or –maxiters 2 +is specified. On benchmark tests, enabling anchors has little or no effect on +accuracy, but if you want to be very conservative and are striving for the best +possible accuracy then –noanchors is a +reasonable choice.

    + +

    4.10 Log +file

    + +

    You can specify a log file by using –log <filename> +or –loga <filename>. Using –log +causes any existing file to be deleted, –loga +appends to any existing file. A message will be written to the log file when muscle +starts and stops. Error and warning messages will also be written to the log. +If –verbose is specified, then more information will be written, +including the command line used to invoke muscle, the resulting internal +parameter settings, and also progress messages. The content and format of +verbose log file output is subject to change in future versions.

    + +

     

    + +

    The use of a log file may seem contrary to Unix conventions for using standard output and standard +error. I like these conventions, but never found a fully satisfactory way to +use them. I like progress messages (see below), but they mess up a file if you +re-direct standard error and there are errors or warning messages too. I could +try to detect whether a standard file handle is a tty device or a disk file and change behavior +accordingly, but I regard this as too complicated and too hard for the user to +understand. On Windows it can be hard to re-direct standard file handles, +especially when working in a GUI debugger. Maybe one day I will figure out a +better solution (suggestions welcomed).

    + +

     

    + +

    I highly recommend using –verbose and ­–log[a], +especially when running muscle in a batch mode. This enables you to +verify whether a particular alignment was completed and to review any errors or +warnings that occurred.

    + +

    4.11 Progress +messages

    + +

    By default, muscle writes progress messages to +standard error periodically so that you know it's doing something and get some +feedback about the time and memory requirements for the alignment. Here is a +typical progress message.

    + +

     

    + +

    00:00:23     25 Mb (5%)  Iter   +2  87.20%  Build guide tree

    + +

     

    + +

    The fields are as follows.

    + +

     

    + + + + + + + + + + + + + + + + + + + + + + +
    +

    00:00:23

    +     		+

    Elapsed time since muscle + started.

    +
    +

    25 Mb (5%)

    +     		+

    Peak memory use in megabytes + (i.e., not the current usage, but the maximum amount of memory used since muscle + started). The number in parentheses is the fraction of physical memory (see –maxmb option for more discussion).

    +
    +

    Iter 2

    +     		+

    Iteration currently in + progress.

    +
    +

    87.20%

    +     		+

    How much of the current step + has been completed (percentage).

    +
    +

    Build...

    +     		+

    A brief description of the current step.

    +
    + +

     

    + +

    The –quiet command-line option disables writing +progress messages to standard error. If the –verbose command-line option +is specified, a progress message will be written to the log file when each iteration completes. So –quiet and –verbose +are not contradictory.

    + +

    4.12 Running +out of memory

    + +

    The muscle code tries to deal gracefully with +low-memory conditions by using the following technique. A block of "emergency +reserve" memory is allocated when muscle starts. If a later request +to allocate memory fails, this reserve block is made available, and muscle +attempts to save the current alignment. With luck, the reserved memory will be +enough to allow muscle to save the alignment and exit gracefully with an +informative error message. See also the –maxmb +option.

    + +

    4.13 Troubleshooting

    + +

    Here is some general advice on what to do if muscle +fails and you don't understand what happened. The code is designed to fail +gracefully with an informative error message when something goes wrong, but +there will no doubt be situations I haven't anticipated (not to mention bugs).

    + +

     

    + +

    Check the MUSCLE web site for updates, bug reports and other +relevant information.

    + +

     

    + +

            http://www.drive5.com/muscle

    + +

     

    + +

    Check the input file to make sure it is in valid FASTA +format. Try giving it to another sequence analysis program that can accept +large FASTA files (e.g., the NCBI formatdb +utility) to see if you get an informative error message. Try dividing the file +into two halves and using each half individually as input. If one half fails +and the other does not, repeat until the problem is +localized as far as possible.

    + +

     

    + +

    Use –log or –loga +and –­verbose and check the log file to see if there are any messages +that give you a hint about the problem. Look at the peak memory requirements +(reported in progress messages) to see if you may be exceeding the physical or +virtual memory capacity of your computer.

    + +

     

    + +

    If muscle crashes without giving an error message, or +hangs, then you may need to refer to the source code or use a debugger. A +"debug" version, muscled, may be provided. This is built from +the same source code but with the DEBUG macro defined and without compiler +optimizations. This version runs much more slowly (perhaps by a factor of three +or more), but does a lot more internal checking and may be able to catch +something that is going wrong in the code. The –­core option specifies +that muscle should not catch exceptions. When –core is specified, +an exception may result in a debugger trap or a core dump, depending on the +execution environment. The –nocore option has +the opposite effect. In muscle, –nocore +is the default, –­core is the default in muscled.

    + +

    4.14 Technical +support

    + +

    I am happy to provide support. But I am busy, and am +offering this program at no charge, so I ask you to make a reasonable effort to +figure things out for yourself before contacting me.

    + +

    5 Command Line Reference

    + +

     

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    Value option

    +     		+

    Legal values

    +     		+

    Default

    +     		+

    Description

    +
    +

    anchorspacing

    +     		+

    Integer

    +     		+

    32

    +     		+

    Minimum spacing between + anchor columns.

    +

     

    +
    +

    center

    +     		+

    Floating point

    +     		+

    [1]

    +     		+

    Center parameter. Should be + negative.

    +

     

    +
    +

    cluster1

    +

    cluster2

    +     		+

    upgma

    +

    upgmb

    +

    neighborjoining

    +     		+

    upgmb

    +     		+

    Clustering method. cluster1 is used in iteration 1 and 2, cluster2 in later + iterations.

    +

     

    +
    +

    clwout

    +     		+

    File name

    +     		+

    None

    +     		+

    Write output in CLUSTALW + format to given file name.

    +
    +

    clwout

    +     		+

    File name

    +     		+

    None

    +     		+

    As -clwout, + except that header is strictly compatible with CLUSTALW 1.81.

    +

     

    +
    +

    diagbreak

    +     		+

    Integer

    +     		+

    1

    +     		+

    Maximum distance between two diagonals that allows them to + merge into one diagonal.

    +

     

    +
    +

    diaglength

    +     		+

    Integer

    +     		+

    24

    +     		+

    Minimum length of diagonal.

    +

     

    +
    +

    diagmargin

    +     		+

    Integer

    +     		+

    5

    +     		+

    Discard this many positions + at ends of diagonal.

    +

     

    +
    +

    distance1

    +

     

    +     		+

    kmer6_6

    +

    kmer20_3

    +

    kmer20_4

    +

    kbit20_3

    +

    kmer4_6

    +

     

    +     		+

    Kmer6_6 + (amino) or Kmer4_6 (nucleo)

    +     		+

    Distance measure for iteration 1.

    +
    +

    distance2

    +

     

    +     		+

    kmer6_6

    +

    kmer20_3

    +

    kmer20_4

    +

    kbit20_3

    +

    pctid_kimura

    +

    pctid_log

    +

     

    +     		+

    pctid_kimura

    +     		+

    Distance measure for iterations 2, 3 ...

    +

     

    +

     

    +

     

    +

     

    +
    +

    fastaout

    +     		+

    File + name

    +     		+

    None

    +     		+

    Write output in FASTA format to the given file.

    +

     

    +
    +

    gapopen

    +     		+

    Floating point

    +     		+

    [1]

    +     		+

    The gap open score. Must be + negative.

    +

     

    +
    +

    hydro

    +     		+

    Integer

    +     		+

    5

    +     		+

    Window size for determining whether a region is + hydrophobic.

    +

     

    +
    +

    hydrofactor

    +     		+

    Floating point

    +     		+

    1.2

    +     		+

    Multiplier for gap open/close penalties in hydrophobic + regions.

    +

     

    +
    +

    in

    +     		+

    Any file name

    +     		+

    standard input

    +     		+

    Where to find the input sequences.

    +

     

    +
    +

    in1

    +     		+

    Any file name

    +     		+

    None

    +     		+

    Where to find an input alignment.

    +

     

    +
    +

    in2

    +     		+

    Any file name

    +     		+

    None

    +     		+

    Where to find an input alignment.

    +

     

    +
    +

    log

    +     		+

    File name

    +     		+

    None.

    +     		+

    Log file name (delete existing file).

    +

     

    +
    +

    loga

    +     		+

    File name

    +     		+

    None.

    +     		+

    Log file name (append to existing file).

    +

     

    +
    +

    matrix

    +     		+

    File name

    +     		+

    None

    +     		+

    File name for substitution matrix in NCBI or WU-BLAST + format. If you specify your own matrix, you should also specify:

    +

     

    +

    -gapopen <g>, -gapextend <e> -center 0.0

    +

     

    +

    Note that <g> and <e> MUST be negative.

    +

     

    +
    +

    maxhours

    +     		+

    Floating point

    +     		+

    None.

    +     		+

    Maximum time to run in hours. The actual time may exceed + the requested limit by a few minutes. Decimals are allowed, so 1.5 means one hour + and 30 minutes.

    +

     

    +
    +

    maxiters

    +     		+

    Integer 1, 2 ...

    +     		+

    16

    +     		+

    Maximum number of iterations.

    +

     

    +
    +

    maxmb

    +     		+

    Integer

    +     		+

    80% + of Physical RAM, or 500 Mb if not known.

    +

     

    +     		+

    Maximum memory to allocate in Mb.

    +
    +

    maxtrees

    +     		+

    Integer

    +     		+

    1

    +     		+

    Maximum number of new trees to build in iteration 2.

    +

     

    +
    +

    minbestcolscore

    +     		+

    Floating point

    +     		+

    [1]

    +     		+

    Minimum score a column must + have to be an anchor.

    +

     

    +
    +

    minsmoothscore

    +     		+

    Floating point

    +     		+

    [1]

    +     		+

    Minimum smoothed score a + column must have to be an anchor.

    +

     

    +
    +

    msaout

    +     		+

    File name

    +     		+

    None

    +     		+

    Write output to given file + name in MSF format.

    +

     

    +
    +

    objscore

    +     		+

    sp

    +

    ps

    +

    dp

    +

    xp

    +

    spf

    +

    spm

    +     		+

    spm

    +     		+

    Objective score used by tree dependent refinement.

    +

    sp=sum-of-pairs score.

    +

    spf=sum-of-pairs score (dimer + approximation)

    +

    spm=sp for < 100 seqs, otherwise spf

    +

    dp=dynamic programming score.

    +

    ps=average profile-sequence score.

    +

    xp=cross profile score.

    +

     

    +
    +

    out

    +     		+

    File name

    +     		+

    standard output

    +     		+

    Where to write the alignment.

    +

     

    +
    +

    phyiout

    +     		+

    File name

    +     		+

    None

    +     		+

    Write output in Phylip + interleaved format to given file name.

    +

     

    +
    +

    physout

    +     		+

    File name

    +     		+

    None

    +     		+

    Write output in Phylip + sequential format to given file name.

    +

     

    +
    +

    refinewindow

    +     		+

    Integer

    +     		+

    200

    +     		+

    Length of window for -refinew.

    +

     

    +
    +

    root1

    +

    root2

    +     		+

    pseudo

    +

    midlongestspan

    +

    minavgleafdist

    +     		+

    psuedo

    +     		+

    Method used to root tree; root1 is used in iteration 1 and + 2, root2 in later iterations.

    +

     

    +

     

    +
    +

    scorefile

    +     		+

    File + name

    +     		+

    None

    +     		+

    File name where to write a score file. This contains one + line for each column in the alignment. The line contains the letters in the + column followed by the average BLOSUM62 score over pairs of letters in the column.

    +

     

    +
    +

    seqtype

    +     		+

    protein

    +

    nucleo

    +

    auto

    +

     

    +     		+

    auto

    +     		+

    Sequence type.

    +
    +

    smoothscoreceil

    +     		+

    Floating point

    +     		+

    [1]

    +     		+

    Maximum value of column score for + smoothing purposes.

    +

     

    +
    +

    smoothwindow

    +     		+

    Integer

    +     		+

    7

    +     		+

    Window used for anchor column smoothing.

    +

     

    +
    +

    spscore

    +     		+

    File name

    +     		+

     

    +     		+

    Compute SP objective score of multiple alignment.

    +

     

    +
    +

    SUEFF

    +     		+

    Floating point value between 0 and 1.

    +

     

    +     		+

    0.1

    +     		+

    Constant used in UPGMB clustering. Determines the relative + fraction of average linkage (SUEFF) vs. nearest-neighbor linkage (1 – SUEFF).
    +
    +

    +
    +

    tree1

    +

    tree2

    +     		+

    File name

    +     		+

    None

    +     		+

    Save tree produced in first or second iteration to given + file in Newick (Phylip-compatible) + format.

    +

     

    +
    +

    usetree

    +     		+

    File name

    +     		+

    None

    +     		+

    Use given tree as guide tree. Must by in Newick (Phyip-compatible) + format.

    +

     

    +
    +

    weight1

    +

    weight2

    +     		+

    none

    +

    henikoff

    +

    henikoffpb

    +

    gsc

    +

    clustalw

    +

    threeway

    +     		+

    clustalw

    +

     

    +     		+

    Sequence weighting scheme.

    +

    weight1 + is used in iterations 1 and 2.

    +

    weight2 + is used for tree-dependent refinement.

    +

    none=all + sequences have equal weight.

    +

    henikoff=Henikoff & + Henikoff weighting scheme.

    +

    henikoffpb=Modified + Henikoff scheme as used in PSI-BLAST.

    +

    clustalw=CLUSTALW method.

    +

    threeway=Gotoh three-way + method.

    +

     

    +
    + +

     

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    Flag option

    +     		+

    Set by default?

    +     		+

    Description

    +
    +

    anchors

    +     		+

    yes

    +     		+

    Use anchor optimization in + tree dependent refinement iterations.

    +

     

    +
    +

    brenner

    +     		+

    no

    +     		+

    Use Steven Brenner's method + for computing the root alignment.

    +

     

    +
    +

    cluster

    +     		+

    no

    +     		+

    Perform fast clustering of + input sequences. Use the –tree1 option to save the tree.

    +

     

    +
    +

    dimer

    +     		+

    no

    +     		+

    Use dimer approximation for + the SP score (faster, slightly less accurate).

    +

     

    +
    +

    clw

    +     		+

    no

    +     		+

    Write output in CLUSTALW + format (default is FASTA).

    +

     

    +
    +

    clwstrict

    +     		+

    no

    +     		+

    Write output in CLUSTALW + format with the "CLUSTAL W (1.81)" header rather than the MUSCLE + version. This is useful when a post-processing step is picky about the file + header.

    +

     

    +
    +

    core

    +     		+

    yes in muscle,

    +

    no + in muscled.

    +     		+

    Do not catch exceptions.

    +

     

    +

     

    +
    +

    diags

    +     		+

    no

    +     		+

    Use diagonal optimizations. + Faster, especially for closely related sequences, but may be less accurate.

    +

     

    +
    +

    diags1

    +     		+

    no

    +     		+

    Use diagonal optimizations + in first iteration.

    +

     

    +
    +

    diags2

    +     		+

    no

    +     		+

    Use diagonal optimizations + in second iteration.

    +

     

    +
    +

    fasta

    +     		+

    yes

    +     		+

    Write output in FASTA + format.

    +

     

    +
    +

    group

    +     		+

    yes

    +     		+

    Group similar sequences + together in the output. This is the default. See also –stable.

    +

     

    +
    +

    html

    +     		+

    no

    +     		+

    Write output in HTML format + (default is FASTA).

    +

     

    +
    +

    le

    +     		+

    maybe

    +     		+

    Use log-expectation profile score (VTML240). Alternatives + are to use –sp or –sv. This is the + default for amino acid sequences.

    +

     

    +
    +

    msf

    +     		+

    no

    +     		+

    Write output in MSF format (default is FASTA). Designed to + be compatible with the GCG package.

    +

     

    +
    +

    noanchors

    +     		+

    no

    +     		+

    Disable anchor optimization. Default is –anchors.

    +

     

    +
    +

    nocore

    +     		+

    no in muscle,

    +

    yes in muscled.

    +     		+

    Catch exceptions and give an error message if possible.

    +

     

    +

     

    +
    +

    phyi

    +     		+

    no

    +     		+

    Write output in Phylip + interleaved format.

    +

     

    +
    +

    phys

    +     		+

    no

    +     		+

    Write output in Phylip + sequential format.

    +

     

    +
    +

    profile

    +     		+

    no

    +     		+

    Compute profile-profile alignment. Input alignments must + be given using –in1 and –in2 options.

    +

     

    +
    +

    quiet

    +     		+

    no

    +     		+

    Do not display progress messages.

    +

     

    +
    +

    refine

    +     		+

    no

    +     		+

    Input file is already aligned, skip first two iterations + and begin tree dependent refinement.

    +

     

    +
    +

    refinew

    +     		+

    no

    +     		+

    Refine an alignment by dividing it into non-overlapping + windows and re-aligning each window. Typically used for whole-genome + nucleotide alignments.

    +

     

    +
    +

    sp

    +     		+

    no

    +     		+

    Use sum-of-pairs protein profile score (PAM200). Default + is –le.

    +

     

    +
    +

    spscore

    +     		+

    no

    +     		+

    Compute alignment score of profile-profile alignment. + Input alignments must be given using –in1 and –in2 options. + These must be pre-aligned with gapped columns as needed, i.e. must be of the + same length (have same number of columns).

    +

     

    +
    +

    spn

    +     		+

    maybe

    +

     

    +     		+

    Use sum-of-pairs nucleotide profile score. This is the + only option for nucleotides, and is therefore the default. The substitution + scores and gap penalty scores are "borrowed" from BLASTZ.

    +

     

    +
    +

    stable

    +     		+

    no

    +     		+

    Preserve input order of sequences in output file. Default + is to group sequences by similarity (–group).

    +

     

    +
    +

    sv

    +     		+

    no

    +     		+

    Use sum-of-pairs profile score (VTML240). Default is –le.

    +

     

    +
    +

    termgaps4

    +     		+

    yes

    +     		+

    Use 4-way test for treatment of terminal gaps. (Cannot be + disabled in this version).

    +

     

    +
    +

    termgapsfull

    +     		+

    no

    +     		+

    Terminal gaps penalized with full penalty.

    +

    [1] Not fully supported in this version.

    +

     

    +
    +

    termgapshalf

    +     		+

    yes

    +     		+

    Terminal gaps penalized with half penalty.

    +

    [1] Not fully supported in this version.

    +

     

    +
    +

    termgapshalflonger

    +     		+

    no

    +     		+

    Terminal gaps penalized with half penalty if gap relative + to

    +

    longer sequence, otherwise with + full penalty.

    +

    [1] Not fully supported in this version.

    +

     

    +
    +

    verbose

    +     		+

    no

    +     		+

    Write parameter settings and progress messages to log + file.

    +

     

    +
    +

    version

    +     		+

    no

    +     		+

    Write version string to stdout + and exit.

    +
    + +

     

    + +

    Notes

    + +

    [1] Default depends on the profile scoring function. To +determine the default, use –verbose –log and check the log file.

    + +

     

    + +
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    + +
    + + + + + +
    +

    Technical

    +
    + +
    + +
    + + +

    Centre National +De LA Recherche scientifique (France)
    +CeNTRO De REGULACIO GENOMICA (SPAIN)

    + +
    + +

    Cédric Notredame
    +www.tcoffee.org

    + +
    + +
    + +

    T-Coffee:
    +Technical Documentation

    + +
    + +
    + +

     

    + +
    + +
    + +
    +     + +
    + +
    + +

    T-Coffee Technical Documentation
    +(Version 8.01, July 2009)
    +www.tcoffee.org
    +
    +T-Coffee, seq_reformat
    + PSI-Coffee, 3D-Coffee, M-Coffee, R-Coffee, +APDB, iRMSD, T-RMSD

    + +
    + +

    ã Cédric Notredame, Centro de Regulacio Genomica, Centre National de +la Recherche Scientifique, France

    + +
    + +
    +     + +
    + +

    License and Terms +of Use. 6

    + +

    T-Coffee is distributed under the Gnu Public License. 6

    + +

    T-Coffee code can be re-used freely. 6

    + +

    T-Coffee can be incorporated in most pipelines: +Plug-in/Plug-outÂ…... 6

    + +

    Addresses and Contacts. 7

    + +

    Contributors. 7

    + +

    Addresses. 7

    + +

    Citations. 8

    + +

    T-Coffee. 8

    + +

    Mocca. 9

    + +

    CORE.. 10

    + +

    Other Contributions. 10

    + +

    Bug Reports and Feedback. 10

    + +

    Installation of The T-Coffee Packages. 11

    + +

    Third Party Packages and On Demand Installations. 11

    + +

    Standard Installation of T-Coffee. 11

    + +

    Unix. 11

    + +

    Microsoft Windows/Cygwin. 13

    + +

    MAC osX, Linux. 13

    + +

    CLUSTER Installation. 13

    + +

    If you have PDB installed: 13

    + +

    Installing BLAST for T-Coffee. 14

    + +

    Why Do I need BLAST with T-Coffee?. 14

    + +

    Using the EBI BLAST Client 14

    + +

    Using the NCBI BLAST Client 15

    + +

    Using another Client 15

    + +

    Using a BLAST local version on UNIX.. 16

    + +

    Using a BLAST local version on Windows/cygwin. 16

    + +

    Installing Other Companion Packages. 17

    + +

    Installation of PSI-Coffee and Expresso. 18

    + +

    Installation of M-Coffee. 19

    + +

    Automated Installation. 19

    + +

    Manual Installation. 20

    + +

    Installation of APDB and iRMSD.. 21

    + +

    Installation of tRMSD.. 21

    + +

    Installation of seq_reformat 22

    + +

    Installation of extract_from_pdb. 22

    + +

    Installation of 3D-Coffee/Expresso. 22

    + +

    Automated Installation. 22

    + +

    Manual Installation. 23

    + +

    Installing Fugue for T-Coffee. 23

    + +

    Installation of R-Coffee. 23

    + +

    Automated Installation. 24

    + +

    Manual Installation. 24

    + +

    Installing ProbbonsRNA for R-Coffee. 24

    + +

    Installing Consan for R-Coffee. 24

    + +

    Quick Start 25

    + +

    T-COFFEE.. 25

    + +

    M-Coffee. 25

    + +

    Expresso. 26

    + +

    R-Coffee. 26

    + +

    iRMSD and APDB.. 27

    + +

    tRMSD.. 27

    + +

    MOCCA.. 28

    + +

    Recent Modifications. 29

    + +

    Reference Manual 30

    + +

    Environment Variables. 30

    + +

    http_proxy_4_TCOFFEE.. 30

    + +

    email_4_TCOFFEE.. 31

    + +

    DIR_4_TCOFFEE.. 31

    + +

    TMP_4_TCOFFEE.. 31

    + +

    CACHE_4_TCOFFEE.. 31

    + +

    NO_ERROR_REPORT_4_TCOFFEE.. 31

    + +

    PDB_DIR.. 31

    + +

    NO_WARNING_4_TCOFFEE.. 31

    + +

    Setting up the T-Coffee environment variables. 31

    + +

    Well Behaved Parameters. 32

    + +

    Separation. 32

    + +

    Posix. 32

    + +

    Entering the right parameters. 32

    + +

    Parameters Syntax. 32

    + +

    No Flag. 32

    + +

    -parameters. 33

    + +

    -t_coffee_defaults. 33

    + +

    -mode. 33

    + +

    -score [Deprecated]. 34

    + +

    -evaluate. 34

    + +

    -convert [cw]. 34

    + +

    -do_align [cw]. 34

    + +

    Special Parameters. 35

    + +

    -version. 35

    + +

    -proxy. 35

    + +

    -email 35

    + +

    -check_configuration. 35

    + +

    -cache. 35

    + +

    -update. 35

    + +

    -full_log. 35

    + +

    -other_pg. 36

    + +

    Input 36

    + +

    Sequence Input 36

    + +

    -infile [cw]. 36

    + +

    -in (Cf –in from the Method and Library Input section) 36

    + +

    -get_type. 36

    + +

    -type [cw]. 36

    + +

    -seq. 37

    + +

    -seq_source. 37

    + +

    Structure Input 37

    + +

    -pdb. 37

    + +

    Tree Input 37

    + +

    -usetree. 37

    + +

    Structures, Sequences Methods and Library Input via the +in Flag. 38

    + +

    -in. 38

    + +

    Profile Input 40

    + +

    -profile. 40

    + +

    -profile1 [cw]. 40

    + +

    -profile2 [cw]. 40

    + +

    Alignment Computation. 40

    + +

    Library Computation: Methods. 40

    + +

    -lalign_n_top. 40

    + +

    -align_pdb_param_file. 41

    + +

    -align_pdb_hasch_mode. 41

    + +

    Library Computation: Extension. 41

    + +

    -lib_list [Unsupported]. 41

    + +

    -do_normalise. 41

    + +

    -extend. 41

    + +

    -extend_mode. 41

    + +

    -max_n_pair. 42

    + +

    -seq_name_for_quadruplet 42

    + +

    -compact 42

    + +

    -clean. 42

    + +

    -maximise. 42

    + +

    -do_self 42

    + +

    -seq_name_for_quadruplet 42

    + +

    -weight 43

    + +

    Tree Computation. 43

    + +

    -distance_matrix_mode. 43

    + +

    -quicktree [CW]. 44

    + +

    Pair-wise Alignment Computation. 44

    + +

    -dp_mode. 44

    + +

    -ktuple. 45

    + +

    -ndiag. 45

    + +

    -diag_mode. 45

    + +

    -diag_threshold. 46

    + +

    -sim_matrix. 46

    + +

    -matrix [CW]. 46

    + +

    -nomatch. 46

    + +

    -gapopen. 46

    + +

    -gapext 47

    + +

    -fgapopen. 47

    + +

    -fgapext 47

    + +

    -cosmetic_penalty. 47

    + +

    -tg_mode. 47

    + +

    Weighting Schemes. 47

    + +

    -seq_weight 47

    + +

    Multiple Alignment Computation. 48

    + +

    -msa_mode. 48

    + +

    -one2all 48

    + +

    -profile_comparison. 48

    + +

    -profile_mode. 49

    + +

    Alignment Post-Processing. 49

    + +

    -clean_aln. 49

    + +

    -clean_threshold. 49

    + +

    -clean_iteration. 49

    + +

    -clean_evaluation_mode. 49

    + +

    -iterate. 49

    + +

    CPU Control 50

    + +

    Multithreading. 50

    + +

    -multi_thread [NOT Supported]. 50

    + +

    Limits. 50

    + +

    -mem_mode. 50

    + +

    -ulimit 50

    + +

    -maxlen. 50

    + +

    Aligning more than 100 sequences with DPA.. 50

    + +

    -maxnseq. 50

    + +

    -dpa_master_aln. 50

    + +

    -dpa_maxnseq. 51

    + +

    -dpa_min_score1. 51

    + +

    -dpa_min_score2. 51

    + +

    -dap_tree [NOT IMPLEMENTED]. 51

    + +

    Using Structures. 51

    + +

    Generic. 51

    + +

    -mode. 51

    + +

    -check_pdb_status. 52

    + +

    3D Coffee: Using SAP.. 52

    + +

    Using/finding PDB templates for the Sequences. 52

    + +

    -template_file. 52

    + +

    -struc_to_use. 54

    + +

    Multiple Local Alignments. 54

    + +

    -domain/-mocca. 55

    + +

    -start 55

    + +

    -len. 55

    + +

    -scale. 55

    + +

    -domain_interactive [Examples]. 56

    + +

    Output Control 57

    + +

    Generic. 57

    + +

    Conventions Regarding Filenames. 57

    + +

    Identifying the Output files automatically. 57

    + +

    -no_warning. 57

    + +

    Alignments. 57

    + +

    -outfile. 57

    + +

    -output 57

    + +

    -outseqweight 58

    + +

    -case. 58

    + +

    -cpu. 58

    + +

    -outseqweight 58

    + +

    -outorder [cw]. 59

    + +

    -inorder [cw]. 59

    + +

    -seqnos. 59

    + +

    Libraries. 59

    + +

    -out_lib. 59

    + +

    -lib_only. 59

    + +

    Trees. 60

    + +

    -newtree. 60

    + +

    Reliability Estimation. 60

    + +

    CORE Computation. 60

    + +

    -evaluate_mode. 60

    + +

    Generic Output 61

    + +

    -run_name. 61

    + +

    -quiet 61

    + +

    -align [CW]. 61

    + +

    APDB, iRMSD and tRMSD Parameters. 61

    + +

    -quiet [Same as T-Coffee]. 61

    + +

    -run_name [Same as T-Coffee]. 61

    + +

    -aln. 61

    + +

    -n_excluded_nb. 62

    + +

    -maximum_distance. 62

    + +

    -similarity_threshold. 62

    + +

    -local_mode. 62

    + +

    -filter. 62

    + +

    -print_rapdb [Unsupported]. 63

    + +

    -outfile [Same as T-Coffee]. 63

    + +

    -color_mode. 63

    + +

    Building a Server 64

    + +

    Environment Variables. 64

    + +

    Output of the .dnd file. 65

    + +

    Permissions. 65

    + +

    Other Programs. 65

    + +

    Formats. 66

    + +

    Parameter files. 66

    + +

    Sequence Name Handling. 66

    + +

    Automatic Format Recognition. 67

    + +

    Structures. 67

    + +

    RNA Structures. 67

    + +

    Sequences. 67

    + +

    Alignments. 67

    + +

    Libraries. 68

    + +

    T-COFFEE_LIB_FORMAT_01. 68

    + +

    T-COFFEE_LIB_FORMAT_02. 69

    + +

    Library List 69

    + +

    Substitution matrices. 69

    + +

    ClustalW Style [Deprecated]. 69

    + +

    BLAST Format [Recommended]. 70

    + +

    Sequences Weights. 70

    + +

    Known Problems. 71

    + +

    Technical Notes. 72

    + +

    Development 72

    + +

    Command Line List 72

    + +

    To DoÂ….. 74

    + +

    + +
    + +
    +     + +
    + + + +

     

    + +

    T-Coffee is distributed +under the Gnu Public License

    + +

     

    + +

    Please make sure you have agreed with the terms +of the license attached to the package before using the T-Coffee package or its +documentation. T-Coffee is a freeware open source distributed under a GPL license. +This means that there are very little restrictions to its use, either in an +academic or a non academic environment.

    + +

    T-Coffee code can be +re-used freely

    + +

    Our philosophy is that code is meant to be re-used, +including ours. No permission is needed for the cut and paste of a few +functions, although we are always happy to receive pieces of improved code.

    + +

    T-Coffee can be +incorporated in most pipelines: Plug-in/Plug-outÂ…

    + +

    Our philosophy is to insure +that as many methods as possible can be used as plug-ins within T-Coffee. +Likewise, we will give as much support as possible to anyone wishing to turn +T-Coffee into a plug-in for another method. For more details on how to do this, +see the plug-in and the plug-out sections of the Tutorial Manual.

    + +

    Again, you do not need our +permission to either use T-Coffee (or your method as a plug-in/out) but if you +let us know, we will insure the stability of T-Coffee within your system +through future releases.

    + +

    The current license only +allows for the incorporation of T-Coffee in non-commercial pipelines (i.e. +where you do not sell the pipeline, or access to it). If your pipeline is +commercial, please get in touch with us.

    + +

     

    + + + +

    Contributors

    + +

    T-coffee is developed, maintained, +monitored, used and debugged by a dedicated team that include or have included:

    + +

                Cédric +Notredame, Fabrice Armougom, Des Higgins, Sebastien Moretti, Orla O’Sullivan. Eamon +O’Toole, Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm

    + +

    Addresses

    + +

    We are always very eager to get some user +feedback. Please do not hesitate to drop us a line  at: cedric.notredame@europe.com The latest updates of T-Coffee +are always available  on: www.tcoffee.org +. On this address you will also find a link to some of the online T-Coffee +servers, including Tcoffee@igs

    + +

     

    + +

    T-Coffee can be used to automatically check if +an updated version is available, however the program will not update +automatically, as this can cause endless reproducibility problems.

    + +
    + +

    PROMPT: +t_coffee –update

    + +
    + +

     

    + +
    + +

    Citations

    + +
    + +

    It is important that you cite T-Coffee when you +use it. Citing us is (almost) like giving us money: it helps us convincing our +institutions that what we do is useful and that they should keep paying our +salaries and deliver Donuts to our offices from time to time (Not that they +ever did it, but it would be nice anyway).

    + +

     

    + +

    Cite the server if you used it, otherwise, cite +the original paper from 2000 (No, it was never named "T-Coffee 2000").

    + + + + + + + + + +
    +

    Notredame + C, Higgins DG, Heringa J.

    +     		+

    Related Articles, Links

    +
    +

    T-Coffee: A novel method for fast + and accurate multiple sequence alignment.
    + J Mol Biol. 2000 Sep 8;302(1):205-17.
    + PMID: 10964570 [PubMed - indexed for MEDLINE]

    +
    + +

    Other useful publications include:

    + +

    T-Coffee

    + + + + + + + + + +
    +

    Claude + JB, Suhre K, Notredame C, Claverie JM, Abergel C.

    +     		+

    Related Articles, Links

    +
    +

    CaspR: a web server for automated + molecular replacement using homology modelling.
    + Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9.
    + PMID: 15215460 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + + + + + + + + + +
    +

    Poirot + O, Suhre K, Abergel C, O'Toole E, Notredame C.

    +     		+

    Related Articles, Links

    +
    +

    3DCoffee@igs: a web server for + combining sequences and structures into a multiple sequence alignment.
    + Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40.
    + PMID: 15215345 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + + + + + + + + + +
    +

    O'Sullivan + O, Suhre K, Abergel C, Higgins DG, Notredame C.

    +     		+

    Related Articles, Links

    +
    +

    3DCoffee: combining protein + sequences and structures within multiple sequence alignments.
    + J Mol Biol. 2004 Jul 2;340(2):385-95.
    + PMID: 15201059 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + + + + + + + + + +
    +

    Poirot + O, O'Toole E, Notredame C.

    +     		+

    Related Articles, Links

    +
    +

    Tcoffee@igs: A web server for + computing, evaluating and combining multiple sequence alignments.
    + Nucleic Acids Res. 2003 Jul 1;31(13):3503-6.
    + PMID: 12824354 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + + + + + + + + + +
    +

    Notredame + C.

    +     		+

    Related Articles, Links

    +
    +

    Mocca: semi-automatic method for + domain hunting.
    + Bioinformatics. 2001 Apr;17(4):373-4.
    + PMID: 11301309 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + + + + + + + + + +
    +

    Notredame + C, Higgins DG, Heringa J.

    +     		+

    Related Articles, Links

    +
    +

    T-Coffee: A novel method for fast + and accurate multiple sequence alignment.
    + J Mol Biol. 2000 Sep 8;302(1):205-17.
    + PMID: 10964570 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + + + + + + + + + +
    +

    Notredame + C, Holm L, Higgins DG.

    +     		+

    Related Articles, Links

    +
    +

    COFFEE: an objective function for + multiple sequence alignments.
    + Bioinformatics. 1998 Jun;14(5):407-22.
    + PMID: 9682054 [PubMed - indexed for MEDLINE]

    +
    + +

     

    + +

    Mocca

    + + + + + + + + + +
    +

    Notredame C.

    +     		+

    Related Articles, Links

    +
    +

    Mocca: semi-automatic method for domain + hunting.
    + Bioinformatics. 2001 Apr;17(4):373-4.
    + PMID: 11301309 [PubMed - indexed for MEDLINE]

    +
    + +

    CORE

    + +

    http://www.tcoffee.org/Publications/Pdf/core.pp.pdf

    + +

    Other Contributions

    + +

    We do not mean to steal code, but we will always +try to re-use pre-existing code whenever that code exists, free of copyright, +just like we expect people to do with our code. However, whenever this happens, +we make a point at properly citing the source of the original contribution. If +ever you recognize a piece of your code improperly cited, please drop us a note +and we will be happy to correct that.

    + +

    In the mean time, here are some important pieces +of code from other packages that have been incorporated within the T-Coffee +package. These include:

    + +

             -The +Sim algorithm of Huang and Miller that given two sequences computes the N best +scoring local alignments.

    + +

             -The +tree reading/computing routines are taken from the ClustalW Package, courtesy +of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson, +1994, 4673-4680,vol. 22, Nucleic Acid Research).

    + +

             -The +implementation of the algorithm for aligning two sequences in linear space was +adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)

    + +

             -Various techniques and algorithms have +been implemented. Whenever relevant, the source of the code/algorithm/idea is +indicated in the corresponding function.

    + +

             -64 +Bits compliance was implemented by Benjamin Sohn, Performance Computing Center +Stuttgart (HLRS), Germany

    + +

             -David +Mathog (Caltech) provided many fixes and useful feedback for improving the code +and making the whole soft behaving more rationally

    + +

    Bug Reports and Feedback

    + +

             -Prof +David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can +align PDB sequences longer than 1000 AA).

    + +

             -Johan +Leckner reported several bugs related to the treatment of PDB structures, +insuring a consistent behavior between version 1.37 and current ones.

    + +

     

    + +

     

    + +
    + +

    Installation of The T-Coffee +Packages

    + +
    + +

    Third Party Packages and On Demand +Installations

    + +

    T-Coffee is a complex package that interacts with many other third part +software. If you only want a standalone version of T-Coffee, you may install +that package on its own. If you want to use a most sophisticated flavor +(3dcoffee, expresso, rcofeee, etc...), the installer will try to install all +the third paparty packages required.

    + +

     

    + +

    Note that since version 7.56, T-Coffee will use 'on demand' +installation and install the third party packages it needs *when* it needs +them. This only works for packages not requiring specific licenses and that can +be installed by the regular installer. Please let us know if you would like +another third party package to be included.

    + +

    Whenver on-demand installation or automated installation fails because +of unforessen system specificities, users should install the third party +package manually. In this documentation gives some tips we have found useful, +but users are encouraged to check the original documentation.

    + +

    Standard +Installation of T-Coffee

    + +

    Unix

    + +

    You need to have: gcc, g77, CPAN and an internet +connection and your root password (to install SOAP). If you cannot log as root, +ask (kindly) your system manager to install SOAP::Lite for you. You may do this +before or after the installation of T-Coffee. Even without SOAP you will still +be able to use the basic functions of T-Coffee (simplest usage).

    + +

     

    + +

    1.        +gunzip t_coffee.tar.gz

    + +

    2.        +tar -xvf t_coffee.tar

    + +

    3.        +cd t_coffee

    + +

    4.        +./install t_coffee

    + +

    This installation will try to install EVERY +flavor of T-Coffee along with the packages it requires. It will not re-install +the packages that are already on your computer.

    + +

    If you want a more specific installation, you +can try:

    + +
    + +

       ./install t_coffee

    + +

       ./install mcoffee

    + +

       ./install 3dcoffee

    + +

       ./install rcoffee

    + +

       ./install psicoffee

    + +

     

    + +
    + +

     

    + +

    Or even

    + +
    + +

       ./install all

    + +
    + +

     

    + +

    -All the corresponding executables will be +downloaded automatically and installed in

    + +
    + +

       $HOME/.t_coffee/plugins

    + +
    + +

     

    + +

    -if you executables are in a different +location, give it to T-Coffee using the -plugins flag.

    + +

    -If the installation of any of the companion +package fails, you should install it yourself using the provided link (see +below) and following the authors instructions.     

    + +

    -If you have not managed to install SOAP::Lite, +you can re-install it later (from anywhere) following steps 1-2.

    + +

     

    + +

    -This procedure attempts 3 things: +installing and Compiling T-Coffee (C program), Installing and compiling TMalign (Fortran), Installing and +compiling SOAP::Lite(Perl Module).

    + +

     

    + +

    -If you have never installed SOAP::Lite, +CPAN will ask you many questions: say Yes to all

    + +

    -If everything went well, the procedure has +created in the bin directory two executables: t_coffee and TMalign (Make +sure these executables are on your $PATH!)

    + +

     

    + +

    Microsoft Windows/Cygwin

    + +

    Install Cygwin

    + +

    Download The Installer (NOT Cygwin/X)

    + +

    Click on view to list ALL the packages

    + +

    Select: gcc-core, make, wget

    + +

    Optional: ssh, xemacs, nano

    + +

    Run mkpasswd in Cywin (as requested when +you start cygwin)

    + +

    Install T-Coffee within Cygwin using the +Unix procedure

    + +

    MAC osX, Linux

    + +

    Make sure you have the Developer's kit installed +(compilers and makefile)

    + +

    Follow the Unix Procedure

    + +

     

    + +

    CLUSTER Installation

    + +

    In order to run, T-Coffee must have a value for +the http_proxy and for the E-mail. In order to do so you can either:

    + +

    export the following values:

    + +

    export +http_proxy_4_TCOFFEE="proxy" or "" if no proxy

    + +

    export EMAIL_4_TCOFFEE="your +email"

    + +

    OR

    + +

    modify the file ~/.t_coffee/t_coffee_env

    + +

    OR

    + +

    add to your command line: t_coffee Â…. +-proxy=<proxy> -email=<email

    + +

    if you have no proxy: t_coffee Â… -proxy +-email=<email>

    + +

     

    + +

     

    + +

    If you have PDB installed:

    + +

    Assuming you have a standard PDB installation +in your file system

    + +

    setenv (or export)  PDB_DIR <abs path>/data/structures/all/pdb/

    + +

    OR

    + +

    setenv (or export)  PDB_DIR <abs +path>/structures/divided/pdb/

    + +

    If you do not have PDB installed, don't worry, +t_coffee will go and fetch any structure it needs directly from the PDB +repository. It will simply be a bit slower than if you had PDB locally.

    + +

    Installing BLAST for T-Coffee

    + +

    BLAST is a program that search sequence databases for homologues of a +query sequence. It works for proteins and Nucleic Acids. In theory BLAST is +just a package like any, but in practice things are a bit more complex. To run +well, BLST requires up to date databases (that can be fairly large, like NR or +UNIPROT) and a powerful computer.

    + +

    Fortunately, an increasing number of institutes or companies are now providing +BLAST clients that run over the net. It means that all you need is a small +program that send your query to the big server and gets the results back. This +prevents you from the hassle of installing and maintaining BLAST, but of course +it is less private and you rely on the network and the current load of these +busy servers.

    + +

    Thanks to its interaction with BLAST, T-Coffee can gather structures +and protein profiles and deliver an alignment significantly more accurate than +the default you would get with T-Coffee or any similar method.

    + +

    Let us go through the various modes available for T-Coffee

    + +

     

    + +

    Why +Do I need BLAST with T-Coffee?

    + +

    The most accurate modes of T-Coffe scan the databases for templates +that they use to align the sequences. There are currently two types of templates +for proteins:

    + +

    structures (PDB) that can be found by a blastp against the PDB database +and profiles that can be constructed with eiether a blastp or a psiblast +against nr or uniprot.

    + +

    These templates are automatically built if you use:

    + +
    + +

       t_coffee <yourseq> -mode expresso

    + +
    + +

             that fetches aand uses +pdb templates, or

    + +
    + +

              t_coffee <your +seq> -mode psicoffee

    + +
    + +

             that fetches and uses +profile templates, or

    + +
    + +

              t_coffee <your +seq> -mode accurate

    + +
    + +

             that does everything and +tries to use the best template. Now that you see why it is useful let's see how +to get BLAST up and running, from the easy solution to tailor made ones.

    + +

     

    + +

    Using +the EBI BLAST Client

    + +

    This is by far the easiest (and the default mode). The perl clients are +already incorporated in T-Coffeem and all you need is the SOAP::Lite perl +library. In theory, T-Coffee should have already installed this library during +the standard installation. Yet, this requires having toot access. If you did +not have it at the time of the installation, or if you need your system administrator +to install SOAP::Lite, simply follow the instruction provided on the website:

    + +

     

    + +
    + +

       http://search.cpan.org/~byrne/SOAP-Lite-0.60a

    + +
    + +

    It really is worth the effort, since the EBI is providing one of the +best webservice available around, and most notably, the only public psiblast +via a web service.

    + +

     

    + +

    Another important point is that the EBI requires your E-mail address to +process your queries. Normally, T-Coffee should have asked you to provide this +address. If you have not, or if you have provided a phony address, you should +correct this by directly editing the file

    + +
    + +

       ~/.t_coffee/email.txt

    + +
    + +

    Be Careful! If you provide a fake E-mail, the +EBI may suspend the service for all machines associated with your IP address +(that could mean your entire lab, or entire institute, or even the entire +country or, but I doubt it, the whole universe).

    + +

    Using +the NCBI BLAST Client

    + +

    The NCBI is the next best alternative. In my hand it was always a bit +slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A +big miss. The NCBI web blast client is a small executable that you should +install on your system following the instructions given on this link

    + +
    + +

    ftp://ftp.ncbi.nih.gov/blast/executables/LATEST

    + +
    + +

    Simply go for netbl, download the executable that corresponds to +your architecture (cygwin users should go for the win executable). Despite all +the files that come along the executable blastcl3 is a stand alone executable +that you can safely move to your $BIN.

    + +

    All you will then need to do is to make sure that T-Coffee uses the +right client, when you run it.

    + +
    + +

    -blast_server=NCBI

    + +
    + +

    No need for any E-mail here, but you don't get psiblast, and whenever +T-Coffee wants to use it, blastp will be used instead.

    + +

    Using +another Client

    + +

    You may have your own client (lucky you). If that is so, all you need +is to make sure that this client is complient with the blast command line. If +your client is named foo.pl, all you need to to is run T-Coffee with

    + +
    + +

    -blast_server=CLIENT_foo.pl

    + +
    + +

    Foo will be called as if it were blastpgp, and it is your responsability +to make sure it can handle the following command line:

    + +
    + +

    foo.pl -p <method> -d +<db> -i <infile> -o <outfile> -m 7

    + +
    + +

    method can either be blastp or psiblast.

    + +

    infile is a FASTA file

    + +

    -m7 triggers the XML output. T-Coffee is able to parse both the EBI XML +output and the NCBI XML output.

    + +

     

    + +

    If foo.pl behaves differently, the easiest will probably be to write a +wrapper around it so that wrapped_foo.pl behaves like blastpgp

    + +

     

    + +

    Using +a BLAST local version on UNIX

    + +

    If you have blastpgp installed, you can run it instead of the remote +clients by using:

    + +
    + +

    -blast_server=LOCAL

    + +
    + +

     The documnentation for blastpgp +can be found on:

    + +
    + +

    www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html

    + +
    + +

    and the package is part of the standard BLAST distribution

    + +
    + +

    ftp://ftp.ncbi.nih.gov/blast/executables/LATEST

    + +
    + +

    Depending on your system, your own skills, your requirements and on +more parameters than I have fingers to count, installing a BLAST server suited +for your needs can range from a 10 minutes job to an achivement spread over +several generations. So at this point, you should roam the NCBI website for +suitable information.

    + +

    If you want to have your own BLAST server to run your own databases, +you should know that it is possible to control both the database and the +program used by BLAST:

    + +

     

    + +
    + +

    -prot_db: will specify the database used by all the psi-blast modes

    + +

    -pdb_db: will specify the database used by the pdb modes

    + +
    + +

    Using +a BLAST local version on Windows/cygwin

    + +

    For those of you using cygwin, be careful. While cygwin behaves like a +UNIX system, the BLAST executable required for cygwin (win32) is expecting +WINDOWS path and not UNIX path. This has three important consequences:

    + +

    1- the ncbi file declaring the Data directory must be:

    + +

             C:WINDOWS//ncbi.init  [at the root of your WINDOWS]

    + +

    2- the address mentionned with this file must be WINDOWS formated, for +instance, on my system:

    + +

    Data=C:\cygwin\home\notredame\blast\data

    + +

    3- When you pass database addresses to BLAST, these must be in Windows +format:

    + +

             -protein_db="c:/somewhere/somewhereelse/database"

    + +

    (using the slash (/) or the andtislash (\) does not matter on new +systems but I would reommand against incorporating white spaces.

    + +

    Installing +Other Companion Packages

    + +

    T-Coffee is meant to interact with as many packages as possible, either +for aligning or using predictions. If you type

    + +
    + +

       t_coffee

    + +
    + +

    You will receive a list of supported packages that looks like the next +table. In theory, most of these packages can be installed by T-Coffee

    + +

     

    + +
    + +

    ****** Pairwise Sequence Alignment Methods:

    + +

    --------------------------------------------

    + +

    fast_pair          built_in

    + +

    exon3_pair         built_in

    + +

    exon2_pair         built_in

    + +

    exon_pair          built_in

    + +

    slow_pair          built_in

    + +

    proba_pair         built_in

    + +

    lalign_id_pair     built_in

    + +

    seq_pair           built_in

    + +

    externprofile_pair built_in

    + +

    hh_pair            built_in

    + +

    profile_pair       built_in

    + +

    cdna_fast_pair     built_in

    + +

    cdna_cfast_pair    built_in

    + +

    clustalw_pair      +ftp://www.ebi.ac.uk/pub/clustalw

    + +

    mafft_pair         +http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    mafftjtt_pair      http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    mafftgins_pair     +http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    dialigntx_pair     +http://dialign-tx.gobics.de/

    + +

    dialignt_pair      +http://dialign-t.gobics.de/

    + +

    poa_pair           http://www.bioinformatics.ucla.edu/poa/

    + +

    probcons_pair      +http://probcons.stanford.edu/

    + +

    muscle_pair        +http://www.drive5.com/muscle/

    + +

    t_coffee_pair      +http://www.tcoffee.org

    + +

    pcma_pair          +ftp://iole.swmed.edu/pub/PCMA/

    + +

    kalign_pair        +http://msa.cgb.ki.se

    + +

    amap_pair          +http://bio.math.berkeley.edu/amap/

    + +

    proda_pair         +http://bio.math.berkeley.edu/proda/

    + +

    prank_pair         +http://www.ebi.ac.uk/goldman-srv/prank/

    + +

    consan_pair        +http://selab.janelia.org/software/consan/

    + +

     

    + +

    ****** Pairwise Structural Alignment Methods:

    + +

    --------------------------------------------

    + +

    align_pdbpair      built_in

    + +

    lalign_pdbpair     built_in

    + +

    extern_pdbpair     built_in

    + +

    thread_pair        built_in

    + +

    fugue_pair         +http://www-cryst.bioc.cam.ac.uk/fugue/download.html

    + +

    pdb_pair           built_in

    + +

    sap_pair           +http://www-cryst.bioc.cam.ac.uk/fugue/download.html

    + +

    mustang_pair       +http://www.cs.mu.oz.au/~arun/mustang/

    + +

    tmalign_pair       +http://zhang.bioinformatics.ku.edu/TM-align/

    + +

     

    + +

    ****** Multiple Sequence Alignment Methods:

    + +

    --------------------------------------------

    + +

    clustalw_msa       +ftp://www.ebi.ac.uk/pub/clustalw

    + +

    mafft_msa          +http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    mafftjtt_msa       +http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    mafftgins_msa      +http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    dialigntx_msa      +http://dialign-tx.gobics.de/

    + +

    dialignt_msa       +http://dialign-t.gobics.de/

    + +

    poa_msa            +http://www.bioinformatics.ucla.edu/poa/

    + +

    probcons_msa       +http://probcons.stanford.edu/

    + +

    muscle_msa         +http://www.drive5.com/muscle/

    + +

    t_coffee_msa       +http://www.tcoffee.org

    + +

    pcma_msa           +ftp://iole.swmed.edu/pub/PCMA/

    + +

    kalign_msa         +http://msa.cgb.ki.se

    + +

    amap_msa           +http://bio.math.berkeley.edu/amap/

    + +

    proda_msa          +http://bio.math.berkeley.edu/proda/

    + +

    prank_msa          +http://www.ebi.ac.uk/goldman-srv/prank/

    + +

     

    + +

    #######   Prediction Methods +available to generate Templates

    + +

    -------------------------------------------------------------

    + +

    RNAplfold          +http://www.tbi.univie.ac.at/~ivo/RNA/

    + +

    HMMtop             +www.enzim.hu/hmmtop/

    + +

    GOR4               +http://mig.jouy.inra.fr/logiciels/gorIV/

    + +

    wublast_client     +http://www.ebi.ac.uk/Tools/webservices/services/wublast

    + +

    blastpgp_client    http://www.ebi.ac.uk/Tools/webservices/services/blastpgp           

    + +

    ==========================================================

    + +
    + +

     

    + +

     

    + +

    Installation +of PSI-Coffee and Expresso

    + +

    PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of +your sequences and makes a multiple profile alignment. If you do not have any +structural information, it is by far the most accurate mode of T-Coffee. To use +it, you must have SOAP installed so that the EBI BLAST client can run on your +system.

