From: pvtroshin Date: Fri, 12 Aug 2011 13:29:30 +0000 (+0000) Subject: remove dm javadoc to update X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d593e4828b2ce526a4e1fd1b11c8f78b112b5f5;p=jabaws.git remove dm javadoc to update git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4505 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/website/dm_javadoc/allclasses-frame.html b/website/dm_javadoc/allclasses-frame.html deleted file mode 100644 index c45a41e..0000000 --- a/website/dm_javadoc/allclasses-frame.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - -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 deleted file mode 100644 index 1120a19..0000000 --- a/website/dm_javadoc/allclasses-noframe.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -

- - - diff --git a/website/dm_javadoc/compbio/data/msa/MsaWS.html b/website/dm_javadoc/compbio/data/msa/MsaWS.html deleted file mode 100644 index 122814d..0000000 --- a/website/dm_javadoc/compbio/data/msa/MsaWS.html +++ /dev/null @@ -1,556 +0,0 @@ - - - - - - -MsaWS - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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- -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
- String align(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- boolean cancelJob(String jobId) - -
-          Stop running the job jobId but leave its output untouched
- String customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- JobStatus getJobStatus(String jobId) - -
-          Return the status of the job.
- Limit<T> getLimit(String presetName) - -
-          Get a Limit for a preset.
- LimitsManager<T> getLimits() - -
-          List Limits supported by a web service.
- PresetManager<T> getPresets() - -
-          Get presets supported by a web service
- Alignment getResult(String jobId) - -
-          Return the result of the job.
- RunnerConfig<T> getRunnerOptions() - -
-          Get options supported by a web service
- String presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
- ChunkHolder pullExecStatistics(String jobId, - long position) - -
-          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
- -

-Method Summary
- `String`	`align(List<FastaSequence> sequences)` - - - Align a list of sequences with default settings.
- `boolean`	`cancelJob(String jobId)` - - - Stop running the job `jobId` but leave its output untouched
- `String`	`customAlign(List<FastaSequence> sequences, - List<Option<T>> options)` - - - Align a list of sequences with options.
- `JobStatus`	`getJobStatus(String jobId)` - - - Return the status of the job.
- `Limit<T>`	`getLimit(String presetName)` - - - Get a Limit for a preset.
- `LimitsManager<T>`	`getLimits()` - - - List Limits supported by a web service.
- `PresetManager<T>`	`getPresets()` - - - Get presets supported by a web service
- `Alignment`	`getResult(String jobId)` - - - Return the result of the job.
- `RunnerConfig<T>`	`getRunnerOptions()` - - - Get options supported by a web service
- `String`	`presetAlign(List<FastaSequence> sequences, - Preset<T> preset)` - - - Align a list of sequences with preset.
- `ChunkHolder`	`pullExecStatistics(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

-String align(List<FastaSequence> sequences)
-             throws UnsupportedRuntimeException,
-                    LimitExceededException,
-                    JobSubmissionException

Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

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

- -

-customAlign

-String customAlign(List<FastaSequence> sequences,
-                   List<Option<T>> options)
-                   throws UnsupportedRuntimeException,
-                          LimitExceededException,
-                          JobSubmissionException,
-                          WrongParameterException

Align a list of sequences with options. -

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

- -

-presetAlign

-String presetAlign(List<FastaSequence> sequences,
-                   Preset<T> preset)
-                   throws UnsupportedRuntimeException,
-                          LimitExceededException,
-                          JobSubmissionException,
-                          WrongParameterException

Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

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

- -

-getResult

-Alignment getResult(String jobId)
-                    throws ResultNotAvailableException

Return the result of the job. This method waits for the job - jobId to complete before return. -

Parameters:: jobId - a unique job identifier -
Returns:: Alignment -
Throws: -: ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -; InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid - format

- -

-cancelJob

-boolean cancelJob(String jobId)

Stop running the job jobId but leave its output untouched -

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

- -

-getJobStatus

-JobStatus getJobStatus(String jobId)

Return the status of the job. -

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

- -

-pullExecStatistics

-ChunkHolder pullExecStatistics(String jobId,
-                               long position)

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

Parameters:: jobId - - unique job identifier; position - - next position within the file to read -
Returns:: ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read -
Throws: -: InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format and also if the position value is negative
See Also:: ChunkHolder

- -

-getRunnerOptions

-RunnerConfig<T> getRunnerOptions()

Get options supported by a web service -

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

- -

-getPresets

-PresetManager<T> getPresets()

Get presets supported by a web service -

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

- -

-getLimit

-Limit<T> getLimit(String presetName)

Get a Limit for a preset. -

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

- -

-getLimits

-LimitsManager<T> getLimits()

List Limits supported by a web service. -

Returns:: LimitManager

- -

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- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html deleted file mode 100644 index 2fd76ec..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.MsaWS - - - - - - - - - - - - -

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-Packages that use MsaWS
compbio.ws.client	A 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(String host, - Services service) - -
- Connects to a web service by the host and the service name
- -

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-Interfaces - -
-MsaWS

- - - - diff --git a/website/dm_javadoc/compbio/data/msa/package-summary.html b/website/dm_javadoc/compbio/data/msa/package-summary.html deleted file mode 100644 index 26b6877..0000000 --- a/website/dm_javadoc/compbio/data/msa/package-summary.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - -compbio.data.msa - - - - - - - - - - - - -

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-Package compbio.data.msa -

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

-See: -
- Description -

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

-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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compbio.data.msa.MsaWS<T>

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-Packages that use compbio.data.msa
compbio.ws.client	A 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
- -

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

- - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html deleted file mode 100644 index 5f14d30..0000000 --- a/website/dm_javadoc/compbio/data/sequence/Alignment.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - -Alignment - - - - - - - - - - - - -

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- -compbio.data.sequence -
-Class Alignment

-java.lang.Object
-  compbio.data.sequence.Alignment
-

@Immutable -public final class Alignment
extends Object
extends Object

- - -

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

- -

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

- -

- - - - - - - - - - - - - - -
-Constructor Summary
Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-
Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- boolean equals(Object obj) - -
-          Please note that this implementation does not take the order of sequences - into account!
- AlignmentMetadata getMetadata() - -
-
- List<FastaSequence> getSequences() - -
-
- int getSize() - -
-
- int hashCode() - -
-
- String toString() - -
-
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
- -

-Constructor Summary
`Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata)` - - -
`Alignment(List<FastaSequence> sequences, - Program program, - char gapchar)` - - -

-Method Summary
- `boolean`	`equals(Object obj)` - - - Please note that this implementation does not take the order of sequences - into account!
- `AlignmentMetadata`	`getMetadata()` - - -
- `List<FastaSequence>`	`getSequences()` - - -
- `int`	`getSize()` - - -
- `int`	`hashCode()` - - -
- `String`	`toString()` - - -

Methods inherited from class java.lang.Object
`clone, finalize, getClass, notify, notifyAll, wait, wait, wait`

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

-Alignment

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

Parameters:: sequences -; program -; gapchar -

- -

-Alignment

-public Alignment(List<FastaSequence> sequences,
-                 AlignmentMetadata metadata)

Parameters:: sequences -; metadata -

- - - - - - - - - -

-Method Detail

- -

-getSequences

-public List<FastaSequence> getSequences()

Returns:: list of FastaSequence records

- -

-getSize

-public int getSize()

Returns:: a number of sequence in the alignment

- -

-getMetadata

-public AlignmentMetadata getMetadata()

Returns:: AlignmentMetadata object

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-equals

-public boolean equals(Object obj)

Please note that this implementation does not take the order of sequences - into account! -

Overrides:: equals in class Object

- -

- - - - - - - - - - - - - - - - - - - -

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- -compbio.data.sequence -
-Class AlignmentMetadata

-java.lang.Object
-  compbio.data.sequence.AlignmentMetadata
-

@Immutable -public class AlignmentMetadata
extends Object
extends Object

- - -

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

- -

Version:: 1.0 September 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Constructor Summary
AlignmentMetadata(Program program, - char gapchar) - -
-
- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- boolean equals(Object obj) - -
-
- char getGapchar() - -
-
- Program getProgram() - -
-
- int hashCode() - -
-
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
- -

-Constructor Summary
`AlignmentMetadata(Program program, - char gapchar)` - - -

-Method Summary
- `boolean`	`equals(Object obj)` - - -
- `char`	`getGapchar()` - - -
- `Program`	`getProgram()` - - -
- `int`	`hashCode()` - - -

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(Object obj)

Overrides:: equals in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index 3cbace7..0000000 --- a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html +++ /dev/null @@ -1,387 +0,0 @@ - - - - - - -ClustalAlignmentUtil - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

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- -compbio.data.sequence -
-Class ClustalAlignmentUtil