    + +

    It is a bit slow, but really worth it if your sequences are hard to +align and if the accuracy of your alignment is important.  

    + +

    To use this mode, try:

    + +
    + +

       t_coffee <yoursequence> -mode psicoffee

    + +
    + +

    Note that because PSI-BLAST is time consuming, T-Coffee stores the runs +in its cache (./tcoffee/cache) so that it does not need to be re-run. It means +that if you re-align your sequences (or add a few extra sequences), things will +be considerably faster.

    + +

    If your installation procedure has managed to compile TMalign, and if +T-Coffee has access to the EBI BLAST server (or any other server) you can also +do the following:

    + +
    + +

       t_coffee <yoursequence> -mode expresso

    + +
    + +

    That will look for structural templates. And if both these modes are +running fine, then you are ready for the best, the "crème de la +crème":

    + +
    + +

       t_coffee <yoursequence> -mode accurate

    + +
    + +

    Installation +of M-Coffee

    + +

     

    + +

    M-Coffee is a special mode of T-Coffee that makes it possible to +combine the output of many multiple sequence alignment packages.

    + +

    Automated +Installation

    + +

    In the T-Coffee distribution, type:

    + +
    + +

    ./install mcoffee

    + +
    + +

     

    + +

    In theory, this command should download and install every required +package. If, however, it fails, you should switch to the manual installation +(see next).

    + +

    By default these packages will be in

    + +
    + +

    $HOME/.t_coffee/plugins

    + +
    + +

    If you want to have these companion packages in a different directory, +you can either set the environement variable

    + +
    + +

    PLUGINS_4_TCOFFEE=<plugins +dir>

    + +
    + +

    Or use the command line flag -plugin (over-rides every other setting)

    + +
    + +

    t_coffee ... +-plugins=<plugins dir>

    + +
    + +

     

    + +

     

    + +

    Manual +Installation

    + +

    M-Coffee requires a standard T-Coffee installation (c.f. previous +section) and the following packages to be installed on your system:

    + +

            

    + +
    + +

    Package           Where From

    + +

    ==========================================================

    + +

    ClustalW          can interact +with t_coffee

    + +

    ----------------------------------------------------------

    + +

    Poa               http://www.bioinformatics.ucla.edu/poa/

    + +

    ----------------------------------------------------------

    + +

    Muscle            http://www.drive5.com

    + +

     ----------------------------------------------------------

    + +

    ProbCons          http://probcons.stanford.edu/

    + +

    ProbConsRNA       http://probcons.stanford.edu/

    + +

    ----------------------------------------------------------

    + +

    MAFFT http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

    + +

    ----------------------------------------------------------

    + +

    Dialign-T         http://dialign-t.gobics.de/

    + +

    Dialign-TX        http://dialign-tx.gobics.de/

    + +

    ----------------------------------------------------------

    + +

    PCMA              ftp://iole.swmed.edu/pub/PCMA/

    + +

    ----------------------------------------------------------

    + +

    kalign            +http://msa.cgb.ki.se

    + +

    ----------------------------------------------------------

    + +

    amap              +http://bio.math.berkeley.edu/amap/

    + +

    -----------------------------------------------------------

    + +

    proda_msa        +http://bio.math.berkeley.edu/proda/

    + +

    -----------------------------------------------------------

    + +

    prank_msa        http://www.ebi.ac.uk/goldman-srv/prank/

    + +

     

    + +
    + +

     

    + +

    In our hands all these packages where very straightforward to compile +and install on a standard cygwin or Linux configuration. Just make sure you +have gcc, the C compiler, properly installed.

    + +

    Once the package is compiled and ready to use, make sure that the +executable is on your path, so that t_coffee can find it automatically. Our +favorite procedure is to create a bin directory in the home. If you do so, make +sure this bin is in your path and fill it with all your executables (this is a +standard Unix practice).

    + +

    If for some reason, you do not want this directory to be on your path, +or you want to specify a precise directory containing the executables, you can +use:

    + +
    + +

       export PLUGINS_4_TCOFFEE=<dir>

    + +
    + +

    By default this directory is set to $HOME/.t_coffee/plugins/$OS, but +you can over-ride it with the environement variable or using the flag:

    + +
    + +

       t_coffee ...-plugins=<dir>

    + +
    + +

     

    + +

    If you cannot, or do not want to use a single bin directory, you can +set the following environment variables to the absolute path values of the +executable you want to use. Whenever they are set, these variables will supersede +any other declaration. This is a convenient way to experiment with multiple +package versions.

    + +
    + +

    POA_4_TCOOFFEE
    +CLUSTALW_4_TCOFFEE
    +POA_4_TCOFFEE
    +TCOFFEE_4_TCOFFEE
    +MAFFT_4_TCOFFEE
    +MUSCLE_4_TCOFFEE
    +DIALIGNT_4_TCOFFEE
    +PRANK_4_TCOFFEE
    +DIALIGNTX_4_TCOFFEE
    + 

    + +
    + +

    For three of these packages, you will need to copy some of the files in +a special T-Coffee directory.

    + +
    + +

       cp POA_DIR/* ~/.t_coffee/mcoffee/

    + +

       cp DIALIGN-T/conf/*  ~/.t_coffee/mcoffee

    + +

       cp DIALIGN-TX/conf/*  +~/.t_coffee/mcoffee

    + +
    + +

    Note that the following files are enough for default usage:

    + +
    + +

    BLOSUM.diag_prob_t10   BLOSUM75.scr  +blosum80_trunc.mat          

    + +

    dna_diag_prob_100_exp_330000  dna_diag_prob_200_exp_110000

    + +

    BLOSUM.scr             BLOSUM90.scr  dna_diag_prob_100_exp_110000

    + +

    dna_diag_prob_100_exp_550000  dna_diag_prob_250_exp_110000

    + +

    BLOSUM75.diag_prob_t2  blosum80.mat  +dna_diag_prob_100_exp_220000 

    + +

    dna_diag_prob_150_exp_110000  dna_matrix.scr

    + +
    + +

     

    + +

    If you would rather have the mcoffee directory in some other location, +set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:

    + +
    + +

       setenv MCOFFEE_4_TCOFFEE <directory containing mcoffee +files>

    + +
    + +

    Installation +of APDB and iRMSD

    + +

    APDB and iRMSD are incorporated in T-Coffee. Once t_coffee is +installed, you can invoque these programs by typing:

    + +
    + +

       t_coffee –other_pg apdb
    +   t_coffee –other_pg irmsd

    + +
    + +

    Installation +of tRMSD

    + +

    tRMSD comes along with t_coffee but it also requires the package +phylip in order to be functional. Phylip can be obtained from:

    + +

            

    + +
    + +

    Package           Function

    + +

    ===================================================

    + +

    ---------------------------------------------------

    + +

    Phylip            Phylogenetic +tree computation

    + +

                      evolution.genetics.washington.edu/phylip.html

    + +

    ---------------------------------------------------

    + +
    + +
    + +

    t_coffee –other_pg trmsd

    + +
    + +

     

    + +

    Installation +of seq_reformat

    + +

    Seq_reformat is a reformatting package that is part of t_coffee. To +use it (and see the available options), type:

    + +
    + +

       t_coffee –other_pg seq_reformat

    + +
    + +

    Installation +of extract_from_pdb

    + +

    Extract_from_pdb is a PDB reformatting package that is part of +t_coffee. To use it (and see the available options), type.

    + +
    + +

       t_coffee –other_pg apdb –h

    + +
    + +

    Extract_from_pdb requires wget in order to automatically fetch PDB +structures.

    + +

     

    + + + +

    Installation of 3D-Coffee/Expresso

    + +

    3D-Coffee/Expresso is a special mode of +T-Coffee that makes it possible to combine sequences and structures. The main +difference between Expresso and 3D-Coffee is that Expresso fetches the +structures itself.

    + +

    Automated Installation

    + +

    In the T-Coffee distribution, type:

    + +
    + +

    ./install +expresso

    + +

    OR

    + +

    ./install +3dcoffee

    + +
    + +

     

    + +

    In theory, this command should download and +install every required package (except fugue). If, however, it fails, +you should switch to the manual installation (see next).

    + +

    Manual Installation

    + +

    In order to make the most out of T-Coffee, you +will need to install the following packages (make sure the executable is named +as indicated below):

    + +

            

    + +
    + +

    Package           Function

    + +

    ===================================================

    + +

    ---------------------------------------------------

    + +

    wget              3DCoffee

    + +

                      Automatic Downloading of Structures

    + +

    ---------------------------------------------------

    + +

    sap               structure/structure comparisons

    + +

    (obtain it from W. Taylor, NIMR-MRC).

    + +

    ---------------------------------------------------

    + +

    TMalign           zhang.bioinformatics.ku.edu/TM-align/

    + +

    ---------------------------------------------------

    + +

    mustang           www.cs.mu.oz.au/~arun/mustang/

    + +

    ---------------------------------------------------

    + +

    wublastclient     www.ebi.ac.uk/Tools/webservices/clients/wublast

    + +

    ---------------------------------------------------

    + +

    Blast             www.ncbi.nih.nlm.gov

    + +

    ---------------------------------------------------

    + +

    Fugue*            protein to structure alignment program

    + +

                      http://www-cryst.bioc.cam.ac.uk/fugue/download.html

    + +

                      ***NOT +COMPULSORY***

    + +
    + +

     

    + +

    Once the package is installed, make sure make +sure that the executable is on your path, so that t_coffee can find it +automatically.

    + +

     

    + +

    The wublast client makes it possible to run +BLAST at the EBI without having to install any database locally. It is an ideal +solution if you are only using expresso occasionally.

    + +

     

    + +

    Installing Fugue for T-Coffee

    + +

    Uses a standard fugue installation. You only +need to install the following packages:

    + +

     joy, +melody, fugueali, sstruc, hbond

    + +

    If you have root privileges, you can install +the common data in:

    + +

    cp fugue/classdef.dat           /data/fugue/SUBST/classdef.dat

    + +

    otherwise

    + +

    Setenv MELODY_CLASSDEF=<location>

    + +

    Setenv MELODY_SUBST=fugue/allmat.dat

    + +

     

    + +

    All the other configuration files must be in +the right location.

    + +

    Installation of R-Coffee

    + +

    R-Coffee is a special mode able to align RNA +sequences while taking into account their secondary structure.

    + +

    Automated Installation

    + +

    In the T-Coffee distribution, type:

    + +
    + +

    ./install +rcoffee

    + +
    + +

     

    + +

    In theory, this command should download and +install every required package (except consan). If, however, it fails, +you should switch to the manual installation (see next).

    + +

    Manual Installation

    + +

    R-Coffee only requires the package Vienna to be installed, in +order to compute multiple sequence alignments. To make the best out of it, you +should also have all the packages required by M-Coffee

    + +

            

    + +
    + +

    Package           Function

    + +

    ===================================================

    + +

    ---------------------------------------------------

    + +

    consan            R-Coffee

    + +

                      Computes highly accurate pairwise Alignments

    + +

                      ***NOT COMPULSORY***

    + +

                      selab.janelia.org/software/consan/

    + +

    ---------------------------------------------------

    + +

    RNAplfold         Computes RNA secondary Structures

    + +

                      www.tbi.univie.ac.at/~ivo/RNA/

    + +

    ---------------------------------------------------

    + +

    probconsRNA       probcons.stanford.edu/

    + +

           

    + +

    ---------------------------------------------------

    + +

    M-Coffee          T-Coffee and the most common MSA Packages

    + +

                      (cf +M-Coffee in this installation guide)

    + +
    + +

    Installing ProbbonsRNA for R-Coffee

    + +

    Follow the installation procedure, but make +sure you rename the probcons executable into probconsRNA.

    + +

    Installing Consan for R-Coffee

    + +

    In order to insure a proper interface beween +consan and R-Coffee, you must make sure that the file mix80.mod is in the +directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.

    + +

     

    + +
    + +

    Quick Start

    + +
    + +

    We only give you the very basics here. +Please use the Tutorial for more detailed information on how to use our tools.

    + + + +

    T-COFFEE

    + +

    Write your sequences in the same file +(Swiss-prot, Fasta or Pir) and type.

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta 

    + +
    + +

    This will output two files:

    + +

    sample_seq1.aln: your Multiple +Sequence Alignment

    + +

    sample_seq1.dnd: The Guide tree +(newick Format)

    + +
    + +

    IMPORTANT:

    + +

    In theory nucleic acids should be +automatically detected and the default methods should be adapted appropriately. +However, sometimes this may fail, either because the sequences are too short or +contain too many ambiguity codes.

    + +

    When this happens, you are advised to +explicitly set the type of your sequences

    + +

    NOTE: the –mode=dna is not needed or +supported anymore

    + +
    + +
    + +

    PROMPT: +t_coffee sample_dnaseq1.fasta –type=dna

    + +
    + +

    M-Coffee

    + +

    M-Coffee is a Meta version of T-Coffee +that makes it possible to combine the output of at least eight packages +(Muscle, probcons, poa, dialignT, mafft, clustalw, PCMA and T-Coffee).

    + +

    If all these packages are already installed on your machine. You must:

    + +

     

    + +

    1-set the following environment variables

    + +
    + +

       export POA_DIR=[absolute path of the POA installation dir]

    + +

       export DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf

    + +
    + +

    Once this is done, write your sequences in a file and run: same file +(Swiss-prot, Fasta or Pir) and type.

    + +
    + +

    PROMPT: t_coffee +sample_seq1.fasta –mode mcoffee

    + +
    + +

    If the program starts complaining one package or the other is missing, +this means you will have to go the hard way and install all these packages +yourself... Proceed to the M-Coffee section for more detailed instructions.

    + +

    Expresso

    + +

    If you have installed the EBI wublast.pl client, Expresso will BLAST +your sequences against PDB, identify the best targets and use these to align +your proteins.

    + +

     

    + +
    + +

    PROMPT: t_coffee +sample_seq1.fasta –mode expresso

    + +
    + +

    If you did not manage to install all the required structural packages +for Expresso, like Fugue or Sap, you can still run expresso by selecting +yourself the structural packages you want to use. For instance, if you'd rather +use TM-Align than sap, try:

    + +

            

    + +
    + +

    PROMPT: t_coffee +sample_seq1.fasta –template_file EXPRESSO -method TMalign_pair

    + +
    + +

     

    + +

    R-Coffee

    + +

    R-Coffee can be used to align RNA sequences, using their RNApfold +predicted secondary structures. The best results are obtained by using the +consan pairwise method. If you have consan installed:

    + +
    + +

    t_coffee +sample_rnaseq1.fasta –special_mode rcoffee_consan

    + +
    + +

    This will only work if your sequences are short enough (less than 200 +nucleotides). A good alternative is the rmcoffee mode that will run Muscle, +Probcons4RNA and MAfft and then use the secondary structures predicted by +RNApfold.

    + +
    + +

    PROMPT: t_coffee +sample_rnaseq1.fasta –mode mrcoffee

    + +
    + +

     

    + +

    If you want to decide yourself which methods should be combined by +R-Coffee, run:

    + +
    + +

    PROMPT: t_coffee +sample_rnaseq1.fasta –mode rcoffee -method lalign_id_pair slow_pair

    + +
    + +

     

    + +

     

    + +


    +iRMSD and APDB

    + +

    All you need is a file containing the alignment of sequences with a +known structure. These sequences must be named according to their PDB ID, +followed by the chain index ( 1aabA for instance). All the sequences do not +need to have a known structure, but at least two need to have it.

    + +

    Given the alignment:

    + +

     

    + +
    + +

    PROMPT: t_coffee –other_pg +irmsd -aln 3d_sample4.aln

    + +
    + +

    tRMSD

    + +

    tRMSD is a structure based clustering method using the iRMSD to drive +the clustering. The T-RMSD supports all the parameters supported by iRMSD or +APDB.

    + +

     

    + +
    + +

    PROMPT: t_coffee –other_pg +trmsd -aln 3d_sample5.aln -template_file 3d_sample5.template_list

    + +
    + +

    3d_sample5.aln is a multiple +alignment in which each sequence has a known structure. The file 3d_sample5.template_list is a fasta like file declaring the structure +associated with each sequence, in the form:

    + +
    + +

    > <seq_name> _P_ <PDB structure file or name>

    + +
    + +

     

    + +
    + +

    ******* 3d_sample5.template_list ********     

    + +

    >2UWI-3A _P_ 2UWI-3.pdb

    + +

    >2UWI-2A _P_ 2UWI-2.pdb

    + +

    >2UWI-1A _P_ 2UWI-1.pdb

    + +

    >2HEY-4R _P_ 2HEY-4.pdb

    + +

    ...

    + +

    **************************************

    + +
    + +

     

    + +

    The program then outputs a series of files

    + +
    + +

    Template Type: [3d_sample5.template_list] +Mode Or File: [3d_sample5.template_list] [Start]

    + +

             +[Sample Columns][TOT=   51][100 +%][ELAPSED TIME:    0 sec.]

    + +

             [Tree Cmp][TOT=   13][ 92 %][ELAPSED TIME:    0 sec.]

    + +

     #### +File Type=   TreeList Format=     newick Name= 3d_sample5.tot_pos_list

    + +

     #### +File Type=       Tree Format=     newick Name= 3d_sample5.struc_tree10

    + +

     #### +File Type=       Tree Format=     newick Name= 3d_sample5.struc_tree50

    + +

     #### +File Type=       Tree Format=     newick Name= 3d_sample5.struc_tree100

    + +

     #### +File Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html

    + +

     

    + +
    + +

     

    + +

    3d_sample5.tot_pos_list       is a +list of the tRMSD tree associated with every position.

    + +

    3d_sample5.struc_tree100   is a +consensus tree (phylip/consense) of the trees contained in the previous file. This +file is the default output

    + +

    3d_sample5.struc_tree10     is a +consensus tree (phylip/consense) of the 10% trees having the higest average +agreement with the rest

    + +

    3d_sample5.struc_tree10     is a +consensus tree (phylip/consense) of the 50% trees having the higest average +agreement with the rest

    + +

    3d_sample5.html      is a colored +version of the output showing in red the positions that give the highest +support to 3d_sample5.struc_tree100

    + +

     

    + +

     

    + +

     

    + +

    MOCCA

    + +

    Write your sequences in the same file +(Swiss-prot, Fasta or Pir) and type.

    + +
    + +

    PROMPT: +t_coffee –other_pg mocca sample_seq1.fasta

    + +
    + +

    This command output one files (<your +sequences>.mocca_lib) and starts an interactive menu.

    + +
    + +

    Recent Modifications

    + +
    + +

    Warning: This log of recent modifications is +not as thorough and accurate as it should be.

    + +

    -5.80 Novel assembly algorithm +(linked_pair_wise) and the primary library is now made of probcons style +pairwise alignments (proba_pair)

    + +

    -4.30 and upward: the FAQ has moved into a new +tutorial document

    + +

    -4.30 and upward: -in has will be deprecated +and replaced by the flags: -profile,-method,-aln,-seq,-pdb

    + +

    -4.02: -mode=dna is still available but not any +more needed or supported. Use type=protein or dna if you need to force things

    + +

    -3.28: corrected a bug that prevents short sequences from being +correctly aligned

    + +

    -Use of @ as a separator when specifying +methods parameters

    + +

    -The most notable modifications have to do with +the structure of the input. From version 2.20, all files must be tagged to +indicate their nature (A: alignment, S: Sequence, L: LibraryÂ…). We are becoming +stricter, but thatÂ’s for your own goodÂ…

    + +

    Another important modification has to do with +the flag -matrix: it now controls the matrix being used for the computation

    + +
    +     + + + +

     

    + +

    This reference manual gives a list of all the +flags that can be used to modify the behavior of T-Coffee. For your +convenience, we have grouped them according to their nature. To display a list +of all the flags used in the version of T-Coffee you are using (along with +their default value), type:

    + +
    + +

    PROMPT: +t_coffee

    + +
    + +

    Or

    + +
    + +

    PROMPT: +t_coffee –help

    + +
    + +

    Or

    + +
    + +

    PROMPT: +t_coffee –help –in

    + +
    + +

    Or any other parameter

    + +

     

    + +

    Environment +Variables

    + +

    It is possible to modify T-Coffee’s behavior by setting any of the +following environement variables. On the bash shell, use export VAR=”value”. On +the cshell, use set $VAR=”xxx”

    + +

    http_proxy_4_TCOFFEE

    + +

    Sets the http_proxy and HTTP_proxy values used by T-Coffee.

    + +

    These values get supersede http_proxy and HTTP_proxy. +http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and +-email)

    + +

    If you have no proxy, just set this value to an empty string.

    + +

    email_4_TCOFFEE

    + +

    Set the E-mail values provided to web services called upon by T-Coffee. +Can be over-riden by the flag -email.

    + +

    DIR_4_TCOFFEE

    + +

    By default this variable is set to $HOME/.t_coffee. This is where +T-Coffee expects to find its cache, tmp dir and possibly any temporary data +stored by the program.

    + +

    TMP_4_TCOFFEE

    + +

    By default this variable is set to $HOME/.t_coffee/tmp. This is where +T-Coffee stores temporary files.

    + +

    CACHE_4_TCOFFEE

    + +

    By default this variable is set to $HOME/.t_coffee/cache. This is where +T-Coffee stores any data expensive to obtain: pdb files, sap alignments....

    + +

    PLUGINS_4_TCOFFEE

    + +

    By default all the companion packages are searched in the directory +DIR_4_TCOFFEE/plugins/<OS>. This variable overrides the default. This +variable can also be overriden by the -plugins T-Coffee flag

    + +

    NO_ERROR_REPORT_4_TCOFFEE

    + +

    By default this variable is no set. Set it if you do not want the +program to generate a verbose error output file (useful for running a server).

    + +

    PDB_DIR

    + +

    Indicate the location of your local PDB installation.

    + +

    NO_WARNING_4_TCOFFEE

    + +

    Suppresses all the warnings.

    + +

     

    + +

    Setting +up the T-Coffee environment variables

    + +

    T-Coffee can have its own environment file. This environment is kept +in a file named $HOME/.t_coffee/t_coffee_env and can be edited. The value of +any legal variable can be modified through that file. For instance, here is an +example of a configuration file when not requiring a proxy.

    + +
    + +

    http_proxy_4_TCOFFEE=

    + +

    EMAIL_4_TCOFFEE=cedric.notredame@europe.com

    + +
    + +
    + +

    IMPORTANT:

    + +

    -proxy, -email >> +t_coffee_env >> env

    + +

     

    + +
    + +

     

    + +

     

    + +

    Well +Behaved Parameters

    + +

    Separation

    + +

    You can use any kind of separator you want +(i.e. ,; <space>=). The syntax used in this document is meant to be +consistent with that of ClustalW. However, in order to take advantage of the +automatic filename compleation provided by many shells, you can replace “=” and +“,” with a space.

    + +

    Posix

    + +

    T-Coffee is not POSIX compliant.

    + +

    Entering the right parameters

    + +

    There are many ways to enter parameters in +T-Coffee, see the -parameter flag in

    + +

     

    + +
    + +

    Parameters Priority

    + +

     

    + +

    In +general you will not need to use these complicated parameters. Yet, if you find +yourself typing long command lines on a regular basis, it may be worth reading +this section.

    + +

     

    + +

    One +may easily feel confused with the various manners in which the parameters can +be passed to t_coffee. The reason for these many mechanisms is that they allow +several levels of intervention. For instance, you may install t_coffee for all +the users and decide that the defaults we provide are not the proper onesÂ… In +this case, you will need to make your own t_coffee_default file.

    + +

     

    + +

    Later +on, a user may find that he/she needs to keep re-using a specific set of +parameters, different from those in t_coffee_default, hence the possibility to +write an extra parameter file: parameters. In summary:

    + +

     

    + +

    -parameters +> prompt parameters > -t_coffee_defaults > -mode

    + +

     

    + +

    This +means that -parameters supersede all the others, while parameters +provided via -special mode are the weakest.

    + +
    + +

     

    + +

     

    + +

    Parameters Syntax

    + +

    No Flag

    + +

    If no flag is used <your +sequence> must be the first argument. See format for further +information.

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta

    + +
    + +

    Which is equivalent to

    + +
    + +

    PROMPT: +t_coffee Ssample_seq1.fasta

    + +
    + +

    When you do so, sample_seq1 is used as a name prefix for every file the program +outputs.

    + +

    -parameters

    + +

    Usage: +-parameters=parameters_file

    + +

    Default: no parameters file

    + +

    Indicates a file containing extra parameters. +Parameters read this way behave as if they had been added on the right end of +the command line that they either supersede(one value parameter) or complete +(list of values). For instance, the following file (parameter.file) could be +used

    + +
    + +

    *******sample_param_file.param********  

    + +

          -in=Ssample_seq1.fasta,Mfast_pair

    + +

          -output=msf_aln

    + +

    **************************************

    + +
    + +

    Note: This is +one of the exceptions (with –infile) where the identifier tag (S,A,L,M…) can be +omitted. Any dataset provided this way will be assumed to be a sequence (S). +These exceptions have been designed to keep the program compatible with +ClustalW.

    + +

    Note: This +parameter file can ONLY contain valid parameters. Comments are not allowed. +Parameters passed this way will be checked like normal parameters.

    + +

    Used with:

    + +
    + +

    PROMPT: +t_coffee -parameters=sample_param_file.param

    + +
    + +

    Will cause t_coffee to apply the +fast_pair method onto to the sequences contained in sample_seq.fasta. If you +wish, you can also pipe these arguments into t_coffee, by naming the parameter +file "stdin" (as a rule, any file named stdin is expected to receive +its content via the stdin)

    + +

    cat sample_param_file.param  | t_coffee -parameters=stdin

    + +

    -t_coffee_defaults

    + +

    Usage: +-t_coffee_defaults=<file_name>

    + +

    Default: not used.

    + +

    This flag tells the program to use +some default parameter file for t_coffee. The format of that file is the same +as the one used with -parameters. The file used is either:

    + +

                1. +<file name> if a name has been specified

    + +

                2.  ~/.t_coffee_defaults if no file was +specified

    + +

                3. +The file indicated by the environment variable TCOFFEE_DEFAULTS

    + +

    -mode

    + +

    Usage: -mode= +hard coded mode

    + +

    Default: not used.

    + +

    It indicates that t_coffee will use +some hard coded parameters. These include:

    + +

                quickaln: very fast approximate +alignment

    + +

                dali: a mode used to combine dali +pairwise alignments

    + +

                evaluate: defaults for evaluating an +alignment

    + +

                3dcoffee: runs t_coffee with the +3dcoffee parameterization

    + +

     

    + +

    Other modes exist that are not yet +fully supported

    + +

    -score [Deprecated]

    + +

    Usage: +-score

    + +

    Default: not used

    + +

    Toggles on the evaluate mode and +causes t_coffee to evaluates a precomputed alignment provided via -infile=<alignment>. +The flag -output must be set to an appropriate format (i.e. +-output=score_ascii, score_html or score_pdf). A better default parameterization +is obtained when using the flag -mode=evaluate.

    + +

    -evaluate

    + +

    Usage: +-evaluate

    + +

    Default: not used

    + +

    Replaces –score. This flag toggles on +the evaluate mode and causes t_coffee to evaluates a pre-computed alignment +provided via -infile=<alignment>. The flag -output must be +set to an appropriate format (i.e. -output=score_ascii, score_html or +score_pdf).

    + +

     

    + +

    The main purpose of –evaluate is to +let you control every aspect of the evaluation. Yet it is advisable to use +pre-defined parameterization: mode=evaluate.

    + +
    + +

    PROMPT: +t_coffee –infile=sample_aln1.aln -mode=evaluate

    + +

    PROMPT: +t_coffee –infile=sample_seq1.aln –in  +Lsample_lib1.tc_lib –mode=evaluate

    + +
    + +

    -convert [cw]

    + +

    Usage: +-convert

    + +

    Default: turned off

    + +

    Toggles on the conversion mode and +causes T-Coffee to convert the sequences, alignments, libraries or structures +provided via the -infile and -in flags. The output format must be +set via the -output flag. This flag can also be used if you simply want +to compute a library (i.e. you have an alignment and you want to turn it into a +library).

    + +

    This flag is ClustalW compliant.

    + +

    -do_align [cw]

    + +

    Usage:  -do_align

    + +

    Default: turned on

    + +

    Special Parameters

    + +

    -version

    + +

    Usage: +-version

    + +

    Default: not used

    + +

    Returns the current version number

    + +

    -proxy

    + +

    Usage: -proxy=<proxy>

    + +

    Default: not used

    + +

    Sets the proxy used by +HTTP_proxy AND http_proxy. Setting with the propmpt supersedes ANY other +setting.

    + +

    Note that if you use no +proxy, you should set

    + +

                -proxy

    + +

    -email

    + +

    Usage: -email=<email>

    + +

    Default: not used

    + +

    Sets your email value as +provided to web services

    + +

    -check_configuration

    + +

    Usage: +-check_configuration

    + +

    Default: not used

    + +

    Checks your system to determine +whether all the programs T-Coffee can interact with are installed.

    + +

    -cache

    + +

    Usage: +-cache=<use, update, ignore, <filename>>

    + +

    Default: -cache=use

    + +

    By default, t_coffee stores in a +cache directory, the results of computationally expensive (structural +alignment) or network intensive (BLAST search) operations.

    + +

    -update

    + +

    Usage: +-update

    + +

    Default: turned off

    + +

    Causes a wget access that checks whether +the t_coffee version you are using needs updating.

    + +

    -full_log

    + +

    Usage: +-full_log=<filename>

    + +

    Default: turned off

    + +

    Causes t_coffee to output a full log +file that contains all the input/output files.

    + +

    -plugins

    + +

    Usage: -plugins=<dir>

    + +

    Default: default

    + +

    Specifies the directory in which the companion packages (other +multiple aligners used by M-Coffee, structural aligners, etcÂ…) are kept as an +alternative, you can also set the environment variable PLUGINS_4_TCOFFEE

    + +

    The default is ~/.t_coffee/plugins/

    + +

    -other_pg

    + +

    Usage: +-other_pg=<filename>

    + +

    Default: turned off

    + +

    Some rumours claim that Tetris is +embedded within T-Coffee and could be ran using some special set of commands. +We wish to deny these rumours, although we may admit that several interesting +reformatting programs are now embedded in t_coffee and can be ran through the +–other_pg flag.

    + +
    + +

    PROMPT: +t_coffee –other_pg=seq_reformat

    + +

    PROMPT: +t_coffee –other_pg=unpack_all

    + +

    PROMPT: +t_coffee –other_pg=unpack_extract_from_pdb

    + +
    + +

    Input

    + +

    Sequence Input

    + +

    -infile [cw]

    + +

    To remain compatible with ClustalW, +it is possible to indicate the sequences with this flag

    + +
    + +

    PROMPT: +t_coffee -infile=sample_seq1.fasta

    + +
    + +

    Note: Common +multiple sequence alignments format constitute a valid input format.

    + +

    Note: T-Coffee +automatically removes the gaps before doing the alignment. This behaviour is different +from that of ClustalW where the gaps are kept.

    + +

    -in (Cf –in from the Method and Library Input section)

    + +

    -get_type

    + +

    Usage: +-get_type

    + +

    Default: turned off

    + +

    Forces t_coffee to identify the +sequences type (PROTEIN, DNA).

    + +

    -type [cw]

    + +

    Usage: +-type=DNA ¦ PROTEIN¦ DNA_PROTEIN

    + +

    Default: -type=<automatically set>

    + +

    This flag sets the type of the +sequences. If omitted, the type is guessed automatically. This flag is +compatible with ClustalW.

    + +
    + +

    Warning:  +In case of low complexity or short sequences, it is recommended to set +the type manually.

    + +
    + +

    -seq

    + +

    Usage: +-seq=[<P,S><name>,]

    + +

    Default: none

    + +

    -seq is now the recommended flag to provide +your sequences. It behaves mostly like the -in flag.

    + +

    -seq_source

    + +

    Usage: +-seq_source=<ANY or  _LS or LS >

    + +

    Default: ANY.

    + +

    You may not want to combine all the +provided sequences into a single sequence list. You can do by specifying that +you do not want to treat all the –in files as potential sequence sources.

    + +

    -seq_source=_LA indicates that +neither sequences provided via the A (Alignment) flag or via the L (Library +flag) should be added to the sequence list.

    + +

    -seq_source=S means that only +sequences provided via the S tag will be considered. All the other sequences +will be ignored.

    + +

    Note:  This flag is mostly designed for interactions +between T-Coffee and T-CoffeeDPA (the large scale version of T-Coffee).

    + +

    Structure Input

    + +

    -pdb

    + +

    Usage:  -pdb=<pdbid1>,<pdbid2>…[Max 200]

    + +

    Default: None

    + +

    Reads or fetch a pdb file. It is +possible to specify a chain or even a sub-chain:

    + +

    PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]

    + +

    It is also possible to input structures via the –in flag. In that +case, you will need to use the TAG identifier:

    + +

    -in +Ppdb1 Ppdb2Â…

    + +

    Tree +Input

    + +

    -usetree

    + +

    Usage: +-usetree=<tree file>

    + +

    Default: No file specified

    + +

    Format: newick tree format (ClustalW +Style)

    + +

    This flag indicates that rather than +computing a new dendrogram, t_coffee must use a pre-computed one. The tree +files are in phylips format and compatible with ClustalW. In most cases, using +a pre-computed tree will halve the computation time required by t_coffee. It is +also possible to use trees output by ClustalW, Phylips and any other program.

    + +

    Structures, Sequences Methods and Library Input via the –in Flag

    + +
    + +

    The -in Flag and +its Identifier TAGS

    + +

     

    + +

    <-in> is the real +grinder of T-Coffee. Sequences, methods and alignments all pass through so that +T-Coffee can turn it all into a single list of constraints (the library). +Everything is done automatically with T-Coffee going through each file to +extract the sequences it contains. The methods are then applied to the +sequences. Pre-compiled constraint list can also be provided. Each file +provided via this flag must be preceded with a symbol (Identifier TAG) that +indicates its nature to T-Coffee. The TAGs currently supported are the +following:

    + +

     

    + +

    P         PDB structure

    + +

    S          for sequences (use it as well to treat an MSA as unaligned +sequences)

    + +

     

    + +

    M        Methods used to build the library

    + +

    L         Pre-computed T-Coffee library

    + +

    A         Multiple Alignments that must be turned into a Library

    + +

     

    + +

    X         Substitution matrices.

    + +

    R                     Profiles. This is a legal multiple +alignments that will be treated as single sequences (the sequences it contains +will not be realigned).

    + +

     

    + +

    If you do not want to use the TAGS, you will +need to use the following flags in replacement of -in. Do not use the TAGS when +using these flags:

    + +

     

    + +

    -aln                             Alignments +   (A)

    + +

    -profile           Profiles +          (R)

    + +

    -method          Method +         (M)

    + +

    -seq                             Sequences +     (S)

    + +

    -lib                              Libraries        (L)

    + +
    + +

    -in

    + +

    Usage: +-in=[<P,S,A,L,M,X><name>,]

    + +

    Default: +-in=Mlalign_id_pair,Mclustalw_pair

    + +
    + +

    Note: -in can be replaced with the combined +usage of -aln, iprofile, .pdb, .lib, -method.

    + +
    + +

    See the box for an explanation of the +-in flag. The following argument passed via -in

    + +

     

    + +
    + +

    PROMPT: +t_coffee +-in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib +–outfile=outaln

    + +
    + +

     

    + +

    This command will trigger the following +chain of events:

    + +

     

    + +

    1-Gather all the sequences

    + +

    Sequences within all the provided +files are pooled together. Format recognition is automatic. Duplicates are +removed (if they have the same name). Duplicates in a single file are only +tolerated in FASTA format file, although they will cause sequences to be +renamed.

    + +

    In the above case, the total set of +sequences will be made of sequences contained in sequences1.seq, +alignment1.aln, alignment2.msf and library.lib, plus the sequences initially +gathered  by -infile.

    + +

    2-Turn alignments into libraries

    + +

    alignment1.aln and alignment2.msf +will be read and turned into libraries. Another library will be produced by +applying the method lalign_id_pair to the set of sequences previously obtained +(1). The final library used for the alignment will be the combination of all +this information.

    + +

    Note as well the following rules:

    + +

     

    + +

    1-Order: The order in which sequences, methods, alignments and libraries are +fed in is irrelevant.

    + +

    2-Heterogeneity: There is no need for each element (A, S, L) to +contain the same sequences.

    + +

    3-No Duplicate: Each file should contain only one copy of each +sequence. Duplicates are only allowed in FASTA files but will cause the +sequences to be renamed.

    + +

    4-Reconciliation: If two files (for instance two alignments) +contain different versions of the same sequence due to an indel, a new sequence +will be reconstructed and used instead:

    + +

    aln 1:hgab1   AAAAABAAAAA

    + +

    aln 2:hgab1   AAAAAAAAAACCC

    + +

    will cause the program to reconstruct +and use the following sequence

    + +

    hgab1   AAAAABAAAAACCC +

    + +

    This can be useful if you are trying +to combine several runs of blast, or structural information where residues may +have been deleted. However substitutions are forbidden. If two sequences with +the same name cannot be merged, they will cause the program to exit with an +information message.

    + +

    5-Methods: The method describer can either be built in +(See ### for a list of all the available methods) or be a file describing the +method to be used. The exact syntax is provided in part 4 of this manual.

    + +

    6-Substitution Matrices: If the method is a substitution matrix (X) then +no other type of information should be provided. For instance:

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta -in=Xpam250mt  +-gapopen=-10  -gapext=-1

    + +
    + +

    This command results in a progressive +alignment carried out on the sequences in seqfile. The procedure does not use +any more the T-Coffee concistency based algorithm, but switches to a standard +progressive alignment algorithm (like ClustalW or Pileup) much less accurate. +In this context, appropriate gap penalties should be provided. The matrices are +in the file source/matrices.h. Add-Hoc matrices can also be provided by the +user (see the matrices format section at the end of this manual).

    + +
    + +

    Warning: Xmatrix does not have the same +effect as using the -matrix flag.  The +-matrix defines the matrix that will be used while compiling the library while +the Xmatrix defines the matrix used when assembling the final alignment.

    + +
    + +

    Profile Input

    + +

    -profile

    + +

    Usage: +-profile=[<name>,] maximum of 200 profiles.

    + +

    Default: no default

    + +

    This flag causes T-Coffee to treat +multiple alignments as a single sequences, thus making it possible to make +multiple profile alignments. The profile-profile alignment is controlled by -profile_mode and -profile_comparison. When provided +with the -in flag, profiles must be +preceded with the letter R.

    + +
    + +

    PROMPT: +t_coffee –profile sample_aln1.aln,sample_aln2.aln –outfile=profile_aln

    + +

    PROMPT: +t_coffee –in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair +–outfile=profile_aln

    + +
    + +

    Note that when using –template_file, +the program will also look for the templates associated with the profiles, even +if the profiles have been provided as templates themselves (however it will not +look for the template of the profile templates of the profile templates…)

    + +

    -profile1 [cw]

    + +

    Usage: +-profile1=[<name>], one name only

    + +

    Default: no default

    + +

    Similar to the previous one and was +provided for compatibility with ClustalW.

    + +

    -profile2 [cw]

    + +

    Usage: +-profile1=[<name>], one name only

    + +

    Default: no default

    + +

    Similar to the previous one and was +provided for compatibility with ClustalW.

    + +

    Alignment Computation

    + +

    Library Computation: Methods

    + +

    -lalign_n_top

    + +

    Usage: +-lalign_n_top=<Integer>

    + +

    Default: -lalign_n_top=10

    + +

    Number of alignment reported by the +local method (lalign).

    + +

    -align_pdb_param_file

    + +

    Unsuported

    + +

    -align_pdb_hasch_mode

    + +

    Unsuported

    + +

    Library +Computation: Extension

    + +

    -lib_list [Unsupported]

    + +

    Usage:  +-lib_list=<filename>

    + +

    Default:unset

    + +

    Use this flag if you do not want the library computation to take +into account all the possible pairs in your dataset. For instance

    + +

    Format:

    + +
    + +

          2 Name1 name2

    + +

          2 Name1 name4

    + +

          3 Name1 Name2 Name3…

    + +
    + +

                (the line 3 would +be used by a multiple alignment method).

    + +

    -do_normalise

    + +

    Usage:  +-do_normalise=<0 or a positive value>

    + +

    Default:-do_normalise=1000

    + +

    Development +Only

    + +

    When using a value different from 0, this flag sets the score of the +highest scoring pair to 1000.

    + +

    -extend

    + +

    Usage:  -extend=<0,1 or a positive value>

    + +

    Default:-extend=1

    + +

    Development Only

    + +

    When turned on, this flag indicates +that the library extension should be carried out when performing the multiple +alignment. If -extend =0, the extension is not made, if it is set to 1, +the extension is made on all the pairs in the library. If the extension is set +to another positive value, the extension is only carried out on pairs having a weight +value superior to the specified limit.

    + +

    -extend_mode

    + +

    Usage:  -extend=<string>

    + +

    Default:-extend=very_fast_triplet

    + +

    Warning: Development Only

    + +

    Controls the algorithm for matrix +extension. Available modes include:

    + +

    relative_triplet                  Unsupported

    + +

    g_coffee                                           Unsupported

    + +

    g_coffee_quadruplets    Unsupported

    + +

    fast_triplet                        Fast triplet extension

    + +

    very_fast_triplet                             slow triplet +extension, limited to the -max_n_pair best sequence pairs when aligning +two profiles

    + +

    slow_triplet                       Exhaustive use of all the triplets

    + +

    mixt                                   Unsupported

    + +

    quadruplet                        Unsupported

    + +

    test                                     Unsupported

    + +

    matrix                                               Use of the matrix -matrix

    + +

    fast_matrix                      Use of the matrix -matrix. Profiles are +turned into consensus

    + +

    -max_n_pair

    + +

    Usage:  -max_n_pair=<integer>

    + +

    Default:-extend=10

    + +

    Development Only

    + +

    Controls the number of pairs +considered by the -extend_mode=very_fast_triplet. Setting it to 0 forces +all the pairs to be considered (equivalent to -extend_mode=slow_triplet).

    + +

    -seq_name_for_quadruplet

    + +

    Usage:  Unsupported

    + +

    -compact

    + +

    Usage:  Unsupported

    + +

    -clean

    + +

    Usage:  Unsupported

    + +

    -maximise

    + +

    Usage:  Unsupported

    + +

    -do_self

    + +

    Usage:  Flag -do_self

    + +

    Default: No

    + +

    This flag causes the extension to +carried out within the sequences (as opposed to between sequences). This is +necessary when looking for internal repeats with Mocca.

    + +

    -seq_name_for_quadruplet

    + +

    Usage:  Unsupported

    + +

    -weight

    + +

    Usage:  -weight=<winsimN, sim or +sim_<matrix_name or matrix_file> or <integer value>

    + +

    Default: -weight=sim

    + +

    Weight defines the way alignments are +weighted when turned into a library.  Overweighting can be obtained with the +OW<X> weight mode.

    + +

     

    + +

    winsimN indicates that the weight +assigned to a given pair will be equal to the percent identity within a window +of 2N+1 length centered on that pair. For instance winsim10 defines a window of +10 residues around the pair being considered. This gives its own weight to each +residue in the output library. In our hands, this type of weighting scheme has +not provided any significant improvement over the standard sim value.

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta -weight=winsim10 –out_lib=test.tc_lib

    + +
    + +

    sim indicates that the weight equals +the average identity within the sequences containing the matched residues.

    + +

    OW<X> Will +cause the sim weight to be multiplied by X

    + +

    sim_matrix_name indicates the average +identity with two residues regarded as identical when their substitution value +is positive. The valid matrices names are in matrices.h (pam250mt) .Matrices not found in this header are +considered to be filenames. See the format section for matrices. For instance, -weight=sim_pam250mt indicates that the +grouping used for similarity will be the set of classes with positive +substitutions.

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta -weight=winsim10 –out_lib=test.tc_lib

    + +
    + +

    Other groups include

    + +

    sim_clustalw_col ( categories of clustalw marked with :)

    + +

    sim_clustalw_dot ( categories of +clustalw marked with .)

    + +

    Value indicates that all the pairs found in +the alignments must be given the same weight equal to value. This is useful +when the alignment one wishes to turn into a library must be given a +pre-specified score (for instance if they come from a structure +super-imposition program). Value is an integer:

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta -weight=1000 –out_lib=test.tc_lib

    + +
    + +

    Tree Computation

    + +

    -distance_matrix_mode

    + +

    Usage: +-distance_matrix_mode=<slow, fast, very_fast>

    + +

    Default: very_fast

    + +

    This flag indicates the method used +for computing the distance matrix (distance between every pair of sequences) +required for the computation of the dendrogram.

    + +

    Slow   The +chosen dp_mode using the extended library,

    + +

    fast:   + The fasta dp_mode using the +extended library.

    + +

    very_fast          The fasta dp_mode using blosum62mt.

    + +

    ktup    Ktup matching (Muscle kind)

    + +

    aln                      Read the distances on a precomputed MSA

    + +

    -quicktree [CW]

    + +

    Usage: +-quicktree

    + +

    Description: Causes T-Coffee to compute a +fast approximate guide tree

    + +

    This flag is kept for compatibility with +ClustalW. It indicates that:

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta –distance_matrix_mode=very_fast

    + +

    PROMPT: +t_coffee sample_seq1.fasta –quicktree

    + +
    + +

    Pair-wise Alignment Computation

    + +

     

    + +
    + +

    Controlling Alignment Computation

    + +

     

    + +

    Most +parameters in this section refer to the alignment mode fasta_pair_wise and +cfatsa_pair_wise. When using these alignment modes, things proceed as follow:

    + +

    1-Sequences +are recoded using a degenerated alphabet provided with <-sim_matrix>

    + +

    2-Recoded +sequences are then hashed into ktuples of size <-ktup>

    + +

    3-Dynamic +programming runs on the <-ndiag> best diagonals whose score is +higher than <-diag_threshold>, the way diagonals are scored is +controlled via <-diag_mode> .

    + +

    4-The +Dynamic computation is made to optimize either the library scoring scheme (as +defined by the -in flag) or a substitution matrix as provided via the -matrix +flag. The penalty scheme is defined by -gapopen and -gapext. If -gapopen +is undefined, the value defined in -cosmetic_penalty is used instead.

    + +

    5-Terminal +gaps are scored according to -tg_mode

    + +
    + +

     

    + +

     

    + +

    -dp_mode

    + +

    Usage:  -dp_mode=<string>

    + +

    Default: -dp_mode=cfasta_fair_wise

    + +

    This flag indicates the type of +dynamic programming used by the program:

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta –dp_mode myers_miller_pair_wise

    + +
    + +

    gotoh_pair_wise: implementation of +the gotoh algorithm (quadratic in memory and time)

    + +

    myers_miller_pair_wise: +implementation of the Myers and Miller dynamic programming algorithm ( +quadratic in time and linear in space). This algorithm is recommended for very +long sequences. It is about 2 times slower than gotoh and only accepts tg_mode=1or 2 (i.e. gaps penalized for +opening).

    + +

    fasta_pair_wise: implementation of the fasta algorithm. +The sequence is hashed, looking for ktuples +words. Dynamic programming is only carried out on the ndiag best scoring diagonals. This is much faster but less accurate +than the two previous. This mode is controlled by the parameters -ktuple, +-diag_mode and -ndiag

    + +

    cfasta_pair_wise: c stands for +checked. It is the same algorithm. The dynamic programming is made on the ndiag best diagonals, and then on the +2*ndiags, and so on until the scores converge. Complexity will depend on the +level of divergence of the sequences, but will usually be L*log(L), with an +accuracy comparable to the two first mode ( this was checked on BaliBase). This +mode is controlled by the parameters -ktuple, -diag_mode and –ndiag

    + +

    Note: Users may +find by looking into the code that other modes with fancy names exists +(viterby_pair_wiseÂ…) Unless mentioned in this documentation, these modes are +not supported.

    + +

    -ktuple

    + +

    Usage:  -ktuple=<value>

    + +

    Default: -ktuple=1 or 2

    + +

    Indicates the ktuple size for +cfasta_pair_wise dp_mode and fasta_pair_wise. It is set to 1 for proteins, and +2 for DNA. The alphabet used for protein can be a degenerated version, set with +-sim_matrix..

    + +

    -ndiag

    + +

    Usage:  -ndiag=<value>

    + +

    Default: -ndiag=0

    + +

    Indicates the number of diagonals +used by the fasta_pair_wise algorithm (cf -dp_mode). When  -ndiag=0, n_diag=Log (length of the +smallest sequence)+1.

    + +

    When –ndiag and +–diag_threshold are set, diagonals are selected if and only if they fulfill +both conditions.

    + +

    -diag_mode

    + +

    Usage:  -diag_mode=<value>

    + +

    Default: -diag_mode=0

    + +

    Indicates the manner in which +diagonals are scored during the fasta hashing.

    + +

    0: indicates that the score of a +diagonal is equal to the sum of the scores of the exact matches it contains.