-java.lang.Object
-  compbio.data.sequence.ClustalAlignmentUtil
-

public final class ClustalAlignmentUtil
extends Object
extends Object

- - -

-Tools to read and write clustal formated files -

- -

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

- -

- - - - - - - - - - - -
-Field Summary
-static char gapchar - -
-          Dash char to be used as gap char in the alignments
- - - - - - - - - - - -
-Constructor Summary
ClustalAlignmentUtil() - -
-
- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static boolean isValidClustalFile(InputStream input) - -
-          Please note this method closes the input stream provided as a parameter
-static Alignment readClustalFile(File file) - -
-
-static Alignment readClustalFile(InputStream instream) - -
-          Read Clustal formatted alignment.
-static void writeClustalAlignment(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(InputStream instream)
-                                 throws IOException,
-                                        UnknownFileFormatException

Read Clustal formatted alignment. Limitations: Does not read consensus - - Sequence names as well as the sequences are not guaranteed to be unique! -

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

- -

-isValidClustalFile

-public static boolean isValidClustalFile(InputStream input)

Please note this method closes the input stream provided as a parameter -

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

- -

-writeClustalAlignment

-public static void writeClustalAlignment(OutputStream outStream,
-                                         Alignment alignment)
-                                  throws IOException

Write Clustal formatted alignment Limitations: does not record the - consensus. Potential bug - records 60 chars length alignment where - Clustal would have recorded 50 chars. -

Parameters:: outStream -; alignment - -
Throws: -: IOException

- -

-readClustalFile

-public static Alignment readClustalFile(File file)
-                                 throws UnknownFileFormatException,
-                                        IOException

Throws: -: UnknownFileFormatException -; IOException

- -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index f7ead48..0000000 --- a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html +++ /dev/null @@ -1,471 +0,0 @@ - - - - - - -FastaSequence - - - - - - - - - - - - -

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- -

- -compbio.data.sequence -
-Class FastaSequence

-java.lang.Object
-  compbio.data.sequence.FastaSequence
-

@Immutable -public class FastaSequence
extends Object
extends Object

- - -

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

- -

Version:: 1.0 September 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Constructor Summary
FastaSequence(String id, - String sequence) - -
-          Upon construction the any whitespace characters are removed from the - sequence
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static int countMatchesInSequence(String theString, - String theRegExp) - -
-
- boolean equals(Object obj) - -
-
- String getFormatedSequence(int width) - -
-          Format sequence per width letter in one string.
- String getFormattedFasta() - -
-
- String getId() - -
-          Gets the value of id
- int getLength() - -
-
- String getOnelineFasta() - -
-
- String getSequence() - -
-          Gets the value of sequence
- int hashCode() - -
-
- String toString() - -
-          Same as oneLineFasta
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
- -

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

-FastaSequence

-public FastaSequence(String id,
-                     String sequence)

Upon construction the any whitespace characters are removed from the - sequence -

Parameters:: id -; sequence -

- - - - - - - - -

-Method Detail

- -

-getId

-public String getId()

Gets the value of id -

Returns:: the value of id

- -

-getSequence

-public String getSequence()

Gets the value of sequence -

Returns:: the value of sequence

- -

-countMatchesInSequence

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

- -

-getFormattedFasta

-public String getFormattedFasta()

- -

-getOnelineFasta

-public String getOnelineFasta()

Returns:: one line name, next line sequence, no matter what the sequence - length is

- -

-getFormatedSequence

-public String getFormatedSequence(int width)

Format sequence per width letter in one string. Without spaces. -

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

- -

-getLength

-public int getLength()

Returns:: sequence length

- -

-toString

-public String toString()

Same as oneLineFasta -

Overrides:: toString in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/Program.html b/website/dm_javadoc/compbio/data/sequence/Program.html deleted file mode 100644 index 909a998..0000000 --- a/website/dm_javadoc/compbio/data/sequence/Program.html +++ /dev/null @@ -1,388 +0,0 @@ - - - - - - -Program - - - - - - - - - - - - -

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- - - -

- -

- -compbio.data.sequence -
-Enum Program

-java.lang.Object
-  java.lang.Enum<Program>
-      compbio.data.sequence.Program
-

All Implemented Interfaces:: Serializable, Comparable<Program>

public enum Program
extends Enum<Program>
extends Enum<Program>

- - -

-The list of programmes that can produce alignments -

- -

Author:: pvtroshin

- -

- - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CLUSTAL - -
-          ClustalW
MAFFT - -
-          Mafft
MUSCLE - -
-          Muscle
Probcons - -
-          Probcons
Tcoffee - -
-          Tcoffee
- - - - - - - - - - - - - - - - -
-Method Summary
-static Program valueOf(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(String name)

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

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

- -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index de2bd93..0000000 --- a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html +++ /dev/null @@ -1,673 +0,0 @@ - - - - - - -SequenceUtil - - - - - - - - - - - - -

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- -

- -compbio.data.sequence -
-Class SequenceUtil

-java.lang.Object
-  compbio.data.sequence.SequenceUtil
-

public final class SequenceUtil
extends Object
extends Object

- - -

-Utility class for operations on sequences -

- -

Version:: 1.0
Author:: Petr Troshin

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static Pattern AA - -
-          Valid Amino acids
-static Pattern AMBIGUOUS_AA - -
-          Same as AA pattern but with two additional letters - XU
-static Pattern AMBIGUOUS_NUCLEOTIDE - -
-          Ambiguous nucleotide
-static Pattern DIGIT - -
-          A digit
-static Pattern NON_AA - -
-          inversion of AA pattern
-static Pattern NON_NUCLEOTIDE - -
-          Non nucleotide
-static Pattern NONWORD - -
-          Non word
-static Pattern NUCLEOTIDE - -
-          Nucleotides a, t, g, c, u
-static Pattern WHITE_SPACE - -
-          A whitespace character: [\t\n\x0B\f\r]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static String cleanSequence(String sequence) - -
-          Removes all whitespace chars in the sequence string
-static void closeSilently(Logger log, - Closeable stream) - -
-          Closes the Closable and logs the exception if any
-static String deepCleanSequence(String sequence) - -
-          Removes all special characters and digits as well as whitespace chars - from the sequence
-static boolean isAmbiguosProtein(String sequence) - -
-          Check whether the sequence confirms to amboguous protein sequence
-static boolean isNonAmbNucleotideSequence(String sequence) - -
-          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char
-static boolean isNucleotideSequence(FastaSequence s) - -
-
-static boolean isProteinSequence(String sequence) - -
-
-static List<FastaSequence> readFasta(InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-static void writeFasta(OutputStream os, - List<FastaSequence> sequences) - -
-          Writes FastaSequence in the file, each sequence will take one line only
-static void writeFasta(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
-          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-static void writeFastaKeepTheStream(OutputStream outstream, - 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 Pattern WHITE_SPACE

A whitespace character: [\t\n\x0B\f\r] -

- -

-DIGIT

-public static final Pattern DIGIT

A digit -

- -

-NONWORD

-public static final Pattern NONWORD

Non word -

- -

-AA

-public static final Pattern AA

Valid Amino acids -

- -

-NON_AA

-public static final Pattern NON_AA

inversion of AA pattern -

- -

-AMBIGUOUS_AA

-public static final Pattern AMBIGUOUS_AA

Same as AA pattern but with two additional letters - XU -

- -

-NUCLEOTIDE

-public static final Pattern NUCLEOTIDE

Nucleotides a, t, g, c, u -

- -

-AMBIGUOUS_NUCLEOTIDE

-public static final Pattern AMBIGUOUS_NUCLEOTIDE

Ambiguous nucleotide -

- -

-NON_NUCLEOTIDE

-public static final Pattern NON_NUCLEOTIDE

Non nucleotide -

- -

- - - - - - - - -

-Method Detail

- -

-isNucleotideSequence

-public static boolean isNucleotideSequence(FastaSequence s)

Returns:: true is the sequence contains only letters a,c, t, g, u

- -

-isNonAmbNucleotideSequence

-public static boolean isNonAmbNucleotideSequence(String sequence)

Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -

- -

-cleanSequence

-public static String cleanSequence(String sequence)

Removes all whitespace chars in the sequence string -

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

- -

-deepCleanSequence

-public static String deepCleanSequence(String sequence)

Removes all special characters and digits as well as whitespace chars - from the sequence -

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

- -

-isProteinSequence

-public static boolean isProteinSequence(String sequence)

Parameters:: sequence - -
Returns:: true is the sequence is a protein sequence, false overwise

- -

-isAmbiguosProtein

-public static boolean isAmbiguosProtein(String sequence)

Check whether the sequence confirms to amboguous protein sequence -

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

- -

-writeFasta

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

Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -

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

- -

-writeFastaKeepTheStream

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

Throws: -: IOException

- -

-readFasta

-public static List<FastaSequence> readFasta(InputStream inStream)
-                                     throws IOException

Reads fasta sequences from inStream into the list of FastaSequence - objects -

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

- -

-writeFasta

-public static void writeFasta(OutputStream os,
-                              List<FastaSequence> sequences)
-                       throws IOException

Writes FastaSequence in the file, each sequence will take one line only -

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

- -

-closeSilently

-public static final void closeSilently(Logger log,
-                                       Closeable stream)

Closes the Closable and logs the exception if any -

Parameters:: log -; stream -

- -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html deleted file mode 100644 index 6163110..0000000 --- a/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - -UnknownFileFormatException - - - - - - - - - - - - -

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- -compbio.data.sequence -
-Class UnknownFileFormatException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.data.sequence.UnknownFileFormatException
-

All Implemented Interfaces:: Serializable

public class UnknownFileFormatException
extends Exception
extends Exception

- - -

See Also:: Serialized Form

- -

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

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

-UnknownFileFormatException

-public UnknownFileFormatException()

- -

-UnknownFileFormatException

-public UnknownFileFormatException(File file,
-                                  Throwable cause)

- -

-UnknownFileFormatException

-public UnknownFileFormatException(String message,
-                                  Throwable cause)

- -

-UnknownFileFormatException

-public UnknownFileFormatException(String message)

- -

-UnknownFileFormatException

-public UnknownFileFormatException(Throwable cause)

- - -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html deleted file mode 100644 index cfddffa..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Alignment - - - - - - - - - - - - -

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-Uses of Class
compbio.data.sequence.Alignment

- - - - - - - - - - - - - - -

-Packages that use Alignment
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
compbio.data.sequence	A 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
- Alignment MsaWS.getResult(String jobId) - -
- Return the result of the job.
- -

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

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

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

- - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html deleted file mode 100644 index 48f1339..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.AlignmentMetadata - - - - - - - - - - - - -

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compbio.data.sequence.AlignmentMetadata

- - - - - - - - - - -

-Packages that use AlignmentMetadata
compbio.data.sequence	A 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
- AlignmentMetadata Alignment.getMetadata() - -
-
- -

- - - - - - - - -
Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-
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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html deleted file mode 100644 index 4b31821..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html +++ /dev/null @@ -1,362 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.FastaSequence - - - - - - - - - - - - -

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-Uses of Class
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- - - - - - - - - - - - - - - - - - -

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

- -

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

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.msa with type arguments of type FastaSequence
- String MsaWS.align(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- String MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- String MsaWS.presetAlign(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
- List<FastaSequence> Alignment.getSequences() - -
-
-static List<FastaSequence> SequenceUtil.readFasta(InputStream inStream) - -
- Reads fasta sequences from inStream into the list of FastaSequence - objects
- -

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

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

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

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

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

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

- - - - - - - - - - - -
Constructors in compbio.data.sequence with parameters of type Program
Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
-
AlignmentMetadata(Program program, - char gapchar) - -
-
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-Packages that use UnknownFileFormatException
compbio.data.sequence	A 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 Alignment ClustalAlignmentUtil.readClustalFile(File file) - -
-
-static Alignment ClustalAlignmentUtil.readClustalFile(InputStream instream) - -
- Read Clustal formatted alignment.
- -

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-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 deleted file mode 100644 index 1609e36..0000000 --- a/website/dm_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -

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-Package compbio.data.sequence -

-A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. -

-See: -
- Description -

- - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
Alignment Multiple sequence alignment.
AlignmentMetadata Alignment metadata e.g.
ClustalAlignmentUtil Tools to read and write clustal formated files
FastaSequence A FASTA formatted sequence.
SequenceUtil Utility class for operations on sequences
- - -

- - - - - - - - - -
-Enum Summary
Program The 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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-Hierarchy For Package compbio.data.sequence -

- -

Package Hierarchies:: All Packages

-Class Hierarchy -

java.lang.Object
- compbio.data.sequence.Alignment
- compbio.data.sequence.AlignmentMetadata
- compbio.data.sequence.ClustalAlignmentUtil
- compbio.data.sequence.FastaSequence
- compbio.data.sequence.SequenceUtil
- java.lang.Throwable (implements java.io.Serializable) -
  - java.lang.Exception
    - compbio.data.sequence.UnknownFileFormatException
    -
  -
-

-Enum Hierarchy -

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) -
  - compbio.data.sequence.Program
  -
-

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

- -

- - - - - - - - - - - -
-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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- - - diff --git a/website/dm_javadoc/compbio/metadata/Argument.html b/website/dm_javadoc/compbio/metadata/Argument.html deleted file mode 100644 index b500d00..0000000 --- a/website/dm_javadoc/compbio/metadata/Argument.html +++ /dev/null @@ -1,327 +0,0 @@ - - - - - - -Argument - - - - - - - - - - - - -

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- -compbio.metadata -
-Interface Argument<T>


Type Parameters:: T - executable type

All Known Implementing Classes:: Option, Parameter

public interface Argument<T>

- - -

-An unmodifiable view for the options and parameters, with one exception - it - allows to set a value -

- -

Author:: pvtroshin - - Date December 2009
See Also:: Parameter, -Option

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- String getDefaultValue() - -
-
- String getDescription() - -
-
- URL getFurtherDetails() - -
-
- String getName() - -
-
- List<String> getPossibleValues() - -
-
- void setValue(String defaultValue) - -
-          Set default values for the parameter or an option
- -

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

-getFurtherDetails

-URL getFurtherDetails()

- -

-getDefaultValue

-String getDefaultValue()

- -

-getDescription

-String getDescription()

- -

-getName

-String getName()

- -

-getPossibleValues

-List<String> getPossibleValues()

Returns:: List of values allowed for an Argument

- -

-setValue

-void setValue(String defaultValue)
-              throws WrongParameterException

Set default values for the parameter or an option -

Parameters:: defaultValue - the value to be set -
Throws: -: WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:: ValueConstrain

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- - - diff --git a/website/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/ChunkHolder.html deleted file mode 100644 index c898bcc..0000000 --- a/website/dm_javadoc/compbio/metadata/ChunkHolder.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -ChunkHolder - - - - - - - - - - - - -

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- -compbio.metadata -
-Class ChunkHolder

-java.lang.Object
-  compbio.metadata.ChunkHolder
-

public class ChunkHolder
extends Object
extends Object

- - -

-Represents a chunk of a string data together with the position in a file for - the next read operation. -

- -

Version:: 1.0 December 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Constructor Summary
ChunkHolder(String chunk, - long position) - -
-
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-Method Summary
- boolean equals(Object obj) - -
-
- String getChunk() - -
-
- long getNextPosition() - -
-
- int hashCode() - -
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- String toString() - -
-
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
- -

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-Constructor Detail
- -

-ChunkHolder

-public ChunkHolder(String chunk,
-                   long position)

- - - - - - - - - -

-Method Detail

- -

-getChunk

-public String getChunk()

- -

-getNextPosition

-public long getNextPosition()

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-hashCode

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Overrides:: hashCode in class Object

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- - - diff --git a/website/dm_javadoc/compbio/metadata/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index 1e83666..0000000 --- a/website/dm_javadoc/compbio/metadata/JobExecutionException.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - -JobExecutionException - - - - - - - - - - - - -

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- -compbio.metadata -
-Class JobExecutionException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.metadata.JobExecutionException
-

All Implemented Interfaces:: Serializable

public class JobExecutionException
extends Exception
extends Exception

- - -

-JobExecutionException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides DrmaaException -

- -

Version:: 1.0 October 2009
Author:: pvtroshin
See Also:: Serialized Form

- -

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

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

-JobExecutionException

-public JobExecutionException(String message)

- -

-JobExecutionException

-public JobExecutionException(Throwable cause)

- -

-JobExecutionException

-public JobExecutionException(String message,
-                             Throwable cause)

- - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/JobStatus.html b/website/dm_javadoc/compbio/metadata/JobStatus.html deleted file mode 100644 index 8728f80..0000000 --- a/website/dm_javadoc/compbio/metadata/JobStatus.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -JobStatus - - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Enum JobStatus

-java.lang.Object
-  java.lang.Enum<JobStatus>
-      compbio.metadata.JobStatus
-

All Implemented Interfaces:: Serializable, Comparable<JobStatus>

public enum JobStatus
extends Enum<JobStatus>
extends Enum<JobStatus>

- - -

-The status of the job. -

- -

Version:: 1.0 October 2009
Author:: pvtroshin

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CANCELLED - -
-          Jobs that has been cancelled
COLLECTED - -
-          Results has been collected
FAILED - -
-          Failed jobs
FINISHED - -
-          Finished jobs
PENDING - -
-          Jobs which are in the queue and awaiting execution reported for cluster - jobs only
RUNNING - -
-          Jobs that are running
STARTED - -
-          Job calculation has been started.
SUBMITTED - -
-          Job has been submitted.
UNDEFINED - -
-          Represents jobs with unknown status
- - - - - - - - - - - - - - - - -
-Method Summary
-static JobStatus valueOf(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(String name)

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

- -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html deleted file mode 100644 index 59f457e..0000000 --- a/website/dm_javadoc/compbio/metadata/JobSubmissionException.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -JobSubmissionException - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