    + +

    1 indicates that this score is set +equal to the score of the best uninterrupted segment (useful when dealing with +fragments of sequences).

    + +

    -diag_threshold

    + +

    Usage:  -diag_threshold=<value>

    + +

    Default: -diag_threshold=0

    + +

    Sets the value of the threshold when +selecting diagonals.

    + +

    0: indicates that –ndiag should be +used to select the diagonals (cf –ndiag section).

    + +

    -sim_matrix

    + +

    Usage:  -sim_matrix=<string>

    + +

    Default: -sim_matrix=vasiliky

    + +

    Indicates the manner in which the +amino acid alphabet is degenerated when hashing in the fasta_pairwise dynamic +programming. Standard ClustalW matrices are all valid. They are used to define +groups of amino acids having positive substitution values. In T-Coffee, the +default is a 13 letter grouping named Vasiliky, with residues grouped as +follows:

    + +

    rk, de, qh, vilm, fy (other residues kept +alone).

    + +

    This alphabet is set with the flag -sim_matrix=vasiliky. +In order to keep the alphabet non degenerated, -sim_matrix=idmat can be +used to retain the standard alphabet.

    + +

    -matrix [CW]

    + +

    Usage:  -matrix=<blosum62mt>

    + +

    Default: -matrix=blosum62mt

    + +

    The usage of this flag has been +modified from previous versions, due to frequent mistakes in its usage. This +flag sets the matrix that will be used by alignment methods within t_coffee +(slow_pair, lalign_id_pair). It does not affect external methods (like +clustal_pair, clustal_alnÂ…).

    + +

    Users can also provide their own +matrices, using the matrix format described in the appendix.

    + +

    -nomatch

    + +

    Usage:  -nomatch=<positive value>

    + +

    Default: -nomatch=0

    + +

    Indicates the penalty to associate +with a match. When using a library, all matches are positive or equal to 0. +Matches equal to 0 are unsupported by the library but non-penalized. Setting +nomatch to a non-negative value makes it possible to penalize these null +matches and prevent unrelated sequences from being aligned (this can be useful +when the alignments are meant to be used for structural modeling).

    + +

    -gapopen

    + +

    Usage:  -gapopen=<negative value>

    + +

    Default: -gapopen=0

    + +

    Indicates the penalty applied for +opening a gap. The penalty must be negative. If no value is provided when using +a substitution matrix, a value will be automatically computed.

    + +

    Here are some guidelines regarding +the tuning of gapopen and gapext. In T-Coffee matches get a score between 0 +(match) and 1000 (match perfectly consistent with the library). The default +cosmetic penalty is set to -50 (5% of a perfect match). If you want to tune +-gapoen and see a strong effect, you should therefore consider values between 0 +and -1000.

    + +

    -gapext

    + +

    Usage:  -gapext=<negative value>

    + +

    Default: -gapext=0

    + +

    Indicates the penalty applied for +extending a gap (cf -gapopen)

    + +

    -fgapopen

    + +

    Unsupported

    + +

    -fgapext

    + +

    Unsupported

    + +

    -cosmetic_penalty

    + +

    Usage:  -cosmetic_penalty=<negative value>

    + +

    Default: -cosmetic_penalty=-50

    + +

    Indicates the penalty applied for +opening a gap. This penalty is set to a very low value. It will only have an +influence on the portions of the alignment that are unalignable. It will not +make them more correct, but only more pleasing to the eye ( i.e. Avoid +stretches of lonely residues).

    + +

    The cosmetic penalty is automatically +turned off if a substitution matrix is used rather than a library.

    + +

    -tg_mode

    + +

    Usage:  -tg_mode=<0, 1, or 2>

    + +

    Default: -tg_mode=1

    + +

    0: terminal gaps penalized with -gapopen + -gapext*len

    + +

    1: terminal gaps penalized with a -gapext*len

    + +

    2: terminal gaps unpenalized.

    + +

     

    + +

    Weighting Schemes

    + +

    -seq_weight

    + +

    Usage: +-seq_weight=<t_coffee or <file_name>>

    + +

    Default: -seq_weight=t_coffee

    + +

    These are the individual weights +assigned to each sequence. The t_coffee weights try to compensate the bias in +consistency caused by redundancy in the sequences.

    + +

                sim(A,B)=%similarity +between A and B, between 0 and 1.

    + +

                weight(A)=1/sum(sim(A,X)^3)

    + +

    Weights are normalized so that their +sum equals the number of sequences. They are applied onto the primary library +in the following manner:

    + +

                res_score(Ax,By)=Min(weight(A), +weight(B))*res_score(Ax, By)

    + +

    These are very simple weights. Their +main goal is to prevent a single sequence present in many copies to dominate +the alignment.

    + +

    Note: The +library output by -out_lib is the un-weighted  +library.

    + +

    Note: Weights +can be output using the -outseqweight flag.

    + +

    Note: You can +use your own weights (see the format section).

    + +

     

    + +

    Multiple Alignment Computation

    + +

    -msa_mode

    + +

    Usage: +-msa_mode=<tree,graph,precomputed>

    + +

    Default: -evaluate_mode=tree

    + +

    Unsupported

    + +

    -one2all

    + +

    Usage: -one2all=<name>

    + +

    Default: not used

    + +

    Will generate a one to all +library with respect to the specified sequence and will then align all the +sequences in turn to that sequence, in a sequence determined by the order in +which the sequences were provided. 

    + +

    –profile_comparison =profile, the MSAs +provided via –profile are vectorized and the function specified by +–profile_comparison is used to make profile profile alignments. In that case, +the complexity is NL^2

    + +

    -profile_comparison

    + +

    Usage: +-profile_mode=<fullN,profile>

    + +

    Default: -profile_mode=full50

    + +

    The profile mode flag controls the +multiple profile alignments in T-Coffee. There are two instances where t_coffee +can make multiple profile alignments:

    + +

    1-When N, the number of sequences is +higher than –maxnseq, the program +switches to its multiple profile alignment mode (t_coffee_dpa).

    + +

    2-When MSAs are provided via the –profile flag or via –profile1 and –profile2.

    + +

    In these situations, the +–profile_mode value influences the alignment computation, these values are:

    + +

    –profile_comparison =profile, the MSAs +provided via –profile are vectorized and the function specified by +–profile_comparison is used to make profile profile alignments. In that case, +the complexity is NL^2

    + +

    -profile_comparison=fullN, N is an integer value that can omitted. Full indicates that given two profiles, the alignment will be based +on a library that includes every possible pair of sequences between the two +profiles. If N is set, then the library will be restricted to the N most +similar pairs of sequences between the two profiles, as judged from a measure +made on a pairwise alignment of these two profiles.

    + +

    -profile_mode

    + +

    Usage: +-profile_mode=<cw_profile_profile, muscle_profile_profile, multi_channel>

    + +

    Default: -profile_mode=cw_profile_profile

    + +

    When –profile_comparison=profile, this flag selects a profile scoring +function.

    + +

    Alignment Post-Processing

    + +

    -clean_aln

    + +

    Usage:  -clean_aln  +

    + +

    Default:-clean_aln

    + +

    This flag causes T-Coffee to +post-process the multiple alignment. Residues that have a reliability score +smaller or equal to -clean_threshold (as given by an evaluation that uses +-clean_evaluate_mode)  are realigned to +the rest of the alignment. Residues with a score higher than the threshold +constitute a rigid framework that cannot be altered.

    + +

    The cleaning algorithm is greedy. It +starts from the top left segment of low constituency residues and works its way +left to right, top to bottom along the alignment. You can require this +operation to be carried out for several cycles using the -clean_iterations +flag.

    + +

    The rationale behind this operation +is mostly cosmetic. In order to ensure a decent looking alignment, the gop is +set to -20 and the gep to -1. There is no penalty for terminal gaps, and the +matrix is blosum62mt.

    + +

    Note: Gaps are +always considered to have a reliability score of 0.

    + +

    Note: The use of the +cleaning option can result in memory overflow when aligning large sequences,

    + +

    -clean_threshold

    + +

    Usage:  -clean_threshold=<0-9> 

    + +

    Default:-clean_aln=1

    + +

    See -clean_aln for details.

    + +

    -clean_iteration

    + +

    Usage:  -clean_iteration=<value between 1 and +> 

    + +

    Default:-clean_iteration=1

    + +

    See -clean_aln for details.

    + +

    -clean_evaluation_mode

    + +

    Usage:  -clean_iteration=<evaluation_mode +> 

    + +

    Default:-clean_iteration=t_coffee_non_extended

    + +

    Indicates the mode used for the +evaluation that will indicate the segments that should be realigned. See +-evaluation_mode for the list of accepted modes.

    + +

    -iterate

    + +

    Usage: +-iterate=<integer>

    + +

    Default: -iterate=0

    + +

    Sequences are extracted in turn and +realigned to the MSA. If iterate is set to -1, each sequence is realigned, +otherwise the number of iterations is set by –iterate.

    + +

    CPU Control

    + +

    Multithreading

    + +

    -multi_core

    + +

    Usage:  -multi_core= templates_jobs_relax_msa

    + +

    Default: 0

    + +

    Specifies that the steps of T-Coffee +that should be multi threaded. by default all relevant steps are.

    + +
    + +

    PROMPT: +t_coffee sample_seq2.fasta -multi_core jobs

    + +
    + +

    -n_core

    + +

    Usage:  -n_core= <number of cores>

    + +

    Default: 0

    + +

    Default indicates that all +cores will be used, as indicated by the environment via:

    + +
    + +

    PROMPT: t_coffee sample_seq2.fasta -multi_core jobs

    + +
    + +

     

    + +

    Limits

    + +

    -mem_mode

    + +

    Usage:  deprecated

    + +

    -ulimit

    + +

    Usage:  -ulimit=<value>

    + +

    Default: -ulimit=0

    + +

    Specifies the upper limit of memory +usage (in Megabytes). Processes exceeding this limit will automatically exit. A +value 0 indicates that no limit applies.

    + +

    -maxlen

    + +

    Usage:  -maxlen=<value, 0=nolimit>

    + +

    Default: -maxlen=1000

    + +

    Indicates the maximum length of the +sequences.

    + +

    Aligning +more than 100 sequences with DPA

    + +

    -maxnseq

    + +

    Usage:  -maxnseq=<value, 0=nolimit>

    + +

    Default: -maxnseq=50

    + +

    Indicates the maximum number of +sequences before triggering the use of t_coffee_dpa.

    + +

    -dpa_master_aln

    + +

    Usage: +-dpa_master_aln=<File, method>

    + +

    Default: -dpa_master_aln=NO

    + +

    When using dpa, t_coffee needs a seed +alignment that can be computed using any appropriate method. By default, +t_coffee computes a fast approximate alignment.

    + +

    A pre-alignment can be provided +through this flag, as well as any program using the following syntax:

    + +

    your_script –in <fasta_file> -out +<file_name>

    + +

    -dpa_maxnseq

    + +

    Usage: +-dpa_maxnseq=<integer value>

    + +

    Default: -dpa_maxnseq=30

    + +

    Maximum number of sequences aligned +simultaneously when DPA is ran. Given the tree computed from the master +alignment, a node is sent to computation if it controls more than –dpa_maxnseq OR if it controls a pair +of sequences having less than –dpa_min_score2 +percent ID.

    + +

    -dpa_min_score1

    + +

    Usage: +-dpa_min_score1=<integer value>

    + +

    Default: -dpa_min_score1=95

    + +

    Threshold for not realigning the +sequences within the master alignment. Given this alignment and the associated +tree, sequences below a node are not realigned if none of them has less than –dpa_min_score1 % identity.

    + +

    -dpa_min_score2

    + +

    Usage: +-dpa_min_score2

    + +

    Default: -dpa_min_score2

    + +

    Maximum number of sequences aligned +simultaneously when DPA is ran. Given the tree computed from the master +alignment, a node is sent to computation if it controls more than –dpa_maxnseq OR if it controls a pair +of sequences having less than –dpa_min_score2 +percent ID.

    + +

    -dap_tree +[NOT IMPLEMENTED]

    + +

    Usage:  -dpa_tree=<filename>

    + +

    Default: -unset

    + +

    Guide tree used in DPA. This is a +newick tree where the distance associated with each node is set to the minimum +pairwise distance among all considered sequences.

    + +

    Using Structures

    + +

    Generic

    + +

    -mode

    + +

    Usage: -mode=3dcoffee

    + +

    Default: turned off

    + +

    Runs t_coffee with the 3dcoffee mode +(cf next section).

    + +

    -check_pdb_status

    + +

    Usage: +-check_pdb_status

    + +

    Default: turned off

    + +

    Forces t_coffee to run +extract_from_pdb to check the pdb status of each sequence. This can +considerably slow down the program.

    + +

     

    + +

    3D Coffee: Using SAP

    + +

    It is possible to use t_coffee to +compute multiple structural alignments. To do so, ensure that you have the sap +program installed.

    + +
    + +

    PROMPT: +t_coffee –pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair

    + +
    + +

    Will combine the pairwise alignments +produced by SAP.  There are currently +four methods that can be interfaced with t_coffee:

    + +

    sap_pair: +that uses the sap algorithm

    + +

    align_pdb: +uses a t_coffee implementation of sap, not as accurate.

    + +

    tmaliagn_pair +(http://zhang.bioinformatics.ku.edu/TM-align/)

    + +

    mustang_pair +(http://www.cs.mu.oz.au/~arun/mustang)

    + +

    When providing a PDB file, the +computation is only carried out on the first chain of this file. If your +original file contains several chain, you should extract the chain you want to +work on. You can use t_coffee –other_pg +extract_from_pdb or any pdb handling program.

    + +

    If you are working with public PDB +files, you can use the PDB identifier and specify the chain by adding its index +to the identifier (i.e. 1pdbC). If your structure is an NMR structure, you are +advised to provide the program with one structure only.

    + +

    If you wish to align only a portion +of the structure, you should extract it yourself from the pdb file, using t_coffee –other_pg extract_from_pdb or +any pdb handling program.

    + +

    You can provide t_coffee with a +mixture of sequences and structure. In this case, you should use the special +mode:

    + +
    + +

    PROMPT: +t_coffee –mode 3dcoffee –seq 3d_sample3.fasta -template_file +template_file.template

    + +
    + +

    Using/finding PDB templates for the Sequences

    + +

    -template_file

    + +

    Usage: +-template_file =

    + +

    <filename,

    + +

    SCRIPT_scriptame,

    + +

    SELF_TAG

    + +

    SEQFILE_TAG_filename,

    + +

    no>

    + +

    Default: no

    + +

    This flag instructs t_coffee on the +templates that will be used when combining several types of information. For +instance, when using structural information, this file will indicate the +structural template that corresponds to your sequences. The identifier T +indicates that the file should be a FASTA like file, formatted as follows. +There are several ways to pass the templates:

    + +

    Predefined Modes

    + +

    EXPRESSO: will use the EBI server to find +_P_ templates

    + +

    PSIBLAST: will use the EBI sever to find +profiles

    + +

     

    + +

    File name

    + +

    This file contains the +sequence/template association it uses a FASTA-like format, as follows:

    + +
    + +

    ><sequence name> _P_ +<pdb template>

    + +

    ><sequence name> _G_ +<gene template>

    + +

    ><sequence name> _R_ +<MSA template>

    + +

    ><sequence name> _F_ +<RNA Secondary Structure>

    + +

    ><sequence name> _T_ +<Transmembrane Secondary Structure>

    + +

    ><sequence name> _E_ +<Protein Secondary Structure>

    + +

     

    + +
    + +

    Each template will be used in place +of the sequence with the appropriate method. For instance, structural templates +will be aligned with sap_pair and the information thus generated will be +transferred onto the alignment.

    + +

    Note the following rule:

    + +

                -Each +sequence can have one template of each type (structural, genomics…)

    + +

                -Each +sequence can only have one template of a given type

    + +

                -Several +sequences can share the same template

    + +

                -All +the sequences do not need to have a template

    + +

    The type of template on which a +method works is declared with the SEQ_TYPE parameter in the method +configuration file:

    + +

                SEQ_TYPE          S: a method that uses sequences

    + +

                SEQ_TYPE          PS: a pairwise method that aligns +sequences and structures

    + +

                SEQ_TYPE          P: a method that aligns structures +(sap for instance)

    + +

    There are 4 tags identifying the +template type:

    + +

    _P_         Structural templates: a pdb identifier +OR a pdb file

    + +

    _G_        Genomic templates: a +protein sequence where boundary amino-acid have been recoded with ( o:0, i:1, +j:2)

    + +

    _R_        Profile Templates: a file containing a +multiple sequence alignment

    + +

    _F_         RNA secondary Structures

    + +

     

    + +

    More than one template file can be +provided. There is no need to have one template for every sequence in the +dataset.

    + +

    _P_, _G_, +and _R_ are known as template TAGS

    + +

    2-SCRIPT_<scriptname>

    + +

    Indicates that filename is a script +that will be used to generate a valid template file. The script will run on a +file containing all your sequences using the following syntax:

    + +

    scriptname –infile=<your sequences> +-outfile=<template_file>

    + +

    It is also possible to pass some +parameters, use @ as a separator and # in place of the = sign. For instance, if +you want to call the a script named blast.pl with the foloowing parameters;

    + +

    blast.pl -db=pdb -dir=/local/test

    + +

    Use

    + +

    SCRIPT_blast.pl@db#pdb@dir#/local/test

    + +

    Bear in mind that the input output +flags will then be concatenated to this command line so that t_coffee ends up +calling the program using the following system call:

    + +

    blast.pl -db=pdb -dir=/local/test +-infile=<some tmp file> -outfile=<another tmp file>

    + +

     

    + +

    3-SELF_TAG

    + +

    TAG can take the value of any of the known +TAGS (_S_, _G_, _P_). SELF indicates that the original name of the sequence +will be used to fetch the template:

    + +
    + +

    PROMPT: +t_coffee 3d_sample2.fasta –template_file SELF_P_

    + +
    + +

    The previous command will work +because the sequences in 3d_sample3 are named

    + +

    4-SEQFILE_TAG_filename

    + +

    Use this flag if your templates are +in filename, and are named according to the sequences. For instance, if your +protein sequences have been recoded with Exon/Intron information, you should +have the recoded sequences names according to the original:

    + +

    SEQFILE_G_recodedprotein.fasta 

    + +

    -struc_to_use

    + +

    Usage: +-struc_to_use=<struc1, struc2Â…>

    + +

    Default: -struc_to_use=NULL

    + +

    Restricts the 3Dcoffee to a set of +pre-defined structures.

    + +

    Multiple Local Alignments

    + +

    It is possible to compute multiple local alignments, +using the moca routine. MOCA is a routine that allows extracting all the local +alignments that show some similarity with another predefined fragment.

    + +

    'mocca' is a perl script that calls t-coffee +and provides it with the appropriate parameters.

    + +

    -domain/-mocca

    + +

    Usage: +-domain

    + +

    Default: not set

    + +

    This flag indicates that t_coffee +will run using the domain mode. All the sequences will be concatenated, and the +resulting sequence will be compared to itself using lalign_rs_s_pair mode +(lalign of the sequence against itself using keeping the lalign raw score). +This step is the most computer intensive, and it is advisable to save the +resulting file.

    + +
    + +

    PROMPT: +t_coffee -in Ssample_seq1.fasta,Mlalign_rs_s_pair +-out_lib=sample_lib1.mocca_lib -domain -start=100 -len=50

    + +
    + +

    This instruction will use the +fragment 100-150 on the concatenated sequences, as a template for the extracted +repeats. The extraction will only be made once. The library will be placed in +the file <lib name>.

    + +

     

    + +

    If you want, you can test other +coordinates for the repeat, such as

    + +
    + +

    PROMPT: +t_coffee -in sample_lib1.mocca_lib -domain -start=100 -len=60

    + +
    + +

    This run will use the fragment +100-160, and will be much faster because it does not need to re-compute the +lalign library.

    + +

    -start

    + +

    Usage: +-start=<int value>

    + +

    Default: not set

    + +

    This flag indicates the starting +position of the portion of sequence that will be used as a template for the +repeat extraction. The value assumes that all the sequences have been +concatenated, and is given on the resulting sequence.

    + +

    -len

    + +

    Usage: +-len=<int value>

    + +

    Default: not set

    + +

    This flag indicates the length of the +portion of sequence that will be used as a template.

    + +

    -scale

    + +

    Usage: +-scale=<int value>

    + +

    Default: -scale=-100

    + +

    This flag indicates the value of the +threshold for extracting the repeats. The actual threshold is equal to:

    + +

                motif_len*scale

    + +

    Increase the scale óIncrease sensitivity ó More +alignments( i.e. -50).

    + +

    -domain_interactive [Examples]

    + +

    Usage: +-domain_interactive

    + +

    Default: unset

    + +

    Launches an interactive mocca +session.

    + +
    + +

    PROMPT: +t_coffee -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60

    + +
    + +
    + +

    TOLB_ECOLI_212_26                     211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA

    + +

    TOLB_ECOLI_165_218    164 TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV

    + +

    TOLB_ECOLI_256_306    255 SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT

    + +

    TOLB_ECOLI_307_350    306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV

    + +

    TOLB_ECOLI_351_393    350 -------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS 

    + +

                            1           *             *    +:          .   +.:.  :   

    + +

     

    + +

            MENU: Type Letter Flag[number] and +Return: ex |10

    + +

            |x      +-->Set     the START to x

    + +

            >x      -->Set     the LEN   +to x

    + +

            Cx      +-->Set     the sCale to x

    + +

            Sname   +-->Save    the  Alignment

    + +

            Bx      +-->Save    Goes back x it

    + +

            return  +-->Compute the  Alignment

    + +

            X       +-->eXit

    + +

     

    + +

    [ITERATION   1] [START=211] [LEN= 50] [SCALE=-100]      YOUR CHOICE:

    + +

    For instance, to set the +length of the domain to 40, type:

    + +

     

    + +

    [ITERATION   1] [START=211] [LEN= 50] [SCALE=-100]      YOUR CHOICE:>40[return]

    + +

    [return]

    + +

     

    + +

    Which will generate:

    + +

     

    + +

    TOLB_ECOLI_212_252    211 +SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF  +251

    + +

    TOLB_ECOLI_256_296    255 +SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW  +295

    + +

    TOLB_ECOLI_300_340    299 +QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV  +339

    + +

    TOLB_ECOLI_344_383    343 +KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL  +382

    + +

    TOLB_ECOLI_387_427    386 +TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW  +426

    + +

                            1   :     +:     :           ::         +.     40

    + +

     

    + +

     

    + +

     

    + +

     

    + +

            MENU: Type Letter Flag[number] and +Return: ex |10

    + +

            |x      +-->Set     the START to x

    + +

            >x      -->Set     the LEN   +to x

    + +

            Cx      +-->Set     the sCale to x

    + +

            Sname   +-->Save    the  Alignment

    + +

            +Bx      -->Save    Goes back x it

    + +

            return  +-->Compute the  Alignment

    + +

            X       +-->eXit

    + +

     

    + +

    [ITERATION   3] [START=211] [LEN= 40] [SCALE=-100]      YOUR CHOICE:

    + +
    + +

     

    + +

    If you want to indicate the +coordinates, relative to a specific sequence, type:

    + +

      |<seq_name>:start

    + +

    Type S<your name> to save the +current alignment, and extract a new motif.

    + +

    Type X when you are done.

    + +

    Output Control

    + +

    Generic

    + +

    Conventions Regarding +Filenames

    + +

    stdout, stderr, stdin, no, /dev/null are valid +filenames. They cause the corresponding file to be output in stderr or stdout, +for an input file, stdin causes the program to requests the corresponding file +through pipe. No causes a suppression of the output, as does /dev/null.

    + +

    Identifying the Output files +automatically

    + +

    In the t_coffee output, each output appears in +a line:

    + +
    + +

    ##### FILENAME <name> TYPE +<Type> FORMAT <Format>

    + +
    + +

    -no_warning

    + +

    Usage:  -no_warning

    + +

    Default: Switched off

    + +

    Suppresseswarning output.

    + +

     

    + +

    Alignments

    + +

    -outfile

    + +

    Usage:  -outfile=<out_aln file,default,no>

    + +

    Default:-outfile=default

    + +

    Indicates the name of the alignment +output by t_coffee. If the default is used, the alignment is named <your sequences>.aln

    + +

    -output

    + +

    Usage:  -output=<format1,format2,...>

    + +

    Default:-output=clustalw

    + +

    Indicates the format used for +outputting the -outfile.

    + +

    Supported formats are:

    + +

               

    + +

    clustalw_aln, clustalw       : ClustalW format.

    + +

    gcg, msf_aln                        : MSF alignment.

    + +

    pir_aln                                  : pir alignment.

    + +

    fasta_aln                             : fasta alignment.

    + +

    phylip                                   : Phylip format.

    + +

    pir_seq                                  : pir sequences (no gap).

    + +

    fasta_seq                             : fasta sequences (no gap).

    + +

                               

    + +

    As well as:

    + +

     

    + +

    score_ascii           : causes the output of a reliability flag

    + +

    score_html           : causes the output to be a reliability plot in HTML

    + +

    score_pdf             : idem in PDF (if ps2pdf is installed on your system).

    + +

    score_ps                               : +idem in postscript.

    + +

     

    + +

    More than one format can be +indicated:

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta -output=clustalw,gcg, score_html

    + +
    + +

    A publication describing the CORE +index is available on:

    + +

    http://www.tcoffee.org/Publications/Pdf/core.pp.pdf

    + +

    -outseqweight

    + +

    Usage:  -outseqweight=<filename>

    + +

    Default: not used

    + +

    Indicates the name of the file in +which the sequences weights should be saved..

    + +

    -case

    + +

    Usage:  -case=<keep,upper,lower>

    + +

    Default: -case=keep

    + +

    Instructs the program on the case to be used in +the output file (Clustalw uses upper case). The default keeps the case and +makes it possible to maintain a mixture of upper and lower case residues.

    + +

    If you need to change the case of your file, +you can use seq_reformat:

    + +
    + +

    PROMPT: +t_coffee –other_pg seq_reformat –in sample_aln1.aln –action +lower –output +clustalw

    + +
    + +

    -cpu

    + +

    Usage:  deprecated

    + +

    -outseqweight

    + +

    Usage: -outseqweight=<name of the file +containing the weights applied>

    + +

    Default: -outseqweight=no

    + +

    Will cause the program to output the weights +associated with every sequence in the dataset.

    + +

    -outorder [cw]

    + +

    Usage:  -outorder=<input OR aligned OR +filename>

    + +

    Default:-outorder=input

    + +

    Sets the order of the sequences in +the output alignment: -outorder=input means the sequences are kept in +the original order. -outorder=aligned means the sequences come in the +order indicated by the tree. This order can be seen as a one-dimensional +projection of the tree distances. –outdorder=<filename>Filename +is a legal fasta file, whose order will be used in the final alignment.

    + +

    -inorder [cw]

    + +

    Usage:  -inorder=<input OR aligned>

    + +

    Default:-inorder=aligned

    + +

    Multiple alignments based on dynamic +programming depend slightly on the order in which the incoming sequences are +provided. To prevent this effect sequences are arbitrarily sorted at the +beginning of the program (-inorder=aligned). However, this affects the sequence +order within the library. You can switch this off by ststing –inorder=input.

    + +

    -seqnos

    + +

    Usage:  -seqnos=<on or off>

    + +

    Default:-seqnos=off

    + +

    Causes the output alignment to contain residue +numbers at the end of each line:

    + +
    + +

    T-COFFEE

    + +

    seq1 aaa---aaaa--------aa 9

    + +

    seq2 a-----aa-----------a 4

    + +

     

    + +

    seq1 a-----------------a 11

    + +

    seq2 aaaaaaaaaaaaaaaaaaa 19

    + +
    + +

    Libraries

    + +

    Although, it does not necessarily do so +explicitly, T-Coffee always end up combining libraries. Libraries are +collections of pairs of residues. Given a set of libraries, T-Coffee makes an +attempt to assemble the alignment with the highest level of consistence. You +can think of the alignment as a timetable. Each library pair would be a request +from students or teachers, and the job of T-Coffee would be to assemble the +time table that makes as many people as possible happyÂ…

    + +

    -out_lib

    + +

    Usage:  +-out_lib=<name of the library,default,no>

    + +

    Default:-out_lib=default

    + +

     

    + +

    Sets the name of the library output. +Default implies <run_name>.tc_lib

    + +

    -lib_only

    + +

    Usage:  -lib_only

    + +

    Default: unset

    + +

    Causes the program to stop once the +library has been computed. Must be used in conjunction with the flag –out_lib

    + +

    Trees

    + +

    -newtree

    + +

    Usage: +-newtree=<tree file>

    + +

    Default: No file specified

    + +

    Indicates the name of the file into +which the guide tree will be written. The default will be +<sequence_name>.dnd, or <run_name.dnd>. The tree is written in the +parenthesis format known as newick or New + Hampshire and used by Phylips (see the format +section).

    + +
    + +

    Do NOT confuse this guide tree with a +phylogenetic tree.

    + +
    + +

    Reliability Estimation

    + +

    CORE Computation

    + +

    The CORE is an index that indicates the +consistency between the library of piarwise alignments and the final multiple +alignment. Our experiment indicate that the higher this consistency, the more +reliable the alignment. A publication describing the CORE index can be found +on:

    + +

    http://www.tcoffee.org/Publications/Pdf/core.pp.pdf

    + +

    -evaluate_mode

    + +

    Usage: +-evaluate_mode=<t_coffee_fast,t_coffee_slow,t_coffee_non_extended >

    + +

    Default: -evaluate_mode=t_coffee_fast

    + +

    This flag indicates the mode used to +normalize the t_coffee score when computing the reliability score.

    + +

    t_coffee_fast: Normalization is made +using the highest score in the MSA. This evaluation mode was validated and in +our hands, pairs of residues with a score of 5 or higher have 90 % chances to +be correctly aligned to one another.

    + +

    t_coffee_slow: Normalization is made +using the library. This usually results in lower score and a scoring scheme +more sensitive to the number of sequences in the dataset. Note that this +scoring scheme is not any more slower, thanks to the implementation of a faster +heuristic algorithm.

    + +

    t_coffee_non_extended: the score of each +residue is the ratio between the sum of its non extended scores with the column +and the sum of all its possible non extended scores.

    + +

    These modes will be useful when +generating colored version of the output, with the –output flag:

    + +
    + +

    PROMPT: +t_coffee sample_seq1.fasta –evaluate_mode t_coffee_slow –output score_ascii, +score_html

    + +

    PROMPT: +t_coffee sample_seq1.fasta –evaluate_mode t_coffee_fast –output score_ascii, +score_html

    + +

    PROMPT: +t_coffee sample_seq1.fasta –evaluate_mode t_coffee_non_extended –output +score_ascii, score_html

    + +
    + +

    Generic Output

    + +

    -run_name

    + +

    Usage: +-run_name=<your run name>

    + +

    Default: no default set

    + +

    This flag causes the prefix <your +sequences> to be replaced by <your run name> when renaming the default +output files.

    + +

    -quiet

    + +

    Usage: +-quiet=<stderr,stdout,file name OR nothing>.

    + +

    Default:-quiet=stderr

    + +

    Redirects the standard output to +either a file. -quiet on its own redirect the output to /dev/null.

    + +

    -align [CW]

    + +

    This flag indicates that the program must +produce the alignment. It is here for compatibility with ClustalW.

    + +

    APDB, iRMSD and tRMSD Parameters

    + +

     

    + +
    + +

    Warning: These flags will only work within +the APDB package that can be invoked via the –other_pg parameter of T-Coffee:

    + +

                                    t_coffee –other_pg apdb –aln <your aln>

    + +

     

    + +
    + +

    -quiet [Same as T-Coffee]

    + +

    -run_name [Same as +T-Coffee]

    + +

    -aln

    + +

    Usage: +-aln=<file_name>.

    + +

    Default:none

    + +

    Indicates the name of the file +containing the sequences that need to be evaluated. The sequences whose +structure is meant to be used must be named according to their PDB identifier.

    + +

    The format can be FASTA, CLUSTAL or +any of the formats supported by T-Coffee. APDB only evaluates residues in +capital and ignores those in lower case. If your sequences are in lower case, +you can upper case them using seq_reformat:

    + +
    + +

    PROMPT: +t_coffee –other_pg seq_reformat –in 3d_sample4.aln –action +upper –output +clustalw > 3d_sample4.cw_aln

    + +
    + +

    The alignment can then be evaluated +using the defaultr of APDB:

    + +
    + +

    PROMPT: +t_coffee –other_pg apdb –aln 3d_sample4.aln

    + +
    + +

    The alignment can contain as many +structures as you wish.

    + +

    -n_excluded_nb

    + +

    Usage: +-n_excluded_nb=<integer>.

    + +

    Default:1

    + +

    When evaluating the local score of a +pair of aligned residues, the residues immediately next to that column should +not contribute to the measure. By default the first to the left and first to +the right are excluded.

    + +

    -maximum_distance

    + +

    Usage: +-maximum_distance=<float>.

    + +

    Default:10

    + +

    Size of the neighborhood considered +around every residue. If .-local_mode is set to sphere, -maximum_distance is +the radius of a sphere centered around each residue. If –local_mode is set to +window, then –maximum_distance is the size of the half window (i.e. +window_size=-maximum_distance*2+1).

    + +

    -similarity_threshold

    + +

    Usage: +-similarity_threshold=<integer>.

    + +

    Default:70

    + +

    Fraction of the neighborhood that +must be supportive for a pair of residue to be considered correct in APDB. The +neighborhood is a sphere defined by –maximum_distance, and the support is +defined by –md_threshold.

    + +

    -local_mode

    + +

    Usage: +-local_mode=<sphere,window>.

    + +

    Default:sphere

    + +

    Defines the shape of a neighborhood, +either as a sphere or as a window.

    + +

    -filter

    + +

    Usage: +-filter=<0.00-1.00>.

    + +

    Default:1.00

    + +

    Defines the centiles that should be +kept when making the local measure. Foir instance, -filter=0.90 means that the +the 10 last centiles will be removed from the evaluation. The filtration is +carried out on the iRMSD values.

    + +

    -print_rapdb [Unsupported]

    + +

    Usage: +-print_rapdb (FLAG)

    + +

    Default:off

    + +

    This causes the prints out of the +exact neighborhood of every considered pair of residues.

    + +

    -outfile [Same as T-Coffee]

    + +

    This flag is meant to control the output name +of the colored APDB output. This file will either display the local APDB score +or the local iRMD, depending on the value of –color_mode. The default format is +defined by –ouptut and is score_html.

    + +

    -color_mode

    + +

    Usage: +-color_mode=<apdb, irmsd>

    + +

    Default:apdb

    + +

    This flag is meant to control the colored APDB +output (local score). This file will either display the local APDB score or the +local iRMD.

    + + + +

    We maintain a T-Coffee server (www.tcoffee.org). +We will be pleased to provide anyone who wants to set up a similar service with +the sources

    + +

    Environment Variables

    + +

    T-Coffee stores a lots of +information in locations that may be unsuitable when running a server.

    + +

    By default, T-Coffee will +generate and rely on the follwing directory structure:

    + +

    /home/youraccount/         #HOME_4_TCOFFEE

    + +

    HOME_4_TCOFFEE/.t_coffee/ #DIR_4_TCOFFEE

    + +

    DIR_4_TCOFFEE/cache        #CACHE_4_TCOFFEE

    + +

    DIR_4_TCOFFEE/tmp          #TMP_4_TCOFFEE

    + +

    DIR_4_TCOFFEE/methods            #METHOS_4_TCOFFEE

    + +

    DIR_4_TCOFFEE/mcoffee            #MCOFFEE_4_TCOFFEE

    + +

     

    + +

    By default, all these +directories are automatically created, following the dependencies suggested +here.

    + +

    The first step is the +determination of the HOME. By default the program tries to use HOME_4_TCOFFEE, +then the HOME variable and TMP or TEMP if HOME is not set on your system or +your account. It is your responsibility to make sure that one of these +variables is set to some valid location where the T-Coffee process is allowed +to read and write.

    + +

    If no valid location can be +found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a +server, we recommend to hard set the following locations, where your scratch is +a valid location.

    + +

     

    + +

    HOME_4_TCOFFEE=”your scratch”

    + +

    TMP_4_TCOFFEE=”your +scratch”

    + +

    DIR_4_TCOFFEE=”your +scratch”

    + +

    CACHE_4_TCOFFEE=”your +scratch”

    + +

    NO_ERROR_REPORT_4_TCOFFEE=1

    + +

    Note that  it is a good idea to have a cron job that +cleans up this scratch area, once in a while.

    + +

     

    + +

    Output of the .dnd file.

    + +

    A common source of error when running a server: +T-Coffee MUST output the .dnd file because it re-reads it to carry out the +progressive alignment. By default T-Coffee outputs this file in the directory +where the process is running. If the T-Coffee process does not have permission +to write in that directory, the computation will abort...

    + +

    To avoid this, simply specify the name of the +output tree:

    + +

             -newtree=<writable +file (usually in /tmp)>

    + +

    Chose the name so that two processes may not +over-write each other dnd file.

    + +

    Permissions

    + +

    The t_coffee process MUST be allowed to write +in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/ +partition is not protected.

    + +

    Other Programs

    + +

    T-Coffee may call various programs while it +runs (lalign2list by defaults). Make sure your process knows where to find +these executables.

    + +
    + +

    Formats

    + +
    + +

    Parameter files

    + +

    Parameter files used with -parameters, +-t_coffee_defaults, -dali_defaults... Must contain a valid parameter string +where line breaks are allowed. These files cannot contain any comment, the +recommended format is one parameter per line:

    + +
    + +

          <parameter +name>=<value1>,<value2>....

    + +

          <parameter +name>=.....

    + +
    + +

    Sequence Name Handling

    + +

    Sequence name handling is meant to be fully +consistent with ClustalW (Version 1.75). This implies that in some cases the +names of your sequences may be edited when coming out of the program. Five +rules apply:

    + +

     

    + +
    + +

    Naming +Your Sequences the Right Way

    + +

    1-No +Space

    + +

    Names +that do contain spaces, for instance:

    + +

                >seq1 human_myc

    + +

    will be +turned into

    + +

                >seq1

    + +

    It is +your responsibility to make sure that the names you provide are not ambiguous +after such an editing. This editing is consistent with Clustalw (Version 1.75)

    + +

     

    + +

    2-No +Strange Character

    + +

    Some non +alphabetical characters are replaced with underscores. These are: ';:()'

    + +

    Other +characters are legal and will be kept unchanged. This editing is meant to keep +in line with Clustalw (Version 1.75).

    + +

     

    + +

    3-> is +NEVER legal (except as a header token in a FASTA file)

    + +

     

    + +

    4-Name +length must be below 100 characters, although 15 is recommended for +compatibility with other programs.

    + +

    5-Duplicated +sequences will be renamed (i.e. sequences with the same name in the same +dataset) are allowed but will be renamed according to their original order. +When sequences come from multiple sources via the –in flag, consistency of the +renaming is not guaranteed. You should avoid duplicated sequences as they will +cause your input to differ from your output thus making it difficult to track +data.

    + +
    + +

    Automatic Format Recognition

    + +

    Most common formats are automatically +recognized by t_coffee. See -in and the next section for more details. If your +format is not recognized, use readseq or clustalw to switch to another format. +We recommend Fasta.

    + +

    Structures

    + +

    PDB format is recognized by T-Coffee. T-Coffee +uses extract_from_pdb (cf –other_pg flag). extract_from_pdb is a small embeded +module that can be used on its own to extract information from pdb files.

    + +

    RNA Structures

    + +

    RNA structures can either be coded as T-Coffee +libraries, with each line indicating two paired residues, or as alifold output. +The selex format is also partly supported (see the seq_reformat tutorial on RNA +sequences handling).

    + +

    Sequences

    + +

    Sequences can come in the following formats: +fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats +are the one automatically recognized. Please replace the '*' sign sometimes +used for stop codons with an X.

    + +

    Alignments

    + +

    Alignments can come in the following formats: +msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to +the ClustalW format, but slightly more flexible. Any interleaved format with +sequence name on each line will be correctly parsed:

    + +
    + +

    <empy line>       [Facultative]n

    + +

    <line of text>    [Required]

    + +

    <line of text>               [Facultative]n

    + +

    <empty line>                 [Required]

    + +

    <empty line>                 [Facultative]n

    + +

    <seq1 +name><space><seq1>

    + +

    <seq2 +name><space><seq2>

    + +

    <seq3 +name><space><seq3>

    + +

    <empty line>                 [Required]

    + +

    <empty line>                 [Facultative]n

    + +

    <seq1 +name><space><seq1>

    + +

    <seq2 +name><space><seq2>

    + +

    <seq3 +name><space><seq3>

    + +

    <empty line>                 [Required]

    + +

    <empty line>                 [Facultative]n

    + +
    + +

    An empty line is a line that does NOT contain +amino-acid. A line that contains the ClustalW annotation (.:*) is empty.

    + +

    Spaces are forbidden in the name. When the +alignment is being read, non character signs are ignored in the sequence field +(such as numbers, annotationÂ…).

    + +

    Note: a +different number of lines in the different blocks will cause the program to +crash or hang.

    + +

    Libraries

    + +

    T-COFFEE_LIB_FORMAT_01

    + +

    This is currently the only supported format.

    + +
    + +

    !<space> TC_LIB_FORMAT_01

    + +

    <nseq>

    + +

    <seq1 name> <seq1 +length> <seq1>

    + +

    <seq2 name> <seq2 +length> <seq2>

    + +

    <seq3 name> <seq3 +length> <seq3>

    + +

    !Comment

    + +

    (!Comment)n

    + +

    #Si1 Si2

    + +

    Ri1 Ri2 V1 (V2, V3)

    + +

    #1 2

    + +

    12 13 99 (12/0 vs 13/1, weight +99)

    + +

    12 14 70

    + +

    15 16 56

    + +

    #1 3

    + +

    12 13 99

    + +

    12 14 70

    + +

    15 16 56

    + +

    !<space>SEQ_1_TO_N

    + +
    + +

    Si1: index of Sequence 1

    + +

    Ri1: index of residue 1 in seq1

    + +

    V1: Integer Value: Weight

    + +

    V2, V3: optional values

    + +

    Note 1: There is +a space between the ! And SEQ_1_TO_N

    + +

    Note 2: The last +line (! SEQ_1_TO_N) indicates that:

    + +

    Sequences and residues are numbered from 1 to +N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are +numbered from 0 to N-1, and residues are from 1 to N.

    + +

    Residues do not need to be sorted, and neither +do the sequences. The same pair can appear several times in the library. For +instance, the following file would be legal:

    + +
    + +

    #1 2

    + +

    12 13 99

    + +

    #1 2

    + +

    15 16 99

    + +

    #1 1

    + +

    12 14 70

    + +
    + +

    It is also poosible to declare +ranges of resdues rather than single pairs. For instance, the following:

    + +
    + +

    #0 1

    + +

    +BLOCK+  10 12 14 99

    + +

    +BLOCK+  15 30 40 99

    + +

    #0 2

    + +

    15 16 99

    + +

    #0 1

    + +

    12 14 70

    + +
    + +

    The first statement BLOCK +declares a BLOCK of length 10, that starts on position 12 of sequence 1 and +position 14 of sequence 2 and where each pair of residues within the block has +a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and +extends for 15 residues.

    + +

    Blocks can overalp and be +incompatible with one another, just like single constraints.

    + +

     

    + +

    T-COFFEE_LIB_FORMAT_02

    + +

    A simpler format is being developed, however it +is not yet fully supported and is only mentioned here for development purpose.

    + +
    + +

    ! TC_LIB_FORMAT_02

    + +

    #S1 SEQ1 [OPTIONAL]

    + +

    #S2 SEQ2 [OPTIONAL]

    + +

    ...

    + +

    !comment [OPTIONAL]

    + +

    S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)

    + +

    => N R1 +Ri1 S2 R2 Ri2 V1 (V2 V3)

    + +

    ...

    + +
    + +

    S1, S2: name of sequence 1 and 2

    + +

    SEQ1: sequence of S1

    + +

    Ri1, Ri2: index of the residues in their +respective sequence

    + +

    R1, R2: Residue type

    + +

    V1, V2, V3: integer Values (V2 and V3 are +optional)

    + +

    Value1, Value 2 and Value3 are optional.

    + +

    Library List

    + +

    These +are lists of pairs of sequences that must be used to compute a library. The +format is:

    + +
    + +

    <nseq> <S1> <S2>

    + +

    2 hamg2 globav

    + +

    3 hamgw hemog singa

    + +

    ...

    + +
    + +

    Substitution +matrices.

    + +

    If the required substitution matrix is not available, +write your own in a file using the following format:

    + +

    ClustalW Style [Deprecated]

    + +
    + +

    # CLUSTALW_MATRIX FORMAT

    + +

    $

    + +

    v1

    + +

    v2 v3

    + +

    v4 v5 v6

    + +

    ...

    + +

    $

    + +
    + +

    v1, v2... are integers, possibly negatives.

    + +

    The order of the amino acids is: +ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs +A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.

    + +

    BLAST Format [Recommended]

    + +
    + +

    # BLAST_MATRIX FORMAT

    + +

    # ALPHABET=AGCT

    + +

     A G C T

    + +

    A 0 1 2 3

    + +

    G 0 2 3 4

    + +

    C 1 1 2 3

    + +

    ...

    + +
    + +

    The alphabet can be freely defined

    + +

    Sequences Weights

    + +

    Create your own weight file, using the +-seq_weight flag:

    + +
    + +

    # SINGLE_SEQ_WEIGHT_FORMAT_01

    + +

    seq_name1 v1

    + +

    seq_name2 v2

    + +

    ...

    + +
    + +

    No duplicate allowed. Sequences not included in +the set of sequences provided to t_coffee will be ignored. Order is free. V1 is +a float. Un-weighted sequences will see their weight set to 1.

    + +
    +     + + + +

    1-Sensitivity to sequence order: It is +difficult to implement a MSA algorithm totally insensitive to the order of +input of the sequences. In t_coffee, robustness is increased by sorting the +sequences alphabetically before aligning them. Beware that this can result in +confusing output where sequences with similar name are unexpectedly close to +one another in the final alignment.

    + +

    2-Nucleotides sequences with long stretches of +Ns will cause problems to lalign, especially when using Mocca. To avoid any +problem, filter out these nucleotides before running mocca.

    + +

    3-Stop codons are sometimes coded with '*' in +protein sequences. This will cause the program to crash or hang. Please replace +the '*' signs with an X.

    + +

    4-Results can differ from one architecture to +another, due rounding differences. This is caused by the tree estimation +procedcure. If you want to make sure an alignment is reproducible, you should +keep the associated dendrogram.

    + +

    5-Deploying the program on a

    + + + +

    These notes are only meant for internal +development.

    + +

    Development

    + +

    The following examples are only meant for +internal development, and are used to insure stability from release to release

    + +

    profile2list

    + +

    prf1: profile containing one structure

    + +

    prf2: profile containing one structure

    + +

     

    + +
    + +

    PROMPT: +t_coffee  +Rsample_profile1.aln,Rsample_profile2.aln -mode=3dcoffee +-outfile=aligned_prf.aln

    + +

     

    + +
    + +

    Command Line List

    + +

    These command lines have been checked before +every release (along with the other CL in this documentation:

    + +

     

    + +

    -external methods;

    + +
    + +

       PROMPT: t_coffee sample_seq1.fasta –in=Mclustalw_pair,Mclustalw_msa,Mslow_pair +–outfile=clustal_text

    + +
    + +

    -fugue_client

    + +
    + +

    PROMPT: +t_coffee –in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair

    + +
    + +

    -A list of command lines kindly provided by +James Watson (used to crash the pg before version 3.40)

    + +
    + +

    PROMPT: +t_coffee -in Sseq.fas P2PTC Mfugue_pair

    + +

    PROMPT: +t_coffee -in S2seqs.fas Mfugue_pair -template_file SELF_P_

    + +

    PROMPT: +t_coffee -mode 3dcoffee -in Sseq.fas P2PTC

    + +

    PROMPT: +t_coffee -mode 3dcoffee -in S2seqs.fas -template_file SELF_P_

    + +
    + +

    -A list of command lines that crashed the +program before 3.81

    + +
    + +

    PROMPT: +t_coffee sample_seq6.fasta –in Mfast_pair Msap_pair Mfugue_pair –template_file +template_file6.template

    + +
    + +

                -A +command line to read “relaxed” pdb files...