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- -compbio.metadata -
-Class JobSubmissionException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.metadata.JobSubmissionException
-

All Implemented Interfaces:: Serializable

Direct Known Subclasses:: LimitExceededException, UnsupportedRuntimeException

public class JobSubmissionException
extends Exception
extends Exception

- - -

-Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException. If - this exception is thrown the task has not been calculated -

- -

Author:: pvtroshin - - Date December 2009
See Also:: Serialized Form

- -

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

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

-JobSubmissionException

-public JobSubmissionException(String message)

- -

-JobSubmissionException

-public JobSubmissionException(Throwable cause)

- -

-JobSubmissionException

-public JobSubmissionException(String message,
-                              Throwable cause)

- - -

- - - - - - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/Limit.html b/website/dm_javadoc/compbio/metadata/Limit.html deleted file mode 100644 index 51efd54..0000000 --- a/website/dm_javadoc/compbio/metadata/Limit.html +++ /dev/null @@ -1,478 +0,0 @@ - - - - - - -Limit - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

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- -compbio.metadata -
-Class Limit<T>

-java.lang.Object
-  compbio.metadata.Limit<T>
-


Type Parameters:: T - the type of an executable for which this limit is defined.

public class Limit<T>
extends Object
extends Object

- - -

-A value object containing a maximum number of sequences and a maximum average - sequence length for a preset. Also contains static method for determining the - number of sequence and their average length in the List -

- -

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

- -

- - - - - - - - - - - - - - -
-Constructor Summary
Limit(int seqNumber, - int seqLength, - String preset) - -
-          Instantiate the limit
Limit(int seqNumber, - int seqLength, - String preset, - boolean isDefault) - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- boolean equals(Object obj) - -
-
- int getAvgSeqLength() - -
-
-static int getAvgSequenceLength(List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- String getPreset() - -
-
- int getSeqNumber() - -
-
- int hashCode() - -
-
- boolean isDefault() - -
-
- boolean isExceeded(List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
- String toString() - -
-
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
- -

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

-Limit

-public Limit(int seqNumber,
-             int seqLength,
-             String preset)

Instantiate the limit -

Parameters:: seqNumber - the maximum number of sequences allowed for calculation. - Required; seqLength - the average length of the sequence, optional; preset - the name of preset if any, optional -
Throws: -: IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative

- -

-Limit

-public Limit(int seqNumber,
-             int seqLength,
-             String preset,
-             boolean isDefault)

- - - - - - - - - -

-Method Detail

- -

-getPreset

-public String getPreset()

- -

-getAvgSeqLength

-public int getAvgSeqLength()

Returns:: the allowed average sequence length

- -

-getSeqNumber

-public int getSeqNumber()

Returns:: the maximum number of sequences allowed

- -

-isDefault

-public boolean isDefault()

Returns:: true is this is a default limit to be used, false otherwise

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-isExceeded

-public boolean isExceeded(List<FastaSequence> data)

Checks if the number of sequences or their average length in the dataset - exceeds this limit. -

Parameters:: data - the dataset to measure -
Returns:: true if a limit is exceeded (what is the dataset is larger then - the limit), false otherwise. First check the number of sequences - in the dataset and if it exceeds the limit return true - irrespective of the average length. If the number of sequences in - the dataset is less than the limit and average length is defined, - then check whether the total number of letters (number of - sequence multiplied by the average sequence length) is greater - then the total number of letters in the dataset. Returns true if - the total number of letters in the dataset is greater than the - limit, false otherwise.

- -

-getAvgSequenceLength

-public static int getAvgSequenceLength(List<FastaSequence> data)

Calculates an average sequence length of the dataset -

Parameters:: data - -
Returns:: an average sequence length in the input dataset

- -

- - - - - - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/LimitExceededException.html deleted file mode 100644 index 9fbf007..0000000 --- a/website/dm_javadoc/compbio/metadata/LimitExceededException.html +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - -LimitExceededException - - - - - - - - - - - - -

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- -compbio.metadata -
-Class LimitExceededException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.metadata.JobSubmissionException
-              compbio.metadata.LimitExceededException
-

All Implemented Interfaces:: Serializable

public class LimitExceededException
extends JobSubmissionException
extends JobSubmissionException

- - -

-This exception is thrown if the task larger in size that the limit that - applies to the calculation. -

- -

Version:: 1.0 February 2010
Author:: pvtroshin
See Also:: Limit, -Serialized Form

- -

- - - - - - - - - - - -
-Constructor Summary
LimitExceededException(String message) - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- int getActualNumberofSequences() - -
-
- int getNumberOfSequencesAllowed() - -
-
- int getSequenceLenghtActual() - -
-
- int getSequenceLenghtAllowed() - -
-
-static LimitExceededException newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
-
- - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
- -

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

-LimitExceededException

-public LimitExceededException(String message)

- - - - - - - - - -

-Method Detail

- -

-newLimitExceeded

-public static LimitExceededException newLimitExceeded(Limit<?> limit,
-                                                      List<FastaSequence> seqs)

- -

-getNumberOfSequencesAllowed

-public int getNumberOfSequencesAllowed()

- -

-getActualNumberofSequences

-public int getActualNumberofSequences()

- -

-getSequenceLenghtAllowed

-public int getSequenceLenghtAllowed()

- -

-getSequenceLenghtActual

-public int getSequenceLenghtActual()

- -

- - -

- - - - - - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/LimitsManager.html b/website/dm_javadoc/compbio/metadata/LimitsManager.html deleted file mode 100644 index 52a8aaf..0000000 --- a/website/dm_javadoc/compbio/metadata/LimitsManager.html +++ /dev/null @@ -1,363 +0,0 @@ - - - - - - -LimitsManager - - - - - - - - - - - - -

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- -compbio.metadata -
-Class LimitsManager<T>

-java.lang.Object
-  compbio.metadata.LimitsManager<T>
-


Type Parameters:: T - executable type

public class LimitsManager<T>
extends Object
extends Object

- - -

-A collection of Limits -

- -

Version:: 1.0 January 2010
Author:: pvtroshin
See Also:: Limit

- -

- - - - - - - - - - - -
-Constructor Summary
LimitsManager() - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Limit<T> getDefaultLimit() - -
-
- Limit<T> getLimitByName(String presetName) - -
-
- List<Limit<T>> getLimits() - -
-
- String toString() - -
-
- void validate(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 List<Limit<T>> getLimits()

Returns:: all limits defined for an executable T

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-getLimitByName

-public Limit<T> getLimitByName(String presetName)

Parameters:: presetName - -
Returns:: Limit defined for the executable T and presetName. If no limit is - defined for the presetName then default Limit is returned. If - presetName is empty or null than the default Limit will be - returned. If not limit defined for the type T than NULL will be - returned

- -

-getDefaultLimit

-public Limit<T> getDefaultLimit()

Returns:: the default Limit for an executable type T

- -

-validate

-public void validate(PresetManager<T> presets)
-              throws ValidationException

Validate Limits -

Parameters:: presets - -
Throws: -: ValidationException - if any of the Limit defined is found to be invalid. That is - when - - 1) No default limit is defined - - 2) More than 1 default limit is defined - - 3) Limit's preset name does not match any presets for type T
See Also:: Limit, -Preset

- -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/Option.html b/website/dm_javadoc/compbio/metadata/Option.html deleted file mode 100644 index 7fc0e28..0000000 --- a/website/dm_javadoc/compbio/metadata/Option.html +++ /dev/null @@ -1,822 +0,0 @@ - - - - - - -Option - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Class Option<T>

-java.lang.Object
-  compbio.metadata.Option<T>
-


Type Parameters:: T - type of executable

All Implemented Interfaces:: Argument<T>

Direct Known Subclasses:: Parameter

public class Option<T>
extends Object
implements Argument<T>
extends Object
implements Argument<T>

- - -

-Command line option/flag or multiple exclusive options with no value. Example - -protein, -dna, -auto -

- -

Version:: 1.0 October 2009
Author:: pvtroshin

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-protected String defaultValue - -
-
-protected String description - -
-
-protected URL furtherDetails - -
-
-protected boolean isRequired - -
-
-protected String name - -
-
- - - - - - - - - - - -
-Constructor Summary
Option(String name, - String description) - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Set<String> addOptionNames(String... value) - -
-          Adds an option to the optionName list
- boolean equals(Object obj) - -
-
- String getDefaultValue() - -
-          A default value of the option.
- String getDescription() - -
-          A long description of the Option
- URL getFurtherDetails() - -
-          The URL where further details about the option can be found
- String getName() - -
-          Human readable name of the option
- List<String> getOptionNames() - -
-
- List<String> getPossibleValues() - -
-          List of possible optionNames
- int hashCode() - -
-
- boolean isRequired() - -
-          Flag that indicated that this option must be specified in the command - line for an executable to run
- void setDefaultValue(String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- void setDescription(String description) - -
-
- void setFurtherDetails(URL furtherDetails) - -
-
- void setName(String name) - -
-
- void setOptionNames(Set<String> optionNames) - -
-
- void setRequired(boolean isRequired) - -
-
- void setValue(String dValue) - -
-          Set default values for the parameter or an option
- String toCommand(String nameValueSeparator) - -
-          Convert the option to the command string.
- String toString() - -
-
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
- -

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

-description

-protected String description

- - -

- -

-name

-protected String name

- - -

- -

-isRequired

-protected boolean isRequired

- - -

- -

-furtherDetails

-protected URL furtherDetails

- - -

- -

-defaultValue

-protected String defaultValue

- - - - - - - - - - -

-Constructor Detail

- -

-Option

-public Option(String name,
-              String description)

- - - - - - - - - -

-Method Detail

- -

-getName

-public String getName()

Human readable name of the option -

Specified by:: getName in interface Argument<T>

- -

-setName

-public void setName(String name)

- -

-getDescription

-public String getDescription()

A long description of the Option -

Specified by:: getDescription in interface Argument<T>

- -

-setDescription

-public void setDescription(String description)

- -

-getFurtherDetails

-public URL getFurtherDetails()

The URL where further details about the option can be found -

Specified by:: getFurtherDetails in interface Argument<T>

- -

-setFurtherDetails

-public void setFurtherDetails(URL furtherDetails)

- -

-getDefaultValue

-public String getDefaultValue()

A default value of the option. Defaults to command line argument name - e.g. -auto -

Specified by:: getDefaultValue in interface Argument<T>

- -

-setDefaultValue

-public void setDefaultValue(String defaultVal)
-                     throws WrongParameterException

Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

- -

Parameters:: defaultVal - -
Throws: -: WrongParameterException - is thrown if the defaultValue is not found in optionList

- -

-isRequired

-public boolean isRequired()

Flag that indicated that this option must be specified in the command - line for an executable to run -

- -

Returns:: true is the option is required, false otherwise

- -

-setRequired

-public void setRequired(boolean isRequired)

- -

-getOptionNames

-public List<String> getOptionNames()

- -

Returns:: List of option names

- -

-setOptionNames

-public void setOptionNames(Set<String> optionNames)

- -

-addOptionNames

-public Set<String> addOptionNames(String... value)

Adds an option to the optionName list -

- -

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

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-toCommand

-public String toCommand(String nameValueSeparator)

Convert the option to the command string. -

- -

Returns:: If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-getPossibleValues

-public List<String> getPossibleValues()

List of possible optionNames -

Specified by:: getPossibleValues in interface Argument<T>

Returns:: List of values allowed for an Argument

- -

-setValue

-public void setValue(String dValue)
-              throws WrongParameterException

Description copied from interface: Argument

Set default values for the parameter or an option -

Specified by:: setValue in interface Argument<T>

Parameters:: dValue - the value to be set -
Throws: -: WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:: ValueConstrain

- -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/Parameter.html b/website/dm_javadoc/compbio/metadata/Parameter.html deleted file mode 100644 index 7a54dc1..0000000 --- a/website/dm_javadoc/compbio/metadata/Parameter.html +++ /dev/null @@ -1,590 +0,0 @@ - - - - - - -Parameter - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Class Parameter<T>

-java.lang.Object
-  compbio.metadata.Option<T>
-      compbio.metadata.Parameter<T>
-

All Implemented Interfaces:: Argument<T>

public class Parameter<T>
extends Option<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(String name, - String description) - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Set<String> addOptionNames(String... value) - -
-          Adds an option to the optionName list
- Set<String> addPossibleValues(String... value) - -
-
- boolean equals(Object obj) - -
-
- String getOptionName() - -
-
- List<String> getPossibleValues() - -
-          List is more convenient to work with
- ValueConstrain getValidValue() - -
-
- int hashCode() - -
-
- void setDefaultValue(String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- void setOptionName(String optionName) - -
-
- void setOptionNames(Set<String> optionName) - -
-
- void setPossibleValues(Set<String> possibleValues) - -
-
- void setValidValue(ValueConstrain validValue) - -
-
- String toCommand(String nameValueSeparator) - -
-          Convert the option to the command string.
- String toString() - -
-
- - - - - - - - -
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(String name,
-                 String description)

- - - - - - - - - -

-Method Detail

- -

-getValidValue

-public ValueConstrain getValidValue()

- -

-setValidValue

-public void setValidValue(ValueConstrain validValue)

- -

-toString

-public String toString()

Overrides:: toString in class Option<T>

- -

-toCommand

-public String toCommand(String nameValueSeparator)

Description copied from class: Option

Convert the option to the command string. -

Overrides:: toCommand in class Option<T>

Returns:: If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Option<T>

- -

-getPossibleValues

-public List<String> getPossibleValues()

List is more convenient to work with -

Specified by:: getPossibleValues in interface Argument<T>
Overrides:: getPossibleValues in class Option<T>

Returns:: List of String

- -

-setPossibleValues

-public void setPossibleValues(Set<String> possibleValues)

- -

-addPossibleValues

-public Set<String> addPossibleValues(String... value)

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Option<T>

- -

-setOptionNames

-public void setOptionNames(Set<String> optionName)

Overrides:: setOptionNames in class Option<T>

- -

-addOptionNames

-public Set<String> addOptionNames(String... value)

Description copied from class: Option

Adds an option to the optionName list -

Overrides:: addOptionNames in class Option<T>

Returns:: modified optionName list

- -

-getOptionName

-public String getOptionName()

- -

-setOptionName

-public void setOptionName(String optionName)

- -

-setDefaultValue

-public void setDefaultValue(String defaultVal)
-                     throws WrongParameterException

Description copied from class: Option

Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

Overrides:: setDefaultValue in class Option<T>

Throws: -: WrongParameterException - is thrown if the defaultValue is not found in optionList

- -

- - - - - - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/Preset.html b/website/dm_javadoc/compbio/metadata/Preset.html deleted file mode 100644 index e42c70d..0000000 --- a/website/dm_javadoc/compbio/metadata/Preset.html +++ /dev/null @@ -1,455 +0,0 @@ - - - - - - -Preset - - - - - - - - - - - - -

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- -compbio.metadata -
-Class Preset<T>

-java.lang.Object
-  compbio.metadata.Preset<T>
-


Type Parameters:: T - executable type

public class Preset<T>
extends Object
extends Object

- - -

-Collection of Options and Parameters with their values -

- -

Version:: 1.0 December 2009
Author:: pvtroshin
See Also:: Option, -Parameter

- -

- - - - - - - - - - - -
-Constructor Summary
Preset() - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- boolean equals(Object obj) - -
-
- List<Option<T>> getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- String getDescription() - -
-
- String getName() - -
-
- List<String> getOptions() - -
-
- int hashCode() - -
-
- void setDescription(String description) - -
-
- void setName(String name) - -
-
- void setOptions(List<String> option) - -
-
- String toString() - -
-
- - - - - - - - -
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(List<String> option)

- -

-setName

-public void setName(String name)

- -

-setDescription

-public void setDescription(String description)

- -

-getOptions

-public List<String> getOptions()

Returns:: a List of Options as a String

- -

-getName

-public String getName()

Returns:: - name of the Preset

- -

-getDescription

-public String getDescription()

Returns:: - a long description of the Preset

- -

-getArguments

-public List<Option<T>> getArguments(RunnerConfig<T> rconfig)
-                             throws WrongParameterException

Converts list of options as String to type Option -

Parameters:: rconfig - -
Returns:: List of Options -
Throws: -: WrongParameterException - if the value of the parameter is invalid @see - Parameter

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

- - - - - - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/PresetManager.html b/website/dm_javadoc/compbio/metadata/PresetManager.html deleted file mode 100644 index 5ecd88a..0000000 --- a/website/dm_javadoc/compbio/metadata/PresetManager.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - -PresetManager - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Class PresetManager<T>

-java.lang.Object
-  compbio.metadata.PresetManager<T>
-


Type Parameters:: T - type of executable.

public class PresetManager<T>
extends Object
extends Object

- - -

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

- -

Version:: 1.0 December 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Field Summary
-static String LOCAL_ENGINE_LIMIT_PRESET - -
-
- - - - - - - - - - - -
-Constructor Summary
PresetManager() - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Preset<T> getPresetByName(String presetName) - -
-
- List<Preset<T>> getPresets() - -
-
- String getRunnerClassName() - -
-
- void setPresets(List<Preset<T>> presets) - -
-
- void setRunnerClassName(String runnerClassName) - -
-
- String toString() - -
-
- void validate(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 String LOCAL_ENGINE_LIMIT_PRESET

See Also:: Constant Field Values

- - - - - - - - - -

-Constructor Detail

- -

-PresetManager

-public PresetManager()

- - - - - - - - - -

-Method Detail

- -

-getPresets

-public List<Preset<T>> getPresets()

- -

-setPresets

-public void setPresets(List<Preset<T>> presets)

- -

-getRunnerClassName

-public String getRunnerClassName()

Returns:: fully qualified class name of type T

- -

-setRunnerClassName

-public void setRunnerClassName(String runnerClassName)

- -

-getPresetByName

-public Preset<T> getPresetByName(String presetName)

Parameters:: presetName - -
Returns:: preset by its name, null if no preset found

- -

-validate

-public void validate(RunnerConfig<T> options)
-              throws ValidationException

Checks whether preset option and parameter are defined in RunnerConfig - object. - - TODO handle parameters with values properly! -

Throws: -: ValidationException - if preset is found to be invalid.