    + +
    + +

    PROMPT: +t_coffee –in Msap_pair Ssample_seq7.fasta –template_file +template_file7.template –weight 1001 –out_lib test_lib7.tc_lib –lib_only

    + +
    + +

                -Parsing +of MARNA libraries

    + +
    + +

    PROMPT: +t_coffee –in Lmarna.tc_lib –outfile maran.test

    + +
    + +

                -Parsing +of long sequence lines:

    + +
    + +

    PROMPT: +t_coffee –in Asample_aln5.aln –outfile test.aln

    + +
    + +

     

    + +
    + +

    To DoÂ…

    + +
    + +

    -implement UPGMA tree computation

    + +

    -implement seq2dpa_tree

    + +

    -debug dpa

    + +

    -Reconciliate sequences and template when +reading the template

    + +

    -Add the server command lines to the checking +procedure

    + +

     

    + +

     

    + +

     

    + +

     

    + +

     

    + +
    + + + + diff --git a/website/prototype-1.6.0.3.js b/website/prototype-1.6.0.3.js new file mode 100644 index 0000000..dfe8ab4 --- /dev/null +++ b/website/prototype-1.6.0.3.js @@ -0,0 +1,4320 @@ +/* Prototype JavaScript framework, version 1.6.0.3 + * (c) 2005-2008 Sam Stephenson + * + * Prototype is freely distributable under the terms of an MIT-style license. + * For details, see the Prototype web site: http://www.prototypejs.org/ + * + *--------------------------------------------------------------------------*/ + +var Prototype = { + Version: '1.6.0.3', + + Browser: { + IE: !!(window.attachEvent && + navigator.userAgent.indexOf('Opera') === -1), + Opera: navigator.userAgent.indexOf('Opera') > -1, + WebKit: navigator.userAgent.indexOf('AppleWebKit/') > -1, + Gecko: navigator.userAgent.indexOf('Gecko') > -1 && + navigator.userAgent.indexOf('KHTML') === -1, + MobileSafari: !!navigator.userAgent.match(/Apple.*Mobile.*Safari/) + }, + + BrowserFeatures: { + XPath: !!document.evaluate, + SelectorsAPI: !!document.querySelector, + ElementExtensions: !!window.HTMLElement, + SpecificElementExtensions: + document.createElement('div')['__proto__'] && + document.createElement('div')['__proto__'] !== + document.createElement('form')['__proto__'] + }, + + ScriptFragment: ']*>([\\S\\s]*?)<\/script>', + JSONFilter: /^\/\*-secure-([\s\S]*)\*\/\s*$/, + + emptyFunction: function() { }, + K: function(x) { return x } +}; + +if (Prototype.Browser.MobileSafari) + Prototype.BrowserFeatures.SpecificElementExtensions = false; + + +/* Based on Alex Arnell's inheritance implementation. */ +var Class = { + create: function() { + var parent = null, properties = $A(arguments); + if (Object.isFunction(properties[0])) + parent = properties.shift(); + + function klass() { + this.initialize.apply(this, arguments); + } + + Object.extend(klass, Class.Methods); + klass.superclass = parent; + klass.subclasses = []; + + if (parent) { + var subclass = function() { }; + subclass.prototype = parent.prototype; + klass.prototype = new subclass; + parent.subclasses.push(klass); + } + + for (var i = 0; i < properties.length; i++) + klass.addMethods(properties[i]); + + if (!klass.prototype.initialize) + klass.prototype.initialize = Prototype.emptyFunction; + + klass.prototype.constructor = klass; + + return klass; + } +}; + +Class.Methods = { + addMethods: function(source) { + var ancestor = this.superclass && this.superclass.prototype; + var properties = Object.keys(source); + + if (!Object.keys({ toString: true }).length) + properties.push("toString", "valueOf"); + + for (var i = 0, length = properties.length; i < length; i++) { + var property = properties[i], value = source[property]; + if (ancestor && Object.isFunction(value) && + value.argumentNames().first() == "$super") { + var method = value; + value = (function(m) { + return function() { return ancestor[m].apply(this, arguments) }; + })(property).wrap(method); + + value.valueOf = method.valueOf.bind(method); + value.toString = method.toString.bind(method); + } + this.prototype[property] = value; + } + + return this; + } +}; + +var Abstract = { }; + +Object.extend = function(destination, source) { + for (var property in source) + destination[property] = source[property]; + return destination; +}; + +Object.extend(Object, { + inspect: function(object) { + try { + if (Object.isUndefined(object)) return 'undefined'; + if (object === null) return 'null'; + return object.inspect ? object.inspect() : String(object); + } catch (e) { + if (e instanceof RangeError) return '...'; + throw e; + } + }, + + toJSON: function(object) { + var type = typeof object; + switch (type) { + case 'undefined': + case 'function': + case 'unknown': return; + case 'boolean': return object.toString(); + } + + if (object === null) return 'null'; + if (object.toJSON) return object.toJSON(); + if (Object.isElement(object)) return; + + var results = []; + for (var property in object) { + var value = Object.toJSON(object[property]); + if (!Object.isUndefined(value)) + results.push(property.toJSON() + ': ' + value); + } + + return '{' + results.join(', ') + '}'; + }, + + toQueryString: function(object) { + return $H(object).toQueryString(); + }, + + toHTML: function(object) { + return object && object.toHTML ? object.toHTML() : String.interpret(object); + }, + + keys: function(object) { + var keys = []; + for (var property in object) + keys.push(property); + return keys; + }, + + values: function(object) { + var values = []; + for (var property in object) + values.push(object[property]); + return values; + }, + + clone: function(object) { + return Object.extend({ }, object); + }, + + isElement: function(object) { + return !!(object && object.nodeType == 1); + }, + + isArray: function(object) { + return object != null && typeof object == "object" && + 'splice' in object && 'join' in object; + }, + + isHash: function(object) { + return object instanceof Hash; + }, + + isFunction: function(object) { + return typeof object == "function"; + }, + + isString: function(object) { + return typeof object == "string"; + }, + + isNumber: function(object) { + return typeof object == "number"; + }, + + isUndefined: function(object) { + return typeof object == "undefined"; + } +}); + +Object.extend(Function.prototype, { + argumentNames: function() { + var names = this.toString().match(/^[\s\(]*function[^(]*\(([^\)]*)\)/)[1] + .replace(/\s+/g, '').split(','); + return names.length == 1 && !names[0] ? [] : names; + }, + + bind: function() { + if (arguments.length < 2 && Object.isUndefined(arguments[0])) return this; + var __method = this, args = $A(arguments), object = args.shift(); + return function() { + return __method.apply(object, args.concat($A(arguments))); + } + }, + + bindAsEventListener: function() { + var __method = this, args = $A(arguments), object = args.shift(); + return function(event) { + return __method.apply(object, [event || window.event].concat(args)); + } + }, + + curry: function() { + if (!arguments.length) return this; + var __method = this, args = $A(arguments); + return function() { + return __method.apply(this, args.concat($A(arguments))); + } + }, + + delay: function() { + var __method = this, args = $A(arguments), timeout = args.shift() * 1000; + return window.setTimeout(function() { + return __method.apply(__method, args); + }, timeout); + }, + + defer: function() { + var args = [0.01].concat($A(arguments)); + return this.delay.apply(this, args); + }, + + wrap: function(wrapper) { + var __method = this; + return function() { + return wrapper.apply(this, [__method.bind(this)].concat($A(arguments))); + } + }, + + methodize: function() { + if (this._methodized) return this._methodized; + var __method = this; + return this._methodized = function() { + return __method.apply(null, [this].concat($A(arguments))); + }; + } +}); + +Date.prototype.toJSON = function() { + return '"' + this.getUTCFullYear() + '-' + + (this.getUTCMonth() + 1).toPaddedString(2) + '-' + + this.getUTCDate().toPaddedString(2) + 'T' + + this.getUTCHours().toPaddedString(2) + ':' + + this.getUTCMinutes().toPaddedString(2) + ':' + + this.getUTCSeconds().toPaddedString(2) + 'Z"'; +}; + +var Try = { + these: function() { + var returnValue; + + for (var i = 0, length = arguments.length; i < length; i++) { + var lambda = arguments[i]; + try { + returnValue = lambda(); + break; + } catch (e) { } + } + + return returnValue; + } +}; + +RegExp.prototype.match = RegExp.prototype.test; + +RegExp.escape = function(str) { + return String(str).replace(/([.*+?^=!:${}()|[\]\/\\])/g, '\\$1'); +}; + +/*--------------------------------------------------------------------------*/ + +var PeriodicalExecuter = Class.create({ + initialize: function(callback, frequency) { + this.callback = callback; + this.frequency = frequency; + this.currentlyExecuting = false; + + this.registerCallback(); + }, + + registerCallback: function() { + this.timer = setInterval(this.onTimerEvent.bind(this), this.frequency * 1000); + }, + + execute: function() { + this.callback(this); + }, + + stop: function() { + if (!this.timer) return; + clearInterval(this.timer); + this.timer = null; + }, + + onTimerEvent: function() { + if (!this.currentlyExecuting) { + try { + this.currentlyExecuting = true; + this.execute(); + } finally { + this.currentlyExecuting = false; + } + } + } +}); +Object.extend(String, { + interpret: function(value) { + return value == null ? '' : String(value); + }, + specialChar: { + '\b': '\\b', + '\t': '\\t', + '\n': '\\n', + '\f': '\\f', + '\r': '\\r', + '\\': '\\\\' + } +}); + +Object.extend(String.prototype, { + gsub: function(pattern, replacement) { + var result = '', source = this, match; + replacement = arguments.callee.prepareReplacement(replacement); + + while (source.length > 0) { + if (match = source.match(pattern)) { + result += source.slice(0, match.index); + result += String.interpret(replacement(match)); + source = source.slice(match.index + match[0].length); + } else { + result += source, source = ''; + } + } + return result; + }, + + sub: function(pattern, replacement, count) { + replacement = this.gsub.prepareReplacement(replacement); + count = Object.isUndefined(count) ? 1 : count; + + return this.gsub(pattern, function(match) { + if (--count < 0) return match[0]; + return replacement(match); + }); + }, + + scan: function(pattern, iterator) { + this.gsub(pattern, iterator); + return String(this); + }, + + truncate: function(length, truncation) { + length = length || 30; + truncation = Object.isUndefined(truncation) ? '...' : truncation; + return this.length > length ? + this.slice(0, length - truncation.length) + truncation : String(this); + }, + + strip: function() { + return this.replace(/^\s+/, '').replace(/\s+$/, ''); + }, + + stripTags: function() { + return this.replace(/<\/?[^>]+>/gi, ''); + }, + + stripScripts: function() { + return this.replace(new RegExp(Prototype.ScriptFragment, 'img'), ''); + }, + + extractScripts: function() { + var matchAll = new RegExp(Prototype.ScriptFragment, 'img'); + var matchOne = new RegExp(Prototype.ScriptFragment, 'im'); + return (this.match(matchAll) || []).map(function(scriptTag) { + return (scriptTag.match(matchOne) || ['', ''])[1]; + }); + }, + + evalScripts: function() { + return this.extractScripts().map(function(script) { return eval(script) }); + }, + + escapeHTML: function() { + var self = arguments.callee; + self.text.data = this; + return self.div.innerHTML; + }, + + unescapeHTML: function() { + var div = new Element('div'); + div.innerHTML = this.stripTags(); + return div.childNodes[0] ? (div.childNodes.length > 1 ? + $A(div.childNodes).inject('', function(memo, node) { return memo+node.nodeValue }) : + div.childNodes[0].nodeValue) : ''; + }, + + toQueryParams: function(separator) { + var match = this.strip().match(/([^?#]*)(#.*)?$/); + if (!match) return { }; + + return match[1].split(separator || '&').inject({ }, function(hash, pair) { + if ((pair = pair.split('='))[0]) { + var key = decodeURIComponent(pair.shift()); + var value = pair.length > 1 ? pair.join('=') : pair[0]; + if (value != undefined) value = decodeURIComponent(value); + + if (key in hash) { + if (!Object.isArray(hash[key])) hash[key] = [hash[key]]; + hash[key].push(value); + } + else hash[key] = value; + } + return hash; + }); + }, + + toArray: function() { + return this.split(''); + }, + + succ: function() { + return this.slice(0, this.length - 1) + + String.fromCharCode(this.charCodeAt(this.length - 1) + 1); + }, + + times: function(count) { + return count < 1 ? '' : new Array(count + 1).join(this); + }, + + camelize: function() { + var parts = this.split('-'), len = parts.length; + if (len == 1) return parts[0]; + + var camelized = this.charAt(0) == '-' + ? parts[0].charAt(0).toUpperCase() + parts[0].substring(1) + : parts[0]; + + for (var i = 1; i < len; i++) + camelized += parts[i].charAt(0).toUpperCase() + parts[i].substring(1); + + return camelized; + }, + + capitalize: function() { + return this.charAt(0).toUpperCase() + this.substring(1).toLowerCase(); + }, + + underscore: function() { + return this.gsub(/::/, '/').gsub(/([A-Z]+)([A-Z][a-z])/,'#{1}_#{2}').gsub(/([a-z\d])([A-Z])/,'#{1}_#{2}').gsub(/-/,'_').toLowerCase(); + }, + + dasherize: function() { + return this.gsub(/_/,'-'); + }, + + inspect: function(useDoubleQuotes) { + var escapedString = this.gsub(/[\x00-\x1f\\]/, function(match) { + var character = String.specialChar[match[0]]; + return character ? character : '\\u00' + match[0].charCodeAt().toPaddedString(2, 16); + }); + if (useDoubleQuotes) return '"' + escapedString.replace(/"/g, '\\"') + '"'; + return "'" + escapedString.replace(/'/g, '\\\'') + "'"; + }, + + toJSON: function() { + return this.inspect(true); + }, + + unfilterJSON: function(filter) { + return this.sub(filter || Prototype.JSONFilter, '#{1}'); + }, + + isJSON: function() { + var str = this; + if (str.blank()) return false; + str = this.replace(/\\./g, '@').replace(/"[^"\\\n\r]*"/g, ''); + return (/^[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t]*$/).test(str); + }, + + evalJSON: function(sanitize) { + var json = this.unfilterJSON(); + try { + if (!sanitize || json.isJSON()) return eval('(' + json + ')'); + } catch (e) { } + throw new SyntaxError('Badly formed JSON string: ' + this.inspect()); + }, + + include: function(pattern) { + return this.indexOf(pattern) > -1; + }, + + startsWith: function(pattern) { + return this.indexOf(pattern) === 0; + }, + + endsWith: function(pattern) { + var d = this.length - pattern.length; + return d >= 0 && this.lastIndexOf(pattern) === d; + }, + + empty: function() { + return this == ''; + }, + + blank: function() { + return /^\s*$/.test(this); + }, + + interpolate: function(object, pattern) { + return new Template(this, pattern).evaluate(object); + } +}); + +if (Prototype.Browser.WebKit || Prototype.Browser.IE) Object.extend(String.prototype, { + escapeHTML: function() { + return this.replace(/&/g,'&').replace(//g,'>'); + }, + unescapeHTML: function() { + return this.stripTags().replace(/&/g,'&').replace(/</g,'<').replace(/>/g,'>'); + } +}); + +String.prototype.gsub.prepareReplacement = function(replacement) { + if (Object.isFunction(replacement)) return replacement; + var template = new Template(replacement); + return function(match) { return template.evaluate(match) }; +}; + +String.prototype.parseQuery = String.prototype.toQueryParams; + +Object.extend(String.prototype.escapeHTML, { + div: document.createElement('div'), + text: document.createTextNode('') +}); + +String.prototype.escapeHTML.div.appendChild(String.prototype.escapeHTML.text); + +var Template = Class.create({ + initialize: function(template, pattern) { + this.template = template.toString(); + this.pattern = pattern || Template.Pattern; + }, + + evaluate: function(object) { + if (Object.isFunction(object.toTemplateReplacements)) + object = object.toTemplateReplacements(); + + return this.template.gsub(this.pattern, function(match) { + if (object == null) return ''; + + var before = match[1] || ''; + if (before == '\\') return match[2]; + + var ctx = object, expr = match[3]; + var pattern = /^([^.[]+|\[((?:.*?[^\\])?)\])(\.|\[|$)/; + match = pattern.exec(expr); + if (match == null) return before; + + while (match != null) { + var comp = match[1].startsWith('[') ? match[2].gsub('\\\\]', ']') : match[1]; + ctx = ctx[comp]; + if (null == ctx || '' == match[3]) break; + expr = expr.substring('[' == match[3] ? match[1].length : match[0].length); + match = pattern.exec(expr); + } + + return before + String.interpret(ctx); + }); + } +}); +Template.Pattern = /(^|.|\r|\n)(#\{(.*?)\})/; + +var $break = { }; + +var Enumerable = { + each: function(iterator, context) { + var index = 0; + try { + this._each(function(value) { + iterator.call(context, value, index++); + }); + } catch (e) { + if (e != $break) throw e; + } + return this; + }, + + eachSlice: function(number, iterator, context) { + var index = -number, slices = [], array = this.toArray(); + if (number < 1) return array; + while ((index += number) < array.length) + slices.push(array.slice(index, index+number)); + return slices.collect(iterator, context); + }, + + all: function(iterator, context) { + iterator = iterator || Prototype.K; + var result = true; + this.each(function(value, index) { + result = result && !!iterator.call(context, value, index); + if (!result) throw $break; + }); + return result; + }, + + any: function(iterator, context) { + iterator = iterator || Prototype.K; + var result = false; + this.each(function(value, index) { + if (result = !!iterator.call(context, value, index)) + throw $break; + }); + return result; + }, + + collect: function(iterator, context) { + iterator = iterator || Prototype.K; + var results = []; + this.each(function(value, index) { + results.push(iterator.call(context, value, index)); + }); + return results; + }, + + detect: function(iterator, context) { + var result; + this.each(function(value, index) { + if (iterator.call(context, value, index)) { + result = value; + throw $break; + } + }); + return result; + }, + + findAll: function(iterator, context) { + var results = []; + this.each(function(value, index) { + if (iterator.call(context, value, index)) + results.push(value); + }); + return results; + }, + + grep: function(filter, iterator, context) { + iterator = iterator || Prototype.K; + var results = []; + + if (Object.isString(filter)) + filter = new RegExp(filter); + + this.each(function(value, index) { + if (filter.match(value)) + results.push(iterator.call(context, value, index)); + }); + return results; + }, + + include: function(object) { + if (Object.isFunction(this.indexOf)) + if (this.indexOf(object) != -1) return true; + + var found = false; + this.each(function(value) { + if (value == object) { + found = true; + throw $break; + } + }); + return found; + }, + + inGroupsOf: function(number, fillWith) { + fillWith = Object.isUndefined(fillWith) ? null : fillWith; + return this.eachSlice(number, function(slice) { + while(slice.length < number) slice.push(fillWith); + return slice; + }); + }, + + inject: function(memo, iterator, context) { + this.each(function(value, index) { + memo = iterator.call(context, memo, value, index); + }); + return memo; + }, + + invoke: function(method) { + var args = $A(arguments).slice(1); + return this.map(function(value) { + return value[method].apply(value, args); + }); + }, + + max: function(iterator, context) { + iterator = iterator || Prototype.K; + var result; + this.each(function(value, index) { + value = iterator.call(context, value, index); + if (result == null || value >= result) + result = value; + }); + return result; + }, + + min: function(iterator, context) { + iterator = iterator || Prototype.K; + var result; + this.each(function(value, index) { + value = iterator.call(context, value, index); + if (result == null || value < result) + result = value; + }); + return result; + }, + + partition: function(iterator, context) { + iterator = iterator || Prototype.K; + var trues = [], falses = []; + this.each(function(value, index) { + (iterator.call(context, value, index) ? + trues : falses).push(value); + }); + return [trues, falses]; + }, + + pluck: function(property) { + var results = []; + this.each(function(value) { + results.push(value[property]); + }); + return results; + }, + + reject: function(iterator, context) { + var results = []; + this.each(function(value, index) { + if (!iterator.call(context, value, index)) + results.push(value); + }); + return results; + }, + + sortBy: function(iterator, context) { + return this.map(function(value, index) { + return { + value: value, + criteria: iterator.call(context, value, index) + }; + }).sort(function(left, right) { + var a = left.criteria, b = right.criteria; + return a < b ? -1 : a > b ? 1 : 0; + }).pluck('value'); + }, + + toArray: function() { + return this.map(); + }, + + zip: function() { + var iterator = Prototype.K, args = $A(arguments); + if (Object.isFunction(args.last())) + iterator = args.pop(); + + var collections = [this].concat(args).map($A); + return this.map(function(value, index) { + return iterator(collections.pluck(index)); + }); + }, + + size: function() { + return this.toArray().length; + }, + + inspect: function() { + return '#'; + } +}; + +Object.extend(Enumerable, { + map: Enumerable.collect, + find: Enumerable.detect, + select: Enumerable.findAll, + filter: Enumerable.findAll, + member: Enumerable.include, + entries: Enumerable.toArray, + every: Enumerable.all, + some: Enumerable.any +}); +function $A(iterable) { + if (!iterable) return []; + if (iterable.toArray) return iterable.toArray(); + var length = iterable.length || 0, results = new Array(length); + while (length--) results[length] = iterable[length]; + return results; +} + +if (Prototype.Browser.WebKit) { + $A = function(iterable) { + if (!iterable) return []; + // In Safari, only use the `toArray` method if it's not a NodeList. + // A NodeList is a function, has an function `item` property, and a numeric + // `length` property. Adapted from Google Doctype. + if (!(typeof iterable === 'function' && typeof iterable.length === + 'number' && typeof iterable.item === 'function') && iterable.toArray) + return iterable.toArray(); + var length = iterable.length || 0, results = new Array(length); + while (length--) results[length] = iterable[length]; + return results; + }; +} + +Array.from = $A; + +Object.extend(Array.prototype, Enumerable); + +if (!Array.prototype._reverse) Array.prototype._reverse = Array.prototype.reverse; + +Object.extend(Array.prototype, { + _each: function(iterator) { + for (var i = 0, length = this.length; i < length; i++) + iterator(this[i]); + }, + + clear: function() { + this.length = 0; + return this; + }, + + first: function() { + return this[0]; + }, + + last: function() { + return this[this.length - 1]; + }, + + compact: function() { + return this.select(function(value) { + return value != null; + }); + }, + + flatten: function() { + return this.inject([], function(array, value) { + return array.concat(Object.isArray(value) ? + value.flatten() : [value]); + }); + }, + + without: function() { + var values = $A(arguments); + return this.select(function(value) { + return !values.include(value); + }); + }, + + reverse: function(inline) { + return (inline !== false ? this : this.toArray())._reverse(); + }, + + reduce: function() { + return this.length > 1 ? this : this[0]; + }, + + uniq: function(sorted) { + return this.inject([], function(array, value, index) { + if (0 == index || (sorted ? array.last() != value : !array.include(value))) + array.push(value); + return array; + }); + }, + + intersect: function(array) { + return this.uniq().findAll(function(item) { + return array.detect(function(value) { return item === value }); + }); + }, + + clone: function() { + return [].concat(this); + }, + + size: function() { + return this.length; + }, + + inspect: function() { + return '[' + this.map(Object.inspect).join(', ') + ']'; + }, + + toJSON: function() { + var results = []; + this.each(function(object) { + var value = Object.toJSON(object); + if (!Object.isUndefined(value)) results.push(value); + }); + return '[' + results.join(', ') + ']'; + } +}); + +// use native browser JS 1.6 implementation if available +if (Object.isFunction(Array.prototype.forEach)) + Array.prototype._each = Array.prototype.forEach; + +if (!Array.prototype.indexOf) Array.prototype.indexOf = function(item, i) { + i || (i = 0); + var length = this.length; + if (i < 0) i = length + i; + for (; i < length; i++) + if (this[i] === item) return i; + return -1; +}; + +if (!Array.prototype.lastIndexOf) Array.prototype.lastIndexOf = function(item, i) { + i = isNaN(i) ? this.length : (i < 0 ? this.length + i : i) + 1; + var n = this.slice(0, i).reverse().indexOf(item); + return (n < 0) ? n : i - n - 1; +}; + +Array.prototype.toArray = Array.prototype.clone; + +function $w(string) { + if (!Object.isString(string)) return []; + string = string.strip(); + return string ? string.split(/\s+/) : []; +} + +if (Prototype.Browser.Opera){ + Array.prototype.concat = function() { + var array = []; + for (var i = 0, length = this.length; i < length; i++) array.push(this[i]); + for (var i = 0, length = arguments.length; i < length; i++) { + if (Object.isArray(arguments[i])) { + for (var j = 0, arrayLength = arguments[i].length; j < arrayLength; j++) + array.push(arguments[i][j]); + } else { + array.push(arguments[i]); + } + } + return array; + }; +} +Object.extend(Number.prototype, { + toColorPart: function() { + return this.toPaddedString(2, 16); + }, + + succ: function() { + return this + 1; + }, + + times: function(iterator, context) { + $R(0, this, true).each(iterator, context); + return this; + }, + + toPaddedString: function(length, radix) { + var string = this.toString(radix || 10); + return '0'.times(length - string.length) + string; + }, + + toJSON: function() { + return isFinite(this) ? this.toString() : 'null'; + } +}); + +$w('abs round ceil floor').each(function(method){ + Number.prototype[method] = Math[method].methodize(); +}); +function $H(object) { + return new Hash(object); +}; + +var Hash = Class.create(Enumerable, (function() { + + function toQueryPair(key, value) { + if (Object.isUndefined(value)) return key; + return key + '=' + encodeURIComponent(String.interpret(value)); + } + + return { + initialize: function(object) { + this._object = Object.isHash(object) ? object.toObject() : Object.clone(object); + }, + + _each: function(iterator) { + for (var key in this._object) { + var value = this._object[key], pair = [key, value]; + pair.key = key; + pair.value = value; + iterator(pair); + } + }, + + set: function(key, value) { + return this._object[key] = value; + }, + + get: function(key) { + // simulating poorly supported hasOwnProperty + if (this._object[key] !== Object.prototype[key]) + return this._object[key]; + }, + + unset: function(key) { + var value = this._object[key]; + delete this._object[key]; + return value; + }, + + toObject: function() { + return Object.clone(this._object); + }, + + keys: function() { + return this.pluck('key'); + }, + + values: function() { + return this.pluck('value'); + }, + + index: function(value) { + var match = this.detect(function(pair) { + return pair.value === value; + }); + return match && match.key; + }, + + merge: function(object) { + return this.clone().update(object); + }, + + update: function(object) { + return new Hash(object).inject(this, function(result, pair) { + result.set(pair.key, pair.value); + return result; + }); + }, + + toQueryString: function() { + return this.inject([], function(results, pair) { + var key = encodeURIComponent(pair.key), values = pair.value; + + if (values && typeof values == 'object') { + if (Object.isArray(values)) + return results.concat(values.map(toQueryPair.curry(key))); + } else results.push(toQueryPair(key, values)); + return results; + }).join('&'); + }, + + inspect: function() { + return '#'; + }, + + toJSON: function() { + return Object.toJSON(this.toObject()); + }, + + clone: function() { + return new Hash(this); + } + } +})()); + +Hash.prototype.toTemplateReplacements = Hash.prototype.toObject; +Hash.from = $H; +var ObjectRange = Class.create(Enumerable, { + initialize: function(start, end, exclusive) { + this.start = start; + this.end = end; + this.exclusive = exclusive; + }, + + _each: function(iterator) { + var value = this.start; + while (this.include(value)) { + iterator(value); + value = value.succ(); + } + }, + + include: function(value) { + if (value < this.start) + return false; + if (this.exclusive) + return value < this.end; + return value <= this.end; + } +}); + +var $R = function(start, end, exclusive) { + return new ObjectRange(start, end, exclusive); +}; + +var Ajax = { + getTransport: function() { + return Try.these( + function() {return new XMLHttpRequest()}, + function() {return new ActiveXObject('Msxml2.XMLHTTP')}, + function() {return new ActiveXObject('Microsoft.XMLHTTP')} + ) || false; + }, + + activeRequestCount: 0 +}; + +Ajax.Responders = { + responders: [], + + _each: function(iterator) { + this.responders._each(iterator); + }, + + register: function(responder) { + if (!this.include(responder)) + this.responders.push(responder); + }, + + unregister: function(responder) { + this.responders = this.responders.without(responder); + }, + + dispatch: function(callback, request, transport, json) { + this.each(function(responder) { + if (Object.isFunction(responder[callback])) { + try { + responder[callback].apply(responder, [request, transport, json]); + } catch (e) { } + } + }); + } +}; + +Object.extend(Ajax.Responders, Enumerable); + +Ajax.Responders.register({ + onCreate: function() { Ajax.activeRequestCount++ }, + onComplete: function() { Ajax.activeRequestCount-- } +}); + +Ajax.Base = Class.create({ + initialize: function(options) { + this.options = { + method: 'post', + asynchronous: true, + contentType: 'application/x-www-form-urlencoded', + encoding: 'UTF-8', + parameters: '', + evalJSON: true, + evalJS: true + }; + Object.extend(this.options, options || { }); + + this.options.method = this.options.method.toLowerCase(); + + if (Object.isString(this.options.parameters)) + this.options.parameters = this.options.parameters.toQueryParams(); + else if (Object.isHash(this.options.parameters)) + this.options.parameters = this.options.parameters.toObject(); + } +}); + +Ajax.Request = Class.create(Ajax.Base, { + _complete: false, + + initialize: function($super, url, options) { + $super(options); + this.transport = Ajax.getTransport(); + this.request(url); + }, + + request: function(url) { + this.url = url; + this.method = this.options.method; + var params = Object.clone(this.options.parameters); + + if (!['get', 'post'].include(this.method)) { + // simulate other verbs over post + params['_method'] = this.method; + this.method = 'post'; + } + + this.parameters = params; + + if (params = Object.toQueryString(params)) { + // when GET, append parameters to URL + if (this.method == 'get') + this.url += (this.url.include('?') ? '&' : '?') + params; + else if (/Konqueror|Safari|KHTML/.test(navigator.userAgent)) + params += '&_='; + } + + try { + var response = new Ajax.Response(this); + if (this.options.onCreate) this.options.onCreate(response); + Ajax.Responders.dispatch('onCreate', this, response); + + this.transport.open(this.method.toUpperCase(), this.url, + this.options.asynchronous); + + if (this.options.asynchronous) this.respondToReadyState.bind(this).defer(1); + + this.transport.onreadystatechange = this.onStateChange.bind(this); + this.setRequestHeaders(); + + this.body = this.method == 'post' ? (this.options.postBody || params) : null; + this.transport.send(this.body); + + /* Force Firefox to handle ready state 4 for synchronous requests */ + if (!this.options.asynchronous && this.transport.overrideMimeType) + this.onStateChange(); + + } + catch (e) { + this.dispatchException(e); + } + }, + + onStateChange: function() { + var readyState = this.transport.readyState; + if (readyState > 1 && !((readyState == 4) && this._complete)) + this.respondToReadyState(this.transport.readyState); + }, + + setRequestHeaders: function() { + var headers = { + 'X-Requested-With': 'XMLHttpRequest', + 'X-Prototype-Version': Prototype.Version, + 'Accept': 'text/javascript, text/html, application/xml, text/xml, */*' + }; + + if (this.method == 'post') { + headers['Content-type'] = this.options.contentType + + (this.options.encoding ? '; charset=' + this.options.encoding : ''); + + /* Force "Connection: close" for older Mozilla browsers to work + * around a bug where XMLHttpRequest sends an incorrect + * Content-length header. See Mozilla Bugzilla #246651. + */ + if (this.transport.overrideMimeType && + (navigator.userAgent.match(/Gecko\/(\d{4})/) || [0,2005])[1] < 2005) + headers['Connection'] = 'close'; + } + + // user-defined headers + if (typeof this.options.requestHeaders == 'object') { + var extras = this.options.requestHeaders; + + if (Object.isFunction(extras.push)) + for (var i = 0, length = extras.length; i < length; i += 2) + headers[extras[i]] = extras[i+1]; + else + $H(extras).each(function(pair) { headers[pair.key] = pair.value }); + } + + for (var name in headers) + this.transport.setRequestHeader(name, headers[name]); + }, + + success: function() { + var status = this.getStatus(); + return !status || (status >= 200 && status < 300); + }, + + getStatus: function() { + try { + return this.transport.status || 0; + } catch (e) { return 0 } + }, + + respondToReadyState: function(readyState) { + var state = Ajax.Request.Events[readyState], response = new Ajax.Response(this); + + if (state == 'Complete') { + try { + this._complete = true; + (this.options['on' + response.status] + || this.options['on' + (this.success() ? 'Success' : 'Failure')] + || Prototype.emptyFunction)(response, response.headerJSON); + } catch (e) { + this.dispatchException(e); + } + + var contentType = response.getHeader('Content-type'); + if (this.options.evalJS == 'force' + || (this.options.evalJS && this.isSameOrigin() && contentType + && contentType.match(/^\s*(text|application)\/(x-)?(java|ecma)script(;.*)?\s*$/i))) + this.evalResponse(); + } + + try { + (this.options['on' + state] || Prototype.emptyFunction)(response, response.headerJSON); + Ajax.Responders.dispatch('on' + state, this, response, response.headerJSON); + } catch (e) { + this.dispatchException(e); + } + + if (state == 'Complete') { + // avoid memory leak in MSIE: clean up + this.transport.onreadystatechange = Prototype.emptyFunction; + } + }, + + isSameOrigin: function() { + var m = this.url.match(/^\s*https?:\/\/[^\/]*/); + return !m || (m[0] == '#{protocol}//#{domain}#{port}'.interpolate({ + protocol: location.protocol, + domain: document.domain, + port: location.port ? ':' + location.port : '' + })); + }, + + getHeader: function(name) { + try { + return this.transport.getResponseHeader(name) || null; + } catch (e) { return null } + }, + + evalResponse: function() { + try { + return eval((this.transport.responseText || '').unfilterJSON()); + } catch (e) { + this.dispatchException(e); + } + }, + + dispatchException: function(exception) { + (this.options.onException || Prototype.emptyFunction)(this, exception); + Ajax.Responders.dispatch('onException', this, exception); + } +}); + +Ajax.Request.Events = + ['Uninitialized', 'Loading', 'Loaded', 'Interactive', 'Complete']; + +Ajax.Response = Class.create({ + initialize: function(request){ + this.request = request; + var transport = this.transport = request.transport, + readyState = this.readyState = transport.readyState; + + if((readyState > 2 && !Prototype.Browser.IE) || readyState == 4) { + this.status = this.getStatus(); + this.statusText = this.getStatusText(); + this.responseText = String.interpret(transport.responseText); + this.headerJSON = this._getHeaderJSON(); + } + + if(readyState == 4) { + var xml = transport.responseXML; + this.responseXML = Object.isUndefined(xml) ? null : xml; + this.responseJSON = this._getResponseJSON(); + } + }, + + status: 0, + statusText: '', + + getStatus: Ajax.Request.prototype.getStatus, + + getStatusText: function() { + try { + return this.transport.statusText || ''; + } catch (e) { return '' } + }, + + getHeader: Ajax.Request.prototype.getHeader, + + getAllHeaders: function() { + try { + return this.getAllResponseHeaders(); + } catch (e) { return null } + }, + + getResponseHeader: function(name) { + return this.transport.getResponseHeader(name); + }, + + getAllResponseHeaders: function() { + return this.transport.getAllResponseHeaders(); + }, + + _getHeaderJSON: function() { + var json = this.getHeader('X-JSON'); + if (!json) return null; + json = decodeURIComponent(escape(json)); + try { + return json.evalJSON(this.request.options.sanitizeJSON || + !this.request.isSameOrigin()); + } catch (e) { + this.request.dispatchException(e); + } + }, + + _getResponseJSON: function() { + var options = this.request.options; + if (!options.evalJSON || (options.evalJSON != 'force' && + !(this.getHeader('Content-type') || '').include('application/json')) || + this.responseText.blank()) + return null; + try { + return this.responseText.evalJSON(options.sanitizeJSON || + !this.request.isSameOrigin()); + } catch (e) { + this.request.dispatchException(e); + } + } +}); + +Ajax.Updater = Class.create(Ajax.Request, { + initialize: function($super, container, url, options) { + this.container = { + success: (container.success || container), + failure: (container.failure || (container.success ? null : container)) + }; + + options = Object.clone(options); + var onComplete = options.onComplete; + options.onComplete = (function(response, json) { + this.updateContent(response.responseText); + if (Object.isFunction(onComplete)) onComplete(response, json); + }).bind(this); + + $super(url, options); + }, + + updateContent: function(responseText) { + var receiver = this.container[this.success() ? 'success' : 'failure'], + options = this.options; + + if (!options.evalScripts) responseText = responseText.stripScripts(); + + if (receiver = $(receiver)) { + if (options.insertion) { + if (Object.isString(options.insertion)) { + var insertion = { }; insertion[options.insertion] = responseText; + receiver.insert(insertion); + } + else options.insertion(receiver, responseText); + } + else receiver.update(responseText); + } + } +}); + +Ajax.PeriodicalUpdater = Class.create(Ajax.Base, { + initialize: function($super, container, url, options) { + $super(options); + this.onComplete = this.options.onComplete; + + this.frequency = (this.options.frequency || 2); + this.decay = (this.options.decay || 1); + + this.updater = { }; + this.container = container; + this.url = url; + + this.start(); + }, + + start: function() { + this.options.onComplete = this.updateComplete.bind(this); + this.onTimerEvent(); + }, + + stop: function() { + this.updater.options.onComplete = undefined; + clearTimeout(this.timer); + (this.onComplete || Prototype.emptyFunction).apply(this, arguments); + }, + + updateComplete: function(response) { + if (this.options.decay) { + this.decay = (response.responseText == this.lastText ? + this.decay * this.options.decay : 1); + + this.lastText = response.responseText; + } + this.timer = this.onTimerEvent.bind(this).delay(this.decay * this.frequency); + }, + + onTimerEvent: function() { + this.updater = new Ajax.Updater(this.container, this.url, this.options); + } +}); +function $(element) { + if (arguments.length > 1) { + for (var i = 0, elements = [], length = arguments.length; i < length; i++) + elements.push($(arguments[i])); + return elements; + } + if (Object.isString(element)) + element = document.getElementById(element); + return Element.extend(element); +} + +if (Prototype.BrowserFeatures.XPath) { + document._getElementsByXPath = function(expression, parentElement) { + var results = []; + var query = document.evaluate(expression, $(parentElement) || document, + null, XPathResult.ORDERED_NODE_SNAPSHOT_TYPE, null); + for (var i = 0, length = query.snapshotLength; i < length; i++) + results.push(Element.extend(query.snapshotItem(i))); + return results; + }; +} + +/*--------------------------------------------------------------------------*/ + +if (!window.Node) var Node = { }; + +if (!Node.ELEMENT_NODE) { + // DOM level 2 ECMAScript Language Binding + Object.extend(Node, { + ELEMENT_NODE: 1, + ATTRIBUTE_NODE: 2, + TEXT_NODE: 3, + CDATA_SECTION_NODE: 4, + ENTITY_REFERENCE_NODE: 5, + ENTITY_NODE: 6, + PROCESSING_INSTRUCTION_NODE: 7, + COMMENT_NODE: 8, + DOCUMENT_NODE: 9, + DOCUMENT_TYPE_NODE: 10, + DOCUMENT_FRAGMENT_NODE: 11, + NOTATION_NODE: 12 + }); +} + +(function() { + var element = this.Element; + this.Element = function(tagName, attributes) { + attributes = attributes || { }; + tagName = tagName.toLowerCase(); + var cache = Element.cache; + if (Prototype.Browser.IE && attributes.name) { + tagName = '<' + tagName + ' name="' + attributes.name + '">'; + delete attributes.name; + return Element.writeAttribute(document.createElement(tagName), attributes); + } + if (!cache[tagName]) cache[tagName] = Element.extend(document.createElement(tagName)); + return Element.writeAttribute(cache[tagName].cloneNode(false), attributes); + }; + Object.extend(this.Element, element || { }); + if (element) this.Element.prototype = element.prototype; +}).call(window); + +Element.cache = { }; + +Element.Methods = { + visible: function(element) { + return $(element).style.display != 'none'; + }, + + toggle: function(element) { + element = $(element); + Element[Element.visible(element) ? 'hide' : 'show'](element); + return element; + }, + + hide: function(element) { + element = $(element); + element.style.display = 'none'; + return element; + }, + + show: function(element) { + element = $(element); + element.style.display = ''; + return element; + }, + + remove: function(element) { + element = $(element); + element.parentNode.removeChild(element); + return element; + }, + + update: function(element, content) { + element = $(element); + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) return element.update().insert(content); + content = Object.toHTML(content); + element.innerHTML = content.stripScripts(); + content.evalScripts.bind(content).defer(); + return element; + }, + + replace: function(element, content) { + element = $(element); + if (content && content.toElement) content = content.toElement(); + else if (!Object.isElement(content)) { + content = Object.toHTML(content); + var range = element.ownerDocument.createRange(); + range.selectNode(element); + content.evalScripts.bind(content).defer(); + content = range.createContextualFragment(content.stripScripts()); + } + element.parentNode.replaceChild(content, element); + return element; + }, + + insert: function(element, insertions) { + element = $(element); + + if (Object.isString(insertions) || Object.isNumber(insertions) || + Object.isElement(insertions) || (insertions && (insertions.toElement || insertions.toHTML))) + insertions = {bottom:insertions}; + + var content, insert, tagName, childNodes; + + for (var position in insertions) { + content = insertions[position]; + position = position.toLowerCase(); + insert = Element._insertionTranslations[position]; + + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) { + insert(element, content); + continue; + } + + content = Object.toHTML(content); + + tagName = ((position == 'before' || position == 'after') + ? element.parentNode : element).tagName.toUpperCase(); + + childNodes = Element._getContentFromAnonymousElement(tagName, content.stripScripts()); + + if (position == 'top' || position == 'after') childNodes.reverse(); + childNodes.each(insert.curry(element)); + + content.evalScripts.bind(content).defer(); + } + + return element; + }, + + wrap: function(element, wrapper, attributes) { + element = $(element); + if (Object.isElement(wrapper)) + $(wrapper).writeAttribute(attributes || { }); + else if (Object.isString(wrapper)) wrapper = new Element(wrapper, attributes); + else wrapper = new Element('div', wrapper); + if (element.parentNode) + element.parentNode.replaceChild(wrapper, element); + wrapper.appendChild(element); + return wrapper; + }, + + inspect: function(element) { + element = $(element); + var result = '<' + element.tagName.toLowerCase(); + $H({'id': 'id', 'className': 'class'}).each(function(pair) { + var property = pair.first(), attribute = pair.last(); + var value = (element[property] || '').toString(); + if (value) result += ' ' + attribute + '=' + value.inspect(true); + }); + return result + '>'; + }, + + recursivelyCollect: function(element, property) { + element = $(element); + var elements = []; + while (element = element[property]) + if (element.nodeType == 1) + elements.push(Element.extend(element)); + return elements; + }, + + ancestors: function(element) { + return $(element).recursivelyCollect('parentNode'); + }, + + descendants: function(element) { + return $(element).select("*"); + }, + + firstDescendant: function(element) { + element = $(element).firstChild; + while (element && element.nodeType != 1) element = element.nextSibling; + return $(element); + }, + + immediateDescendants: function(element) { + if (!(element = $(element).firstChild)) return []; + while (element && element.nodeType != 1) element = element.nextSibling; + if (element) return [element].concat($(element).nextSiblings()); + return []; + }, + + previousSiblings: function(element) { + return $(element).recursivelyCollect('previousSibling'); + }, + + nextSiblings: function(element) { + return $(element).recursivelyCollect('nextSibling'); + }, + + siblings: function(element) { + element = $(element); + return element.previousSiblings().reverse().concat(element.nextSiblings()); + }, + + match: function(element, selector) { + if (Object.isString(selector)) + selector = new Selector(selector); + return selector.match($(element)); + }, + + up: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return $(element.parentNode); + var ancestors = element.ancestors(); + return Object.isNumber(expression) ? ancestors[expression] : + Selector.findElement(ancestors, expression, index); + }, + + down: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return element.firstDescendant(); + return Object.isNumber(expression) ? element.descendants()[expression] : + Element.select(element, expression)[index || 0]; + }, + + previous: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return $(Selector.handlers.previousElementSibling(element)); + var previousSiblings = element.previousSiblings(); + return Object.isNumber(expression) ? previousSiblings[expression] : + Selector.findElement(previousSiblings, expression, index); + }, + + next: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return $(Selector.handlers.nextElementSibling(element)); + var nextSiblings = element.nextSiblings(); + return Object.isNumber(expression) ? nextSiblings[expression] : + Selector.findElement(nextSiblings, expression, index); + }, + + select: function() { + var args = $A(arguments), element = $(args.shift()); + return Selector.findChildElements(element, args); + }, + + adjacent: function() { + var args = $A(arguments), element = $(args.shift()); + return Selector.findChildElements(element.parentNode, args).without(element); + }, + + identify: function(element) { + element = $(element); + var id = element.readAttribute('id'), self = arguments.callee; + if (id) return id; + do { id = 'anonymous_element_' + self.counter++ } while ($(id)); + element.writeAttribute('id', id); + return id; + }, + + readAttribute: function(element, name) { + element = $(element); + if (Prototype.Browser.IE) { + var t = Element._attributeTranslations.read; + if (t.values[name]) return t.values[name](element, name); + if (t.names[name]) name = t.names[name]; + if (name.include(':')) { + return (!element.attributes || !element.attributes[name]) ? null : + element.attributes[name].value; + } + } + return element.getAttribute(name); + }, + + writeAttribute: function(element, name, value) { + element = $(element); + var attributes = { }, t = Element._attributeTranslations.write; + + if (typeof name == 'object') attributes = name; + else attributes[name] = Object.isUndefined(value) ? true : value; + + for (var attr in attributes) { + name = t.names[attr] || attr; + value = attributes[attr]; + if (t.values[attr]) name = t.values[attr](element, value); + if (value === false || value === null) + element.removeAttribute(name); + else if (value === true) + element.setAttribute(name, name); + else element.setAttribute(name, value); + } + return element; + }, + + getHeight: function(element) { + return $(element).getDimensions().height; + }, + + getWidth: function(element) { + return $(element).getDimensions().width; + }, + + classNames: function(element) { + return new Element.ClassNames(element); + }, + + hasClassName: function(element, className) { + if (!(element = $(element))) return; + var elementClassName = element.className; + return (elementClassName.length > 0 && (elementClassName == className || + new RegExp("(^|\\s)" + className + "(\\s|$)").test(elementClassName))); + }, + + addClassName: function(element, className) { + if (!(element = $(element))) return; + if (!element.hasClassName(className)) + element.className += (element.className ? ' ' : '') + className; + return element; + }, + + removeClassName: function(element, className) { + if (!(element = $(element))) return; + element.className = element.className.replace( + new RegExp("(^|\\s+)" + className + "(\\s+|$)"), ' ').strip(); + return element; + }, + + toggleClassName: function(element, className) { + if (!(element = $(element))) return; + return element[element.hasClassName(className) ? + 'removeClassName' : 'addClassName'](className); + }, + + // removes whitespace-only text node children + cleanWhitespace: function(element) { + element = $(element); + var node = element.firstChild; + while (node) { + var nextNode = node.nextSibling; + if (node.nodeType == 3 && !/\S/.test(node.nodeValue)) + element.removeChild(node); + node = nextNode; + } + return element; + }, + + empty: function(element) { + return $(element).innerHTML.blank(); + }, + + descendantOf: function(element, ancestor) { + element = $(element), ancestor = $(ancestor); + + if (element.compareDocumentPosition) + return (element.compareDocumentPosition(ancestor) & 8) === 8; + + if (ancestor.contains) + return ancestor.contains(element) && ancestor !== element; + + while (element = element.parentNode) + if (element == ancestor) return true; + + return false; + }, + + scrollTo: function(element) { + element = $(element); + var pos = element.cumulativeOffset(); + window.scrollTo(pos[0], pos[1]); + return element; + }, + + getStyle: function(element, style) { + element = $(element); + style = style == 'float' ? 'cssFloat' : style.camelize(); + var value = element.style[style]; + if (!value || value == 'auto') { + var css = document.defaultView.getComputedStyle(element, null); + value = css ? css[style] : null; + } + if (style == 'opacity') return value ? parseFloat(value) : 1.0; + return value == 'auto' ? null : value; + }, + + getOpacity: function(element) { + return $(element).getStyle('opacity'); + }, + + setStyle: function(element, styles) { + element = $(element); + var elementStyle = element.style, match; + if (Object.isString(styles)) { + element.style.cssText += ';' + styles; + return styles.include('opacity') ? + element.setOpacity(styles.match(/opacity:\s*(\d?\.?\d*)/)[1]) : element; + } + for (var property in styles) + if (property == 'opacity') element.setOpacity(styles[property]); + else + elementStyle[(property == 'float' || property == 'cssFloat') ? + (Object.isUndefined(elementStyle.styleFloat) ? 'cssFloat' : 'styleFloat') : + property] = styles[property]; + + return element; + }, + + setOpacity: function(element, value) { + element = $(element); + element.style.opacity = (value == 1 || value === '') ? '' : + (value < 0.00001) ? 0 : value; + return element; + }, + + getDimensions: function(element) { + element = $(element); + var display = element.getStyle('display'); + if (display != 'none' && display != null) // Safari bug + return {width: element.offsetWidth, height: element.offsetHeight}; + + // All *Width and *Height properties give 0 on elements with display none, + // so enable the element temporarily + var els = element.style; + var originalVisibility = els.visibility; + var originalPosition = els.position; + var originalDisplay = els.display; + els.visibility = 'hidden'; + els.position = 'absolute'; + els.display = 'block'; + var originalWidth = element.clientWidth; + var originalHeight = element.clientHeight; + els.display = originalDisplay; + els.position = originalPosition; + els.visibility = originalVisibility; + return {width: originalWidth, height: originalHeight}; + }, + + makePositioned: function(element) { + element = $(element); + var pos = Element.getStyle(element, 'position'); + if (pos == 'static' || !pos) { + element._madePositioned = true; + element.style.position = 'relative'; + // Opera returns the offset relative to the positioning context, when an + // element is position relative but top and left have not been defined + if (Prototype.Browser.Opera) { + element.style.top = 0; + element.style.left = 0; + } + } + return element; + }, + + undoPositioned: function(element) { + element = $(element); + if (element._madePositioned) { + element._madePositioned = undefined; + element.style.position = + element.style.top = + element.style.left = + element.style.bottom = + element.style.right = ''; + } + return element; + }, + + makeClipping: function(element) { + element = $(element); + if (element._overflow) return element; + element._overflow = Element.getStyle(element, 'overflow') || 'auto'; + if (element._overflow !== 'hidden') + element.style.overflow = 'hidden'; + return element; + }, + + undoClipping: function(element) { + element = $(element); + if (!element._overflow) return element; + element.style.overflow = element._overflow == 'auto' ? '' : element._overflow; + element._overflow = null; + return element; + }, + + cumulativeOffset: function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + element = element.offsetParent; + } while (element); + return Element._returnOffset(valueL, valueT); + }, + + positionedOffset: function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + element = element.offsetParent; + if (element) { + if (element.tagName.toUpperCase() == 'BODY') break; + var p = Element.getStyle(element, 'position'); + if (p !== 'static') break; + } + } while (element); + return Element._returnOffset(valueL, valueT); + }, + + absolutize: function(element) { + element = $(element); + if (element.getStyle('position') == 'absolute') return element; + // Position.prepare(); // To be done manually by Scripty when it needs it. + + var offsets = element.positionedOffset(); + var top = offsets[1]; + var left = offsets[0]; + var width = element.clientWidth; + var height = element.clientHeight; + + element._originalLeft = left - parseFloat(element.style.left || 0); + element._originalTop = top - parseFloat(element.style.top || 0); + element._originalWidth = element.style.width; + element._originalHeight = element.style.height; + + element.style.position = 'absolute'; + element.style.top = top + 'px'; + element.style.left = left + 'px'; + element.style.width = width + 'px'; + element.style.height = height + 'px'; + return element; + }, + + relativize: function(element) { + element = $(element); + if (element.getStyle('position') == 'relative') return element; + // Position.prepare(); // To be done manually by Scripty when it needs it. + + element.style.position = 'relative'; + var top = parseFloat(element.style.top || 0) - (element._originalTop || 0); + var left = parseFloat(element.style.left || 0) - (element._originalLeft || 0); + + element.style.top = top + 'px'; + element.style.left = left + 'px'; + element.style.height = element._originalHeight; + element.style.width = element._originalWidth; + return element; + }, + + cumulativeScrollOffset: function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.scrollTop || 0; + valueL += element.scrollLeft || 0; + element = element.parentNode; + } while (element); + return Element._returnOffset(valueL, valueT); + }, + + getOffsetParent: function(element) { + if (element.offsetParent) return $(element.offsetParent); + if (element == document.body) return $(element); + + while ((element = element.parentNode) && element != document.body) + if (Element.getStyle(element, 'position') != 'static') + return $(element); + + return $(document.body); + }, + + viewportOffset: function(forElement) { + var valueT = 0, valueL = 0; + + var element = forElement; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + + // Safari fix + if (element.offsetParent == document.body && + Element.getStyle(element, 'position') == 'absolute') break; + + } while (element = element.offsetParent); + + element = forElement; + do { + if (!Prototype.Browser.Opera || (element.tagName && (element.tagName.toUpperCase() == 'BODY'))) { + valueT -= element.scrollTop || 0; + valueL -= element.scrollLeft || 0; + } + } while (element = element.parentNode); + + return Element._returnOffset(valueL, valueT); + }, + + clonePosition: function(element, source) { + var options = Object.extend({ + setLeft: true, + setTop: true, + setWidth: true, + setHeight: true, + offsetTop: 0, + offsetLeft: 0 + }, arguments[2] || { }); + + // find page position of source + source = $(source); + var p = source.viewportOffset(); + + // find coordinate system to use + element = $(element); + var delta = [0, 0]; + var parent = null; + // delta [0,0] will do fine with position: fixed elements, + // position:absolute needs offsetParent deltas + if (Element.getStyle(element, 'position') == 'absolute') { + parent = element.getOffsetParent(); + delta = parent.viewportOffset(); + } + + // correct by body offsets (fixes Safari) + if (parent == document.body) { + delta[0] -= document.body.offsetLeft; + delta[1] -= document.body.offsetTop; + } + + // set position + if (options.setLeft) element.style.left = (p[0] - delta[0] + options.offsetLeft) + 'px'; + if (options.setTop) element.style.top = (p[1] - delta[1] + options.offsetTop) + 'px'; + if (options.setWidth) element.style.width = source.offsetWidth + 'px'; + if (options.setHeight) element.style.height = source.offsetHeight + 'px'; + return element; + } +}; + +Element.Methods.identify.counter = 1; + +Object.extend(Element.Methods, { + getElementsBySelector: Element.Methods.select, + childElements: Element.Methods.immediateDescendants +}); + +Element._attributeTranslations = { + write: { + names: { + className: 'class', + htmlFor: 'for' + }, + values: { } + } +}; + +if (Prototype.Browser.Opera) { + Element.Methods.getStyle = Element.Methods.getStyle.wrap( + function(proceed, element, style) { + switch (style) { + case 'left': case 'top': case 'right': case 'bottom': + if (proceed(element, 'position') === 'static') return null; + case 'height': case 'width': + // returns '0px' for hidden elements; we want it to return null + if (!Element.visible(element)) return null; + + // returns the border-box dimensions rather than the content-box + // dimensions, so we subtract padding and borders from the value + var dim = parseInt(proceed(element, style), 10); + + if (dim !