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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-DETAIL: FIELD | CONSTR | METHOD

- - - -

- - - diff --git a/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html deleted file mode 100644 index 423c8b1..0000000 --- a/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -ResultNotAvailableException - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Class ResultNotAvailableException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.metadata.ResultNotAvailableException
-

All Implemented Interfaces:: Serializable

public class ResultNotAvailableException
extends Exception
extends Exception

- - -

-ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides lower level exceptions - like DrmaaException -

- -

Author:: pvtroshin - - Date October 2009
See Also:: Serialized Form

- -

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

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

-ResultNotAvailableException

-public ResultNotAvailableException(String message)

- -

-ResultNotAvailableException

-public ResultNotAvailableException(Throwable cause)

- -

-ResultNotAvailableException

-public ResultNotAvailableException(String message,
-                                   Throwable cause)

- - -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html deleted file mode 100644 index 0e8948a..0000000 --- a/website/dm_javadoc/compbio/metadata/RunnerConfig.html +++ /dev/null @@ -1,706 +0,0 @@ - - - - - - -RunnerConfig - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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- - - -

- -

- -compbio.metadata -
-Class RunnerConfig<T>

-java.lang.Object
-  compbio.metadata.RunnerConfig<T>
-


Type Parameters:: T - type of an Executable

@NotThreadSafe -public class RunnerConfig<T>
extends Object
extends Object

- - -

-The list of Parameters and Options supported by executable. - The lists is defined in and loaded from Parameters.xml file. -

- -

Version:: 1.0 October 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Constructor Summary
RunnerConfig() - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- void addOption(Option<T> option) - -
-          Adds Option to the internal list of options
- void addParameter(Parameter<T> param) - -
-          Adds parameter to the internal parameter list
- RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
-
- boolean equals(Object obj) - -
-
- Option<T> getArgument(String name) - -
-          Returns the argument by its name if found, NULL otherwise.
- Option<T> getArgumentByOptionName(String optionName) - -
-          Returns the argument by option name, NULL if the argument is not found
- List<Option<T>> getArguments() - -
-          Returns list of Parameter and Option supported by current - runner
- List<Option<T>> getOptions() - -
-          Returns the list of the Options supported by the executable of type T
- List<Parameter<T>> getParameters() - -
-          Returns the list of parameters supported executable of type T.
- String getPrmSeparator() - -
-
- String getRunnerClassName() - -
-
- boolean removeArgument(String name) - -
-          Removes the argument Argument if found.
- boolean removeArgumentByOptionName(String optionName) - -
-          Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor.
- void setOptions(List<Option<T>> parameters) - -
-          Adds the list of options or parameters to the internal list of options
- void setParameters(List<Parameter<T>> parameters) - -
-          Sets the list of parameters as internal list
- void setPrmSeparator(String prmSeparator) - -
-          Sets name value separator character
- void setRunnerClassName(String runnerClassName) - -
-          Set the name of a runner class
- String toString() - -
-
- void validate() - -
-          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 List<Option<T>> getOptions()

Returns the list of the Options supported by the executable of type T -

Returns:: list of Option supported by type T
See Also:: Option

- -

-addParameter

-public void addParameter(Parameter<T> param)

Adds parameter to the internal parameter list -

Parameters:: param - the Parameter to add
See Also:: Parameter

- -

-addOption

-public void addOption(Option<T> option)

Adds Option to the internal list of options -

Parameters:: option - the Option to add

- -

-getArguments

-public List<Option<T>> getArguments()

Returns list of Parameter and Option supported by current - runner -

Returns:: list of Option and Parameter supported by type T

- -

-getPrmSeparator

-public String getPrmSeparator()

Returns:: name value separator character

- -

-setPrmSeparator

-public void setPrmSeparator(String prmSeparator)

Sets name value separator character -

Parameters:: prmSeparator - the separator char

- -

-setOptions

-public void setOptions(List<Option<T>> parameters)

Adds the list of options or parameters to the internal list of options -

Parameters:: parameters - the list of parameters to add

- -

-getRunnerClassName

-public String getRunnerClassName()

Returns:: fully qualified class name for type T

- -

-setRunnerClassName

-public void setRunnerClassName(String runnerClassName)

Set the name of a runner class -

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

- -

-setParameters

-public void setParameters(List<Parameter<T>> parameters)

Sets the list of parameters as internal list -

Parameters:: parameters - the list of parameters

- -

-getParameters

-public List<Parameter<T>> getParameters()

Returns the list of parameters supported executable of type T. Where - Parameter is an Option with value. -

Returns:: List of Parameter supported by type T.

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

-getArgument

-public Option<T> getArgument(String name)

Returns the argument by its name if found, NULL otherwise. Where the - Argument is a common interface for Option and Parameter - therefore this method can return either. If you need to retrieve the - Option by its optionNames use @link - getArgumentByOptionName(String) method. The - difference between option name and optionName is explained by the - following example: - -

- Sequence type
-         
-         --nuc - Assume the sequences are nucleotide.
-         --amino - Assume the sequences are amino acid. 
-         --amino
-         --nuc
-         --auto
-

- - In the example, the "Sequence type" is a name whereas --amino, --nuc and - --auto are all optionNames. This dichotomy only manifests in - Option never in Parameters as the latter can - only have single element -

Parameters:: name - the Parameter of Option name -
Returns:: Argument

- -

-removeArgument

-public boolean removeArgument(String name)

Removes the argument Argument if found. Where Argument is either - Option or Parameter. -

Parameters:: name - of the argument -
Returns:: true if argument was removed, false otherwise

- -

-getArgumentByOptionName

-public Option<T> getArgumentByOptionName(String optionName)

Returns the argument by option name, NULL if the argument is not found -

Parameters:

optionName - - the optionName. This is not the same as an Option name. - - For example: - -

-            Output sequences order
-                          --inputorder - Output order: same as input. 
-                           --reorder - Output order: aligned. Default: same as input
-                          --inputorder
-                          --reorder
-

- - The name of the option in the example is - "Output sequences order" whereas optionNames are - "--inputorder" and "--reorder". If you need to retrieve the - Option or Parameter by its names use - getArgument(String) method -

Returns:

Option

- -

-removeArgumentByOptionName

-public boolean removeArgumentByOptionName(String optionName)

Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -

Parameters:: optionName - the optionName of the option, do not confuse with the name! -
Returns:: true if argument with optionName exists and was removed, false - otherwise
See Also:: for destinctions - between optionNames and the name of the Option

- -

-validate

-public void validate()
-              throws ValidationException

Validate the value of the argument. Checks whether the argument value is - in the valid values range. -

Throws: -

ValidationException - if any of the arguments found invalid which is when -

Parameter value outside ValueConstrain boundary

Parameter name is not listed in possible values

- -

- - - - - - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html deleted file mode 100644 index dd5739b..0000000 --- a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Class UnsupportedRuntimeException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.metadata.JobSubmissionException
-              compbio.metadata.UnsupportedRuntimeException
-

All Implemented Interfaces:: Serializable

public class UnsupportedRuntimeException
extends JobSubmissionException
extends JobSubmissionException

- - -

-Indicates that the server could not execute native executables. e.g. If Mafft - (unix executable) is asked to be run on Windows. In context of JABAWS this - exception indicates that the service is deployed but is not able to run. -

- -

Author:: pvtroshin - - Date February 2010
See Also:: Serialized Form

- -

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

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

-UnsupportedRuntimeException

-public UnsupportedRuntimeException(String message)

- -

-UnsupportedRuntimeException

-public UnsupportedRuntimeException(Throwable cause)

- - -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html deleted file mode 100644 index fbbe56c..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - -ValueConstrain.Type - - - - - - - - - - - - -

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- -

- -compbio.metadata -
-Enum ValueConstrain.Type

-java.lang.Object
-  java.lang.Enum<ValueConstrain.Type>
-      compbio.metadata.ValueConstrain.Type
-

All Implemented Interfaces:: Serializable, Comparable<ValueConstrain.Type>

Enclosing class:: ValueConstrain

public static enum ValueConstrain.Type
extends Enum<ValueConstrain.Type>
extends Enum<ValueConstrain.Type>

- - -

- -

- - - - - - - - - - - - - -
-Enum Constant Summary
Float - -
-
Integer - -
-
- - - - - - - - - - - - - - - - -
-Method Summary
-static ValueConstrain.Type valueOf(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(String name)

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

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- - - diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index 5968d9e..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -ValueConstrain - - - - - - - - - - - - -

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- -compbio.metadata -
-Class ValueConstrain

-java.lang.Object
-  compbio.metadata.ValueConstrain
-

public class ValueConstrain
extends Object
extends Object

- - -

-The type and the lower and upper boundaries for numerical value. -

- -

Version:: 1.0 November 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Nested Class Summary
-static class ValueConstrain.Type - -
-
- - - - - - - - - - - -
-Constructor Summary
ValueConstrain() - -
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- boolean equals(Object obj) - -
-
- Number getMax() - -
-
- Number getMin() - -
-
- ValueConstrain.Type getType() - -
-
- int hashCode() - -
-
- void setMax(String max) - -
-
- void setMin(String min) - -
-
- void setType(ValueConstrain.Type type) - -
-
- String toString() - -
-
- - - - - - - - -
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 Number getMax()

- -

-setMax

-public void setMax(String max)

- -

-getMin

-public Number getMin()

- -

-setMin

-public void setMin(String min)

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

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- - - diff --git a/website/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/WrongParameterException.html deleted file mode 100644 index f8703fe..0000000 --- a/website/dm_javadoc/compbio/metadata/WrongParameterException.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -WrongParameterException - - - - - - - - - - - - -

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- -compbio.metadata -
-Class WrongParameterException

-java.lang.Object
-  java.lang.Throwable
-      java.lang.Exception
-          compbio.metadata.WrongParameterException
-

All Implemented Interfaces:: Serializable

public class WrongParameterException
extends Exception
extends Exception

- - -

-WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value. -

- -

Version:: 1.0 October 2009
Author:: pvtroshin
See Also:: Serialized Form

- -

- - - - - - - - - - - - - - - - - - - - -
-Constructor Summary
WrongParameterException(Option<?> option) - -
-
WrongParameterException(String message) - -
-
WrongParameterException(String message, - Throwable cause) - -
-
WrongParameterException(Throwable cause) - -
-
- - - - - - - - -
-Method Summary
- - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
- - - - - - - - -
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
- -

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

-WrongParameterException

-public WrongParameterException(Option<?> option)

- -

-WrongParameterException

-public WrongParameterException(String message)

- -

-WrongParameterException

-public WrongParameterException(Throwable cause)

- -

-WrongParameterException

-public WrongParameterException(String message,
-                               Throwable cause)

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Argument.html b/website/dm_javadoc/compbio/metadata/class-use/Argument.html deleted file mode 100644 index 59618f6..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Argument.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.metadata.Argument - - - - - - - - - - - - -

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compbio.metadata.Argument

- - - - - - - - - - -

-Packages that use Argument
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.

- -

- - - - - -
-Uses of Argument in compbio.metadata
- -

- - - - - - - - - - - - - -
Classes in compbio.metadata that implement Argument
- class Option<T> - -
- Command line option/flag or multiple exclusive options with no value.
- class Parameter<T> - -
- A single value containing an option supported by the web service e.g.
- -

- - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html deleted file mode 100644 index c36b0c5..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,182 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.ChunkHolder - - - - - - - - - - - - -

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- - - - - - - - - - -

-Packages that use ChunkHolder
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.

- -

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

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

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html deleted file mode 100644 index 27480e2..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.JobExecutionException - - - - - - - - - - - - -

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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 deleted file mode 100644 index e3d7c98..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html +++ /dev/null @@ -1,219 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.JobStatus - - - - - - - - - - - - -

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- - - - - - - - - - - - - - -

-Packages that use JobStatus
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - -
Methods in compbio.data.msa that return JobStatus
- JobStatus MsaWS.getJobStatus(String jobId) - -
- Return the status of the job.
- -

- - - - - -
-Uses of JobStatus in compbio.metadata
- -

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

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html deleted file mode 100644 index 1f7c42c..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html +++ /dev/null @@ -1,237 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.JobSubmissionException - - - - - - - - - - - - -

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- - - - - - - - - - - - - - -

-Packages that use JobSubmissionException
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.msa that throw JobSubmissionException
- String MsaWS.align(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- String MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- String MsaWS.presetAlign(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
- class LimitExceededException - -
- This exception is thrown if the task larger in size that the limit that - applies to the calculation.
- class UnsupportedRuntimeException - -
- Indicates that the server could not execute native executables.
- -

- - - - - - - - - - - - - - - -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Limit.html b/website/dm_javadoc/compbio/metadata/class-use/Limit.html deleted file mode 100644 index aad5361..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Limit.html +++ /dev/null @@ -1,251 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Limit - - - - - - - - - - - - -

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-Uses of Class
compbio.metadata.Limit

- - - - - - - - - - - - - - -

-Packages that use Limit
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - -
Methods in compbio.data.msa that return Limit
- Limit<T> MsaWS.getLimit(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(String presetName) - -
-
- -

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

- - - - - - - - - -
Methods in compbio.metadata with parameters of type Limit
-static LimitExceededException LimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
-
- -

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- - - - - - - - - - - - - - -

-Packages that use LimitExceededException
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.msa that throw LimitExceededException
- String MsaWS.align(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- String MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- String MsaWS.presetAlign(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 LimitExceededException LimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
-
- -

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html deleted file mode 100644 index d097a36..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.LimitsManager - - - - - - - - - - - - -

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compbio.metadata.LimitsManager

- - - - - - - - - - -

-Packages that use LimitsManager
compbio.data.msa	Web 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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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Option.html b/website/dm_javadoc/compbio/metadata/class-use/Option.html deleted file mode 100644 index 9a7fff7..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Option.html +++ /dev/null @@ -1,314 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Option - - - - - - - - - - - - -

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compbio.metadata.Option

- - - - - - - - - - - - - - -

-Packages that use Option
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - -
Method parameters in compbio.data.msa with type arguments of type Option
- String MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
- Align a list of sequences with options.
- -

- - - - - -
-Uses of Option in compbio.metadata
- -

- - - - - - - - - -
Subclasses of Option in compbio.metadata
- class Parameter<T> - -
- A single value containing an option supported by the web service e.g.
- -

- - - - - - - - - - - - - -
Methods in compbio.metadata that return Option
- Option<T> RunnerConfig.getArgument(String name) - -
- Returns the argument by its name if found, NULL otherwise.
- Option<T> RunnerConfig.getArgumentByOptionName(String optionName) - -
- Returns the argument by option name, NULL if the argument is not found
- -

- - - - - - - - - - - - - - - - - -
Methods in compbio.metadata that return types with arguments of type Option
- List<Option<T>> RunnerConfig.getArguments() - -
-          Returns list of Parameter and Option supported by current - runner
- List<Option<T>> Preset.getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- List<Option<T>> RunnerConfig.getOptions() - -
-          Returns the list of the Options supported by the executable of type T
- -

- - - - - - - - - -
Methods in compbio.metadata with parameters of type Option
- void RunnerConfig.addOption(Option<T> option) - -
- Adds Option to the internal list of options
- -

- - - - - - - - - -
Method parameters in compbio.metadata with type arguments of type Option
- void RunnerConfig.setOptions(List<Option<T>> parameters) - -
- Adds the list of options or parameters to the internal list of options
- -

- - - - - - - - -
Constructors in compbio.metadata with parameters of type Option
WrongParameterException(Option<?> option) - -
-
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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.

- -

- - - - - -
-Uses of Parameter in compbio.metadata
- -

- - - - - - - - - -
Methods in compbio.metadata that return types with arguments of type Parameter
- List<Parameter<T>> RunnerConfig.getParameters() - -
- Returns the list of parameters supported executable of type T.
- -

- - - - - - - - - -
Methods in compbio.metadata with parameters of type Parameter
- void RunnerConfig.addParameter(Parameter<T> param) - -
- Adds parameter to the internal parameter list
- -

- - - - - - - - - -
Method parameters in compbio.metadata with type arguments of type Parameter
- void RunnerConfig.setParameters(List<Parameter<T>> parameters) - -
- Sets the list of parameters as internal list
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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Preset.html b/website/dm_javadoc/compbio/metadata/class-use/Preset.html deleted file mode 100644 index 5f4b0d5..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Preset.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Preset - - - - - - - - - - - - -

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-Packages that use Preset
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - -
Methods in compbio.data.msa with parameters of type Preset
- String MsaWS.presetAlign(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(String presetName) - -
-
- -

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

- - - - - - - - - -
Method parameters in compbio.metadata with type arguments of type Preset
- void PresetManager.setPresets(List<Preset<T>> presets) - -
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compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

- - - - - -
-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
- void LimitsManager.validate(PresetManager<T> presets) - -
- Validate Limits
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compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.