== element['offset' + style.capitalize()]) + return dim + 'px'; + + var properties; + if (style === 'height') { + properties = ['border-top-width', 'padding-top', + 'padding-bottom', 'border-bottom-width']; + } + else { + properties = ['border-left-width', 'padding-left', + 'padding-right', 'border-right-width']; + } + return properties.inject(dim, function(memo, property) { + var val = proceed(element, property); + return val === null ? memo : memo - parseInt(val, 10); + }) + 'px'; + default: return proceed(element, style); + } + } + ); + + Element.Methods.readAttribute = Element.Methods.readAttribute.wrap( + function(proceed, element, attribute) { + if (attribute === 'title') return element.title; + return proceed(element, attribute); + } + ); +} + +else if (Prototype.Browser.IE) { + // IE doesn't report offsets correctly for static elements, so we change them + // to "relative" to get the values, then change them back. + Element.Methods.getOffsetParent = Element.Methods.getOffsetParent.wrap( + function(proceed, element) { + element = $(element); + // IE throws an error if element is not in document + try { element.offsetParent } + catch(e) { return $(document.body) } + var position = element.getStyle('position'); + if (position !== 'static') return proceed(element); + element.setStyle({ position: 'relative' }); + var value = proceed(element); + element.setStyle({ position: position }); + return value; + } + ); + + $w('positionedOffset viewportOffset').each(function(method) { + Element.Methods[method] = Element.Methods[method].wrap( + function(proceed, element) { + element = $(element); + try { element.offsetParent } + catch(e) { return Element._returnOffset(0,0) } + var position = element.getStyle('position'); + if (position !== 'static') return proceed(element); + // Trigger hasLayout on the offset parent so that IE6 reports + // accurate offsetTop and offsetLeft values for position: fixed. + var offsetParent = element.getOffsetParent(); + if (offsetParent && offsetParent.getStyle('position') === 'fixed') + offsetParent.setStyle({ zoom: 1 }); + element.setStyle({ position: 'relative' }); + var value = proceed(element); + element.setStyle({ position: position }); + return value; + } + ); + }); + + Element.Methods.cumulativeOffset = Element.Methods.cumulativeOffset.wrap( + function(proceed, element) { + try { element.offsetParent } + catch(e) { return Element._returnOffset(0,0) } + return proceed(element); + } + ); + + Element.Methods.getStyle = function(element, style) { + element = $(element); + style = (style == 'float' || style == 'cssFloat') ? 'styleFloat' : style.camelize(); + var value = element.style[style]; + if (!value && element.currentStyle) value = element.currentStyle[style]; + + if (style == 'opacity') { + if (value = (element.getStyle('filter') || '').match(/alpha\(opacity=(.*)\)/)) + if (value[1]) return parseFloat(value[1]) / 100; + return 1.0; + } + + if (value == 'auto') { + if ((style == 'width' || style == 'height') && (element.getStyle('display') != 'none')) + return element['offset' + style.capitalize()] + 'px'; + return null; + } + return value; + }; + + Element.Methods.setOpacity = function(element, value) { + function stripAlpha(filter){ + return filter.replace(/alpha\([^\)]*\)/gi,''); + } + element = $(element); + var currentStyle = element.currentStyle; + if ((currentStyle && !currentStyle.hasLayout) || + (!currentStyle && element.style.zoom == 'normal')) + element.style.zoom = 1; + + var filter = element.getStyle('filter'), style = element.style; + if (value == 1 || value === '') { + (filter = stripAlpha(filter)) ? + style.filter = filter : style.removeAttribute('filter'); + return element; + } else if (value < 0.00001) value = 0; + style.filter = stripAlpha(filter) + + 'alpha(opacity=' + (value * 100) + ')'; + return element; + }; + + Element._attributeTranslations = { + read: { + names: { + 'class': 'className', + 'for': 'htmlFor' + }, + values: { + _getAttr: function(element, attribute) { + return element.getAttribute(attribute, 2); + }, + _getAttrNode: function(element, attribute) { + var node = element.getAttributeNode(attribute); + return node ? node.value : ""; + }, + _getEv: function(element, attribute) { + attribute = element.getAttribute(attribute); + return attribute ? attribute.toString().slice(23, -2) : null; + }, + _flag: function(element, attribute) { + return $(element).hasAttribute(attribute) ? attribute : null; + }, + style: function(element) { + return element.style.cssText.toLowerCase(); + }, + title: function(element) { + return element.title; + } + } + } + }; + + Element._attributeTranslations.write = { + names: Object.extend({ + cellpadding: 'cellPadding', + cellspacing: 'cellSpacing' + }, Element._attributeTranslations.read.names), + values: { + checked: function(element, value) { + element.checked = !!value; + }, + + style: function(element, value) { + element.style.cssText = value ? value : ''; + } + } + }; + + Element._attributeTranslations.has = {}; + + $w('colSpan rowSpan vAlign dateTime accessKey tabIndex ' + + 'encType maxLength readOnly longDesc frameBorder').each(function(attr) { + Element._attributeTranslations.write.names[attr.toLowerCase()] = attr; + Element._attributeTranslations.has[attr.toLowerCase()] = attr; + }); + + (function(v) { + Object.extend(v, { + href: v._getAttr, + src: v._getAttr, + type: v._getAttr, + action: v._getAttrNode, + disabled: v._flag, + checked: v._flag, + readonly: v._flag, + multiple: v._flag, + onload: v._getEv, + onunload: v._getEv, + onclick: v._getEv, + ondblclick: v._getEv, + onmousedown: v._getEv, + onmouseup: v._getEv, + onmouseover: v._getEv, + onmousemove: v._getEv, + onmouseout: v._getEv, + onfocus: v._getEv, + onblur: v._getEv, + onkeypress: v._getEv, + onkeydown: v._getEv, + onkeyup: v._getEv, + onsubmit: v._getEv, + onreset: v._getEv, + onselect: v._getEv, + onchange: v._getEv + }); + })(Element._attributeTranslations.read.values); +} + +else if (Prototype.Browser.Gecko && /rv:1\.8\.0/.test(navigator.userAgent)) { + Element.Methods.setOpacity = function(element, value) { + element = $(element); + element.style.opacity = (value == 1) ? 0.999999 : + (value === '') ? '' : (value < 0.00001) ? 0 : value; + return element; + }; +} + +else if (Prototype.Browser.WebKit) { + Element.Methods.setOpacity = function(element, value) { + element = $(element); + element.style.opacity = (value == 1 || value === '') ? '' : + (value < 0.00001) ? 0 : value; + + if (value == 1) + if(element.tagName.toUpperCase() == 'IMG' && element.width) { + element.width++; element.width--; + } else try { + var n = document.createTextNode(' '); + element.appendChild(n); + element.removeChild(n); + } catch (e) { } + + return element; + }; + + // Safari returns margins on body which is incorrect if the child is absolutely + // positioned. For performance reasons, redefine Element#cumulativeOffset for + // KHTML/WebKit only. + Element.Methods.cumulativeOffset = function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + if (element.offsetParent == document.body) + if (Element.getStyle(element, 'position') == 'absolute') break; + + element = element.offsetParent; + } while (element); + + return Element._returnOffset(valueL, valueT); + }; +} + +if (Prototype.Browser.IE || Prototype.Browser.Opera) { + // IE and Opera are missing .innerHTML support for TABLE-related and SELECT elements + Element.Methods.update = function(element, content) { + element = $(element); + + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) return element.update().insert(content); + + content = Object.toHTML(content); + var tagName = element.tagName.toUpperCase(); + + if (tagName in Element._insertionTranslations.tags) { + $A(element.childNodes).each(function(node) { element.removeChild(node) }); + Element._getContentFromAnonymousElement(tagName, content.stripScripts()) + .each(function(node) { element.appendChild(node) }); + } + else element.innerHTML = content.stripScripts(); + + content.evalScripts.bind(content).defer(); + return element; + }; +} + +if ('outerHTML' in document.createElement('div')) { + Element.Methods.replace = function(element, content) { + element = $(element); + + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) { + element.parentNode.replaceChild(content, element); + return element; + } + + content = Object.toHTML(content); + var parent = element.parentNode, tagName = parent.tagName.toUpperCase(); + + if (Element._insertionTranslations.tags[tagName]) { + var nextSibling = element.next(); + var fragments = Element._getContentFromAnonymousElement(tagName, content.stripScripts()); + parent.removeChild(element); + if (nextSibling) + fragments.each(function(node) { parent.insertBefore(node, nextSibling) }); + else + fragments.each(function(node) { parent.appendChild(node) }); + } + else element.outerHTML = content.stripScripts(); + + content.evalScripts.bind(content).defer(); + return element; + }; +} + +Element._returnOffset = function(l, t) { + var result = [l, t]; + result.left = l; + result.top = t; + return result; +}; + +Element._getContentFromAnonymousElement = function(tagName, html) { + var div = new Element('div'), t = Element._insertionTranslations.tags[tagName]; + if (t) { + div.innerHTML = t[0] + html + t[1]; + t[2].times(function() { div = div.firstChild }); + } else div.innerHTML = html; + return $A(div.childNodes); +}; + +Element._insertionTranslations = { + before: function(element, node) { + element.parentNode.insertBefore(node, element); + }, + top: function(element, node) { + element.insertBefore(node, element.firstChild); + }, + bottom: function(element, node) { + element.appendChild(node); + }, + after: function(element, node) { + element.parentNode.insertBefore(node, element.nextSibling); + }, + tags: { + TABLE: ['', '
    ', 1], + TBODY: ['', '
    ', 2], + TR: ['', '
    ', 3], + TD: ['
    ', '
    ', 4], + SELECT: ['', 1] + } +}; + +(function() { + Object.extend(this.tags, { + THEAD: this.tags.TBODY, + TFOOT: this.tags.TBODY, + TH: this.tags.TD + }); +}).call(Element._insertionTranslations); + +Element.Methods.Simulated = { + hasAttribute: function(element, attribute) { + attribute = Element._attributeTranslations.has[attribute] || attribute; + var node = $(element).getAttributeNode(attribute); + return !!(node && node.specified); + } +}; + +Element.Methods.ByTag = { }; + +Object.extend(Element, Element.Methods); + +if (!Prototype.BrowserFeatures.ElementExtensions && + document.createElement('div')['__proto__']) { + window.HTMLElement = { }; + window.HTMLElement.prototype = document.createElement('div')['__proto__']; + Prototype.BrowserFeatures.ElementExtensions = true; +} + +Element.extend = (function() { + if (Prototype.BrowserFeatures.SpecificElementExtensions) + return Prototype.K; + + var Methods = { }, ByTag = Element.Methods.ByTag; + + var extend = Object.extend(function(element) { + if (!element || element._extendedByPrototype || + element.nodeType != 1 || element == window) return element; + + var methods = Object.clone(Methods), + tagName = element.tagName.toUpperCase(), property, value; + + // extend methods for specific tags + if (ByTag[tagName]) Object.extend(methods, ByTag[tagName]); + + for (property in methods) { + value = methods[property]; + if (Object.isFunction(value) && !(property in element)) + element[property] = value.methodize(); + } + + element._extendedByPrototype = Prototype.emptyFunction; + return element; + + }, { + refresh: function() { + // extend methods for all tags (Safari doesn't need this) + if (!Prototype.BrowserFeatures.ElementExtensions) { + Object.extend(Methods, Element.Methods); + Object.extend(Methods, Element.Methods.Simulated); + } + } + }); + + extend.refresh(); + return extend; +})(); + +Element.hasAttribute = function(element, attribute) { + if (element.hasAttribute) return element.hasAttribute(attribute); + return Element.Methods.Simulated.hasAttribute(element, attribute); +}; + +Element.addMethods = function(methods) { + var F = Prototype.BrowserFeatures, T = Element.Methods.ByTag; + + if (!methods) { + Object.extend(Form, Form.Methods); + Object.extend(Form.Element, Form.Element.Methods); + Object.extend(Element.Methods.ByTag, { + "FORM": Object.clone(Form.Methods), + "INPUT": Object.clone(Form.Element.Methods), + "SELECT": Object.clone(Form.Element.Methods), + "TEXTAREA": Object.clone(Form.Element.Methods) + }); + } + + if (arguments.length == 2) { + var tagName = methods; + methods = arguments[1]; + } + + if (!tagName) Object.extend(Element.Methods, methods || { }); + else { + if (Object.isArray(tagName)) tagName.each(extend); + else extend(tagName); + } + + function extend(tagName) { + tagName = tagName.toUpperCase(); + if (!Element.Methods.ByTag[tagName]) + Element.Methods.ByTag[tagName] = { }; + Object.extend(Element.Methods.ByTag[tagName], methods); + } + + function copy(methods, destination, onlyIfAbsent) { + onlyIfAbsent = onlyIfAbsent || false; + for (var property in methods) { + var value = methods[property]; + if (!Object.isFunction(value)) continue; + if (!onlyIfAbsent || !(property in destination)) + destination[property] = value.methodize(); + } + } + + function findDOMClass(tagName) { + var klass; + var trans = { + "OPTGROUP": "OptGroup", "TEXTAREA": "TextArea", "P": "Paragraph", + "FIELDSET": "FieldSet", "UL": "UList", "OL": "OList", "DL": "DList", + "DIR": "Directory", "H1": "Heading", "H2": "Heading", "H3": "Heading", + "H4": "Heading", "H5": "Heading", "H6": "Heading", "Q": "Quote", + "INS": "Mod", "DEL": "Mod", "A": "Anchor", "IMG": "Image", "CAPTION": + "TableCaption", "COL": "TableCol", "COLGROUP": "TableCol", "THEAD": + "TableSection", "TFOOT": "TableSection", "TBODY": "TableSection", "TR": + "TableRow", "TH": "TableCell", "TD": "TableCell", "FRAMESET": + "FrameSet", "IFRAME": "IFrame" + }; + if (trans[tagName]) klass = 'HTML' + trans[tagName] + 'Element'; + if (window[klass]) return window[klass]; + klass = 'HTML' + tagName + 'Element'; + if (window[klass]) return window[klass]; + klass = 'HTML' + tagName.capitalize() + 'Element'; + if (window[klass]) return window[klass]; + + window[klass] = { }; + window[klass].prototype = document.createElement(tagName)['__proto__']; + return window[klass]; + } + + if (F.ElementExtensions) { + copy(Element.Methods, HTMLElement.prototype); + copy(Element.Methods.Simulated, HTMLElement.prototype, true); + } + + if (F.SpecificElementExtensions) { + for (var tag in Element.Methods.ByTag) { + var klass = findDOMClass(tag); + if (Object.isUndefined(klass)) continue; + copy(T[tag], klass.prototype); + } + } + + Object.extend(Element, Element.Methods); + delete Element.ByTag; + + if (Element.extend.refresh) Element.extend.refresh(); + Element.cache = { }; +}; + +document.viewport = { + getDimensions: function() { + var dimensions = { }, B = Prototype.Browser; + $w('width height').each(function(d) { + var D = d.capitalize(); + if (B.WebKit && !document.evaluate) { + // Safari <3.0 needs self.innerWidth/Height + dimensions[d] = self['inner' + D]; + } else if (B.Opera && parseFloat(window.opera.version()) < 9.5) { + // Opera <9.5 needs document.body.clientWidth/Height + dimensions[d] = document.body['client' + D] + } else { + dimensions[d] = document.documentElement['client' + D]; + } + }); + return dimensions; + }, + + getWidth: function() { + return this.getDimensions().width; + }, + + getHeight: function() { + return this.getDimensions().height; + }, + + getScrollOffsets: function() { + return Element._returnOffset( + window.pageXOffset || document.documentElement.scrollLeft || document.body.scrollLeft, + window.pageYOffset || document.documentElement.scrollTop || document.body.scrollTop); + } +}; +/* Portions of the Selector class are derived from Jack Slocum's DomQuery, + * part of YUI-Ext version 0.40, distributed under the terms of an MIT-style + * license. Please see http://www.yui-ext.com/ for more information. */ + +var Selector = Class.create({ + initialize: function(expression) { + this.expression = expression.strip(); + + if (this.shouldUseSelectorsAPI()) { + this.mode = 'selectorsAPI'; + } else if (this.shouldUseXPath()) { + this.mode = 'xpath'; + this.compileXPathMatcher(); + } else { + this.mode = "normal"; + this.compileMatcher(); + } + + }, + + shouldUseXPath: function() { + if (!Prototype.BrowserFeatures.XPath) return false; + + var e = this.expression; + + // Safari 3 chokes on :*-of-type and :empty + if (Prototype.Browser.WebKit && + (e.include("-of-type") || e.include(":empty"))) + return false; + + // XPath can't do namespaced attributes, nor can it read + // the "checked" property from DOM nodes + if ((/(\[[\w-]*?:|:checked)/).test(e)) + return false; + + return true; + }, + + shouldUseSelectorsAPI: function() { + if (!Prototype.BrowserFeatures.SelectorsAPI) return false; + + if (!Selector._div) Selector._div = new Element('div'); + + // Make sure the browser treats the selector as valid. Test on an + // isolated element to minimize cost of this check. + try { + Selector._div.querySelector(this.expression); + } catch(e) { + return false; + } + + return true; + }, + + compileMatcher: function() { + var e = this.expression, ps = Selector.patterns, h = Selector.handlers, + c = Selector.criteria, le, p, m; + + if (Selector._cache[e]) { + this.matcher = Selector._cache[e]; + return; + } + + this.matcher = ["this.matcher = function(root) {", + "var r = root, h = Selector.handlers, c = false, n;"]; + + while (e && le != e && (/\S/).test(e)) { + le = e; + for (var i in ps) { + p = ps[i]; + if (m = e.match(p)) { + this.matcher.push(Object.isFunction(c[i]) ? c[i](m) : + new Template(c[i]).evaluate(m)); + e = e.replace(m[0], ''); + break; + } + } + } + + this.matcher.push("return h.unique(n);\n}"); + eval(this.matcher.join('\n')); + Selector._cache[this.expression] = this.matcher; + }, + + compileXPathMatcher: function() { + var e = this.expression, ps = Selector.patterns, + x = Selector.xpath, le, m; + + if (Selector._cache[e]) { + this.xpath = Selector._cache[e]; return; + } + + this.matcher = ['.//*']; + while (e && le != e && (/\S/).test(e)) { + le = e; + for (var i in ps) { + if (m = e.match(ps[i])) { + this.matcher.push(Object.isFunction(x[i]) ? x[i](m) : + new Template(x[i]).evaluate(m)); + e = e.replace(m[0], ''); + break; + } + } + } + + this.xpath = this.matcher.join(''); + Selector._cache[this.expression] = this.xpath; + }, + + findElements: function(root) { + root = root || document; + var e = this.expression, results; + + switch (this.mode) { + case 'selectorsAPI': + // querySelectorAll queries document-wide, then filters to descendants + // of the context element. That's not what we want. + // Add an explicit context to the selector if necessary. + if (root !== document) { + var oldId = root.id, id = $(root).identify(); + e = "#" + id + " " + e; + } + + results = $A(root.querySelectorAll(e)).map(Element.extend); + root.id = oldId; + + return results; + case 'xpath': + return document._getElementsByXPath(this.xpath, root); + default: + return this.matcher(root); + } + }, + + match: function(element) { + this.tokens = []; + + var e = this.expression, ps = Selector.patterns, as = Selector.assertions; + var le, p, m; + + while (e && le !== e && (/\S/).test(e)) { + le = e; + for (var i in ps) { + p = ps[i]; + if (m = e.match(p)) { + // use the Selector.assertions methods unless the selector + // is too complex. + if (as[i]) { + this.tokens.push([i, Object.clone(m)]); + e = e.replace(m[0], ''); + } else { + // reluctantly do a document-wide search + // and look for a match in the array + return this.findElements(document).include(element); + } + } + } + } + + var match = true, name, matches; + for (var i = 0, token; token = this.tokens[i]; i++) { + name = token[0], matches = token[1]; + if (!Selector.assertions[name](element, matches)) { + match = false; break; + } + } + + return match; + }, + + toString: function() { + return this.expression; + }, + + inspect: function() { + return "#"; + } +}); + +Object.extend(Selector, { + _cache: { }, + + xpath: { + descendant: "//*", + child: "/*", + adjacent: "/following-sibling::*[1]", + laterSibling: '/following-sibling::*', + tagName: function(m) { + if (m[1] == '*') return ''; + return "[local-name()='" + m[1].toLowerCase() + + "' or local-name()='" + m[1].toUpperCase() + "']"; + }, + className: "[contains(concat(' ', @class, ' '), ' #{1} ')]", + id: "[@id='#{1}']", + attrPresence: function(m) { + m[1] = m[1].toLowerCase(); + return new Template("[@#{1}]").evaluate(m); + }, + attr: function(m) { + m[1] = m[1].toLowerCase(); + m[3] = m[5] || m[6]; + return new Template(Selector.xpath.operators[m[2]]).evaluate(m); + }, + pseudo: function(m) { + var h = Selector.xpath.pseudos[m[1]]; + if (!h) return ''; + if (Object.isFunction(h)) return h(m); + return new Template(Selector.xpath.pseudos[m[1]]).evaluate(m); + }, + operators: { + '=': "[@#{1}='#{3}']", + '!=': "[@#{1}!='#{3}']", + '^=': "[starts-with(@#{1}, '#{3}')]", + '$=': "[substring(@#{1}, (string-length(@#{1}) - string-length('#{3}') + 1))='#{3}']", + '*=': "[contains(@#{1}, '#{3}')]", + '~=': "[contains(concat(' ', @#{1}, ' '), ' #{3} ')]", + '|=': "[contains(concat('-', @#{1}, '-'), '-#{3}-')]" + }, + pseudos: { + 'first-child': '[not(preceding-sibling::*)]', + 'last-child': '[not(following-sibling::*)]', + 'only-child': '[not(preceding-sibling::* or following-sibling::*)]', + 'empty': "[count(*) = 0 and (count(text()) = 0)]", + 'checked': "[@checked]", + 'disabled': "[(@disabled) and (@type!='hidden')]", + 'enabled': "[not(@disabled) and (@type!='hidden')]", + 'not': function(m) { + var e = m[6], p = Selector.patterns, + x = Selector.xpath, le, v; + + var exclusion = []; + while (e && le != e && (/\S/).test(e)) { + le = e; + for (var i in p) { + if (m = e.match(p[i])) { + v = Object.isFunction(x[i]) ? x[i](m) : new Template(x[i]).evaluate(m); + exclusion.push("(" + v.substring(1, v.length - 1) + ")"); + e = e.replace(m[0], ''); + break; + } + } + } + return "[not(" + exclusion.join(" and ") + ")]"; + }, + 'nth-child': function(m) { + return Selector.xpath.pseudos.nth("(count(./preceding-sibling::*) + 1) ", m); + }, + 'nth-last-child': function(m) { + return Selector.xpath.pseudos.nth("(count(./following-sibling::*) + 1) ", m); + }, + 'nth-of-type': function(m) { + return Selector.xpath.pseudos.nth("position() ", m); + }, + 'nth-last-of-type': function(m) { + return Selector.xpath.pseudos.nth("(last() + 1 - position()) ", m); + }, + 'first-of-type': function(m) { + m[6] = "1"; return Selector.xpath.pseudos['nth-of-type'](m); + }, + 'last-of-type': function(m) { + m[6] = "1"; return Selector.xpath.pseudos['nth-last-of-type'](m); + }, + 'only-of-type': function(m) { + var p = Selector.xpath.pseudos; return p['first-of-type'](m) + p['last-of-type'](m); + }, + nth: function(fragment, m) { + var mm, formula = m[6], predicate; + if (formula == 'even') formula = '2n+0'; + if (formula == 'odd') formula = '2n+1'; + if (mm = formula.match(/^(\d+)$/)) // digit only + return '[' + fragment + "= " + mm[1] + ']'; + if (mm = formula.match(/^(-?\d*)?n(([+-])(\d+))?/)) { // an+b + if (mm[1] == "-") mm[1] = -1; + var a = mm[1] ? Number(mm[1]) : 1; + var b = mm[2] ? Number(mm[2]) : 0; + predicate = "[((#{fragment} - #{b}) mod #{a} = 0) and " + + "((#{fragment} - #{b}) div #{a} >= 0)]"; + return new Template(predicate).evaluate({ + fragment: fragment, a: a, b: b }); + } + } + } + }, + + criteria: { + tagName: 'n = h.tagName(n, r, "#{1}", c); c = false;', + className: 'n = h.className(n, r, "#{1}", c); c = false;', + id: 'n = h.id(n, r, "#{1}", c); c = false;', + attrPresence: 'n = h.attrPresence(n, r, "#{1}", c); c = false;', + attr: function(m) { + m[3] = (m[5] || m[6]); + return new Template('n = h.attr(n, r, "#{1}", "#{3}", "#{2}", c); c = false;').evaluate(m); + }, + pseudo: function(m) { + if (m[6]) m[6] = m[6].replace(/"/g, '\\"'); + return new Template('n = h.pseudo(n, "#{1}", "#{6}", r, c); c = false;').evaluate(m); + }, + descendant: 'c = "descendant";', + child: 'c = "child";', + adjacent: 'c = "adjacent";', + laterSibling: 'c = "laterSibling";' + }, + + patterns: { + // combinators must be listed first + // (and descendant needs to be last combinator) + laterSibling: /^\s*~\s*/, + child: /^\s*>\s*/, + adjacent: /^\s*\+\s*/, + descendant: /^\s/, + + // selectors follow + tagName: /^\s*(\*|[\w\-]+)(\b|$)?/, + id: /^#([\w\-\*]+)(\b|$)/, + className: /^\.([\w\-\*]+)(\b|$)/, + pseudo: +/^:((first|last|nth|nth-last|only)(-child|-of-type)|empty|checked|(en|dis)abled|not)(\((.*?)\))?(\b|$|(?=\s|[:+~>]))/, + attrPresence: /^\[((?:[\w]+:)?[\w]+)\]/, + attr: /\[((?:[\w-]*:)?[\w-]+)\s*(?:([!^$*~|]?=)\s*((['"])([^\4]*?)\4|([^'"][^\]]*?)))?\]/ + }, + + // for Selector.match and Element#match + assertions: { + tagName: function(element, matches) { + return matches[1].toUpperCase() == element.tagName.toUpperCase(); + }, + + className: function(element, matches) { + return Element.hasClassName(element, matches[1]); + }, + + id: function(element, matches) { + return element.id === matches[1]; + }, + + attrPresence: function(element, matches) { + return Element.hasAttribute(element, matches[1]); + }, + + attr: function(element, matches) { + var nodeValue = Element.readAttribute(element, matches[1]); + return nodeValue && Selector.operators[matches[2]](nodeValue, matches[5] || matches[6]); + } + }, + + handlers: { + // UTILITY FUNCTIONS + // joins two collections + concat: function(a, b) { + for (var i = 0, node; node = b[i]; i++) + a.push(node); + return a; + }, + + // marks an array of nodes for counting + mark: function(nodes) { + var _true = Prototype.emptyFunction; + for (var i = 0, node; node = nodes[i]; i++) + node._countedByPrototype = _true; + return nodes; + }, + + unmark: function(nodes) { + for (var i = 0, node; node = nodes[i]; i++) + node._countedByPrototype = undefined; + return nodes; + }, + + // mark each child node with its position (for nth calls) + // "ofType" flag indicates whether we're indexing for nth-of-type + // rather than nth-child + index: function(parentNode, reverse, ofType) { + parentNode._countedByPrototype = Prototype.emptyFunction; + if (reverse) { + for (var nodes = parentNode.childNodes, i = nodes.length - 1, j = 1; i >= 0; i--) { + var node = nodes[i]; + if (node.nodeType == 1 && (!ofType || node._countedByPrototype)) node.nodeIndex = j++; + } + } else { + for (var i = 0, j = 1, nodes = parentNode.childNodes; node = nodes[i]; i++) + if (node.nodeType == 1 && (!ofType || node._countedByPrototype)) node.nodeIndex = j++; + } + }, + + // filters out duplicates and extends all nodes + unique: function(nodes) { + if (nodes.length == 0) return nodes; + var results = [], n; + for (var i = 0, l = nodes.length; i < l; i++) + if (!(n = nodes[i])._countedByPrototype) { + n._countedByPrototype = Prototype.emptyFunction; + results.push(Element.extend(n)); + } + return Selector.handlers.unmark(results); + }, + + // COMBINATOR FUNCTIONS + descendant: function(nodes) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) + h.concat(results, node.getElementsByTagName('*')); + return results; + }, + + child: function(nodes) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) { + for (var j = 0, child; child = node.childNodes[j]; j++) + if (child.nodeType == 1 && child.tagName != '!') results.push(child); + } + return results; + }, + + adjacent: function(nodes) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + var next = this.nextElementSibling(node); + if (next) results.push(next); + } + return results; + }, + + laterSibling: function(nodes) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) + h.concat(results, Element.nextSiblings(node)); + return results; + }, + + nextElementSibling: function(node) { + while (node = node.nextSibling) + if (node.nodeType == 1) return node; + return null; + }, + + previousElementSibling: function(node) { + while (node = node.previousSibling) + if (node.nodeType == 1) return node; + return null; + }, + + // TOKEN FUNCTIONS + tagName: function(nodes, root, tagName, combinator) { + var uTagName = tagName.toUpperCase(); + var results = [], h = Selector.handlers; + if (nodes) { + if (combinator) { + // fastlane for ordinary descendant combinators + if (combinator == "descendant") { + for (var i = 0, node; node = nodes[i]; i++) + h.concat(results, node.getElementsByTagName(tagName)); + return results; + } else nodes = this[combinator](nodes); + if (tagName == "*") return nodes; + } + for (var i = 0, node; node = nodes[i]; i++) + if (node.tagName.toUpperCase() === uTagName) results.push(node); + return results; + } else return root.getElementsByTagName(tagName); + }, + + id: function(nodes, root, id, combinator) { + var targetNode = $(id), h = Selector.handlers; + if (!targetNode) return []; + if (!nodes && root == document) return [targetNode]; + if (nodes) { + if (combinator) { + if (combinator == 'child') { + for (var i = 0, node; node = nodes[i]; i++) + if (targetNode.parentNode == node) return [targetNode]; + } else if (combinator == 'descendant') { + for (var i = 0, node; node = nodes[i]; i++) + if (Element.descendantOf(targetNode, node)) return [targetNode]; + } else if (combinator == 'adjacent') { + for (var i = 0, node; node = nodes[i]; i++) + if (Selector.handlers.previousElementSibling(targetNode) == node) + return [targetNode]; + } else nodes = h[combinator](nodes); + } + for (var i = 0, node; node = nodes[i]; i++) + if (node == targetNode) return [targetNode]; + return []; + } + return (targetNode && Element.descendantOf(targetNode, root)) ? [targetNode] : []; + }, + + className: function(nodes, root, className, combinator) { + if (nodes && combinator) nodes = this[combinator](nodes); + return Selector.handlers.byClassName(nodes, root, className); + }, + + byClassName: function(nodes, root, className) { + if (!nodes) nodes = Selector.handlers.descendant([root]); + var needle = ' ' + className + ' '; + for (var i = 0, results = [], node, nodeClassName; node = nodes[i]; i++) { + nodeClassName = node.className; + if (nodeClassName.length == 0) continue; + if (nodeClassName == className || (' ' + nodeClassName + ' ').include(needle)) + results.push(node); + } + return results; + }, + + attrPresence: function(nodes, root, attr, combinator) { + if (!nodes) nodes = root.getElementsByTagName("*"); + if (nodes && combinator) nodes = this[combinator](nodes); + var results = []; + for (var i = 0, node; node = nodes[i]; i++) + if (Element.hasAttribute(node, attr)) results.push(node); + return results; + }, + + attr: function(nodes, root, attr, value, operator, combinator) { + if (!nodes) nodes = root.getElementsByTagName("*"); + if (nodes && combinator) nodes = this[combinator](nodes); + var handler = Selector.operators[operator], results = []; + for (var i = 0, node; node = nodes[i]; i++) { + var nodeValue = Element.readAttribute(node, attr); + if (nodeValue === null) continue; + if (handler(nodeValue, value)) results.push(node); + } + return results; + }, + + pseudo: function(nodes, name, value, root, combinator) { + if (nodes && combinator) nodes = this[combinator](nodes); + if (!nodes) nodes = root.getElementsByTagName("*"); + return Selector.pseudos[name](nodes, value, root); + } + }, + + pseudos: { + 'first-child': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + if (Selector.handlers.previousElementSibling(node)) continue; + results.push(node); + } + return results; + }, + 'last-child': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + if (Selector.handlers.nextElementSibling(node)) continue; + results.push(node); + } + return results; + }, + 'only-child': function(nodes, value, root) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (!h.previousElementSibling(node) && !h.nextElementSibling(node)) + results.push(node); + return results; + }, + 'nth-child': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root); + }, + 'nth-last-child': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root, true); + }, + 'nth-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root, false, true); + }, + 'nth-last-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root, true, true); + }, + 'first-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, "1", root, false, true); + }, + 'last-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, "1", root, true, true); + }, + 'only-of-type': function(nodes, formula, root) { + var p = Selector.pseudos; + return p['last-of-type'](p['first-of-type'](nodes, formula, root), formula, root); + }, + + // handles the an+b logic + getIndices: function(a, b, total) { + if (a == 0) return b > 0 ? [b] : []; + return $R(1, total).inject([], function(memo, i) { + if (0 == (i - b) % a && (i - b) / a >= 0) memo.push(i); + return memo; + }); + }, + + // handles nth(-last)-child, nth(-last)-of-type, and (first|last)-of-type + nth: function(nodes, formula, root, reverse, ofType) { + if (nodes.length == 0) return []; + if (formula == 'even') formula = '2n+0'; + if (formula == 'odd') formula = '2n+1'; + var h = Selector.handlers, results = [], indexed = [], m; + h.mark(nodes); + for (var i = 0, node; node = nodes[i]; i++) { + if (!node.parentNode._countedByPrototype) { + h.index(node.parentNode, reverse, ofType); + indexed.push(node.parentNode); + } + } + if (formula.match(/^\d+$/)) { // just a number + formula = Number(formula); + for (var i = 0, node; node = nodes[i]; i++) + if (node.nodeIndex == formula) results.push(node); + } else if (m = formula.match(/^(-?\d*)?n(([+-])(\d+))?/)) { // an+b + if (m[1] == "-") m[1] = -1; + var a = m[1] ? Number(m[1]) : 1; + var b = m[2] ? Number(m[2]) : 0; + var indices = Selector.pseudos.getIndices(a, b, nodes.length); + for (var i = 0, node, l = indices.length; node = nodes[i]; i++) { + for (var j = 0; j < l; j++) + if (node.nodeIndex == indices[j]) results.push(node); + } + } + h.unmark(nodes); + h.unmark(indexed); + return results; + }, + + 'empty': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + // IE treats comments as element nodes + if (node.tagName == '!' || node.firstChild) continue; + results.push(node); + } + return results; + }, + + 'not': function(nodes, selector, root) { + var h = Selector.handlers, selectorType, m; + var exclusions = new Selector(selector).findElements(root); + h.mark(exclusions); + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (!node._countedByPrototype) results.push(node); + h.unmark(exclusions); + return results; + }, + + 'enabled': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (!node.disabled && (!node.type || node.type !== 'hidden')) + results.push(node); + return results; + }, + + 'disabled': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (node.disabled) results.push(node); + return results; + }, + + 'checked': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (node.checked) results.push(node); + return results; + } + }, + + operators: { + '=': function(nv, v) { return nv == v; }, + '!=': function(nv, v) { return nv != v; }, + '^=': function(nv, v) { return nv == v || nv && nv.startsWith(v); }, + '$=': function(nv, v) { return nv == v || nv && nv.endsWith(v); }, + '*=': function(nv, v) { return nv == v || nv && nv.include(v); }, + '$=': function(nv, v) { return nv.endsWith(v); }, + '*=': function(nv, v) { return nv.include(v); }, + '~=': function(nv, v) { return (' ' + nv + ' ').include(' ' + v + ' '); }, + '|=': function(nv, v) { return ('-' + (nv || "").toUpperCase() + + '-').include('-' + (v || "").toUpperCase() + '-'); } + }, + + split: function(expression) { + var expressions = []; + expression.scan(/(([\w#:.~>+()\s-]+|\*|\[.*?\])+)\s*(,|$)/, function(m) { + expressions.push(m[1].strip()); + }); + return expressions; + }, + + matchElements: function(elements, expression) { + var matches = $$(expression), h = Selector.handlers; + h.mark(matches); + for (var i = 0, results = [], element; element = elements[i]; i++) + if (element._countedByPrototype) results.push(element); + h.unmark(matches); + return results; + }, + + findElement: function(elements, expression, index) { + if (Object.isNumber(expression)) { + index = expression; expression = false; + } + return Selector.matchElements(elements, expression || '*')[index || 0]; + }, + + findChildElements: function(element, expressions) { + expressions = Selector.split(expressions.join(',')); + var results = [], h = Selector.handlers; + for (var i = 0, l = expressions.length, selector; i < l; i++) { + selector = new Selector(expressions[i].strip()); + h.concat(results, selector.findElements(element)); + } + return (l > 1) ? h.unique(results) : results; + } +}); + +if (Prototype.Browser.IE) { + Object.extend(Selector.handlers, { + // IE returns comment nodes on getElementsByTagName("*"). + // Filter them out. + concat: function(a, b) { + for (var i = 0, node; node = b[i]; i++) + if (node.tagName !== "!") a.push(node); + return a; + }, + + // IE improperly serializes _countedByPrototype in (inner|outer)HTML. + unmark: function(nodes) { + for (var i = 0, node; node = nodes[i]; i++) + node.removeAttribute('_countedByPrototype'); + return nodes; + } + }); +} + +function $$() { + return Selector.findChildElements(document, $A(arguments)); +} +var Form = { + reset: function(form) { + $(form).reset(); + return form; + }, + + serializeElements: function(elements, options) { + if (typeof options != 'object') options = { hash: !!options }; + else if (Object.isUndefined(options.hash)) options.hash = true; + var key, value, submitted = false, submit = options.submit; + + var data = elements.inject({ }, function(result, element) { + if (!element.disabled && element.name) { + key = element.name; value = $(element).getValue(); + if (value != null && element.type != 'file' && (element.type != 'submit' || (!submitted && + submit !== false && (!submit || key == submit) && (submitted = true)))) { + if (key in result) { + // a key is already present; construct an array of values + if (!Object.isArray(result[key])) result[key] = [result[key]]; + result[key].push(value); + } + else result[key] = value; + } + } + return result; + }); + + return options.hash ? data : Object.toQueryString(data); + } +}; + +Form.Methods = { + serialize: function(form, options) { + return Form.serializeElements(Form.getElements(form), options); + }, + + getElements: function(form) { + return $A($(form).getElementsByTagName('*')).inject([], + function(elements, child) { + if (Form.Element.Serializers[child.tagName.toLowerCase()]) + elements.push(Element.extend(child)); + return elements; + } + ); + }, + + getInputs: function(form, typeName, name) { + form = $(form); + var inputs = form.getElementsByTagName('input'); + + if (!typeName && !name) return $A(inputs).map(Element.extend); + + for (var i = 0, matchingInputs = [], length = inputs.length; i < length; i++) { + var input = inputs[i]; + if ((typeName && input.type != typeName) || (name && input.name != name)) + continue; + matchingInputs.push(Element.extend(input)); + } + + return matchingInputs; + }, + + disable: function(form) { + form = $(form); + Form.getElements(form).invoke('disable'); + return form; + }, + + enable: function(form) { + form = $(form); + Form.getElements(form).invoke('enable'); + return form; + }, + + findFirstElement: function(form) { + var elements = $(form).getElements().findAll(function(element) { + return 'hidden' != element.type && !element.disabled; + }); + var firstByIndex = elements.findAll(function(element) { + return element.hasAttribute('tabIndex') && element.tabIndex >= 0; + }).sortBy(function(element) { return element.tabIndex }).first(); + + return firstByIndex ? firstByIndex : elements.find(function(element) { + return ['input', 'select', 'textarea'].include(element.tagName.toLowerCase()); + }); + }, + + focusFirstElement: function(form) { + form = $(form); + form.findFirstElement().activate(); + return form; + }, + + request: function(form, options) { + form = $(form), options = Object.clone(options || { }); + + var params = options.parameters, action = form.readAttribute('action') || ''; + if (action.blank()) action = window.location.href; + options.parameters = form.serialize(true); + + if (params) { + if (Object.isString(params)) params = params.toQueryParams(); + Object.extend(options.parameters, params); + } + + if (form.hasAttribute('method') && !options.method) + options.method = form.method; + + return new Ajax.Request(action, options); + } +}; + +/*--------------------------------------------------------------------------*/ + +Form.Element = { + focus: function(element) { + $(element).focus(); + return element; + }, + + select: function(element) { + $(element).select(); + return element; + } +}; + +Form.Element.Methods = { + serialize: function(element) { + element = $(element); + if (!element.disabled && element.name) { + var value = element.getValue(); + if (value != undefined) { + var pair = { }; + pair[element.name] = value; + return Object.toQueryString(pair); + } + } + return ''; + }, + + getValue: function(element) { + element = $(element); + var method = element.tagName.toLowerCase(); + return Form.Element.Serializers[method](element); + }, + + setValue: function(element, value) { + element = $(element); + var method = element.tagName.toLowerCase(); + Form.Element.Serializers[method](element, value); + return element; + }, + + clear: function(element) { + $(element).value = ''; + return element; + }, + + present: function(element) { + return $(element).value != ''; + }, + + activate: function(element) { + element = $(element); + try { + element.focus(); + if (element.select && (element.tagName.toLowerCase() != 'input' || + !['button', 'reset', 'submit'].include(element.type))) + element.select(); + } catch (e) { } + return element; + }, + + disable: function(element) { + element = $(element); + element.disabled = true; + return element; + }, + + enable: function(element) { + element = $(element); + element.disabled = false; + return element; + } +}; + +/*--------------------------------------------------------------------------*/ + +var Field = Form.Element; +var $F = Form.Element.Methods.getValue; + +/*--------------------------------------------------------------------------*/ + +Form.Element.Serializers = { + input: function(element, value) { + switch (element.type.toLowerCase()) { + case 'checkbox': + case 'radio': + return Form.Element.Serializers.inputSelector(element, value); + default: + return Form.Element.Serializers.textarea(element, value); + } + }, + + inputSelector: function(element, value) { + if (Object.isUndefined(value)) return element.checked ? element.value : null; + else element.checked = !!value; + }, + + textarea: function(element, value) { + if (Object.isUndefined(value)) return element.value; + else element.value = value; + }, + + select: function(element, value) { + if (Object.isUndefined(value)) + return this[element.type == 'select-one' ? + 'selectOne' : 'selectMany'](element); + else { + var opt, currentValue, single = !Object.isArray(value); + for (var i = 0, length = element.length; i < length; i++) { + opt = element.options[i]; + currentValue = this.optionValue(opt); + if (single) { + if (currentValue == value) { + opt.selected = true; + return; + } + } + else opt.selected = value.include(currentValue); + } + } + }, + + selectOne: function(element) { + var index = element.selectedIndex; + return index >= 0 ? this.optionValue(element.options[index]) : null; + }, + + selectMany: function(element) { + var values, length = element.length; + if (!length) return null; + + for (var i = 0, values = []; i < length; i++) { + var opt = element.options[i]; + if (opt.selected) values.push(this.optionValue(opt)); + } + return values; + }, + + optionValue: function(opt) { + // extend element because hasAttribute may not be native + return Element.extend(opt).hasAttribute('value') ? opt.value : opt.text; + } +}; + +/*--------------------------------------------------------------------------*/ + +Abstract.TimedObserver = Class.create(PeriodicalExecuter, { + initialize: function($super, element, frequency, callback) { + $super(callback, frequency); + this.element = $(element); + this.lastValue = this.getValue(); + }, + + execute: function() { + var value = this.getValue(); + if (Object.isString(this.lastValue) && Object.isString(value) ? + this.lastValue != value : String(this.lastValue) != String(value)) { + this.callback(this.element, value); + this.lastValue = value; + } + } +}); + +Form.Element.Observer = Class.create(Abstract.TimedObserver, { + getValue: function() { + return Form.Element.getValue(this.element); + } +}); + +Form.Observer = Class.create(Abstract.TimedObserver, { + getValue: function() { + return Form.serialize(this.element); + } +}); + +/*--------------------------------------------------------------------------*/ + +Abstract.EventObserver = Class.create({ + initialize: function(element, callback) { + this.element = $(element); + this.callback = callback; + + this.lastValue = this.getValue(); + if (this.element.tagName.toLowerCase() == 'form') + this.registerFormCallbacks(); + else + this.registerCallback(this.element); + }, + + onElementEvent: function() { + var value = this.getValue(); + if (this.lastValue != value) { + this.callback(this.element, value); + this.lastValue = value; + } + }, + + registerFormCallbacks: function() { + Form.getElements(this.element).each(this.registerCallback, this); + }, + + registerCallback: function(element) { + if (element.type) { + switch (element.type.toLowerCase()) { + case 'checkbox': + case 'radio': + Event.observe(element, 'click', this.onElementEvent.bind(this)); + break; + default: + Event.observe(element, 'change', this.onElementEvent.bind(this)); + break; + } + } + } +}); + +Form.Element.EventObserver = Class.create(Abstract.EventObserver, { + getValue: function() { + return Form.Element.getValue(this.element); + } +}); + +Form.EventObserver = Class.create(Abstract.EventObserver, { + getValue: function() { + return Form.serialize(this.element); + } +}); +if (!window.Event) var Event = { }; + +Object.extend(Event, { + KEY_BACKSPACE: 8, + KEY_TAB: 9, + KEY_RETURN: 13, + KEY_ESC: 27, + KEY_LEFT: 37, + KEY_UP: 38, + KEY_RIGHT: 39, + KEY_DOWN: 40, + KEY_DELETE: 46, + KEY_HOME: 36, + KEY_END: 35, + KEY_PAGEUP: 33, + KEY_PAGEDOWN: 34, + KEY_INSERT: 45, + + cache: { }, + + relatedTarget: function(event) { + var element; + switch(event.type) { + case 'mouseover': element = event.fromElement; break; + case 'mouseout': element = event.toElement; break; + default: return null; + } + return Element.extend(element); + } +}); + +Event.Methods = (function() { + var isButton; + + if (Prototype.Browser.IE) { + var buttonMap = { 0: 1, 1: 4, 2: 2 }; + isButton = function(event, code) { + return event.button == buttonMap[code]; + }; + + } else if (Prototype.Browser.WebKit) { + isButton = function(event, code) { + switch (code) { + case 0: return event.which == 1 && !event.metaKey; + case 1: return event.which == 1 && event.metaKey; + default: return false; + } + }; + + } else { + isButton = function(event, code) { + return event.which ? (event.which === code + 1) : (event.button === code); + }; + } + + return { + isLeftClick: function(event) { return isButton(event, 0) }, + isMiddleClick: function(event) { return isButton(event, 1) }, + isRightClick: function(event) { return isButton(event, 2) }, + + element: function(event) { + event = Event.extend(event); + + var node = event.target, + type = event.type, + currentTarget = event.currentTarget; + + if (currentTarget && currentTarget.tagName) { + // Firefox screws up the "click" event when moving between radio buttons + // via arrow keys. It also screws up the "load" and "error" events on images, + // reporting the document as the target instead of the original image. + if (type === 'load' || type === 'error' || + (type === 'click' && currentTarget.tagName.toLowerCase() === 'input' + && currentTarget.type === 'radio')) + node = currentTarget; + } + if (node.nodeType == Node.TEXT_NODE) node = node.parentNode; + return Element.extend(node); + }, + + findElement: function(event, expression) { + var element = Event.element(event); + if (!expression) return element; + var elements = [element].concat(element.ancestors()); + return Selector.findElement(elements, expression, 0); + }, + + pointer: function(event) { + var docElement = document.documentElement, + body = document.body || { scrollLeft: 0, scrollTop: 0 }; + return { + x: event.pageX || (event.clientX + + (docElement.scrollLeft || body.scrollLeft) - + (docElement.clientLeft || 0)), + y: event.pageY || (event.clientY + + (docElement.scrollTop || body.scrollTop) - + (docElement.clientTop || 0)) + }; + }, + + pointerX: function(event) { return Event.pointer(event).x }, + pointerY: function(event) { return Event.pointer(event).y }, + + stop: function(event) { + Event.extend(event); + event.preventDefault(); + event.stopPropagation(); + event.stopped = true; + } + }; +})(); + +Event.extend = (function() { + var methods = Object.keys(Event.Methods).inject({ }, function(m, name) { + m[name] = Event.Methods[name].methodize(); + return m; + }); + + if (Prototype.Browser.IE) { + Object.extend(methods, { + stopPropagation: function() { this.cancelBubble = true }, + preventDefault: function() { this.returnValue = false }, + inspect: function() { return "[object Event]" } + }); + + return function(event) { + if (!event) return false; + if (event._extendedByPrototype) return event; + + event._extendedByPrototype = Prototype.emptyFunction; + var pointer = Event.pointer(event); + Object.extend(event, { + target: event.srcElement, + relatedTarget: Event.relatedTarget(event), + pageX: pointer.x, + pageY: pointer.y + }); + return Object.extend(event, methods); + }; + + } else { + Event.prototype = Event.prototype || document.createEvent("HTMLEvents")['__proto__']; + Object.extend(Event.prototype, methods); + return Prototype.K; + } +})(); + +Object.extend(Event, (function() { + var cache = Event.cache; + + function getEventID(element) { + if (element._prototypeEventID) return element._prototypeEventID[0]; + arguments.callee.id = arguments.callee.id || 1; + return element._prototypeEventID = [++arguments.callee.id]; + } + + function getDOMEventName(eventName) { + if (eventName && eventName.include(':')) return "dataavailable"; + return eventName; + } + + function getCacheForID(id) { + return cache[id] = cache[id] || { }; + } + + function getWrappersForEventName(id, eventName) { + var c = getCacheForID(id); + return c[eventName] = c[eventName] || []; + } + + function createWrapper(element, eventName, handler) { + var id = getEventID(element); + var c = getWrappersForEventName(id, eventName); + if (c.pluck("handler").include(handler)) return false; + + var wrapper = function(event) { + if (!Event || !Event.extend || + (event.eventName && event.eventName != eventName)) + return false; + + Event.extend(event); + handler.call(element, event); + }; + + wrapper.handler = handler; + c.push(wrapper); + return wrapper; + } + + function findWrapper(id, eventName, handler) { + var c = getWrappersForEventName(id, eventName); + return c.find(function(wrapper) { return wrapper.handler == handler }); + } + + function destroyWrapper(id, eventName, handler) { + var c = getCacheForID(id); + if (!c[eventName]) return false; + c[eventName] = c[eventName].without(findWrapper(id, eventName, handler)); + } + + function destroyCache() { + for (var id in cache) + for (var eventName in cache[id]) + cache[id][eventName] = null; + } + + + // Internet Explorer needs to remove event handlers on page unload + // in order to avoid memory leaks. + if (window.attachEvent) { + window.attachEvent("onunload", destroyCache); + } + + // Safari has a dummy event handler on page unload so that it won't + // use its bfcache. Safari <= 3.1 has an issue with restoring the "document" + // object when page is returned to via the back button using its bfcache. + if (Prototype.Browser.WebKit) { + window.addEventListener('unload', Prototype.emptyFunction, false); + } + + return { + observe: function(element, eventName, handler) { + element = $(element); + var name = getDOMEventName(eventName); + + var wrapper = createWrapper(element, eventName, handler); + if (!wrapper) return element; + + if (element.addEventListener) { + element.addEventListener(name, wrapper, false); + } else { + element.attachEvent("on" + name, wrapper); + } + + return element; + }, + + stopObserving: function(element, eventName, handler) { + element = $(element); + var id = getEventID(element), name = getDOMEventName(eventName); + + if (!handler && eventName) { + getWrappersForEventName(id, eventName).each(function(wrapper) { + element.stopObserving(eventName, wrapper.handler); + }); + return element; + + } else if (!eventName) { + Object.keys(getCacheForID(id)).each(function(eventName) { + element.stopObserving(eventName); + }); + return element; + } + + var wrapper = findWrapper(id, eventName, handler); + if (!wrapper) return element; + + if (element.removeEventListener) { + element.removeEventListener(name, wrapper, false); + } else { + element.detachEvent("on" + name, wrapper); + } + + destroyWrapper(id, eventName, handler); + + return element; + }, + + fire: function(element, eventName, memo) { + element = $(element); + if (element == document && document.createEvent && !element.dispatchEvent) + element = document.documentElement; + + var event; + if (document.createEvent) { + event = document.createEvent("HTMLEvents"); + event.initEvent("dataavailable", true, true); + } else { + event = document.createEventObject(); + event.eventType = "ondataavailable"; + } + + event.eventName = eventName; + event.memo = memo || { }; + + if (document.createEvent) { + element.dispatchEvent(event); + } else { + element.fireEvent(event.eventType, event); + } + + return Event.extend(event); + } + }; +})()); + +Object.extend(Event, Event.Methods); + +Element.addMethods({ + fire: Event.fire, + observe: Event.observe, + stopObserving: Event.stopObserving +}); + +Object.extend(document, { + fire: Element.Methods.fire.methodize(), + observe: Element.Methods.observe.methodize(), + stopObserving: Element.Methods.stopObserving.methodize(), + loaded: false +}); + +(function() { + /* Support for the DOMContentLoaded event is based on work by Dan Webb, + Matthias Miller, Dean Edwards and John Resig. */ + + var timer; + + function fireContentLoadedEvent() { + if (document.loaded) return; + if (timer) window.clearInterval(timer); + document.fire("dom:loaded"); + document.loaded = true; + } + + if (document.addEventListener) { + if (Prototype.Browser.WebKit) { + timer = window.setInterval(function() { + if (/loaded|complete/.test(document.readyState)) + fireContentLoadedEvent(); + }, 0); + + Event.observe(window, "load", fireContentLoadedEvent); + + } else { + document.addEventListener("DOMContentLoaded", + fireContentLoadedEvent, false); + } + + } else { + document.write(" + + + +
    + + +
    + + +
    + +

    Authors

    +

    SVN soued.

    +

    Structure of the project

    +
    + + +
    +
    + + + + diff --git a/website/tests/Ant suite/Ant test.html b/website/tests/Ant suite/Ant test.html new file mode 100644 index 0000000..98af8e8 --- /dev/null +++ b/website/tests/Ant suite/Ant test.html @@ -0,0 +1,1621 @@ + + +TestNG: Ant test + + + + + + + + +

    Ant test

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:165/0/0
    Started on:Wed Feb 17 15:34:08 GMT 2010
    Total time:524 seconds (524407 ms)
    Included groups:
    Excluded groups:performance

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    marshallPreset
    Test class:Ant test    		compbio.metadata.PresetTester@50009f0d0
    readStatistics
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e1
    readStatistics
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a84160
    readStatistics
    Test class:Ant test    		compbio.runner.msa.MuscleTester@37b994de0
    readStatistics
    Test class:Ant test    		compbio.runner.msa.ProbconsTester@5a57e7870
    readStatistics
    Test class:Ant test    		compbio.runner.msa.TcoffeeTester@7df1bd980
    readStatisticsClusterExecution
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e8
    test
    Test class:Ant test    		compbio.engine.PulledFileCacheTester@1164b9b65
    testArguments
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba3
    testArguments
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722436
    testArguments
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a37
    testArguments
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc97662
    testArguments
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e678
    testAsyncCancelOperation
    Test class:Ant test    		compbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testAsyncRetrievOperation
    Test class:Ant test    		compbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testCache
    Test class:Ant test    		compbio.engine.FilePullerTester@5fa80aea6
    testCancel
    Test class:Ant test    		compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e181
    compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
+	at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
+	at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
+	at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
+	at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
+Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
+	at compbio.runner.Util.readClustalFile(Util.java:126)
+	at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
+	... 25 more
+... Removed 22 stack frames
    Click to show all stack frames +
    compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
+	at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
+	at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
+	at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
+	at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
+	at compbio.runner.Util.readClustalFile(Util.java:126)
+	at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
+	... 25 more
+
    testCancel
    Test class:Ant test    		compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac931
    testCancelCompletedTaskLocally
    Test class:Ant test    		compbio.engine.local.AsyncLocalRunnerTester@7461f5333
    testCancelCompletedTaskLocally
    Test class:Ant test    		compbio.engine.local.LocalRunnerTester@4b2922f60
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
+	at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
+	at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testCancelLocally
    Test class:Ant test    		compbio.engine.local.AsyncLocalRunnerTester@7461f5330
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
+	at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
+	at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testCancelLocally
    Test class:Ant test    		compbio.engine.local.LocalRunnerTester@4b2922f60
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
+	at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
+	at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testCleanSequence
    Test class:Ant test    		compbio.data.sequence.SequenceUtilTester@ad722000
    testClusterEngineConf
    Test class:Ant test    		compbio.engine.conf.PropertyHelperManagerTester@307bd0d0
    testClusterExecute
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a841611
    testClusterExecute
    Test class:Ant test    		compbio.runner.msa.ProbconsTester@5a57e78719
    testClusterExecute
    Test class:Ant test    		compbio.runner.msa.TcoffeeTester@7df1bd985
    testCommandBuilding
    Test class:Ant test    		compbio.engine.client.CommandBuilderTester@6bdc64a50
    testConfiguration
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba0
    testConfiguration
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722430
    testConfiguration
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a30
    testConfiguration
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc97660
    testConfiguration
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e670
    testConfigurationLoading
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e0
    testConfigurationLoading
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a84160
    testConfigurationLoading
    Test class:Ant test    		compbio.runner.msa.MuscleTester@37b994de0
    testConfigurationLoading
    Test class:Ant test    		compbio.runner.msa.ProbconsTester@5a57e7870
    testConfigurationLoading
    Test class:Ant test    		compbio.runner.msa.TcoffeeTester@7df1bd980
    testConstrainedParametersMaxValues
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba1
    testConstrainedParametersMaxValues
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722433
    testConstrainedParametersMaxValues
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a31
    testConstrainedParametersMaxValues
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc976638
    testConstrainedParametersMaxValues
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e6711
    testConstrainedParametersMinValues
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba1
    testConstrainedParametersMinValues
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722431
    testConstrainedParametersMinValues
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a30
    testConstrainedParametersMinValues
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc97660
    testConstrainedParametersMinValues
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e675
    testConstrainedParametersRandomValues
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba3
    testConstrainedParametersRandomValues
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722437
    testConstrainedParametersRandomValues
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a37
    testConstrainedParametersRandomValues
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc976661
    testConstrainedParametersRandomValues
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e6721
    testCreateNumParameterWithoutValidValue
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
+Description: DNA weight matrix
+URL: null
+Is required: false
+
+ Without possible values! Please define possible value first!
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
+	at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
+Description: DNA weight matrix
+URL: null
+Is required: false
+
+ Without possible values! Please define possible value first!
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
+	at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testCreateParameter
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+POSSIBLE VALUES:
+BLOSUM
+GONNET
+ID
+PAM
+
+
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
+	at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
+... Removed 22 stack frames
    Click to show all stack frames +
    compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+POSSIBLE VALUES:
+BLOSUM
+GONNET
+ID
+PAM
+
+
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
+	at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testCreateParameterWithValidValueConstrain
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    testDeepCleanSequence
    Test class:Ant test    		compbio.data.sequence.SequenceUtilTester@ad722000
    testDefaultParameters
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba0
    testDefaultParameters
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc7224320
    testDefaultParameters
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a30
    testDefaultParameters
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc976614
    testDefaultParameters
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e6710
    testExecute
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a84160
    testExecute
    Test class:Ant test    		compbio.runner.msa.ProbconsTester@5a57e7870
    testExecute
    Test class:Ant test    		compbio.runner.msa.TcoffeeTester@7df1bd980
    testGet
    Test class:Ant test    		compbio.engine.FilePullerTester@5fa80aea0
    testGetAsyncEngine
    Test class:Ant test    		compbio.engine.EngineConfiguratorTester@31f9338f0
    testGetClassPath
    Test class:Ant test    		compbio.engine.client.PathValidatorTester@5253c3f50
    testGetDelay
    Test class:Ant test    		compbio.engine.FilePullerTester@5fa80aea0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@1c1474ea0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@1c1474ea0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@1c1474ea0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@1c1474ea0
    testGetFormattedFasta
    Test class:Ant test    		compbio.data.sequence.FastaSequenceTester@ec0a9f90
    testGetJobStatus
    Test class:Ant test    		compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e1820
    testGetStatuscompbio.engine.local.AsyncLocalRunnerTester@7461f53320
    testGetStatuscompbio.engine.local.AsyncLocalRunnerTester@7461f53320
    testGetStatuscompbio.engine.local.AsyncLocalRunnerTester@7461f53321
    testGetStatuscompbio.engine.local.AsyncLocalRunnerTester@7461f53340
    testGetStatuscompbio.engine.local.AsyncLocalRunnerTester@7461f53320
    testGetSyncEngine
    Test class:Ant test    		compbio.engine.EngineConfiguratorTester@31f9338f0
    testGetTestArgsCommand
    Test class:Ant test    		compbio.runner._impl.OBTester@327124af0
    testGetTestArgsCommand
    Test class:Ant test    		compbio.runner._impl.RPSBlastTester@221f77080
    testGetTestCommand
    Test class:Ant test    		compbio.runner._impl.MclTester@4402a6ff0
    testGetTestCommand
    Test class:Ant test    		compbio.runner._impl.NetNglycTester@a21d23b0
    testGetTestCommand
    Test class:Ant test    		compbio.runner._impl.OBTester@327124af0
    testGetTestCommand
    Test class:Ant test    		compbio.runner._impl.RPSBlastTester@221f77080
    testGetTestCommand
    Test class:Ant test    		compbio.runner._impl.RonnTester@3fbfbfb80
    testGetTestCommand
    Test class:Ant test    		compbio.runner._impl.Tmhmm2Tester@45c3e9ba0
    testIsAbsolutePath
    Test class:Ant test    		compbio.engine.client.PathValidatorTester@5253c3f50
    testLoadLimits
    Test class:Ant test    		compbio.runner.msa.LimitTester@1b0c6cfc0
    testMarshalling
    Test class:Ant test    		compbio.engine.conf.RunnerConfigMarshallerTester@710ca2080
    testMarshalling
    Test class:Ant test    		compbio.metadata.OptionMarshallerTester@372c95570
    javax.xml.bind.MarshalException
+ - with linked exception:
+[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
+	at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
+	at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
+	at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
+Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
+	at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
+	at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
+	at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
+	at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
+	at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
+	... 26 more
+... Removed 22 stack frames
    Click to show all stack frames +
    javax.xml.bind.MarshalException
+ - with linked exception:
+[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
+	at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
+	at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
+	at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
+	at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
+	at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
+	at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
+	at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
+	at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
+	... 26 more
+
    testMultipleCancelLocally
    Test class:Ant test    		compbio.engine.local.AsyncLocalRunnerTester@7461f5330
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
+	at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
+	at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testMultipleCancelLocally
    Test class:Ant test    		compbio.engine.local.LocalRunnerTester@4b2922f60
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
+	at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.util.concurrent.CancellationException
+	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
+	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
+	at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
+	at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
+	at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testNcore
    Test class:Ant test    		compbio.runner.msa.TcoffeeTester@7df1bd980
    testOptionNoDefaultValidate
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+--ABMAT
+--BBBB
+
+	at compbio.metadata.Option.validate(Option.java:317)
+	at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
+... Removed 22 stack frames
    Click to show all stack frames +
    javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+--ABMAT
+--BBBB
+
+	at compbio.metadata.Option.validate(Option.java:317)
+	at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testOptionSetInvalidValue
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+--ABMAT
+--BBBB
+
+	at compbio.metadata.Option.setDefaultValue(Option.java:130)
+	at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
+... Removed 22 stack frames
    Click to show all stack frames +
    compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+--ABMAT
+--BBBB
+
+	at compbio.metadata.Option.setDefaultValue(Option.java:130)
+	at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testOptionToCommand
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    testOptions
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba2
    testOptions
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722434
    testOptions
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a32
    testOptions
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc97660
    testOptions
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e670
    testOptionsLocally
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e1
    testOptionsToCommand
    Test class:Ant test    		compbio.engine.client.CommandBuilderTester@6bdc64a50
    testParameterToCommand
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    testParameters
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba2
    testParameters
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722432
    testParameters
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a34
    testParameters
    Test class:Ant test    		compbio.runner.msa.ProbconsParametersTester@78dc97661
    testParameters
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e6712
    testParser
    Test class:Ant test    		compbio.engine.cluster.drmaa.UtilTester@22e909430
    testPersistance
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e0
    testPersistance
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a84161
    testPersistance
    Test class:Ant test    		compbio.runner.msa.MuscleTester@37b994de0
    testPersistance
    Test class:Ant test    		compbio.runner.msa.ProbconsTester@5a57e7870
    testPersistance
    Test class:Ant test    		compbio.runner.msa.TcoffeeTester@7df1bd981
    testPresets
    Test class:Ant test    		compbio.runner.msa.ClustalWParametersTester@132803ba0
    testPresets
    Test class:Ant test    		compbio.runner.msa.MafftParametersTester@4cc722432
    testPresets
    Test class:Ant test    		compbio.runner.msa.MuscleParametersTester@4355d3a30
    testPresets
    Test class:Ant test    		compbio.runner.msa.TcoffeeParametersTester@41217e671
    testProteinSequenceGeneration
    Test class:Ant test    		compbio.data.sequence.FastaSequenceGeneratorTester@163b4b1e0
    testPull
    Test class:Ant test    		compbio.engine.FilePullerTester@5fa80aea0
    testQueue
    Test class:Ant test    		compbio.engine.cluster.dundee._QueueTester@715f1f9c0
    testReadClustalFile
    Test class:Ant test    		compbio.data.sequence.ClustalAlignmentUtilTester@38c522000
    testReadClustalFileLongNames
    Test class:Ant test    		compbio.data.sequence.ClustalAlignmentUtilTester@38c522000
    testReadClustalFileShortNames
    Test class:Ant test    		compbio.data.sequence.ClustalAlignmentUtilTester@38c522000
    testReadWriteFasta
    Test class:Ant test    		compbio.data.sequence.SequenceUtilTester@ad722000
    testRunLocally
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e0
    testRunLocally
    Test class:Ant test    		compbio.runner.msa.MuscleTester@37b994de0
    testRunOnCluster
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e15
    testRunOnCluster
    Test class:Ant test    		compbio.runner.msa.MuscleTester@37b994de8
    testRunOnClusterAsyncCheckStatusLongPoolingTime
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a841621
    testRunWithMatrix
    Test class:Ant test    		compbio.runner.msa.ClustalWTester@4125d61e0
    testSchemaFromCodeGeneration
    Test class:Ant test    		compbio.engine.conf.RunnerConfigMarshallerTester@710ca2080
    testSetInputTester
    Test class:Ant test    		compbio.runner.msa.MafftTester@259a84160
    testSetInputTester
    Test class:Ant test    		compbio.runner.msa.ProbconsTester@5a57e7870
    testSpaceDelimiterExecutable
    Test class:Ant test    		compbio.engine.client.CommandBuilderTester@6bdc64a50
    testSubmit
    Test class:Ant test    		compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e1818
    testSubmit
    Test class:Ant test    		compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac9317
    testSubmitLocallycompbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testSubmitLocallycompbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testSubmitLocallycompbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testSubmitLocallycompbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testSubmitLocallycompbio.engine.local.AsyncLocalRunnerTester@7461f5330
    testTaskList
    Test class:Ant test    		compbio.engine.cluster.drmaa.ClusterSessionTester@7966340c8
    testUnMarshalling
    Test class:Ant test    		compbio.engine.conf.RunnerConfigMarshallerTester@710ca2080
    testUnMarshalling
    Test class:Ant test    		compbio.metadata.OptionMarshallerTester@372c95570
    testValidate
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    testValidateBoundaryConstrainCheck
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    testValidateLowerBoundaryConstrainCheck
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
+Min: -10.12
+Max: 0
+
+ For parameter: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+Type: Float
+Min: -10.12
+Max: 0
+
+
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
+	at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
+... Removed 22 stack frames
    Click to show all stack frames +
    compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
+Min: -10.12
+Max: 0
+
+ For parameter: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+Type: Float
+Min: -10.12
+Max: 0
+
+
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
+	at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testValidateUpperBoundaryConstrainCheck
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
+Min: -10.12
+Max: 0
+
+ For parameter: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+Type: Float
+Min: -10.12
+Max: 0
+
+
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
+	at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
+... Removed 22 stack frames
    Click to show all stack frames +
    compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
+Min: -10.12
+Max: 0
+
+ For parameter: Option name: Matrix1
+Description: Protein weight matrix
+URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
+Is required: true
+Option Names: 
+--AAMATRIX
+Type: Float
+Min: -10.12
+Max: 0
+
+
+	at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
+	at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testValidateValueConstrain
    Test class:Ant test    		compbio.metadata.RunnerConfigTester@58ca37830
    javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
+
+	at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
+	at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
+... Removed 22 stack frames
    Click to show all stack frames +
    javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
+
+	at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
+	at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testValidation
    Test class:Ant test    		compbio.engine.conf.RunnerConfigMarshallerTester@710ca2080
    testValidationOnMarshalling
    Test class:Ant test    		compbio.engine.conf.RunnerConfigMarshallerTester@710ca2080
    javax.xml.bind.MarshalException
+ - with linked exception:
+[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
+	at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
+	at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
+	at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
+Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
+	at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
+	at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
+	at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
+	at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
+	at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
+	... 26 more
+... Removed 22 stack frames
    Click to show all stack frames +
    javax.xml.bind.MarshalException
+ - with linked exception:
+[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
+	at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
+	at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
+	at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
+	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
+	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
+	at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
+	at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
+	at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
+	at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
+	at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
+	at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
+	at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
+	at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
+	at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
+	at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
+	... 26 more
+
    testgetAllOptions
    Test class:Ant test    		compbio.metadata.OptionCombinatorTester@79b66b060
    testgetAllParameters
    Test class:Ant test    		compbio.metadata.OptionCombinatorTester@79b66b060
    testisNonAmbNucleotideSequence
    Test class:Ant test    		compbio.data.sequence.SequenceUtilTester@ad722000
    testisProteinSequence
    Test class:Ant test    		compbio.data.sequence.SequenceUtilTester@ad722000
    validateClustalConfiguration
    Test class:Ant test    		compbio.engine.conf.PropertyHelperManagerTester@307bd0d0
    validateMafftConfiguration
    Test class:Ant test    		compbio.engine.conf.PropertyHelperManagerTester@307bd0d0
    validateMuscleConfiguration
    Test class:Ant test    		compbio.engine.conf.PropertyHelperManagerTester@307bd0d0
    validatePresets
    Test class:Ant test    		compbio.metadata.PresetTester@50009f0d0
    validateTcoffeeConfiguration
    Test class:Ant test    		compbio.engine.conf.PropertyHelperManagerTester@307bd0d0

    + + \ No newline at end of file diff --git a/website/tests/Ant suite/Ant test.properties b/website/tests/Ant suite/Ant test.properties new file mode 100644 index 0000000..688741c --- /dev/null +++ b/website/tests/Ant suite/Ant test.properties @@ -0,0 +1 @@ +[SuiteResult Ant test] \ No newline at end of file diff --git a/website/tests/Ant suite/Ant test.xml b/website/tests/Ant suite/Ant test.xml new file mode 100644 index 0000000..7af5c76 --- /dev/null +++ b/website/tests/Ant suite/Ant test.xml @@ -0,0 +1,169 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/tests/Ant suite/classes.html b/website/tests/Ant suite/classes.html new file mode 100644 index 0000000..34aa37e --- /dev/null +++ b/website/tests/Ant suite/classes.html @@ -0,0 +1,1550 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Class nameMethod nameGroups
    compbio.engine.client.CommandBuilderTester  
    @Test
     testOptionsToCommand 
     testSpaceDelimiterExecutable 
     testCommandBuilding 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.metadata.RunnerConfigTester  
    @Test
     testValidateUpperBoundaryConstrainCheck 
     testOptionSetInvalidValue 
     testValidateBoundaryConstrainCheck 
     testValidateValueConstrain 
     testCreateParameterWithValidValueConstrain 
     testValidateLowerBoundaryConstrainCheck 
     testOptionNoDefaultValidate 
     testCreateParameter 
     testOptionToCommand 
     testParameterToCommand 
     testCreateNumParameterWithoutValidValue 
     testValidate 
    @BeforeClass
    @BeforeMethod
     setup 
    @AfterMethod
    @AfterClass
    compbio.runner._impl.NetNglycTester  
    @Test
     testGetTestCommand 
     testBuildCommandcluster runner
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner.msa.MafftParametersTester  
    @Test
     testConstrainedParametersMaxValuesrunner non_windows
     testConstrainedParametersRandomValuesrunner non_windows
     testConstrainedParametersMinValuesrunner non_windows
     testArgumentsrunner non_windows
     testOptionsrunner non_windows
     testDefaultParametersrunner non_windows
     testParametersrunner non_windows
     testPresetsrunner non_windows
     testConfiguration 
    @BeforeClass
    @BeforeMethod
     setuprunner non_windows
    @AfterMethod
    @AfterClass
    compbio.engine.EngineConfiguratorTester  
    @Test
     testGetAsyncEngine 
     testGetSyncEngine 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner._impl.RonnTester  
    @Test
     testGetTestCommand 
     testBuildCommandcluster runner
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner.msa.ProbconsTester  
    @Test
     testExecuterunner non_windows
     testPersistancerunner non_windows
     testClusterExecutecluster runner non_windows
     testSetInputTesterrunner non_windows
     testConfigurationLoadingrunner
     readStatisticsrunner non_windows
    @BeforeClass
    @BeforeMethod
     initcluster runner non_windows
    @AfterMethod
    @AfterClass
    compbio.engine.conf.PropertyHelperManagerTester  
    @Test
     testClusterEngineConfcluster
     validateClustalConfiguration 
     validateTcoffeeConfiguration 
     validateMuscleConfiguration 
     validateMafftConfiguration 
    @BeforeClass
     testLoadResources 
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.FilePullerTester  
    @Test
     testGet 
     testCacheengine
     testGetDelayengine
     testPullengine
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.metadata.OptionCombinatorTester  
    @Test
     testgetAllParameters 
     testgetAllOptions 
    @BeforeClass
    @BeforeMethod
     setup 
    @AfterMethod
    @AfterClass
    compbio.runner.msa.MuscleTester  
    @Test
     testRunOnClustercluster runner
     testRunOnClusterAsynccluster runner
     testPersistancerunner
     testConfigurationLoadingrunner
     readStatisticsrunner
     testRunLocallyrunner
    @BeforeClass
    @BeforeMethod
     init 
    @AfterMethod
    @AfterClass
    compbio.runner.msa.TcoffeeTester  
    @Test
     testExecuterunner non_windows
     testPersistancecluster runner non_windows
     testNcorerunner non_windows
     testClusterExecutecluster runner non_windows
     testConfigurationLoadingrunner
     readStatisticsrunner non_windows
    @BeforeClass
    @BeforeMethod
     initcluster runner non_windows
    @AfterMethod
    @AfterClass
    compbio.runner.msa.LimitTester  
    @Test
     testLoadLimits 
    @BeforeClass
    @BeforeMethod
     setuprunner
    @AfterMethod
    @AfterClass
    compbio.runner._impl.OBTester  
    @Test
     testGetTestCommand 
     testBuildCommandcluster runner
     testGetTestArgsCommand 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.local.AsyncLocalRunnerTester  
    @Test
     testCancelLocallyengine
     testMultipleCancelLocallyengine
     testAsyncCancelOperationengine
     testAsyncRetrievOperationengine
     testSubmitLocallyengine
     testCancelCompletedTaskLocallyengine
     testGetStatusengine
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.local.LocalRunnerTester  
    @Test
     testCancelLocallyengine
     testMultipleCancelLocallyengine
     testCancelCompletedTaskLocallyengine
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner._impl.Tmhmm2Tester  
    @Test
     testGetTestCommand 
     testBuildCommandcluster runner
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner.msa.MafftTester  
    @Test
     testExecuterunner non_windows
     testRunOnClusterAsyncCheckStatusShortPoolingTimecluster runner non_windows
     testPersistancerunner non_windows
     testClusterExecutecluster runner non_windows
     testSetInputTesterrunner non_windows
     testConfigurationLoadingrunner
     readStatisticsrunner non_windows
     testRunOnClusterAsyncCheckStatusLongPoolingTimecluster runner non_windows
    @BeforeClass
    @BeforeMethod
     initcluster runner non_windows
    @AfterMethod
    @AfterClass
    compbio.data.sequence.ClustalAlignmentUtilTester  
    @Test
     testReadClustalFile 
     testReadClustalFileLongNames 
     testReadClustalFileShortNames 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner.msa.MuscleParametersTester  
    @Test
     testConstrainedParametersMaxValuesrunner
     testConstrainedParametersRandomValuesrunner
     testConstrainedParametersMinValuesrunner
     testArgumentsrunner
     testOptionsrunner
     testDefaultParametersrunner
     testParametersrunner
     testPresetsrunner
     testConfiguration 
    @BeforeClass
    @BeforeMethod
     setuprunner
    @AfterMethod
    @AfterClass
    compbio.data.sequence.FastaSequenceGeneratorTester  
    @Test
     testProteinSequenceGeneration 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.cluster.drmaa.ClusterSessionTester  
    @Test
     testTaskListengine cluster
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.data.sequence.FastaSequenceTester  
    @Test
     testGetFormattedFasta 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.client.PathValidatorTester  
    @Test
     testIsAbsolutePath 
     testGetClassPath 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.data.sequence.SequenceUtilTester  
    @Test
     testDeepCleanSequence 
     testReadWriteFasta 
     testisNonAmbNucleotideSequence 
     testisProteinSequence 
     testCleanSequence 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner.msa.TcoffeeParametersTester  
    @Test
     testConstrainedParametersMaxValuesrunner non_windows
     testConstrainedParametersRandomValuesrunner non_windows
     testConstrainedParametersMinValuesrunner non_windows
     testArgumentsrunner non_windows
     testOptionsrunner non_windows
     testDefaultParametersrunner non_windows
     testParametersrunner non_windows
     testPresetsrunner non_windows
     testConfiguration 
    @BeforeClass
    @BeforeMethod
     setuprunner non_windows
    @AfterMethod
    @AfterClass
    compbio.runner.msa.ClustalWTester  
    @Test
     testRunOnClustercluster runner
     testPersistancerunner
     testAddParameters 
     testOptionsLocallyrunner
     readStatisticsClusterExecutioncluster runner
     testConfigurationLoadingrunner
     testRunWithMatrixrunner
     readStatisticsrunner
     testRunLocallyrunner
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.cluster.drmaa.UtilTester  
    @Test
     testParser 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.conf.DirectoryManagerTester  
    @Test
     testGetDirectory 
     testNanoTime 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester  
    @Test
     testSubmitengine cluster
     testCancelengine cluster
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester  
    @Test
     testSubmitengine cluster
     testCancelengine cluster
     testGetJobStatusengine cluster
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.metadata.PresetTester  
    @Test
     marshallPreset 
     validatePresets 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.metadata.OptionMarshallerTester  
    @Test
     testUnMarshalling 
     testMarshalling 
    @BeforeClass
    @BeforeMethod
     setup 
    @AfterMethod
    @AfterClass
    compbio.runner.msa.ClustalWParametersTester  
    @Test
     testConstrainedParametersMaxValuesrunner
     testConstrainedParametersRandomValuesrunner
     testConstrainedParametersMinValuesrunner
     testArgumentsrunner
     testOptionsrunner
     testDefaultParametersrunner
     testParametersrunner
     testPresetsrunner
     testConfiguration 
    @BeforeClass
    @BeforeMethod
     setuprunner
    @AfterMethod
    @AfterClass
    compbio.runner._impl.RPSBlastTester  
    @Test
     testGetTestCommand 
     testBuildCommandcluster runner
     testGetTestArgsCommand 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.PulledFileCacheTester  
    @Test
     test 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner._impl.MclTester  
    @Test
     testGetTestCommand 
     testBuildCommandcluster runner
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.engine.cluster.dundee._QueueTester  
    @Test
     testQueue 
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    compbio.runner.msa.ProbconsParametersTester  
    @Test
     testConstrainedParametersMaxValuesrunner non_windows
     testConstrainedParametersRandomValuesrunner non_windows
     testConstrainedParametersMinValuesrunner non_windows
     testArgumentsrunner non_windows
     testOptionsrunner non_windows
     testDefaultParametersrunner non_windows
     testParametersrunner non_windows
     testConfiguration 
    @BeforeClass
    @BeforeMethod
     setuprunner non_windows
    @AfterMethod
    @AfterClass
    compbio.engine.conf.RunnerConfigMarshallerTester  
    @Test
     testValidationOnMarshalling 
     testUnMarshalling 
     testValidation 
     testSchemaFromCodeGeneration 
     testMarshalling 
    @BeforeClass
    @BeforeMethod
     setup 
    @AfterMethod
    @AfterClass
    diff --git a/website/tests/Ant suite/groups.html b/website/tests/Ant suite/groups.html new file mode 100644 index 0000000..de93281 --- /dev/null +++ b/website/tests/Ant suite/groups.html @@ -0,0 +1,6 @@ +

    Groups used for this test run

    + + + + +
    Group nameMethods
    clustercompbio.runner.msa.TcoffeeTester.testPersistance()
    compbio.runner.msa.ProbconsTester.testClusterExecute()
    compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()
    compbio.runner.msa.ClustalWTester.testRunOnCluster()
    compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()
    compbio.runner.msa.MuscleTester.testRunOnCluster()
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()
    compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()
    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()
    compbio.runner.msa.MafftTester.testClusterExecute()
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()
    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()
    compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()
    compbio.runner.msa.TcoffeeTester.testClusterExecute()
    enginecompbio.engine.local.AsyncLocalRunnerTester.testGetStatus()
    compbio.engine.local.LocalRunnerTester.testCancelLocally()
    compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()
    compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()
    compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()
    compbio.engine.FilePullerTester.testCache()
    compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()
    compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()
    compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()
    compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()
    compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()
    compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()
    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()
    compbio.engine.FilePullerTester.testGetDelay()
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()
    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()
    compbio.engine.FilePullerTester.testPull()
    non_windowscompbio.runner.msa.MafftTester.readStatistics()
    compbio.runner.msa.MafftParametersTester.testParameters()
    compbio.runner.msa.MafftParametersTester.testDefaultParameters()
    compbio.runner.msa.TcoffeeTester.testExecute()
    compbio.runner.msa.MafftParametersTester.testPresets()
    compbio.runner.msa.MafftTester.testSetInputTester()
    compbio.runner.msa.ProbconsParametersTester.testArguments()
    compbio.runner.msa.TcoffeeTester.readStatistics()
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.MafftTester.testExecute()
    compbio.runner.msa.ProbconsTester.readStatistics()
    compbio.runner.msa.TcoffeeParametersTester.testArguments()
    compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()
    compbio.runner.msa.TcoffeeTester.testNcore()
    compbio.runner.msa.MafftParametersTester.testOptions()
    compbio.runner.msa.ProbconsTester.testSetInputTester()
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.ProbconsTester.testExecute()
    compbio.runner.msa.TcoffeeParametersTester.testParameters()
    compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()
    compbio.runner.msa.TcoffeeTester.testPersistance()
    compbio.runner.msa.ProbconsParametersTester.testOptions()
    compbio.runner.msa.ProbconsTester.testClusterExecute()
    compbio.runner.msa.TcoffeeParametersTester.testPresets()
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.MafftTester.testPersistance()
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.MafftParametersTester.testArguments()
    compbio.runner.msa.TcoffeeParametersTester.testOptions()
    compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()
    compbio.runner.msa.ProbconsParametersTester.testParameters()
    compbio.runner.msa.MafftTester.testClusterExecute()
    compbio.runner.msa.ProbconsTester.testPersistance()
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.TcoffeeTester.testClusterExecute()
    runnercompbio.runner.msa.ClustalWTester.testConfigurationLoading()
    compbio.runner.msa.MafftTester.readStatistics()
    compbio.runner.msa.MafftParametersTester.testParameters()
    compbio.runner.msa.MafftParametersTester.testDefaultParameters()
    compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.MafftTester.testSetInputTester()
    compbio.runner.msa.ProbconsParametersTester.testArguments()
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.ClustalWTester.testRunOnCluster()
    compbio.runner.msa.MafftTester.testExecute()
    compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.TcoffeeTester.testNcore()
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.MuscleTester.testRunLocally()
    compbio.runner.msa.TcoffeeParametersTester.testParameters()
    compbio.runner.msa.ProbconsTester.testConfigurationLoading()
    compbio.runner.msa.ClustalWTester.testRunWithMatrix()
    compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()
    compbio.runner.msa.ClustalWTester.testRunLocally()
    compbio.runner.msa.ProbconsParametersTester.testOptions()
    compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.MafftTester.testPersistance()
    compbio.runner.msa.MuscleParametersTester.testParameters()
    compbio.runner.msa.MuscleParametersTester.testDefaultParameters()
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.MuscleTester.testRunOnCluster()
    compbio.runner.msa.ClustalWTester.testOptionsLocally()
    compbio.runner.msa.MafftTester.testClusterExecute()
    compbio.runner.msa.TcoffeeTester.testConfigurationLoading()
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.ClustalWParametersTester.testParameters()
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()
    compbio.runner.msa.MuscleTester.testConfigurationLoading()
    compbio.runner.msa.TcoffeeTester.testExecute()
    compbio.runner.msa.MafftParametersTester.testPresets()
    compbio.runner.msa.TcoffeeTester.readStatistics()
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.MuscleTester.readStatistics()
    compbio.runner.msa.ClustalWParametersTester.testArguments()
    compbio.runner.msa.ProbconsTester.readStatistics()
    compbio.runner.msa.TcoffeeParametersTester.testArguments()
    compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()
    compbio.runner.msa.MafftParametersTester.testOptions()
    compbio.runner.msa.ProbconsTester.testSetInputTester()
    compbio.runner.msa.MuscleParametersTester.testArguments()
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()
    compbio.runner.msa.ClustalWTester.testPersistance()
    compbio.runner.msa.ProbconsTester.testExecute()
    compbio.runner.msa.TcoffeeTester.testPersistance()
    compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.ProbconsTester.testClusterExecute()
    compbio.runner.msa.TcoffeeParametersTester.testPresets()
    compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()
    compbio.runner.msa.MuscleTester.testPersistance()
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.ClustalWParametersTester.testOptions()
    compbio.runner.msa.MuscleParametersTester.testPresets()
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()
    compbio.runner.msa.MafftParametersTester.testArguments()
    compbio.runner.msa.MafftTester.testConfigurationLoading()
    compbio.runner.msa.TcoffeeParametersTester.testOptions()
    compbio.runner.msa.ClustalWTester.readStatistics()
    compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()
    compbio.runner.msa.ProbconsParametersTester.testParameters()
    compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()
    compbio.runner.msa.ProbconsTester.testPersistance()
    compbio.runner.msa.ClustalWParametersTester.testPresets()
    compbio.runner.msa.MuscleParametersTester.testOptions()
    compbio.runner.msa.TcoffeeTester.testClusterExecute()
    diff --git a/website/tests/Ant suite/index.html b/website/tests/Ant suite/index.html new file mode 100644 index 0000000..7c18f73 --- /dev/null +++ b/website/tests/Ant suite/index.html @@ -0,0 +1,6 @@ +Results for Ant suite + + + + + diff --git a/website/tests/Ant suite/main.html b/website/tests/Ant suite/main.html new file mode 100644 index 0000000..0198e44 --- /dev/null +++ b/website/tests/Ant suite/main.html @@ -0,0 +1,2 @@ +Results for Ant suite +Select a result on the left-hand pane. diff --git a/website/tests/Ant suite/methods-alphabetical.html b/website/tests/Ant suite/methods-alphabetical.html new file mode 100644 index 0000000..7cfdc6e --- /dev/null +++ b/website/tests/Ant suite/methods-alphabetical.html @@ -0,0 +1,520 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    Ant suite

    (Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/02/17 15:34:08 0  >>init     main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:34:10 1737  >>loadPresets     main@277466206
    10/02/17 15:36:38 149837      marshallPresetmain@277466206
    10/02/17 15:36:39 151131      readStatisticsmain@277466206
    10/02/17 15:37:57 228724      readStatisticsmain@277466206
    10/02/17 15:38:59 290965      readStatisticsmain@277466206
    10/02/17 15:41:09 421361      readStatisticsmain@277466206
    10/02/17 15:42:43 515257      readStatisticsmain@277466206
    10/02/17 15:36:40 152310      readStatisticsClusterExecutionmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:36:37 149279     >>setup  main@277466206
    10/02/17 15:36:37 149279     >>setup  main@277466206
    10/02/17 15:36:38 149451     >>setup  main@277466206
    10/02/17 15:36:38 149451     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:37:09 180414     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:34:33 24806      testmain@277466206
    10/02/17 15:34:17 8754      testArgumentsmain@277466206
    10/02/17 15:37:09 180523      testArgumentsmain@277466206
    10/02/17 15:38:32 264102      testArgumentsmain@277466206
    10/02/17 15:39:09 300748      testArgumentsmain@277466206
    10/02/17 15:41:30 442182      testArgumentsmain@277466206
    10/02/17 15:35:50 102119      testAsyncCancelOperationmain@277466206
    10/02/17 15:35:50 102168      testAsyncRetrievOperationmain@277466206
    10/02/17 15:34:11 2379      testCachemain@277466206
    10/02/17 15:34:48 39760      testCancelmain@277466206
    10/02/17 15:35:29 80525      testCancelmain@277466206
    10/02/17 15:35:51 102728      testCancelCompletedTaskLocallymain@277466206
    10/02/17 15:36:37 148461      testCancelCompletedTaskLocallymain@277466206
    10/02/17 15:35:54 105781      testCancelLocallymain@277466206
    10/02/17 15:36:37 148798      testCancelLocallymain@277466206
    10/02/17 15:34:33 24445      testCleanSequencemain@277466206
    10/02/17 15:35:48 100065      testClusterEngineConfmain@277466206
    10/02/17 15:37:57 229363      testClusterExecutemain@277466206
    10/02/17 15:41:10 421803      testClusterExecutemain@277466206
    10/02/17 15:42:44 516133      testClusterExecutemain@277466206
    10/02/17 15:34:38 29993      testCommandBuildingmain@277466206
    10/02/17 15:34:20 12305      testConfigurationmain@277466206
    10/02/17 15:37:15 186680      testConfigurationmain@277466206
    10/02/17 15:38:40 271944      testConfigurationmain@277466206
    10/02/17 15:39:12 303651      testConfigurationmain@277466206
    10/02/17 15:41:39 450947      testConfigurationmain@277466206
    10/02/17 15:36:49 160431      testConfigurationLoadingmain@277466206
    10/02/17 15:38:09 240703      testConfigurationLoadingmain@277466206
    10/02/17 15:39:00 291898      testConfigurationLoadingmain@277466206
    10/02/17 15:41:29 441129      testConfigurationLoadingmain@277466206
    10/02/17 15:42:50 521659      testConfigurationLoadingmain@277466206
    10/02/17 15:34:20 12333      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:37:15 186725      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:38:40 271986      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:39:12 303681      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:41:39 450948      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:34:22 14199      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:37:18 190008      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:38:42 273564      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:39:50 342135      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:41:50 462115      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:34:24 15492      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:37:20 191380      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:38:43 274453      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:39:51 342932      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:41:56 467622      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:36:39 150771      testCreateNumParameterWithoutValidValuemain@277466206
    10/02/17 15:36:39 150787      testCreateParametermain@277466206
    10/02/17 15:36:39 150802      testCreateParameterWithValidValueConstrainmain@277466206
    10/02/17 15:34:33 24446      testDeepCleanSequencemain@277466206
    10/02/17 15:34:27 18651      testDefaultParametersmain@277466206
    10/02/17 15:37:27 199100      testDefaultParametersmain@277466206
    10/02/17 15:38:50 282098      testDefaultParametersmain@277466206
    10/02/17 15:40:53 404843      testDefaultParametersmain@277466206
    10/02/17 15:42:18 489565      testDefaultParametersmain@277466206
    10/02/17 15:38:09 241138      testExecutemain@277466206
    10/02/17 15:41:29 441236      testExecutemain@277466206
    10/02/17 15:42:50 521758      testExecutemain@277466206
    10/02/17 15:34:33 24760      testGetmain@277466206
    10/02/17 15:34:33 24462      testGetAsyncEnginemain@277466206
    10/02/17 15:34:39 30561      testGetClassPathmain@277466206
    10/02/17 15:34:33 24760      testGetDelaymain@277466206
    10/02/17 15:35:48 99951      testGetDirectorypool-4-thread-1@98491205
    10/02/17 15:35:48 99957      testGetDirectorypool-4-thread-2@1476184699
    10/02/17 15:35:48 99959      testGetDirectorypool-4-thread-3@819697057
    10/02/17 15:35:48 99959      testGetDirectorypool-4-thread-4@709342045
    10/02/17 15:34:33 24445      testGetFormattedFastamain@277466206
    10/02/17 15:34:49 41033      testGetJobStatusmain@277466206
    10/02/17 15:35:54 105819      testGetStatuspool-5-thread-1@764103883
    10/02/17 15:35:54 105819      testGetStatuspool-5-thread-2@341752521
    10/02/17 15:35:54 105823      testGetStatuspool-5-thread-4@409692872
    10/02/17 15:35:54 105823      testGetStatuspool-5-thread-3@1513312339
    10/02/17 15:36:15 126691      testGetStatuspool-5-thread-2@341752521
    10/02/17 15:34:33 24759      testGetSyncEnginemain@277466206
    10/02/17 15:36:39 151130      testGetTestArgsCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestArgsCommandmain@277466206
    10/02/17 15:36:39 151129      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151131      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151131      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151131      testGetTestCommandmain@277466206
    10/02/17 15:34:39 30795      testIsAbsolutePathmain@277466206
    10/02/17 15:37:09 180475      testLoadLimitsmain@277466206
    10/02/17 15:35:48 100064   >>testLoadResources    main@277466206
    10/02/17 15:35:48 100251      testMarshallingmain@277466206
    10/02/17 15:36:38 149393      testMarshallingmain@277466206
    10/02/17 15:36:36 147556      testMultipleCancelLocallymain@277466206
    10/02/17 15:36:37 148818      testMultipleCancelLocallymain@277466206
    10/02/17 15:42:51 522626      testNcoremain@277466206
    10/02/17 15:36:39 150817      testOptionNoDefaultValidatemain@277466206
    10/02/17 15:36:39 150832      testOptionSetInvalidValuemain@277466206
    10/02/17 15:36:39 150848      testOptionToCommandmain@277466206
    10/02/17 15:34:27 19210      testOptionsmain@277466206
    10/02/17 15:37:48 219617      testOptionsmain@277466206
    10/02/17 15:38:51 282763      testOptionsmain@277466206
    10/02/17 15:41:08 419575      testOptionsmain@277466206
    10/02/17 15:42:29 500553      testOptionsmain@277466206
    10/02/17 15:36:49 161119      testOptionsLocallymain@277466206
    10/02/17 15:34:38 29994      testOptionsToCommandmain@277466206
    10/02/17 15:36:39 150863      testParameterToCommandmain@277466206
    10/02/17 15:34:30 21374      testParametersmain@277466206
    10/02/17 15:37:52 224118      testParametersmain@277466206
    10/02/17 15:38:53 285288      testParametersmain@277466206
    10/02/17 15:41:08 420039      testParametersmain@277466206
    10/02/17 15:42:30 501445      testParametersmain@277466206
    10/02/17 15:35:48 99948      testParsermain@277466206
    10/02/17 15:36:51 163051      testPersistancemain@277466206
    10/02/17 15:38:10 241567      testPersistancemain@277466206
    10/02/17 15:39:00 292212      testPersistancemain@277466206
    10/02/17 15:41:30 441672      testPersistancemain@277466206
    10/02/17 15:42:51 522627      testPersistancemain@277466206
    10/02/17 15:34:32 24131      testPresetsmain@277466206
    10/02/17 15:37:55 226587      testPresetsmain@277466206
    10/02/17 15:38:58 290109      testPresetsmain@277466206
    10/02/17 15:42:42 514162      testPresetsmain@277466206
    10/02/17 15:34:33 24437      testProteinSequenceGenerationmain@277466206
    10/02/17 15:34:10 1923      testPullmain@277466206
    10/02/17 15:35:48 99948      testQueuemain@277466206
    10/02/17 15:34:32 24308      testReadClustalFilemain@277466206
    10/02/17 15:34:32 24330      testReadClustalFileLongNamesmain@277466206
    10/02/17 15:34:33 24382      testReadClustalFileShortNamesmain@277466206
    10/02/17 15:34:33 24446      testReadWriteFastamain@277466206
    10/02/17 15:36:52 163482      testRunLocallymain@277466206
    10/02/17 15:39:01 292454      testRunLocallymain@277466206
    10/02/17 15:36:52 163653      testRunOnClustermain@277466206
    10/02/17 15:39:01 292556      testRunOnClustermain@277466206
    10/02/17 15:38:11 242600      testRunOnClusterAsyncCheckStatusLongPoolingTimemain@277466206
    10/02/17 15:37:08 179590      testRunWithMatrixmain@277466206
    10/02/17 15:35:48 100287      testSchemaFromCodeGenerationmain@277466206
    10/02/17 15:38:32 264017      testSetInputTestermain@277466206
    10/02/17 15:41:30 442181      testSetInputTestermain@277466206
    10/02/17 15:34:39 30561      testSpaceDelimiterExecutablemain@277466206
    10/02/17 15:35:10 61811      testSubmitmain@277466206
    10/02/17 15:35:30 82112      testSubmitmain@277466206
    10/02/17 15:36:36 147825      testSubmitLocallypool-6-thread-1@97575625
    10/02/17 15:36:36 147826      testSubmitLocallypool-6-thread-2@598639019
    10/02/17 15:36:36 147826      testSubmitLocallypool-6-thread-3@772581038
    10/02/17 15:36:36 147828      testSubmitLocallypool-6-thread-4@1330799835
    10/02/17 15:36:36 147951      testSubmitLocallypool-6-thread-3@772581038
    10/02/17 15:34:39 30795      testTaskListmain@277466206
    10/02/17 15:35:49 100858      testUnMarshallingmain@277466206
    10/02/17 15:36:38 149451      testUnMarshallingmain@277466206
    10/02/17 15:36:39 150878      testValidatemain@277466206
    10/02/17 15:36:39 151082      testValidateBoundaryConstrainCheckmain@277466206
    10/02/17 15:36:39 151098      testValidateLowerBoundaryConstrainCheckmain@277466206
    10/02/17 15:36:39 151114      testValidateUpperBoundaryConstrainCheckmain@277466206
    10/02/17 15:36:39 151129      testValidateValueConstrainmain@277466206
    10/02/17 15:35:50 101456      testValidationmain@277466206
    10/02/17 15:35:50 102108      testValidationOnMarshallingmain@277466206
    10/02/17 15:36:37 149278      testgetAllOptionsmain@277466206
    10/02/17 15:36:38 149390      testgetAllParametersmain@277466206
    10/02/17 15:34:33 24462      testisNonAmbNucleotideSequencemain@277466206
    10/02/17 15:34:33 24462      testisProteinSequencemain@277466206
    10/02/17 15:35:48 100169      validateClustalConfigurationmain@277466206
    10/02/17 15:35:48 100212      validateMafftConfigurationmain@277466206
    10/02/17 15:35:48 100214      validateMuscleConfigurationmain@277466206
    10/02/17 15:36:39 150736      validatePresetsmain@277466206
    10/02/17 15:35:48 100218      validateTcoffeeConfigurationmain@277466206
    diff --git a/website/tests/Ant suite/methods-not-run.html b/website/tests/Ant suite/methods-not-run.html new file mode 100644 index 0000000..1580dbc --- /dev/null +++ b/website/tests/Ant suite/methods-not-run.html @@ -0,0 +1,15 @@ +

    Methods that were not run

    + + + + + + + + + + + + + +
    compbio.runner._impl.RPSBlastTester.testBuildCommand
    compbio.runner._impl.OBTester.testBuildCommand
    compbio.runner.msa.MuscleTester.testRunOnClusterAsync
    compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce
    compbio.runner.msa.ClustalWTester.testAddParameters
    compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes
    compbio.runner._impl.MclTester.testBuildCommand
    compbio.runner._impl.DisEMBLTester.testBuildCommand
    compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime
    compbio.runner._impl.Tmhmm2Tester.testBuildCommand
    compbio.engine.conf.DirectoryManagerTester.testNanoTime
    compbio.runner._impl.NetNglycTester.testBuildCommand
    compbio.runner._impl.RonnTester.testBuildCommand
    \ No newline at end of file diff --git a/website/tests/Ant suite/methods.html b/website/tests/Ant suite/methods.html new file mode 100644 index 0000000..78a4826 --- /dev/null +++ b/website/tests/Ant suite/methods.html @@ -0,0 +1,520 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    Ant suite

    (Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/02/17 15:34:08 0  >>init     main@277466206
    10/02/17 15:34:10 1737  >>loadPresets     main@277466206
    10/02/17 15:34:10 1923      testPullmain@277466206
    10/02/17 15:34:11 2379      testCachemain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:17 8754      testArgumentsmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:20 12305      testConfigurationmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:20 12333      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:22 14199      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:24 15492      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:27 18651      testDefaultParametersmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:27 19210      testOptionsmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:30 21374      testParametersmain@277466206
    10/02/17 15:34:32 24054     >>setup  main@277466206
    10/02/17 15:34:32 24131      testPresetsmain@277466206
    10/02/17 15:34:32 24308      testReadClustalFilemain@277466206
    10/02/17 15:34:32 24330      testReadClustalFileLongNamesmain@277466206
    10/02/17 15:34:33 24382      testReadClustalFileShortNamesmain@277466206
    10/02/17 15:34:33 24437      testProteinSequenceGenerationmain@277466206
    10/02/17 15:34:33 24445      testGetFormattedFastamain@277466206
    10/02/17 15:34:33 24445      testCleanSequencemain@277466206
    10/02/17 15:34:33 24446      testDeepCleanSequencemain@277466206
    10/02/17 15:34:33 24446      testReadWriteFastamain@277466206
    10/02/17 15:34:33 24462      testisNonAmbNucleotideSequencemain@277466206
    10/02/17 15:34:33 24462      testisProteinSequencemain@277466206
    10/02/17 15:34:33 24462      testGetAsyncEnginemain@277466206
    10/02/17 15:34:33 24759      testGetSyncEnginemain@277466206
    10/02/17 15:34:33 24760      testGetDelaymain@277466206
    10/02/17 15:34:33 24760      testGetmain@277466206
    10/02/17 15:34:33 24806      testmain@277466206
    10/02/17 15:34:38 29993      testCommandBuildingmain@277466206
    10/02/17 15:34:38 29994      testOptionsToCommandmain@277466206
    10/02/17 15:34:39 30561      testSpaceDelimiterExecutablemain@277466206
    10/02/17 15:34:39 30561      testGetClassPathmain@277466206
    10/02/17 15:34:39 30795      testIsAbsolutePathmain@277466206
    10/02/17 15:34:39 30795      testTaskListmain@277466206
    10/02/17 15:34:48 39760      testCancelmain@277466206
    10/02/17 15:34:49 41033      testGetJobStatusmain@277466206
    10/02/17 15:35:10 61811      testSubmitmain@277466206
    10/02/17 15:35:29 80525      testCancelmain@277466206
    10/02/17 15:35:30 82112      testSubmitmain@277466206
    10/02/17 15:35:48 99948      testParsermain@277466206
    10/02/17 15:35:48 99948      testQueuemain@277466206
    10/02/17 15:35:48 99951      testGetDirectorypool-4-thread-1@98491205
    10/02/17 15:35:48 99957      testGetDirectorypool-4-thread-2@1476184699
    10/02/17 15:35:48 99959      testGetDirectorypool-4-thread-3@819697057
    10/02/17 15:35:48 99959      testGetDirectorypool-4-thread-4@709342045
    10/02/17 15:35:48 100064   >>testLoadResources    main@277466206
    10/02/17 15:35:48 100065      testClusterEngineConfmain@277466206
    10/02/17 15:35:48 100169      validateClustalConfigurationmain@277466206
    10/02/17 15:35:48 100212      validateMafftConfigurationmain@277466206
    10/02/17 15:35:48 100214      validateMuscleConfigurationmain@277466206
    10/02/17 15:35:48 100218      validateTcoffeeConfigurationmain@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:48 100251      testMarshallingmain@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:48 100287      testSchemaFromCodeGenerationmain@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:49 100858      testUnMarshallingmain@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:50 101456      testValidationmain@277466206
    10/02/17 15:35:50 102092     >>setup  main@277466206
    10/02/17 15:35:50 102108      testValidationOnMarshallingmain@277466206
    10/02/17 15:35:50 102119      testAsyncCancelOperationmain@277466206
    10/02/17 15:35:50 102168      testAsyncRetrievOperationmain@277466206
    10/02/17 15:35:51 102728      testCancelCompletedTaskLocallymain@277466206
    10/02/17 15:35:54 105781      testCancelLocallymain@277466206
    10/02/17 15:35:54 105819      testGetStatuspool-5-thread-1@764103883
    10/02/17 15:35:54 105819      testGetStatuspool-5-thread-2@341752521
    10/02/17 15:35:54 105823      testGetStatuspool-5-thread-4@409692872
    10/02/17 15:35:54 105823      testGetStatuspool-5-thread-3@1513312339
    10/02/17 15:36:15 126691      testGetStatuspool-5-thread-2@341752521
    10/02/17 15:36:36 147556      testMultipleCancelLocallymain@277466206
    10/02/17 15:36:36 147825      testSubmitLocallypool-6-thread-1@97575625
    10/02/17 15:36:36 147826      testSubmitLocallypool-6-thread-2@598639019
    10/02/17 15:36:36 147826      testSubmitLocallypool-6-thread-3@772581038
    10/02/17 15:36:36 147828      testSubmitLocallypool-6-thread-4@1330799835
    10/02/17 15:36:36 147951      testSubmitLocallypool-6-thread-3@772581038
    10/02/17 15:36:37 148461      testCancelCompletedTaskLocallymain@277466206
    10/02/17 15:36:37 148798      testCancelLocallymain@277466206
    10/02/17 15:36:37 148818      testMultipleCancelLocallymain@277466206
    10/02/17 15:36:37 149279     >>setup  main@277466206
    10/02/17 15:36:37 149278      testgetAllOptionsmain@277466206
    10/02/17 15:36:37 149279     >>setup  main@277466206
    10/02/17 15:36:38 149390      testgetAllParametersmain@277466206
    10/02/17 15:36:38 149451     >>setup  main@277466206
    10/02/17 15:36:38 149393      testMarshallingmain@277466206
    10/02/17 15:36:38 149451     >>setup  main@277466206
    10/02/17 15:36:38 149451      testUnMarshallingmain@277466206
    10/02/17 15:36:38 149837      marshallPresetmain@277466206
    10/02/17 15:36:39 150736      validatePresetsmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150771      testCreateNumParameterWithoutValidValuemain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150787      testCreateParametermain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150802      testCreateParameterWithValidValueConstrainmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150817      testOptionNoDefaultValidatemain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150832      testOptionSetInvalidValuemain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150848      testOptionToCommandmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150863      testParameterToCommandmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 150878      testValidatemain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151082      testValidateBoundaryConstrainCheckmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151098      testValidateLowerBoundaryConstrainCheckmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151114      testValidateUpperBoundaryConstrainCheckmain@277466206
    10/02/17 15:36:39 151114     >>setup  main@277466206
    10/02/17 15:36:39 151129      testValidateValueConstrainmain@277466206
    10/02/17 15:36:39 151129      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestArgsCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151130      testGetTestArgsCommandmain@277466206
    10/02/17 15:36:39 151131      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151131      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151131      testGetTestCommandmain@277466206
    10/02/17 15:36:39 151131      readStatisticsmain@277466206
    10/02/17 15:36:40 152310      readStatisticsClusterExecutionmain@277466206
    10/02/17 15:36:49 160431      testConfigurationLoadingmain@277466206
    10/02/17 15:36:49 161119      testOptionsLocallymain@277466206
    10/02/17 15:36:51 163051      testPersistancemain@277466206
    10/02/17 15:36:52 163482      testRunLocallymain@277466206
    10/02/17 15:36:52 163653      testRunOnClustermain@277466206
    10/02/17 15:37:08 179590      testRunWithMatrixmain@277466206
    10/02/17 15:37:09 180414     >>setup  main@277466206
    10/02/17 15:37:09 180475      testLoadLimitsmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:09 180523      testArgumentsmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:15 186680      testConfigurationmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:15 186725      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:18 190008      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:20 191380      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:27 199100      testDefaultParametersmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:48 219617      testOptionsmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:52 224118      testParametersmain@277466206
    10/02/17 15:37:55 226540     >>setup  main@277466206
    10/02/17 15:37:55 226587      testPresetsmain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:37:57 228724      readStatisticsmain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:37:57 229363      testClusterExecutemain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:09 240703      testConfigurationLoadingmain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:09 241138      testExecutemain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:10 241567      testPersistancemain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:11 242600      testRunOnClusterAsyncCheckStatusLongPoolingTimemain@277466206
    10/02/17 15:38:32 264017     >>init  main@277466206
    10/02/17 15:38:32 264017      testSetInputTestermain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:32 264102      testArgumentsmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:40 271944      testConfigurationmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:40 271986      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:42 273564      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:43 274453      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:50 282098      testDefaultParametersmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:51 282763      testOptionsmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:53 285288      testParametersmain@277466206
    10/02/17 15:38:58 290061     >>setup  main@277466206
    10/02/17 15:38:58 290109      testPresetsmain@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:38:59 290965      readStatisticsmain@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:00 291898      testConfigurationLoadingmain@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:00 292212      testPersistancemain@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:01 292454      testRunLocallymain@277466206
    10/02/17 15:39:01 292556     >>init  main@277466206
    10/02/17 15:39:01 292556      testRunOnClustermain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:39:09 300748      testArgumentsmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:39:12 303651      testConfigurationmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:39:12 303681      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:39:50 342135      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:39:51 342932      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:40:53 404843      testDefaultParametersmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 419575      testOptionsmain@277466206
    10/02/17 15:41:08 420008     >>setup  main@277466206
    10/02/17 15:41:08 420039      testParametersmain@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:09 421361      readStatisticsmain@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:10 421803      testClusterExecutemain@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:29 441129      testConfigurationLoadingmain@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:29 441236      testExecutemain@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 441672      testPersistancemain@277466206
    10/02/17 15:41:30 442181     >>init  main@277466206
    10/02/17 15:41:30 442181      testSetInputTestermain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:41:30 442182      testArgumentsmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:41:39 450947      testConfigurationmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:41:39 450948      testConstrainedParametersMaxValuesmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:41:50 462115      testConstrainedParametersMinValuesmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:41:56 467622      testConstrainedParametersRandomValuesmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:18 489565      testDefaultParametersmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:29 500553      testOptionsmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:30 501445      testParametersmain@277466206
    10/02/17 15:42:42 514162     >>setup  main@277466206
    10/02/17 15:42:42 514162      testPresetsmain@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:43 515257      readStatisticsmain@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:44 516133      testClusterExecutemain@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:50 521659      testConfigurationLoadingmain@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:50 521758      testExecutemain@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522626      testNcoremain@277466206
    10/02/17 15:42:51 522627     >>init  main@277466206
    10/02/17 15:42:51 522627      testPersistancemain@277466206
    diff --git a/website/tests/Ant suite/reporter-output.html b/website/tests/Ant suite/reporter-output.html new file mode 100644 index 0000000..063bc2e --- /dev/null +++ b/website/tests/Ant suite/reporter-output.html @@ -0,0 +1 @@ +

    Reporter output

    \ No newline at end of file diff --git a/website/tests/Ant suite/testng-failed.xml b/website/tests/Ant suite/testng-failed.xml new file mode 100644 index 0000000..2a331c9 --- /dev/null +++ b/website/tests/Ant suite/testng-failed.xml @@ -0,0 +1,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/tests/Ant suite/testng.xml.html b/website/tests/Ant suite/testng.xml.html new file mode 100644 index 0000000..40f9b9a --- /dev/null +++ b/website/tests/Ant suite/testng.xml.html @@ -0,0 +1 @@ +testng.xml for Ant suite<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
    <suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Ant suite" junit="false" annotations="JDK" data-provider-thread-count="10">
      <test name="Ant test" junit="false">
        <groups>
          <run>
            <exclude name="performance"/>
          </run>
        </groups>
        <classes>
          <class name="compbio.data._structure.JnetAnnotation$AType"/>
          <class name="compbio.data._structure.JnetAnnotation"/>
          <class name="compbio.data._structure.JpredAnnotation"/>
          <class name="compbio.data._structure.JpredResult"/>
          <class name="compbio.data.msa.MsaWS"/>
          <class name="compbio.data.msa.jaxws.Align"/>
          <class name="compbio.data.msa.jaxws.AlignResponse"/>
          <class name="compbio.data.msa.jaxws.CancelJob"/>
          <class name="compbio.data.msa.jaxws.CancelJobResponse"/>
          <class name="compbio.data.msa.jaxws.CustomAlign"/>
          <class name="compbio.data.msa.jaxws.CustomAlignResponse"/>
          <class name="compbio.data.msa.jaxws.GetJobStatus"/>
          <class name="compbio.data.msa.jaxws.GetJobStatusResponse"/>
          <class name="compbio.data.msa.jaxws.GetLimit"/>
          <class name="compbio.data.msa.jaxws.GetLimitResponse"/>
          <class name="compbio.data.msa.jaxws.GetLimits"/>
          <class name="compbio.data.msa.jaxws.GetLimitsResponse"/>
          <class name="compbio.data.msa.jaxws.GetPresets"/>
          <class name="compbio.data.msa.jaxws.GetPresetsResponse"/>
          <class name="compbio.data.msa.jaxws.GetProgress"/>
          <class name="compbio.data.msa.jaxws.GetProgressResponse"/>
          <class name="compbio.data.msa.jaxws.GetResult"/>
          <class name="compbio.data.msa.jaxws.GetResultResponse"/>
          <class name="compbio.data.msa.jaxws.GetRunnerOptions"/>
          <class name="compbio.data.msa.jaxws.GetRunnerOptionsResponse"/>
          <class name="compbio.data.msa.jaxws.JobExecutionExceptionBean"/>
          <class name="compbio.data.msa.jaxws.JobSubmissionExceptionBean"/>
          <class name="compbio.data.msa.jaxws.LimitExceededExceptionBean"/>
          <class name="compbio.data.msa.jaxws.PresetAlign"/>
          <class name="compbio.data.msa.jaxws.PresetAlignResponse"/>
          <class name="compbio.data.msa.jaxws.PullExecStatistics"/>
          <class name="compbio.data.msa.jaxws.PullExecStatisticsResponse"/>
          <class name="compbio.data.msa.jaxws.PullFile"/>
          <class name="compbio.data.msa.jaxws.PullFileResponse"/>
          <class name="compbio.data.msa.jaxws.ResultNotAvailableExceptionBean"/>
          <class name="compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean"/>
          <class name="compbio.data.msa.jaxws.WrongParameterExceptionBean"/>
          <class name="compbio.data.sequence.Alignment"/>
          <class name="compbio.data.sequence.AlignmentMetadata"/>
          <class name="compbio.data.sequence.ClustalAlignmentUtil"/>
          <class name="compbio.data.sequence.ClustalAlignmentUtilTester"/>
          <class name="compbio.data.sequence.FastaGeneratorManager"/>
          <class name="compbio.data.sequence.FastaSequence"/>
          <class name="compbio.data.sequence.FastaSequenceGenerator$1"/>
          <class name="compbio.data.sequence.FastaSequenceGenerator$DNAAlphabet"/>
          <class name="compbio.data.sequence.FastaSequenceGenerator$Letters"/>
          <class name="compbio.data.sequence.FastaSequenceGenerator$ProteinAlphabet"/>
          <class name="compbio.data.sequence.FastaSequenceGenerator$SeqType"/>
          <class name="compbio.data.sequence.FastaSequenceGenerator"/>
          <class name="compbio.data.sequence.FastaSequenceGeneratorTester"/>
          <class name="compbio.data.sequence.FastaSequenceTester"/>
          <class name="compbio.data.sequence.Program"/>
          <class name="compbio.data.sequence.SequenceUtil"/>
          <class name="compbio.data.sequence.SequenceUtilTester"/>
          <class name="compbio.data.sequence.UnknownFileFormatException"/>
          <class name="compbio.engine.AsyncExecutor"/>
          <class name="compbio.engine.Cleaner"/>
          <class name="compbio.engine.ClusterJobId"/>
          <class name="compbio.engine.Configurator"/>
          <class name="compbio.engine.EngineConfiguratorTester"/>
          <class name="compbio.engine.FilePuller"/>
          <class name="compbio.engine.FilePullerTester"/>
          <class name="compbio.engine.Job"/>
          <class name="compbio.engine.LoadBalancer"/>
          <class name="compbio.engine.ProgressGetter"/>
          <class name="compbio.engine.PulledFileCache"/>
          <class name="compbio.engine.PulledFileCacheTester"/>
          <class name="compbio.engine.SubmissionManager"/>
          <class name="compbio.engine.SyncExecutor"/>
          <class name="compbio.engine.client.ClusterNativeSpecExecutable"/>
          <class name="compbio.engine.client.CommandBuilder$Parameter"/>
          <class name="compbio.engine.client.CommandBuilder"/>
          <class name="compbio.engine.client.CommandBuilderTester"/>
          <class name="compbio.engine.client.ConfExecutable"/>
          <class name="compbio.engine.client.ConfiguredExecutable"/>
          <class name="compbio.engine.client.EnvVariableProcessor"/>
          <class name="compbio.engine.client.Executable$ExecProvider"/>
          <class name="compbio.engine.client.Executable"/>
          <class name="compbio.engine.client.PathValidator"/>
          <class name="compbio.engine.client.PathValidatorTester"/>
          <class name="compbio.engine.client.PipedExecutable"/>
          <class name="compbio.engine.client.RunConfiguration"/>
          <class name="compbio.engine.client.SkeletalExecutable"/>
          <class name="compbio.engine.client.Util"/>
          <class name="compbio.engine.cluster.drmaa.AsyncJobRunner"/>
          <class name="compbio.engine.cluster.drmaa.ClusterSession$1"/>
          <class name="compbio.engine.cluster.drmaa.ClusterSession"/>
          <class name="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
          <class name="compbio.engine.cluster.drmaa.ClusterUtil"/>
          <class name="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
          <class name="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
          <class name="compbio.engine.cluster.drmaa.JobRunner"/>
          <class name="compbio.engine.cluster.drmaa.StatisticManager"/>
          <class name="compbio.engine.cluster.drmaa.UtilTester"/>
          <class name="compbio.engine.cluster.drmaa._DrmaaExample"/>
          <class name="compbio.engine.cluster.drmaa._JobStatus"/>
          <class name="compbio.engine.cluster.dundee._Queue$1"/>
          <class name="compbio.engine.cluster.dundee._Queue"/>
          <class name="compbio.engine.cluster.dundee._QueueConstraints"/>
          <class name="compbio.engine.cluster.dundee._QueueTester"/>
          <class name="compbio.engine.conf.DirectoryManager"/>
          <class name="compbio.engine.conf.DirectoryManagerTester"/>
          <class name="compbio.engine.conf.PropertyHelperManager"/>
          <class name="compbio.engine.conf.PropertyHelperManagerTester"/>
          <class name="compbio.engine.conf.RunnerConfigMarshaller$MySchemaOutputResolver"/>
          <class name="compbio.engine.conf.RunnerConfigMarshaller"/>
          <class name="compbio.engine.conf.RunnerConfigMarshallerTester"/>
          <class name="compbio.engine.conf._Key"/>
          <class name="compbio.engine.local.AsyncLocalRunner"/>
          <class name="compbio.engine.local.AsyncLocalRunnerTester"/>
          <class name="compbio.engine.local.EngineResourcesLeakTester"/>
          <class name="compbio.engine.local.ExecutableWrapper$1"/>
          <class name="compbio.engine.local.ExecutableWrapper"/>
          <class name="compbio.engine.local.LocalEngineUtil"/>
          <class name="compbio.engine.local.LocalExecutorService$1"/>
          <class name="compbio.engine.local.LocalExecutorService"/>
          <class name="compbio.engine.local.LocalRunner"/>
          <class name="compbio.engine.local.LocalRunnerTester"/>
          <class name="compbio.engine.local.StreamGobbler$OutputType"/>
          <class name="compbio.engine.local.StreamGobbler"/>
          <class name="compbio.engine.local._TrackingExecutor$1"/>
          <class name="compbio.engine.local._TrackingExecutor$2"/>
          <class name="compbio.engine.local._TrackingExecutor"/>
          <class name="compbio.metadata.AllTestSuit"/>
          <class name="compbio.metadata.Argument"/>
          <class name="compbio.metadata.ChunkHolder"/>
          <class name="compbio.metadata.JobExecutionException"/>
          <class name="compbio.metadata.JobStatus"/>
          <class name="compbio.metadata.JobSubmissionException"/>
          <class name="compbio.metadata.Limit"/>
          <class name="compbio.metadata.LimitExceededException"/>
          <class name="compbio.metadata.LimitsManager"/>
          <class name="compbio.metadata.Option"/>
          <class name="compbio.metadata.OptionCombinatorTester"/>
          <class name="compbio.metadata.OptionMarshallerTester"/>
          <class name="compbio.metadata.Parameter"/>
          <class name="compbio.metadata.Preset"/>
          <class name="compbio.metadata.PresetManager"/>
          <class name="compbio.metadata.PresetTester"/>
          <class name="compbio.metadata.ResultNotAvailableException"/>
          <class name="compbio.metadata.RunnerConfig"/>
          <class name="compbio.metadata.RunnerConfigTester"/>
          <class name="compbio.metadata.UnsupportedRuntimeException"/>
          <class name="compbio.metadata.ValueConstrain$1"/>
          <class name="compbio.metadata.ValueConstrain$Type"/>
          <class name="compbio.metadata.ValueConstrain"/>
          <class name="compbio.metadata.WrongParameterException"/>
          <class name="compbio.pipeline._jpred.BlastParser$Psiseq"/>
          <class name="compbio.pipeline._jpred.BlastParser"/>
          <class name="compbio.pipeline._jpred.Jpred4"/>
          <class name="compbio.pipeline._jpred.PScore"/>
          <class name="compbio.pipeline._jpred.Pairwise"/>
          <class name="compbio.runner.OptionCombinator"/>
          <class name="compbio.runner.Util"/>
          <class name="compbio.runner._NativeSpecHelper"/>
          <class name="compbio.runner._SkeletalCommandBuilder"/>
          <class name="compbio.runner._impl.BlastAll$blastType"/>
          <class name="compbio.runner._impl.BlastAll$dataBase"/>
          <class name="compbio.runner._impl.BlastAll"/>
          <class name="compbio.runner._impl.BlastParameters"/>
          <class name="compbio.runner._impl.DisEMBLTester"/>
          <class name="compbio.runner._impl.Disembl"/>
          <class name="compbio.runner._impl.Environment"/>
          <class name="compbio.runner._impl.Mcl"/>
          <class name="compbio.runner._impl.MclTester"/>
          <class name="compbio.runner._impl.NetNglyc"/>
          <class name="compbio.runner._impl.NetNglycTester"/>
          <class name="compbio.runner._impl.OB"/>
          <class name="compbio.runner._impl.OBTester"/>
          <class name="compbio.runner._impl.PSIBlast$blastType"/>
          <class name="compbio.runner._impl.PSIBlast$dataBase"/>
          <class name="compbio.runner._impl.PSIBlast"/>
          <class name="compbio.runner._impl.RPSBlast$DB"/>
          <class name="compbio.runner._impl.RPSBlast"/>
          <class name="compbio.runner._impl.RPSBlastTester"/>
          <class name="compbio.runner._impl.Ronn"/>
          <class name="compbio.runner._impl.RonnTester"/>
          <class name="compbio.runner._impl.Runners"/>
          <class name="compbio.runner._impl.Tmhmm2"/>
          <class name="compbio.runner._impl.Tmhmm2Tester"/>
          <class name="compbio.runner._jpred._Jpred"/>
          <class name="compbio.runner.msa.ClustalW"/>
          <class name="compbio.runner.msa.ClustalWParametersTester"/>
          <class name="compbio.runner.msa.ClustalWTester"/>
          <class name="compbio.runner.msa.LimitTester"/>
          <class name="compbio.runner.msa.Mafft"/>
          <class name="compbio.runner.msa.MafftParametersTester"/>
          <class name="compbio.runner.msa.MafftTester"/>
          <class name="compbio.runner.msa.Muscle"/>
          <class name="compbio.runner.msa.MuscleParametersTester"/>
          <class name="compbio.runner.msa.MuscleTester"/>
          <class name="compbio.runner.msa.Probcons"/>
          <class name="compbio.runner.msa.ProbconsParametersTester"/>
          <class name="compbio.runner.msa.ProbconsTester"/>
          <class name="compbio.runner.msa.Tcoffee"/>
          <class name="compbio.runner.msa.TcoffeeParametersTester"/>
          <class name="compbio.runner.msa.TcoffeeTester"/>
          <class name="compbio.runner.psiblast.PsiBlast"/>
          <class name="compbio.ws.client.Jws2Client$Services"/>
          <class name="compbio.ws.client.Jws2Client"/>
          <class name="compbio.ws.client.WSTester"/>
          <class name="compbio.ws.server.ClustalWS"/>
          <class name="compbio.ws.server.MafftWS"/>
          <class name="compbio.ws.server.MuscleWS"/>
          <class name="compbio.ws.server.ProbconsWS"/>
          <class name="compbio.ws.server.SimpleWSPublisher"/>
          <class name="compbio.ws.server.TcoffeeWS"/>
          <class name="compbio.ws.server.WSUtil"/>
        </classes>
      </test>
    </suite>
     \ No newline at end of file diff --git a/website/tests/Ant suite/toc.html b/website/tests/Ant suite/toc.html new file mode 100644 index 0000000..bfce6b9 --- /dev/null +++ b/website/tests/Ant suite/toc.html @@ -0,0 +1,30 @@ + + +Results for Ant suite + + + + +

    Results for
    Ant suite

    + + + + + + + + + + +
    1 test40 classes154 methods:
    +  chronological
    +  alphabetical
    +  not run (13)
    4 groupsreporter outputtestng.xml
    + +

    +

    +
    Ant test (165/0/0) + Results +
    +
    + \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/Ant test(failed).html b/website/tests/Failed suite [Ant suite]/Ant test(failed).html new file mode 100644 index 0000000..77319bf --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/Ant test(failed).html @@ -0,0 +1,84 @@ + + +TestNG: Ant test(failed) + + + + + + + + +

    Ant test(failed)

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Mon Feb 08 18:30:13 GMT 2010
    Total time:1 seconds (1098 ms)
    Included groups:
    Excluded groups:performance

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    readStatistics
    Test class:Ant test(failed)    		compbio.runner.msa.ProbconsTester@60cbf9bd0

    + + \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/Ant test(failed).properties b/website/tests/Failed suite [Ant suite]/Ant test(failed).properties new file mode 100644 index 0000000..840adb8 --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/Ant test(failed).properties @@ -0,0 +1 @@ +[SuiteResult Ant test(failed)] \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/Ant test(failed).xml b/website/tests/Failed suite [Ant suite]/Ant test(failed).xml new file mode 100644 index 0000000..a488254 --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/Ant test(failed).xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/Failed suite [Ant suite]/classes.html b/website/tests/Failed suite [Ant suite]/classes.html new file mode 100644 index 0000000..08936eb --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/classes.html @@ -0,0 +1,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Class nameMethod nameGroups
    compbio.runner.msa.ProbconsTester  
    @Test
     testExecuterunner non_windows
     testPersistancerunner non_windows
     testClusterExecutecluster runner non_windows
     testSetInputTesterrunner non_windows
     testConfigurationLoadingrunner
     readStatisticsrunner non_windows
    @BeforeClass
    @BeforeMethod
     initcluster runner non_windows
    @AfterMethod
    @AfterClass
    diff --git a/website/tests/Failed suite [Ant suite]/groups.html b/website/tests/Failed suite [Ant suite]/groups.html new file mode 100644 index 0000000..1fc18ba --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/groups.html @@ -0,0 +1,4 @@ +

    Groups used for this test run

    + + +
    Group nameMethods
    non_windowscompbio.runner.msa.ProbconsTester.readStatistics()
    runnercompbio.runner.msa.ProbconsTester.readStatistics()
    diff --git a/website/tests/Failed suite [Ant suite]/index.html b/website/tests/Failed suite [Ant suite]/index.html new file mode 100644 index 0000000..7746c5f --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/index.html @@ -0,0 +1,6 @@ +Results for Failed suite [Ant suite] + + + + + diff --git a/website/tests/Failed suite [Ant suite]/main.html b/website/tests/Failed suite [Ant suite]/main.html new file mode 100644 index 0000000..62581b7 --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/main.html @@ -0,0 +1,2 @@ +Results for Failed suite [Ant suite] +Select a result on the left-hand pane. diff --git a/website/tests/Failed suite [Ant suite]/methods-alphabetical.html b/website/tests/Failed suite [Ant suite]/methods-alphabetical.html new file mode 100644 index 0000000..a133bb8 --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/methods-alphabetical.html @@ -0,0 +1,12 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    Failed suite [Ant suite]

    (Hover the method name to see the test class name)

    + + + + + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/02/08 18:30:13 0  >>init     main@1369543768
    10/02/08 18:30:14 525     >>init  main@1369543768
    10/02/08 18:30:14 452  >>loadPresets     main@1369543768
    10/02/08 18:30:14 526      readStatisticsmain@1369543768
    diff --git a/website/tests/Failed suite [Ant suite]/methods-not-run.html b/website/tests/Failed suite [Ant suite]/methods-not-run.html new file mode 100644 index 0000000..909d7cb --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/methods-not-run.html @@ -0,0 +1,105 @@ +

    Methods that were not run

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    compbio.metadata.OptionCombinatorTester.testgetAllParameters
    compbio.runner.msa.MafftParametersTester.testParameters
    compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues
    compbio.runner.msa.ProbconsParametersTester.testArguments
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues
    compbio.runner.msa.MafftTester.testExecute
    compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration
    compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime
    compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues
    compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue
    compbio.metadata.OptionMarshallerTester.testMarshalling
    compbio.engine.FilePullerTester.testGetDelay
    compbio.runner.msa.TcoffeeParametersTester.testParameters
    compbio.runner.msa.ProbconsTester.testConfigurationLoading
    compbio.engine.conf.RunnerConfigMarshallerTester.testValidation
    compbio.runner.msa.MuscleParametersTester.testParameters
    compbio.runner.msa.MafftTester.testPersistance
    compbio.metadata.RunnerConfigTester.testParameterToCommand
    compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues
    compbio.runner.msa.MafftTester.testClusterExecute
    compbio.runner.msa.TcoffeeTester.testConfigurationLoading
    compbio.runner.msa.ClustalWParametersTester.testParameters
    compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration
    compbio.runner.msa.LimitTester.testLoadLimits
    compbio.metadata.PresetTester.marshallPreset
    compbio.runner.msa.TcoffeeTester.readStatistics
    compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues
    compbio.metadata.RunnerConfigTester.testValidateValueConstrain
    compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime
    compbio.runner.msa.MafftParametersTester.testOptions
    compbio.runner.msa.ProbconsTester.testSetInputTester
    compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling
    compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues
    compbio.runner.msa.MuscleTester.testPersistance
    compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues
    compbio.runner.msa.ClustalWParametersTester.testOptions
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues
    compbio.runner.msa.TcoffeeParametersTester.testOptions
    compbio.runner.msa.ProbconsParametersTester.testConfiguration
    compbio.runner.msa.ProbconsParametersTester.testDefaultParameters
    compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration
    compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues
    compbio.runner.msa.MuscleParametersTester.testOptions
    compbio.metadata.RunnerConfigTester.testOptionToCommand
    compbio.runner.msa.MafftTester.readStatistics
    compbio.runner.msa.MafftParametersTester.testDefaultParameters
    compbio.runner.msa.MafftParametersTester.testConfiguration
    compbio.runner.msa.MafftTester.testSetInputTester
    compbio.metadata.RunnerConfigTester.testCreateParameter
    compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling
    compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling
    compbio.runner.msa.TcoffeeTester.testNcore
    compbio.metadata.OptionCombinatorTester.testgetAllOptions
    compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues
    compbio.engine.FilePullerTester.testPull
    compbio.runner.msa.MuscleTester.testRunLocally
    compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters
    compbio.runner.msa.TcoffeeParametersTester.testConfiguration
    compbio.runner.msa.ProbconsParametersTester.testOptions
    compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues
    compbio.runner.msa.MuscleParametersTester.testDefaultParameters
    compbio.runner.msa.MuscleParametersTester.testConfiguration
    compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues
    compbio.runner.msa.MuscleTester.testRunOnCluster
    compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck
    compbio.runner.msa.ClustalWParametersTester.testConfiguration
    compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues
    compbio.runner.msa.ClustalWParametersTester.testDefaultParameters
    compbio.runner.msa.MuscleTester.testConfigurationLoading
    compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf
    compbio.runner.msa.MafftParametersTester.testPresets
    compbio.runner.msa.TcoffeeTester.testExecute
    compbio.metadata.RunnerConfigTester.testValidate
    compbio.metadata.PresetTester.validatePresets
    compbio.engine.FilePullerTester.testCache
    compbio.runner.msa.MuscleTester.readStatistics
    compbio.runner.msa.ClustalWParametersTester.testArguments
    compbio.metadata.OptionMarshallerTester.testUnMarshalling
    compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain
    compbio.runner.msa.TcoffeeParametersTester.testArguments
    compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration
    compbio.runner.msa.MuscleParametersTester.testArguments
    compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues
    compbio.runner.msa.ProbconsTester.testExecute
    compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck
    compbio.runner.msa.TcoffeeTester.testPersistance
    compbio.engine.conf.PropertyHelperManagerTester.testLocalEngineConf
    compbio.runner.msa.ProbconsTester.testClusterExecute
    compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck
    compbio.runner.msa.TcoffeeParametersTester.testPresets
    compbio.runner.msa.MuscleTester.testRunOnClusterAsync
    compbio.runner.msa.MuscleParametersTester.testPresets
    compbio.runner.msa.MafftParametersTester.testArguments
    compbio.runner.msa.MafftTester.testConfigurationLoading
    compbio.runner.msa.ProbconsParametersTester.testParameters
    compbio.engine.FilePullerTester.testGet
    compbio.runner.msa.ProbconsTester.testPersistance
    compbio.runner.msa.ClustalWParametersTester.testPresets
    compbio.runner.msa.TcoffeeTester.testClusterExecute
    \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/methods.html b/website/tests/Failed suite [Ant suite]/methods.html new file mode 100644 index 0000000..632a9da --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/methods.html @@ -0,0 +1,12 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    Failed suite [Ant suite]

    (Hover the method name to see the test class name)

    + + + + + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/02/08 18:30:13 0  >>init     main@1369543768
    10/02/08 18:30:14 452  >>loadPresets     main@1369543768
    10/02/08 18:30:14 525     >>init  main@1369543768
    10/02/08 18:30:14 526      readStatisticsmain@1369543768
    diff --git a/website/tests/Failed suite [Ant suite]/reporter-output.html b/website/tests/Failed suite [Ant suite]/reporter-output.html new file mode 100644 index 0000000..063bc2e --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/reporter-output.html @@ -0,0 +1 @@ +

    Reporter output

    \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/testng-failed.xml b/website/tests/Failed suite [Ant suite]/testng-failed.xml new file mode 100644 index 0000000..624888d --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/testng-failed.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/tests/Failed suite [Ant suite]/testng.xml.html b/website/tests/Failed suite [Ant suite]/testng.xml.html new file mode 100644 index 0000000..0a8a7ad --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/testng.xml.html @@ -0,0 +1 @@ +testng.xml for Failed suite [Ant suite]<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
    <suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Failed suite [Ant suite]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
      <test name="Ant test(failed)" junit="false" annotations="JDK">
        <groups>
          <run>
            <exclude name="performance"/>
          </run>
        </groups>
        <classes>
          <class name="compbio.runner.msa.MuscleTester">
            <methods>
              <include name="init"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.LimitTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.ClustalWParametersTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.TcoffeeParametersTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.metadata.OptionMarshallerTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.metadata.PresetTester">
            <methods>
              <include name="loadPresets"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.MafftTester">
            <methods>
              <include name="init"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.ProbconsTester">
            <methods>
              <include name="readStatistics"/>
              <include name="init"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.MuscleParametersTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.engine.conf.PropertyHelperManagerTester">
            <methods>
              <include name="testLoadResources"/>
            </methods>
          </class>
          <class name="compbio.metadata.RunnerConfigTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.MafftParametersTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.metadata.OptionCombinatorTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.ProbconsParametersTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
          <class name="compbio.runner.msa.TcoffeeTester">
            <methods>
              <include name="init"/>
            </methods>
          </class>
          <class name="compbio.engine.FilePullerTester">
            <methods>
              <include name="init"/>
            </methods>
          </class>
          <class name="compbio.engine.conf.RunnerConfigMarshallerTester">
            <methods>
              <include name="setup"/>
            </methods>
          </class>
        </classes>
      </test>
    </suite>
     \ No newline at end of file diff --git a/website/tests/Failed suite [Ant suite]/toc.html b/website/tests/Failed suite [Ant suite]/toc.html new file mode 100644 index 0000000..ad058ee --- /dev/null +++ b/website/tests/Failed suite [Ant suite]/toc.html @@ -0,0 +1,30 @@ + + +Results for Failed suite [Ant suite] + + + + +

    Results for
    Failed suite [Ant suite]

    + + + + + + + + + + +
    1 test1 class1 method:
    +  chronological
    +  alphabetical
    +  not run (103)
    2 groupsreporter outputtestng.xml
    + +

    +

    +
    Ant test(failed) (1/0/0) + Results +
    +
    + \ No newline at end of file diff --git a/website/tests/JWS2/classes.html b/website/tests/JWS2/classes.html new file mode 100644 index 0000000..52eb8da --- /dev/null +++ b/website/tests/JWS2/classes.html @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Class nameMethod nameGroups
    compbio.engine.local.EngineResourcesLeakTester  
    @Test
     loadEngineRetrieveResultsManyTimesengine
     loadEngineRetrieveResultsOnceengine
    @BeforeClass
    @BeforeMethod
    @AfterMethod
    @AfterClass
    diff --git a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.html b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.html new file mode 100644 index 0000000..2b3cebd --- /dev/null +++ b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.html @@ -0,0 +1,153 @@ + + +TestNG: compbio.engine.local.EngineResourcesLeakTester + + + + + + + + +

    compbio.engine.local.EngineResourcesLeakTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/2/0
    Started on:Wed Jan 27 15:33:57 GMT 2010
    Total time:1 seconds (1330 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + +
    FAILED TESTS
    Test methodInstanceTime (seconds)Exception
    loadEngineRetrieveResultsManyTimes
    Test class:compbio.engine.local.EngineResourcesLeakTester    		compbio.engine.local.EngineResourcesLeakTester@444cee321
    java.lang.AssertionError: expected:<true> but was:<false>
+	at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45)
+... Removed 27 stack frames
    Click to show all stack frames +
    java.lang.AssertionError: expected:<true> but was:<false>
+	at org.testng.Assert.fail(Assert.java:86)
+	at org.testng.Assert.failNotEquals(Assert.java:440)
+	at org.testng.Assert.assertTrue(Assert.java:34)
+	at org.testng.Assert.assertNotNull(Assert.java:354)
+	at org.testng.Assert.assertNotNull(Assert.java:344)
+	at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    loadEngineRetrieveResultsOnce
    Test class:compbio.engine.local.EngineResourcesLeakTester    		compbio.engine.local.EngineResourcesLeakTester@444cee320
    java.lang.AssertionError: expected:<true> but was:<false>
+	at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113)
+... Removed 27 stack frames
    Click to show all stack frames +
    java.lang.AssertionError: expected:<true> but was:<false>
+	at org.testng.Assert.fail(Assert.java:86)
+	at org.testng.Assert.failNotEquals(Assert.java:440)
+	at org.testng.Assert.assertTrue(Assert.java:34)
+	at org.testng.Assert.assertNotNull(Assert.java:354)
+	at org.testng.Assert.assertNotNull(Assert.java:344)
+	at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+

    + + \ No newline at end of file diff --git a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.properties b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.properties new file mode 100644 index 0000000..221a183 --- /dev/null +++ b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.local.EngineResourcesLeakTester] \ No newline at end of file diff --git a/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.xml b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.xml new file mode 100644 index 0000000..34e2af7 --- /dev/null +++ b/website/tests/JWS2/compbio.engine.local.EngineResourcesLeakTester.xml @@ -0,0 +1,18 @@ + + + + + + but was: + at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45) +... Removed 27 stack frames]]> + + + + + but was: + at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113) +... Removed 27 stack frames]]> + + + diff --git a/website/tests/JWS2/groups.html b/website/tests/JWS2/groups.html new file mode 100644 index 0000000..16b0e43 --- /dev/null +++ b/website/tests/JWS2/groups.html @@ -0,0 +1,3 @@ +

    Groups used for this test run

    + +
    Group nameMethods
    enginecompbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce()
    compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes()
    diff --git a/website/tests/JWS2/index.html b/website/tests/JWS2/index.html new file mode 100644 index 0000000..bc45584 --- /dev/null +++ b/website/tests/JWS2/index.html @@ -0,0 +1,6 @@ +Results for JWS2 + + + + + diff --git a/website/tests/JWS2/main.html b/website/tests/JWS2/main.html new file mode 100644 index 0000000..9acc40e --- /dev/null +++ b/website/tests/JWS2/main.html @@ -0,0 +1,2 @@ +Results for JWS2 +Select a result on the left-hand pane. diff --git a/website/tests/JWS2/methods-alphabetical.html b/website/tests/JWS2/methods-alphabetical.html new file mode 100644 index 0000000..9249041 --- /dev/null +++ b/website/tests/JWS2/methods-alphabetical.html @@ -0,0 +1,8 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    JWS2

    (Hover the method name to see the test class name)

    + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/01/27 15:33:57 0      loadEngineRetrieveResultsManyTimesmain@1663273938
    10/01/27 15:33:58 1249      loadEngineRetrieveResultsOncemain@1663273938
    diff --git a/website/tests/JWS2/methods-not-run.html b/website/tests/JWS2/methods-not-run.html new file mode 100644 index 0000000..54b14cb --- /dev/null +++ b/website/tests/JWS2/methods-not-run.html @@ -0,0 +1,2 @@ +

    Methods that were not run

    +
    \ No newline at end of file diff --git a/website/tests/JWS2/methods.html b/website/tests/JWS2/methods.html new file mode 100644 index 0000000..9249041 --- /dev/null +++ b/website/tests/JWS2/methods.html @@ -0,0 +1,8 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    JWS2

    (Hover the method name to see the test class name)

    + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/01/27 15:33:57 0      loadEngineRetrieveResultsManyTimesmain@1663273938
    10/01/27 15:33:58 1249      loadEngineRetrieveResultsOncemain@1663273938
    diff --git a/website/tests/JWS2/reporter-output.html b/website/tests/JWS2/reporter-output.html new file mode 100644 index 0000000..063bc2e --- /dev/null +++ b/website/tests/JWS2/reporter-output.html @@ -0,0 +1 @@ +

    Reporter output

    \ No newline at end of file diff --git a/website/tests/JWS2/testng-failed.xml b/website/tests/JWS2/testng-failed.xml new file mode 100644 index 0000000..58cda06 --- /dev/null +++ b/website/tests/JWS2/testng-failed.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/website/tests/JWS2/testng.xml.html b/website/tests/JWS2/testng.xml.html new file mode 100644 index 0000000..3d0e061 --- /dev/null +++ b/website/tests/JWS2/testng.xml.html @@ -0,0 +1 @@ +testng.xml for JWS2<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
    <suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="JWS2" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
      <test verbose="2" name="compbio.engine.local.EngineResourcesLeakTester" junit="false" annotations="JDK">
        <classes>
          <class name="compbio.engine.local.EngineResourcesLeakTester"/>
        </classes>
      </test>
    </suite>
     \ No newline at end of file diff --git a/website/tests/JWS2/toc.html b/website/tests/JWS2/toc.html new file mode 100644 index 0000000..94b16d1 --- /dev/null +++ b/website/tests/JWS2/toc.html @@ -0,0 +1,30 @@ + + +Results for JWS2 + + + + +

    Results for
    JWS2

    + + + + + + + + + + +
    1 test1 class2 methods:
    +  chronological
    +  alphabetical
    +  not run (0)
    1 groupreporter outputtestng.xml
    + +

    +

    +
    compbio.engine.local.EngineResourcesLeakTester (0/2/0) + Results +
    +
    + \ No newline at end of file diff --git a/website/tests/clustengine/classes.html b/website/tests/clustengine/classes.html new file mode 100644 index 0000000..ca7c305 --- /dev/null +++ b/website/tests/clustengine/classes.html @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Class nameMethod nameGroups
    compbio.engine.conf.PropertyHelperManagerTester  
    @Test
     testClusterEngineConfcluster
     validateClustalConfiguration 
     validateTcoffeeConfiguration 
     validateMuscleConfiguration 
     validateMafftConfiguration 
    @BeforeClass
     testLoadResources 
    @BeforeMethod
    @AfterMethod
    @AfterClass
    diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.html b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.html new file mode 100644 index 0000000..5e1694d --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.html @@ -0,0 +1,84 @@ + + +TestNG: compbio.engine.cluster.drmaa.ClusterSessionTester + + + + + + + + +

    compbio.engine.cluster.drmaa.ClusterSessionTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Mon Dec 21 16:10:22 GMT 2009
    Total time:13 seconds (13917 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testTaskList
    Test class:compbio.engine.cluster.drmaa.ClusterSessionTester    		compbio.engine.cluster.drmaa.ClusterSessionTester@2321ab8013

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.properties b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.properties new file mode 100644 index 0000000..cdc5679 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.cluster.drmaa.ClusterSessionTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.xml b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.xml new file mode 100644 index 0000000..b238c95 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.ClusterSessionTester.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.html b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.html new file mode 100644 index 0000000..30abc5d --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.html @@ -0,0 +1,129 @@ + + +TestNG: compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester + + + + + + + + +

    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:3/0/0
    Started on:Mon Dec 21 16:16:04 GMT 2009
    Total time:31 seconds (31283 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testCancel
    Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester    		compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e3690
    compbio.engine.ResultNotAvailableException: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/ClustalW#556313082813930709 with file name TO1381.clustal.cluster.out is not found!
+	at compbio.data.sequence.ClustalAlignmentUtil.readClustalFile(ClustalAlignmentUtil.java:258)
+	at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:54)
+	at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:15)
+	at compbio.runner.ConfExecutable.getResults(ConfExecutable.java:158)
+	at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:94)
+... Removed 22 stack frames
    Click to show all stack frames +
    compbio.engine.ResultNotAvailableException: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/ClustalW#556313082813930709 with file name TO1381.clustal.cluster.out is not found!
+	at compbio.data.sequence.ClustalAlignmentUtil.readClustalFile(ClustalAlignmentUtil.java:258)
+	at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:54)
+	at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:15)
+	at compbio.runner.ConfExecutable.getResults(ConfExecutable.java:158)
+	at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:94)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+
    testGetJobStatus
    Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester    		compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e36911
    testSubmit
    Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester    		compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e36918

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.properties b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.properties new file mode 100644 index 0000000..c90302d --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.xml b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.xml new file mode 100644 index 0000000..8e5131c --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.xml @@ -0,0 +1,7 @@ + + + + + + + diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.html b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.html new file mode 100644 index 0000000..d48dd63 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.html @@ -0,0 +1,84 @@ + + +TestNG: compbio.engine.cluster.drmaa.DrmaaClusterEngineTester + + + + + + + + +

    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Mon Dec 21 13:38:22 GMT 2009
    Total time:4 seconds (4831 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testSubmit
    Test class:compbio.engine.cluster.drmaa.DrmaaClusterEngineTester    		compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@13b8f8644

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.properties b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.properties new file mode 100644 index 0000000..4b7bcd4 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.cluster.drmaa.DrmaaClusterEngineTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.xml b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.xml new file mode 100644 index 0000000..1b02fe9 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.html b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.html new file mode 100644 index 0000000..316b0a9 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.html @@ -0,0 +1,109 @@ + + +TestNG: compbio.engine.conf.DirectoryManagerTester + + + + + + + + +

    compbio.engine.conf.DirectoryManagerTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:6/0/0
    Started on:Thu Jan 07 16:48:50 GMT 2010
    Total time:0 seconds (209 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@2ca6d51e0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@2ca6d51e0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@2ca6d51e0
    testGetDirectorycompbio.engine.conf.DirectoryManagerTester@2ca6d51e0
    testLongDirName
    Test class:compbio.engine.conf.DirectoryManagerTester    		compbio.engine.conf.DirectoryManagerTester@2ca6d51e0
    testNanoTime
    Test class:compbio.engine.conf.DirectoryManagerTester    		compbio.engine.conf.DirectoryManagerTester@2ca6d51e0

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.properties b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.properties new file mode 100644 index 0000000..9df1de2 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.conf.DirectoryManagerTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.xml b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.xml new file mode 100644 index 0000000..d20c2da --- /dev/null +++ b/website/tests/clustengine/compbio.engine.conf.DirectoryManagerTester.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.html b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.html new file mode 100644 index 0000000..3b0cffc --- /dev/null +++ b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.html @@ -0,0 +1,104 @@ + + +TestNG: compbio.engine.conf.PropertyHelperManagerTester + + + + + + + + +

    compbio.engine.conf.PropertyHelperManagerTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:5/0/0
    Started on:Wed Feb 17 15:33:15 GMT 2010
    Total time:0 seconds (723 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testClusterEngineConf
    Test class:compbio.engine.conf.PropertyHelperManagerTester    		compbio.engine.conf.PropertyHelperManagerTester@4e99353f0
    validateClustalConfiguration
    Test class:compbio.engine.conf.PropertyHelperManagerTester    		compbio.engine.conf.PropertyHelperManagerTester@4e99353f0
    validateMafftConfiguration
    Test class:compbio.engine.conf.PropertyHelperManagerTester    		compbio.engine.conf.PropertyHelperManagerTester@4e99353f0
    validateMuscleConfiguration
    Test class:compbio.engine.conf.PropertyHelperManagerTester    		compbio.engine.conf.PropertyHelperManagerTester@4e99353f0
    validateTcoffeeConfiguration
    Test class:compbio.engine.conf.PropertyHelperManagerTester    		compbio.engine.conf.PropertyHelperManagerTester@4e99353f0

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.properties b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.properties new file mode 100644 index 0000000..3272d4d --- /dev/null +++ b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.conf.PropertyHelperManagerTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.xml b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.xml new file mode 100644 index 0000000..eedcc52 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.conf.PropertyHelperManagerTester.xml @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.html b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.html new file mode 100644 index 0000000..61ec4fe --- /dev/null +++ b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.html @@ -0,0 +1,119 @@ + + +TestNG: compbio.engine.local.EngineResourcesLeakTester + + + + + + + + +

    compbio.engine.local.EngineResourcesLeakTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/1/0
    Started on:Tue Jan 26 17:00:52 GMT 2010
    Total time:0 seconds (782 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    FAILED TESTS
    Test methodInstanceTime (seconds)Exception
    loadEngine
    Test class:compbio.engine.local.EngineResourcesLeakTester    		compbio.engine.local.EngineResourcesLeakTester@116471f0
    java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist!
+	at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)
+	at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75)
+	at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist!
+	at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)
+	at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75)
+	at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:546)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:908)
+	at org.testng.TestRunner.privateRun(TestRunner.java:617)
+	at org.testng.TestRunner.run(TestRunner.java:498)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:201)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:879)
+	at org.testng.TestNG.run(TestNG.java:787)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127)
+

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.properties b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.properties new file mode 100644 index 0000000..221a183 --- /dev/null +++ b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.engine.local.EngineResourcesLeakTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.xml b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.xml new file mode 100644 index 0000000..4bc270f --- /dev/null +++ b/website/tests/clustengine/compbio.engine.local.EngineResourcesLeakTester.xml @@ -0,0 +1,15 @@ + + + + + + (ExecutableWrapper.java:87) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) + at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75) + at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28) +... Removed 22 stack frames]]> + + + diff --git a/website/tests/clustengine/compbio.metadata.PresetTester.html b/website/tests/clustengine/compbio.metadata.PresetTester.html new file mode 100644 index 0000000..6ff65b4 --- /dev/null +++ b/website/tests/clustengine/compbio.metadata.PresetTester.html @@ -0,0 +1,127 @@ + + +TestNG: compbio.metadata.PresetTester + + + + + + + + +

    compbio.metadata.PresetTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/0/2
    Started on:Mon Jan 25 15:45:52 GMT 2010
    Total time:0 seconds (110 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    FAILED CONFIGURATIONS
    Test methodInstanceTime (seconds)Exception
    loadPresets
    Test class:compbio.metadata.PresetTester    		null0
    java.lang.AssertionError: null
+	at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85)
+... Removed 20 stack frames
    Click to show all stack frames +
    java.lang.AssertionError: null
+	at org.testng.Assert.fail(Assert.java:87)
+	at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)
+	at org.testng.internal.Invoker.invokeConfigurationMethod(Invoker.java:443)
+	at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:160)
+	at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:90)
+	at org.testng.TestRunner.beforeRun(TestRunner.java:522)
+	at org.testng.TestRunner.run(TestRunner.java:490)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:201)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:879)
+	at org.testng.TestNG.run(TestNG.java:787)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127)
+

    + + + + + + + + + + + + + + + + + +
    SKIPPED TESTS
    Test methodInstanceTime (seconds)Exception
    marshallPreset
    Test class:compbio.metadata.PresetTester    		compbio.metadata.PresetTester@1171b260
    validatePresets
    Test class:compbio.metadata.PresetTester    		compbio.metadata.PresetTester@1171b260

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.metadata.PresetTester.properties b/website/tests/clustengine/compbio.metadata.PresetTester.properties new file mode 100644 index 0000000..604ca3e --- /dev/null +++ b/website/tests/clustengine/compbio.metadata.PresetTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.metadata.PresetTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.metadata.PresetTester.xml b/website/tests/clustengine/compbio.metadata.PresetTester.xml new file mode 100644 index 0000000..a425b4d --- /dev/null +++ b/website/tests/clustengine/compbio.metadata.PresetTester.xml @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + diff --git a/website/tests/clustengine/compbio.runner.CommandBuilderTester.html b/website/tests/clustengine/compbio.runner.CommandBuilderTester.html new file mode 100644 index 0000000..794bf77 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.CommandBuilderTester.html @@ -0,0 +1,84 @@ + + +TestNG: compbio.runner.CommandBuilderTester + + + + + + + + +

    compbio.runner.CommandBuilderTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Thu Jan 14 14:12:38 GMT 2010
    Total time:0 seconds (32 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testCommandBuilding
    Test class:compbio.runner.CommandBuilderTester    		compbio.runner.CommandBuilderTester@34a1fc0

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.CommandBuilderTester.properties b/website/tests/clustengine/compbio.runner.CommandBuilderTester.properties new file mode 100644 index 0000000..b4c9fb5 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.CommandBuilderTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.CommandBuilderTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.CommandBuilderTester.xml b/website/tests/clustengine/compbio.runner.CommandBuilderTester.xml new file mode 100644 index 0000000..cb26c89 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.CommandBuilderTester.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.html b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.html new file mode 100644 index 0000000..1b2d8f5 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.html @@ -0,0 +1,406 @@ + + +TestNG: compbio.runner.clustal.ClustalWParametersTester + + + + + + + + +

    compbio.runner.clustal.ClustalWParametersTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/8/0
    Started on:Mon Dec 21 18:09:47 GMT 2009
    Total time:2 seconds (2219 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    FAILED TESTS
    Test methodTime (seconds)Exception
    testArguments0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)
+	at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)
+	at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testConstrainedParametersMaxValues0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)
+	at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)
+	at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testConstrainedParametersMinValues0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)
+	at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)
+	at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testConstrainedParametersRandomValues0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testDefaultParameters0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testOptions0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)
+	at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)
+	at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testParameters0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)
+	at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)
+	at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+
    testPresets0
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist!
+	at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)
+	at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)
+	at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:842)
+	at org.testng.TestNG.run(TestNG.java:751)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)
+

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.properties b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.properties new file mode 100644 index 0000000..89fb9a5 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.clustal.ClustalWParametersTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.xml b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.xml new file mode 100644 index 0000000..9b22c51 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.ClustalWParametersTester.xml @@ -0,0 +1,96 @@ + + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) + at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) + at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183) + at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) + at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174) + at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151) +... Removed 22 stack frames]]> + + + + + (ExecutableWrapper.java:57) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69) + at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202) + at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164) +... Removed 22 stack frames]]> + + + diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.html b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.html new file mode 100644 index 0000000..225516c --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.html @@ -0,0 +1,84 @@ + + +TestNG: compbio.runner.clustal.ClustalWTester + + + + + + + + +

    compbio.runner.clustal.ClustalWTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Fri Jan 15 16:55:36 GMT 2010
    Total time:0 seconds (285 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testRunWithMatrix
    Test class:compbio.runner.clustal.ClustalWTester    		compbio.runner.clustal.ClustalWTester@3d8600380

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.properties b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.properties new file mode 100644 index 0000000..41b902e --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.clustal.ClustalWTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.xml b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.xml new file mode 100644 index 0000000..28e3f4a --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.ClustalWTester.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/clustengine/compbio.runner.clustal.LimitTester.html b/website/tests/clustengine/compbio.runner.clustal.LimitTester.html new file mode 100644 index 0000000..ecf2617 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.LimitTester.html @@ -0,0 +1,83 @@ + + +TestNG: compbio.runner.clustal.LimitTester + + + + + + + + +

    compbio.runner.clustal.LimitTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Mon Dec 21 17:22:34 GMT 2009
    Total time:0 seconds (719 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + +
    PASSED TESTS
    Test methodTime (seconds)Exception
    testLoadLimits0

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.LimitTester.properties b/website/tests/clustengine/compbio.runner.clustal.LimitTester.properties new file mode 100644 index 0000000..5bece15 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.LimitTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.clustal.LimitTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.clustal.LimitTester.xml b/website/tests/clustengine/compbio.runner.clustal.LimitTester.xml new file mode 100644 index 0000000..1d5674a --- /dev/null +++ b/website/tests/clustengine/compbio.runner.clustal.LimitTester.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/clustengine/compbio.runner.mafft.MafftTester.html b/website/tests/clustengine/compbio.runner.mafft.MafftTester.html new file mode 100644 index 0000000..364217f --- /dev/null +++ b/website/tests/clustengine/compbio.runner.mafft.MafftTester.html @@ -0,0 +1,84 @@ + + +TestNG: compbio.runner.mafft.MafftTester + + + + + + + + +

    compbio.runner.mafft.MafftTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:1/0/0
    Started on:Mon Jan 25 17:07:55 GMT 2010
    Total time:0 seconds (682 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testExecute
    Test class:compbio.runner.mafft.MafftTester    		compbio.runner.mafft.MafftTester@13b8f8640

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.mafft.MafftTester.properties b/website/tests/clustengine/compbio.runner.mafft.MafftTester.properties new file mode 100644 index 0000000..b36a025 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.mafft.MafftTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.mafft.MafftTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.mafft.MafftTester.xml b/website/tests/clustengine/compbio.runner.mafft.MafftTester.xml new file mode 100644 index 0000000..4b8fe84 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.mafft.MafftTester.xml @@ -0,0 +1,5 @@ + + + + + diff --git a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.html b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.html new file mode 100644 index 0000000..3a62862 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.html @@ -0,0 +1,117 @@ + + +TestNG: compbio.runner.muscle.MuscleTester + + + + + + + + +

    compbio.runner.muscle.MuscleTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/1/0
    Started on:Mon Jan 25 17:08:34 GMT 2010
    Total time:6 seconds (6782 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    FAILED TESTS
    Test methodInstanceTime (seconds)Exception
    testRunLocally
    Test class:compbio.runner.muscle.MuscleTester    		compbio.runner.muscle.MuscleTester@18020cc1
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist!
+	at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)
+	at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173)
+... Removed 22 stack frames
    Click to show all stack frames +
    java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist!
+	at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)
+	at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)
+	at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)
+	at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:546)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:908)
+	at org.testng.TestRunner.privateRun(TestRunner.java:617)
+	at org.testng.TestRunner.run(TestRunner.java:498)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:201)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:879)
+	at org.testng.TestNG.run(TestNG.java:787)
+	at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75)
+	at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127)
+

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.properties b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.properties new file mode 100644 index 0000000..87d54e7 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.muscle.MuscleTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.muscle.MuscleTester.xml b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.xml new file mode 100644 index 0000000..bbcd8d6 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.muscle.MuscleTester.xml @@ -0,0 +1,14 @@ + + + + + + (ExecutableWrapper.java:87) + at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89) + at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173) +... Removed 22 stack frames]]> + + + diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.html b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.html new file mode 100644 index 0000000..e93ca5d --- /dev/null +++ b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.html @@ -0,0 +1,114 @@ + + +TestNG: compbio.runner.probcons.ProbconsParametersTester + + + + + + + + +

    compbio.runner.probcons.ProbconsParametersTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:7/0/0
    Started on:Mon Jan 11 16:11:14 GMT 2010
    Total time:140 seconds (140484 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testArguments
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf01
    testConstrainedParametersMaxValues
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf037
    testConstrainedParametersMinValues
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf00
    testConstrainedParametersRandomValues
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf074
    testDefaultParameters
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf024
    testOptions
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf00
    testParameters
    Test class:compbio.runner.probcons.ProbconsParametersTester    		compbio.runner.probcons.ProbconsParametersTester@6513cf01

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.properties b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.properties new file mode 100644 index 0000000..a9fa110 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.probcons.ProbconsParametersTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.xml b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.xml new file mode 100644 index 0000000..96f8857 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.probcons.ProbconsParametersTester.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.html b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.html new file mode 100644 index 0000000..b824aff --- /dev/null +++ b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.html @@ -0,0 +1,112 @@ + + +TestNG: compbio.runner.probcons.ProbconsTester + + + + + + + + +

    compbio.runner.probcons.ProbconsTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/1/0
    Started on:Fri Jan 15 17:16:57 GMT 2010
    Total time:0 seconds (549 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    FAILED TESTS
    Test methodInstanceTime (seconds)Exception
    testExecute
    Test class:compbio.runner.probcons.ProbconsTester    		compbio.runner.probcons.ProbconsTester@5cbfe9d0
    java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found!
+	at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99)
+... Removed 23 stack frames
    Click to show all stack frames +
    java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found!
+	at org.testng.Assert.fail(Assert.java:86)
+	at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.properties b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.properties new file mode 100644 index 0000000..6110b4f --- /dev/null +++ b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.probcons.ProbconsTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.xml b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.xml new file mode 100644 index 0000000..5822b7c --- /dev/null +++ b/website/tests/clustengine/compbio.runner.probcons.ProbconsTester.xml @@ -0,0 +1,11 @@ + + + + + + + + + diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.html b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.html new file mode 100644 index 0000000..18d211c --- /dev/null +++ b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.html @@ -0,0 +1,119 @@ + + +TestNG: compbio.runner.tcoffee.TcoffeeParametersTester + + + + + + + + +

    compbio.runner.tcoffee.TcoffeeParametersTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:8/0/0
    Started on:Fri Jan 15 12:35:10 GMT 2010
    Total time:69 seconds (69406 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PASSED TESTS
    Test methodInstanceTime (seconds)Exception
    testArguments
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f75
    testConstrainedParametersMaxValues
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f78
    testConstrainedParametersMinValues
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f74
    testConstrainedParametersRandomValues
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f717
    testDefaultParameters
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f721
    testOptions
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f71
    testParameters
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f79
    testPresets
    Test class:compbio.runner.tcoffee.TcoffeeParametersTester    		compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f70

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.properties b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.properties new file mode 100644 index 0000000..f22ffc3 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.tcoffee.TcoffeeParametersTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.xml b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.xml new file mode 100644 index 0000000..882a0d1 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeParametersTester.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.html b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.html new file mode 100644 index 0000000..fae5fe0 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.html @@ -0,0 +1,112 @@ + + +TestNG: compbio.runner.tcoffee.TcoffeeTester + + + + + + + + +

    compbio.runner.tcoffee.TcoffeeTester

    + + + + + + + + + + + +
    Tests passed/Failed/Skipped:0/1/0
    Started on:Fri Jan 15 17:10:30 GMT 2010
    Total time:1 seconds (1723 ms)
    Included groups:
    Excluded groups:

    +(Hover the method name to see the test class name)

    + + + + + + + + + + + + +
    FAILED TESTS
    Test methodInstanceTime (seconds)Exception
    testExecute
    Test class:compbio.runner.tcoffee.TcoffeeTester    		compbio.runner.tcoffee.TcoffeeTester@13b8f8641
    java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found!
+	at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92)
+... Removed 23 stack frames
    Click to show all stack frames +
    java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found!
+	at org.testng.Assert.fail(Assert.java:86)
+	at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
+	at java.lang.reflect.Method.invoke(Method.java:597)
+	at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
+	at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
+	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
+	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
+	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
+	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
+	at org.testng.TestRunner.runWorkers(TestRunner.java:759)
+	at org.testng.TestRunner.privateRun(TestRunner.java:592)
+	at org.testng.TestRunner.run(TestRunner.java:486)
+	at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
+	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
+	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
+	at org.testng.SuiteRunner.run(SuiteRunner.java:204)
+	at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
+	at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
+	at org.testng.TestNG.run(TestNG.java:784)
+	at org.testng.TestNG.privateMain(TestNG.java:949)
+	at org.testng.TestNG.main(TestNG.java:922)
+

    + + \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.properties b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.properties new file mode 100644 index 0000000..b30cf76 --- /dev/null +++ b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.properties @@ -0,0 +1 @@ +[SuiteResult compbio.runner.tcoffee.TcoffeeTester] \ No newline at end of file diff --git a/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.xml b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.xml new file mode 100644 index 0000000..573ffeb --- /dev/null +++ b/website/tests/clustengine/compbio.runner.tcoffee.TcoffeeTester.xml @@ -0,0 +1,11 @@ + + + + + + + + + diff --git a/website/tests/clustengine/groups.html b/website/tests/clustengine/groups.html new file mode 100644 index 0000000..1910670 --- /dev/null +++ b/website/tests/clustengine/groups.html @@ -0,0 +1,3 @@ +

    Groups used for this test run

    + +
    Group nameMethods
    clustercompbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()
    diff --git a/website/tests/clustengine/index.html b/website/tests/clustengine/index.html new file mode 100644 index 0000000..4b5a4d2 --- /dev/null +++ b/website/tests/clustengine/index.html @@ -0,0 +1,6 @@ +Results for clustengine + + + + + diff --git a/website/tests/clustengine/main.html b/website/tests/clustengine/main.html new file mode 100644 index 0000000..280992c --- /dev/null +++ b/website/tests/clustengine/main.html @@ -0,0 +1,2 @@ +Results for clustengine +Select a result on the left-hand pane. diff --git a/website/tests/clustengine/methods-alphabetical.html b/website/tests/clustengine/methods-alphabetical.html new file mode 100644 index 0000000..a993f34 --- /dev/null +++ b/website/tests/clustengine/methods-alphabetical.html @@ -0,0 +1,16 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    clustengine

    (Hover the method name to see the test class name)

    + + + + + + + + + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/02/17 15:33:16 0      testClusterEngineConfmain@1421571929
    10/02/17 15:33:15 -606   >>testLoadResources    main@1421571929
    10/02/17 15:33:16 13      validateClustalConfigurationmain@1421571929
    10/02/17 15:33:16 68      validateMafftConfigurationmain@1421571929
    10/02/17 15:33:16 80      validateMuscleConfigurationmain@1421571929
    10/02/17 15:33:16 92      validateTcoffeeConfigurationmain@1421571929
    diff --git a/website/tests/clustengine/methods-not-run.html b/website/tests/clustengine/methods-not-run.html new file mode 100644 index 0000000..54b14cb --- /dev/null +++ b/website/tests/clustengine/methods-not-run.html @@ -0,0 +1,2 @@ +

    Methods that were not run

    +
    \ No newline at end of file diff --git a/website/tests/clustengine/methods.html b/website/tests/clustengine/methods.html new file mode 100644 index 0000000..e499aaf --- /dev/null +++ b/website/tests/clustengine/methods.html @@ -0,0 +1,16 @@ +

    Methods run, sorted chronologically

    >> means before, << means after


    clustengine

    (Hover the method name to see the test class name)

    + + + + + + + + + + + + + + +
    TimeDelta (ms)Suite
    configuration    		Test
    configuration    		Class
    configuration    		Groups
    configuration    		Method
    configuration    		Test
    method    		ThreadInstances
    10/02/17 15:33:15 0   >>testLoadResources    main@1421571929
    10/02/17 15:33:16 606      testClusterEngineConfmain@1421571929
    10/02/17 15:33:16 619      validateClustalConfigurationmain@1421571929
    10/02/17 15:33:16 674      validateMafftConfigurationmain@1421571929
    10/02/17 15:33:16 686      validateMuscleConfigurationmain@1421571929
    10/02/17 15:33:16 698      validateTcoffeeConfigurationmain@1421571929
    diff --git a/website/tests/clustengine/reporter-output.html b/website/tests/clustengine/reporter-output.html new file mode 100644 index 0000000..063bc2e --- /dev/null +++ b/website/tests/clustengine/reporter-output.html @@ -0,0 +1 @@ +

    Reporter output

    \ No newline at end of file diff --git a/website/tests/clustengine/testng-failed.xml b/website/tests/clustengine/testng-failed.xml new file mode 100644 index 0000000..b9ea5c6 --- /dev/null +++ b/website/tests/clustengine/testng-failed.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/website/tests/clustengine/testng.xml.html b/website/tests/clustengine/testng.xml.html new file mode 100644 index 0000000..dec3522 --- /dev/null +++ b/website/tests/clustengine/testng.xml.html @@ -0,0 +1 @@ +testng.xml for clustengine<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
    <suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="clustengine" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
      <test verbose="2" name="compbio.engine.conf.PropertyHelperManagerTester" junit="false" annotations="JDK">
        <classes>
          <class name="compbio.engine.conf.PropertyHelperManagerTester"/>
        </classes>
      </test>
    </suite>
     \ No newline at end of file diff --git a/website/tests/clustengine/toc.html b/website/tests/clustengine/toc.html new file mode 100644 index 0000000..0c29c08 --- /dev/null +++ b/website/tests/clustengine/toc.html @@ -0,0 +1,30 @@ + + +Results for clustengine + + + + +

    Results for
    clustengine

    + + + + + + + + + + +
    1 test1 class5 methods:
    +  chronological
    +  alphabetical
    +  not run (0)
    1 groupreporter outputtestng.xml
    + +

    +

    +
    compbio.engine.conf.PropertyHelperManagerTester (5/0/0) + Results +
    +
    + \ No newline at end of file diff --git a/website/tests/emailable-report.html b/website/tests/emailable-report.html new file mode 100644 index 0000000..25d37af --- /dev/null +++ b/website/tests/emailable-report.html @@ -0,0 +1,626 @@ + + + +TestNG: Unit Test + + + + + + +
    TestMethods
    Passed    		Scenarios
    Passed    		# skipped# failedTotal
    Time    		Included
    Groups    		Excluded
    Groups
    Ant test15416500524.4 secondsperformance
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    ClassMethod# of
    Scenarios    		Time
    (Msecs)
    Ant test — passed
    compbio.data.sequence.ClustalAlignmentUtilTestertestReadClustalFile 122
    testReadClustalFileLongNames 152
    testReadClustalFileShortNames 154
    compbio.data.sequence.FastaSequenceGeneratorTestertestProteinSequenceGeneration 18
    compbio.data.sequence.FastaSequenceTestertestGetFormattedFasta 10
    compbio.data.sequence.SequenceUtilTestertestCleanSequence 10
    testDeepCleanSequence 10
    testReadWriteFasta 116
    testisNonAmbNucleotideSequence 10
    testisProteinSequence 10
    compbio.engine.EngineConfiguratorTestertestGetAsyncEngine 1296
    testGetSyncEngine 10
    compbio.engine.FilePullerTestertestCache (engine) 16006
    testGet 146
    testGetDelay (engine) 10
    testPull (engine) 1450
    compbio.engine.PulledFileCacheTestertest 15187
    compbio.engine.client.CommandBuilderTestertestCommandBuilding 11
    testOptionsToCommand 1567
    testSpaceDelimiterExecutable 10
    compbio.engine.client.PathValidatorTestertestGetClassPath 1234
    testIsAbsolutePath 10
    compbio.engine.cluster.drmaa.ClusterSessionTestertestTaskList (engine, cluster) 18964
    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTestertestCancel (engine, cluster) 11273
    testGetJobStatus (engine, cluster) 120778
    testSubmit (engine, cluster) 118714
    compbio.engine.cluster.drmaa.DrmaaClusterEngineTestertestCancel (engine, cluster) 11587
    testSubmit (engine, cluster) 117835
    compbio.engine.cluster.drmaa.UtilTestertestParser 10
    compbio.engine.cluster.dundee._QueueTestertestQueue 10
    compbio.engine.conf.DirectoryManagerTestertestGetDirectory 4111
    compbio.engine.conf.PropertyHelperManagerTestertestClusterEngineConf (cluster) 1104
    validateClustalConfiguration 143
    validateMafftConfiguration 11
    validateMuscleConfiguration 14
    validateTcoffeeConfiguration 14
    compbio.engine.conf.RunnerConfigMarshallerTestertestMarshalling 120
    testSchemaFromCodeGeneration 1504
    testUnMarshalling 1580
    testValidation 1636
    testValidationOnMarshalling 111
    compbio.engine.local.AsyncLocalRunnerTestertestAsyncCancelOperation (engine) 148
    testAsyncRetrievOperation (engine) 1560
    testCancelCompletedTaskLocally (engine) 13053
    testCancelLocally (engine) 127
    testGetStatus (engine) 541735
    testMultipleCancelLocally (engine) 1267
    testSubmitLocally (engine) 5634
    compbio.engine.local.LocalRunnerTestertestCancelCompletedTaskLocally (engine) 1336
    testCancelLocally (engine) 120
    testMultipleCancelLocally (engine) 158
    compbio.metadata.OptionCombinatorTestertestgetAllOptions 11
    testgetAllParameters 13
    compbio.metadata.OptionMarshallerTestertestMarshalling 158
    testUnMarshalling 1386
    compbio.metadata.PresetTestermarshallPreset 1899
    validatePresets 11
    compbio.metadata.RunnerConfigTestertestCreateNumParameterWithoutValidValue 11
    testCreateParameter 10
    testCreateParameterWithValidValueConstrain 10
    testOptionNoDefaultValidate 10
    testOptionSetInvalidValue 11
    testOptionToCommand 10
    testParameterToCommand 10
    testValidate 10
    testValidateBoundaryConstrainCheck 11
    testValidateLowerBoundaryConstrainCheck 10
    testValidateUpperBoundaryConstrainCheck 10
    testValidateValueConstrain 10
    compbio.runner._impl.MclTestertestGetTestCommand 11
    compbio.runner._impl.NetNglycTestertestGetTestCommand 10
    compbio.runner._impl.OBTestertestGetTestArgsCommand 10
    testGetTestCommand 10
    compbio.runner._impl.RPSBlastTestertestGetTestArgsCommand 10
    testGetTestCommand 10
    compbio.runner._impl.RonnTestertestGetTestCommand 10
    compbio.runner._impl.Tmhmm2TestertestGetTestCommand 10
    compbio.runner.msa.ClustalWParametersTestertestArguments (runner) 13518
    testConfiguration 11
    testConstrainedParametersMaxValues (runner) 11835
    testConstrainedParametersMinValues (runner) 11232
    testConstrainedParametersRandomValues (runner) 13105
    testDefaultParameters (runner) 1502
    testOptions (runner) 12109
    testParameters (runner) 12680
    testPresets (runner) 1177
    compbio.runner.msa.ClustalWTesterreadStatistics (runner) 11178
    readStatisticsClusterExecution (cluster, runner) 18121
    testConfigurationLoading (runner) 1688
    testOptionsLocally (runner) 11932
    testPersistance (runner) 1431
    testRunLocally (runner) 1171
    testRunOnCluster (cluster, runner) 115937
    testRunWithMatrix (runner) 1824
    compbio.runner.msa.LimitTestertestLoadLimits 10
    compbio.runner.msa.MafftParametersTestertestArguments (runner, non_windows) 16103
    testConfiguration 11
    testConstrainedParametersMaxValues (runner, non_windows) 13235
    testConstrainedParametersMinValues (runner, non_windows) 11326
    testConstrainedParametersRandomValues (runner, non_windows) 17672
    testDefaultParameters (runner, non_windows) 120463
    testOptions (runner, non_windows) 14449
    testParameters (runner, non_windows) 12422
    testPresets (runner, non_windows) 12136
    compbio.runner.msa.MafftTesterreadStatistics (runner, non_windows) 1639
    testClusterExecute (cluster, runner, non_windows) 111340
    testConfigurationLoading (runner) 1435
    testExecute (runner, non_windows) 1428
    testPersistance (runner, non_windows) 11033
    testRunOnClusterAsyncCheckStatusLongPoolingTime (cluster, runner, non_windows) 121418
    testSetInputTester (runner, non_windows) 10
    compbio.runner.msa.MuscleParametersTestertestArguments (runner) 17798
    testConfiguration 10
    testConstrainedParametersMaxValues (runner) 11534
    testConstrainedParametersMinValues (runner) 1845
    testConstrainedParametersRandomValues (runner) 17603
    testDefaultParameters (runner) 1622
    testOptions (runner) 12481
    testParameters (runner) 14773
    testPresets (runner) 1856
    compbio.runner.msa.MuscleTesterreadStatistics (runner) 1932
    testConfigurationLoading (runner) 1313
    testPersistance (runner) 1241
    testRunLocally (runner) 1101
    testRunOnCluster (cluster, runner) 18142
    compbio.runner.msa.ProbconsParametersTestertestArguments (runner, non_windows) 12874
    testConfiguration 11
    testConstrainedParametersMaxValues (runner, non_windows) 138416
    testConstrainedParametersMinValues (runner, non_windows) 1768
    testConstrainedParametersRandomValues (runner, non_windows) 161881
    testDefaultParameters (runner, non_windows) 114704
    testOptions (runner, non_windows) 1433
    testParameters (runner, non_windows) 11321
    compbio.runner.msa.ProbconsTesterreadStatistics (runner, non_windows) 1441
    testClusterExecute (cluster, runner, non_windows) 119326
    testConfigurationLoading (runner) 1107
    testExecute (runner, non_windows) 1436
    testPersistance (runner, non_windows) 1509
    testSetInputTester (runner, non_windows) 10
    compbio.runner.msa.TcoffeeParametersTestertestArguments (runner, non_windows) 18765
    testConfiguration 10
    testConstrainedParametersMaxValues (runner, non_windows) 111166
    testConstrainedParametersMinValues (runner, non_windows) 15507
    testConstrainedParametersRandomValues (runner, non_windows) 121942
    testDefaultParameters (runner, non_windows) 110988
    testOptions (runner, non_windows) 1891
    testParameters (runner, non_windows) 112717
    testPresets (runner, non_windows) 11094
    compbio.runner.msa.TcoffeeTester
    "Ant test"    		readStatistics (runner, non_windows) 1876
    testClusterExecute (cluster, runner, non_windows) 15526
    testConfigurationLoading (runner) 199
    testExecute (runner, non_windows) 1868
    testNcore (runner, non_windows) 11
    testPersistance (cluster, runner, non_windows) 11771
    +

    Ant test

    +

    compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile

    +

    back to summary

    +

    compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames

    +

    back to summary

    +

    compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames

    +

    back to summary

    +

    compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration

    +

    back to summary

    +

    compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta

    +

    back to summary

    +

    compbio.data.sequence.SequenceUtilTester:testCleanSequence

    +

    back to summary

    +

    compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence

    +

    back to summary

    +

    compbio.data.sequence.SequenceUtilTester:testReadWriteFasta

    +

    back to summary

    +

    compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence

    +

    back to summary

    +

    compbio.data.sequence.SequenceUtilTester:testisProteinSequence

    +

    back to summary

    +

    compbio.engine.EngineConfiguratorTester:testGetAsyncEngine

    +

    back to summary

    +

    compbio.engine.EngineConfiguratorTester:testGetSyncEngine

    +

    back to summary

    +

    compbio.engine.FilePullerTester:testCache

    +

    back to summary

    +

    compbio.engine.FilePullerTester:testGet

    +

    back to summary

    +

    compbio.engine.FilePullerTester:testGetDelay

    +

    back to summary

    +

    compbio.engine.FilePullerTester:testPull

    +

    back to summary

    +

    compbio.engine.PulledFileCacheTester:test

    +

    back to summary

    +

    compbio.engine.client.CommandBuilderTester:testCommandBuilding

    +

    back to summary

    +

    compbio.engine.client.CommandBuilderTester:testOptionsToCommand

    +

    back to summary

    +

    compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable

    +

    back to summary

    +

    compbio.engine.client.PathValidatorTester:testGetClassPath

    +

    back to summary

    +

    compbio.engine.client.PathValidatorTester:testIsAbsolutePath

    +

    back to summary

    +

    compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList

    +

    back to summary

    +

    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testCancel

    +
    +

    java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!

    +compbio.runner.msa.ClustalW.getResults(ClustalW.java:79) +
    at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37) +
    at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206) +
    at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109) +
    23 lines not shown +

    Caused by Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!

    +compbio.runner.Util.readClustalFile(Util.java:126) +
    at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76) +
    at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37) +
    at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206) +
    at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus

    +

    back to summary

    +

    compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit

    +

    back to summary

    +

    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel

    +

    back to summary

    +

    compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit

    +

    back to summary

    +

    compbio.engine.cluster.drmaa.UtilTester:testParser

    +

    back to summary

    +

    compbio.engine.cluster.dundee._QueueTester:testQueue

    +

    back to summary

    +

    compbio.engine.conf.DirectoryManagerTester:testGetDirectory

    +

    back to summary

    +

    compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf

    +

    back to summary

    +

    compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration

    +

    back to summary

    +

    compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration

    +

    back to summary

    +

    compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration

    +

    back to summary

    +

    compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration

    +

    back to summary

    +

    compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling

    +

    back to summary

    +

    compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration

    +

    back to summary

    +

    compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling

    +

    back to summary

    +

    compbio.engine.conf.RunnerConfigMarshallerTester:testValidation

    +

    back to summary

    +

    compbio.engine.conf.RunnerConfigMarshallerTester:testValidationOnMarshalling

    +
    +

    null

    +com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328) +
    at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) +
    at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) +
    at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) +
    at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258) +
    23 lines not shown +

    Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.

    +com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195) +
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131) +
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384) +
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685) +
    at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549) +
    at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527) +
    at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124) +
    at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697) +
    at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65) +
    at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168) +
    at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152) +
    at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592) +
    at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493) +
    at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325) +
    at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) +
    at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) +
    at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) +
    at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation

    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation

    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally

    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testCancelLocally

    +
    +

    null

    +java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) +
    at java.util.concurrent.FutureTask.get(FutureTask.java:83) +
    at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) +
    at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130) +
    at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testGetStatus

    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testMultipleCancelLocally

    +
    +

    null

    +java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) +
    at java.util.concurrent.FutureTask.get(FutureTask.java:83) +
    at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) +
    at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130) +
    at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally

    +

    back to summary

    +

    compbio.engine.local.LocalRunnerTester:testCancelCompletedTaskLocally

    +
    +

    null

    +java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) +
    at java.util.concurrent.FutureTask.get(FutureTask.java:83) +
    at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) +
    at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) +
    at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.engine.local.LocalRunnerTester:testCancelLocally

    +
    +

    null

    +java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) +
    at java.util.concurrent.FutureTask.get(FutureTask.java:83) +
    at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) +
    at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) +
    at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.engine.local.LocalRunnerTester:testMultipleCancelLocally

    +
    +

    null

    +java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220) +
    at java.util.concurrent.FutureTask.get(FutureTask.java:83) +
    at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108) +
    at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99) +
    at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.OptionCombinatorTester:testgetAllOptions

    +

    back to summary

    +

    compbio.metadata.OptionCombinatorTester:testgetAllParameters

    +

    back to summary

    +

    compbio.metadata.OptionMarshallerTester:testMarshalling

    +
    +

    null

    +com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328) +
    at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) +
    at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) +
    at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) +
    at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140) +
    23 lines not shown +

    Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.

    +com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195) +
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131) +
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384) +
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777) +
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685) +
    at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549) +
    at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527) +
    at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124) +
    at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697) +
    at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65) +
    at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168) +
    at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152) +
    at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592) +
    at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320) +
    at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493) +
    at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325) +
    at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254) +
    at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75) +
    at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88) +
    at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.OptionMarshallerTester:testUnMarshalling

    +

    back to summary

    +

    compbio.metadata.PresetTester:marshallPreset

    +

    back to summary

    +

    compbio.metadata.PresetTester:validatePresets

    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testCreateNumParameterWithoutValidValue

    +
    +

    Attempting to set default value for parameter: Option name: Matrix +Description: DNA weight matrix +URL: null +Is required: false + + Without possible values! Please define possible value first!

    +compbio.metadata.Parameter.setDefaultValue(Parameter.java:234) +
    at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testCreateParameter

    +
    +

    Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1 +Description: Protein weight matrix +URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html +Is required: true +Option Names: +--AAMATRIX +POSSIBLE VALUES: +BLOSUM +GONNET +ID +PAM + +

    +compbio.metadata.Parameter.setDefaultValue(Parameter.java:240) +
    at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain

    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testOptionNoDefaultValidate

    +
    +

    Default value is required as multiple optionNames are defined for option: Option name: Matrix1 +Description: Protein weight matrix +URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html +Is required: true +Option Names: +--AAMATRIX +--ABMAT +--BBBB +

    +compbio.metadata.Option.validate(Option.java:317) +
    at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testOptionSetInvalidValue

    +
    +

    Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1 +Description: Protein weight matrix +URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html +Is required: true +Option Names: +--AAMATRIX +--ABMAT +--BBBB +

    +compbio.metadata.Option.setDefaultValue(Option.java:130) +
    at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testOptionToCommand

    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testParameterToCommand

    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testValidate

    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testValidateBoundaryConstrainCheck

    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testValidateLowerBoundaryConstrainCheck

    +
    +

    Attempting to set default value outside boundaries defined by the constraint: Type: Float +Min: -10.12 +Max: 0 + + For parameter: Option name: Matrix1 +Description: Protein weight matrix +URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html +Is required: true +Option Names: +--AAMATRIX +Type: Float +Min: -10.12 +Max: 0 + +

    +compbio.metadata.Parameter.setDefaultValue(Parameter.java:248) +
    at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testValidateUpperBoundaryConstrainCheck

    +
    +

    Attempting to set default value outside boundaries defined by the constraint: Type: Float +Min: -10.12 +Max: 0 + + For parameter: Option name: Matrix1 +Description: Protein weight matrix +URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html +Is required: true +Option Names: +--AAMATRIX +Type: Float +Min: -10.12 +Max: 0 + +

    +compbio.metadata.Parameter.setDefaultValue(Parameter.java:248) +
    at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.metadata.RunnerConfigTester:testValidateValueConstrain

    +
    +

    Both boundaries (min and max) is undefined for ValueConstrain: Type: Float +

    +compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208) +
    at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341) +
    23 lines not shown +
    +

    back to summary

    +

    compbio.runner._impl.MclTester:testGetTestCommand

    +

    back to summary

    +

    compbio.runner._impl.NetNglycTester:testGetTestCommand

    +

    back to summary

    +

    compbio.runner._impl.OBTester:testGetTestArgsCommand

    +

    back to summary

    +

    compbio.runner._impl.OBTester:testGetTestCommand

    +

    back to summary

    +

    compbio.runner._impl.RPSBlastTester:testGetTestArgsCommand

    +

    back to summary

    +

    compbio.runner._impl.RPSBlastTester:testGetTestCommand

    +

    back to summary

    +

    compbio.runner._impl.RonnTester:testGetTestCommand

    +

    back to summary

    +

    compbio.runner._impl.Tmhmm2Tester:testGetTestCommand

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testArguments

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testConfiguration

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMaxValues

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMinValues

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersRandomValues

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testDefaultParameters

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testOptions

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testParameters

    +

    back to summary

    +

    compbio.runner.msa.ClustalWParametersTester:testPresets

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:readStatistics

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:readStatisticsClusterExecution

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:testConfigurationLoading

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:testOptionsLocally

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:testPersistance

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:testRunLocally

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:testRunOnCluster

    +

    back to summary

    +

    compbio.runner.msa.ClustalWTester:testRunWithMatrix

    +

    back to summary

    +

    compbio.runner.msa.LimitTester:testLoadLimits

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testArguments

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testConfiguration

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testConstrainedParametersMaxValues

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testConstrainedParametersMinValues

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testConstrainedParametersRandomValues

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testDefaultParameters

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testOptions

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testParameters

    +

    back to summary

    +

    compbio.runner.msa.MafftParametersTester:testPresets

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:readStatistics

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:testClusterExecute

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:testConfigurationLoading

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:testExecute

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:testPersistance

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:testRunOnClusterAsyncCheckStatusLongPoolingTime

    +

    back to summary

    +

    compbio.runner.msa.MafftTester:testSetInputTester

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testArguments

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testConfiguration

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMaxValues

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMinValues

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testConstrainedParametersRandomValues

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testDefaultParameters

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testOptions

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testParameters

    +

    back to summary

    +

    compbio.runner.msa.MuscleParametersTester:testPresets

    +

    back to summary

    +

    compbio.runner.msa.MuscleTester:readStatistics

    +

    back to summary

    +

    compbio.runner.msa.MuscleTester:testConfigurationLoading

    +

    back to summary

    +

    compbio.runner.msa.MuscleTester:testPersistance

    +

    back to summary

    +

    compbio.runner.msa.MuscleTester:testRunLocally

    +

    back to summary

    +

    compbio.runner.msa.MuscleTester:testRunOnCluster

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testArguments

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testConfiguration

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMaxValues

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMinValues

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersRandomValues

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testDefaultParameters

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testOptions

    +

    back to summary

    +

    compbio.runner.msa.ProbconsParametersTester:testParameters

    +

    back to summary

    +

    compbio.runner.msa.ProbconsTester:readStatistics

    +

    back to summary

    +

    compbio.runner.msa.ProbconsTester:testClusterExecute

    +

    back to summary

    +

    compbio.runner.msa.ProbconsTester:testConfigurationLoading

    +

    back to summary

    +

    compbio.runner.msa.ProbconsTester:testExecute

    +

    back to summary

    +

    compbio.runner.msa.ProbconsTester:testPersistance

    +

    back to summary

    +

    compbio.runner.msa.ProbconsTester:testSetInputTester

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testArguments

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testConfiguration

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMaxValues

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMinValues

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersRandomValues

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testDefaultParameters

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testOptions

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testParameters

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeParametersTester:testPresets

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeTester:readStatistics

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeTester:testClusterExecute

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeTester:testConfigurationLoading

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeTester:testExecute

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeTester:testNcore

    +

    back to summary

    +

    compbio.runner.msa.TcoffeeTester:testPersistance

    +

    back to summary

    + diff --git a/website/tests/index.html b/website/tests/index.html new file mode 100644 index 0000000..1b6147b --- /dev/null +++ b/website/tests/index.html @@ -0,0 +1,9 @@ + +Test results + + +

    Test results

    + + + +
    SuitePassedFailedSkippedtestng.xml
    Total16500 
    Ant suite16500Link
    diff --git a/website/tests/testng-failed.xml b/website/tests/testng-failed.xml new file mode 100644 index 0000000..b9ea5c6 --- /dev/null +++ b/website/tests/testng-failed.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/website/tests/testng-results.xml b/website/tests/testng-results.xml new file mode 100644 index 0000000..399a8e0 --- /dev/null +++ b/website/tests/testng-results.xml @@ -0,0 +1,1435 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/tests/testng.css b/website/tests/testng.css new file mode 100644 index 0000000..3904800 --- /dev/null +++ b/website/tests/testng.css @@ -0,0 +1,9 @@ +.invocation-failed, .test-failed { background-color: #DD0000; } +.invocation-percent, .test-percent { background-color: #006600; } +.invocation-passed, .test-passed { background-color: #00AA00; } +.invocation-skipped, .test-skipped { background-color: #CCCC00; } + +.main-page { + font-size: x-large; +} + diff --git a/website/ws.css b/website/ws.css new file mode 100644 index 0000000..6e28bc4 --- /dev/null +++ b/website/ws.css @@ -0,0 +1,227 @@ + +#banner { background-color:white; } + +/* +See index.html banner commented out code for an example of use +.uniicon { overflow: hidden; display:inline; padding:0; margin:0; float:right; position:relative; top:1em; } +.uniicon a img {border:none;} +*/ +#panel { width:150px; background:url("images/panel_bg.gif") repeat-y ; float:left; + font-family:Verdana, Arial, Helvetica, sans-serif; + } + +#content { margin-left:150px; border-bottom:solid 1px #6994af; } + +#page { margin: 0.5em; } + +#copyright { text-align:right; + color:#999999; + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:smaller; + line-height:1em; + } + +#wrapper { background:url("images/panel_bg.gif") repeat-y left top; } + +ul { + list-style-type: circle; +} + +#panel a:link, #panel a:visited { + text-decoration: none; + display:block; + line-height: 1em; + padding:10px; + color:#000000; + } + +#panel a:hover { + background-color: transparent; + text-decoration: underline; + } + +#panel a.selected { + text-decoration:underline; + font-weight:bolder; +} + +strong { + font-weight:bold; + color:#003366; +} + +pre { + font-family:Arial, Helvetica, sans-serif; +} + +p { + line-height: 1.4em; +} + +.hightlight { +font-style:italic; +font-family:"Courier New", Courier, monospace; +} + +.code { + font-size-adjust:0.4; + color:black; + background-color:#F5F5F5; + font-family:"Courier New",Courier,monospace; + font-style:normal; + margin:1em 0; + padding: 0.5em; + border: 1px dashed black; + display:block; +} + +.box { + color:black; + background-color:#F5F5F5; + font-family:Arial, Helvetica, sans-serif; + font-style:normal; + margin:1em 0; + font-size:0.9em; + padding: 0.5em; + border: 1px solid black; + display:block; +} + +.u { text-decoration: underline; } +/* .headeru { text-shadow: #CCCCCC 15px -14px 2px;} font-size-adjust:+0.7 */ +/*.headeru { text-shadow: 1px 0 black, 0 -1px black;} */ +.headeru { text-shadow: black 0.05em 0.05em 0.01em ;} +/* .headeru { border-bottom:1px solid white; } */ + +/* Table styles */ + + +#wrapper table { + border-collapse: collapse; + border: 1px solid #666; + margin: 20px 0 20px 0; + width: 100%; +} +#wrapper th, #wrapper td { + margin: 2px 4px 2px 4px; + padding: 0 5px; + text-align: left; + vertical-align: top; + border: 1px solid #666; +} + +#wrapper table caption { + font: 1.5em Georgia, "Times New Roman", Times, serif; + padding: 1em; + background-color: #9c9; +} + + +#wrapper tr { + background-color: #eee; +} + +#wrapper tr:nth-child(odd) { + background-color: #ccc; +} + + +span.directory { +background: transparent url(images/dir.gif) no-repeat scroll left center; +color:#666666; +font-family:"Courier New",Courier,monospace; +font-style:normal; +padding:0 0 0 15px; +} + +.attention { +color:#993333; +} + +/* open/closed box related styles */ + +.source { + border:1px solid #858789; + display:block; + margin:26px 0; + overflow:visible; +} + +/* OPEN state styles */ +.source .body { + background:#F5F5F5 none repeat scroll right 0; + color:#434546; + padding:7px 15px; +/* white-space:pre-wrap; */ + white-space:normal; +/* word-wrap:break-word; # this prop does not exits*/ +} + +.source .header { + background:#E9EAEC url(images/minus.png) no-repeat scroll 98% center; + color:#3B3D3F; + cursor:pointer; + font-weight:bold; + height:30px; + line-height:30px; + padding:0 15px 0 15px; +} + +/* CLOSED state styles */ +.source .body.collapsed { + display:none; +} + +.source .header.collapsed { + background:#E9EAEC url(images/plus.png) no-repeat scroll 98% center; + padding:0 15px 0 15px; +} + +.body .code { + margin:0; + padding:0; + border:0; + font-family:"Courier New",Courier,monospace; + font-style:normal; +} + +body { + font-family:Arial, Helvetica, sans-serif; + font-size: 9pt; + background-color: white; + line-height: 2em; + min-width:35em; +} + + +#banner table { + border-collapse: collapse; + border: none; + padding:0; + margin:0; + color:white; + text-align:center; + vertical-align:middle; + line-height:1.5em; + width: 100%; +} + +h3 {border-bottom: 1px solid grey; margin-top: 2em; } + +#banner td.bg { + border-collapse: collapse; + background-image:url("images/banner_bg.gif"); + background-repeat: repeat-x; + background-color:transparent; + background-position:inherit; +} + +img.logo { + border-top:1px solid #003b62; + border-left:1px solid #003b62; + border-right:none; + border-bottom: none; + margin:0; + padding:0; + display:inline +} \ No newline at end of file -- 1.7.10.2

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    + + + +
    + + + +
    +

    What is JABAWS?

    + +

    JAva Bioinformatics Analysis Web Services (JABAWS) is a +collection of SOAP web +services for bioinformatics.
    + JABAWS is designed to make it easy to access bioinformatics +analysis programs and databases over the web from anywhere, at +anytime. Unlike other web services, JABAWS can be easily installed on different platforms and work straight out of the box with minimum configuration. JABA Web Services are designed for use by other programs rather +than people. + The current version of JABAWS is compatible with version 2.6 of Jalview, and provides five web +services for multiple sequence alignment:

    + + + +

    Why JABAWS?

    + +

    JABAWS can be deployed on nearly any operation system, it can operate on a stand alone server as well as submit the jobs to the cluster. Thanks to DRMAA it integrates well with a large variety of cluster job management systems. Jalview from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. Please look in the how to for more information on JABAWS benefits.

    +

    Public JABAWS Server

    + + + + + + + + + + + + + + + + + + + + + + +
    FeatureDescription
    URL http://www.compbio.dundee.ac.uk/jabaws
    Execution limitsJABAWS installation is backed up by the College of +Life Sciences HPC cluster. Tasks exceeding 1000×1000 +(sequences per letters) will not be accepted for alignment. If you +would like to work with bigger alignments consider installing +JABAWS in your lab.
    Web Services DescriptionWSDL List
    + +For programmatic access to JABAWS please refer to the How To section using JABAWS in your program. +

    Authors

    +

    Peter Troshin and Geoff Barton are the authors of the JABA Web +Services. Jim Procter helped with the JABAWS design process and web +pages, and developed the interface and management components in +Jalview to access JABAWS servers.

    +
    + + + +
    + + +