- -

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

- - - - - - - - - -
Methods in compbio.data.msa that throw ResultNotAvailableException
- Alignment MsaWS.getResult(String jobId) - -
- Return the result of the job.
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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/class-use/RunnerConfig.html deleted file mode 100644 index 077e951..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/RunnerConfig.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.RunnerConfig - - - - - - - - - - - - -

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-Packages that use RunnerConfig
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

- - - - - -
-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
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- - - - - - - - - -
Methods in compbio.metadata that return RunnerConfig
- RunnerConfig<T> RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
-
- -

- - - - - - - - - - - - - - - - - -
Methods in compbio.metadata with parameters of type RunnerConfig
- RunnerConfig<T> RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
-
- List<Option<T>> Preset.getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- void PresetManager.validate(RunnerConfig<T> options) - -
-          Checks whether preset option and parameter are defined in RunnerConfig - object.
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-Packages that use UnsupportedRuntimeException
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.

- -

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

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

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- - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html deleted file mode 100644 index 29605fc..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html +++ /dev/null @@ -1,214 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.ValueConstrain.Type - - - - - - - - - - - - -

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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.

- -

- - - - - -
-Uses of ValueConstrain.Type in compbio.metadata
- -

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

- - - - - - - - - -
Methods in compbio.metadata with parameters of type ValueConstrain.Type
- void ValueConstrain.setType(ValueConstrain.Type type) - -
-
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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.

- -

- - - - - -
-Uses of ValueConstrain in compbio.metadata
- -

- - - - - - - - - -
Methods in compbio.metadata that return ValueConstrain
- ValueConstrain Parameter.getValidValue() - -
-
- -

- - - - - - - - - -
Methods in compbio.metadata with parameters of type ValueConstrain
- void Parameter.setValidValue(ValueConstrain validValue) - -
-
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compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

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

- - - - - - - - - - - - - -
Methods in compbio.data.msa that throw WrongParameterException
- String MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
- Align a list of sequences with options.
- String MsaWS.presetAlign(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
- List<Option<T>> Preset.getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- void Parameter.setDefaultValue(String defaultVal) - -
-
- void Option.setDefaultValue(String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- void Argument.setValue(String defaultValue) - -
-          Set default values for the parameter or an option
- void Option.setValue(String dValue) - -
-
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-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 deleted file mode 100644 index 6256e43..0000000 --- a/website/dm_javadoc/compbio/metadata/package-summary.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -compbio.metadata - - - - - - - - - - - - -

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-Package compbio.metadata -

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

-See: -
- Description -

- - - - - - - - - -
-Interface Summary
Argument<T> An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
- - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
ChunkHolder Represents 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.
ValueConstrain The type and the lower and upper boundaries for numerical value.
- - -

- - - - - - - - - - - - - -
-Enum Summary
JobStatus The status of the job.
ValueConstrain.Type
- - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Exception Summary
JobExecutionException JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
JobSubmissionException Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
LimitExceededException This exception is thrown if the task larger in size that the limit that - applies to the calculation.
ResultNotAvailableException ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
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.
- - -

-Package compbio.metadata Description -

- -

-A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS) -

- -

Version:: 1.0 January 2010
Author:: Peter Troshin

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-Hierarchy For Package compbio.metadata -

- -

Package Hierarchies:: All Packages

-Class Hierarchy -

java.lang.Object
- compbio.metadata.ChunkHolder
- compbio.metadata.Limit<T>
- compbio.metadata.LimitsManager<T>
- compbio.metadata.Option<T> (implements compbio.metadata.Argument<T>) -
  - compbio.metadata.Parameter<T>
  -
- compbio.metadata.Preset<T>
- compbio.metadata.PresetManager<T>
- compbio.metadata.RunnerConfig<T>
- java.lang.Throwable (implements java.io.Serializable) -
  - java.lang.Exception
    - compbio.metadata.JobExecutionException
    - compbio.metadata.JobSubmissionException
      - compbio.metadata.LimitExceededException
      - compbio.metadata.UnsupportedRuntimeException
      -
    - compbio.metadata.ResultNotAvailableException
    - compbio.metadata.WrongParameterException
    -
  -
- compbio.metadata.ValueConstrain
-

-Interface Hierarchy -

compbio.metadata.Argument<T>

-Enum Hierarchy -

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) -
  - compbio.metadata.ValueConstrain.Type
  - compbio.metadata.JobStatus
  -
-

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- - - diff --git a/website/dm_javadoc/compbio/metadata/package-use.html b/website/dm_javadoc/compbio/metadata/package-use.html deleted file mode 100644 index 3c74190..0000000 --- a/website/dm_javadoc/compbio/metadata/package-use.html +++ /dev/null @@ -1,347 +0,0 @@ - - - - - - -Uses of Package compbio.metadata - - - - - - - - - - - - -

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compbio.metadata

- - - - - - - - - - - - - - -

-Packages that use compbio.metadata
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.metadata used by compbio.data.msa
ChunkHolder - -
-          Represents a chunk of a string data together with the position in a file for - the next read operation.
JobStatus - -
-          The status of the job.
JobSubmissionException - -
-          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
Limit - -
-          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
LimitExceededException - -
-          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
LimitsManager - -
-          A collection of Limits
Option - -
-          Command line option/flag or multiple exclusive options with no value.
Preset - -
-          Collection of Options and Parameters with their values
PresetManager - -
-          Collection of presets and methods to manipulate them @see Preset
ResultNotAvailableException - -
-          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
RunnerConfig - -
-          The list of Parameters and Options supported by executable.
UnsupportedRuntimeException - -
-          Indicates that the server could not execute native executables.
WrongParameterException - -
-          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.metadata used by compbio.metadata
Argument - -
-          An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
JobStatus - -
-          The status of the job.
JobSubmissionException - -
-          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
Limit - -
-          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
LimitExceededException - -
-          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
Option - -
-          Command line option/flag or multiple exclusive options with no value.
Parameter - -
-          A single value containing an option supported by the web service e.g.
Preset - -
-          Collection of Options and Parameters with their values
PresetManager - -
-          Collection of presets and methods to manipulate them @see Preset
RunnerConfig - -
-          The list of Parameters and Options supported by executable.
ValueConstrain - -
-          The type and the lower and upper boundaries for numerical value.
ValueConstrain.Type - -
-
WrongParameterException - -
-          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
- -

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- -compbio.ws.client -
-Class Jws2Client

-java.lang.Object
-  compbio.ws.client.Jws2Client
-

public class Jws2Client
extends Object
extends Object

- - -

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

- -

Version:: 1.0
Author:: pvtroshin

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static - - - - - -<T> MsaWS<T> - connect(String host, - Services service) - -
-          Connects to a web service by the host and the service name
-static String getHost(String[] cmd) - -
-          Extracts host name from the command line
-static String getServiceName(String[] cmd) - -
-          Extracts service name from the command line
-static void main(String[] args) - -
-          Starts command line client, if no parameter are supported print help.
-static boolean validURL(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(String urlstr)

Attempt to construct the URL object from the string -

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

- -

-getServiceName

-public static String getServiceName(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 String getHost(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(String host,
-                                   Services service)
-                        throws 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: -: WebServiceException

- -

-main

-public static void main(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!

- -

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- -compbio.ws.client -
-Enum Services

-java.lang.Object
-  java.lang.Enum<Services>
-      compbio.ws.client.Services
-

All Implemented Interfaces:: Serializable, Comparable<Services>

public enum Services
extends Enum<Services>
extends Enum<Services>

- - -

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

- -

- - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
ClustalWS - -
-
MafftWS - -
-
MuscleWS - -
-
ProbconsWS - -
-
TcoffeeWS - -
-
- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static Services getService(Class wsImplClass) - -
-
-static Services getService(String servName) - -
-
-static Services valueOf(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(String name)

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

- -

-getService

-public static Services getService(String servName)

- -

-getService

-public static Services getService(Class wsImplClass)

- -

- - -

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- - - diff --git a/website/dm_javadoc/compbio/ws/client/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html deleted file mode 100644 index ce5d917..0000000 --- a/website/dm_javadoc/compbio/ws/client/WSTester.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -WSTester - - - - - - - - - - - - -

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- -compbio.ws.client -
-Class WSTester

-java.lang.Object
-  compbio.ws.client.WSTester
-

public class WSTester
extends Object
extends Object

- - -

-Class for testing web services -

- -

Version:: 1.0 February 2010
Author:: pvtroshin

- -

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

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

-WSTester

-public WSTester()

- - - - - - - - - -

-Method Detail

- -

-main

-public static <T> void main(String[] args)
-                 throws IOException

Test JWS2 web services -

Type Parameters:: T - web service type
Parameters:: args - -h= - - -s= which is optional. If service name is not - provided then all known JWS2 web services are tested -
Throws: -: IOException

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- - - - - - - - - - -

-Packages that use Services
compbio.ws.client	A 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 Services Services.getService(Class wsImplClass) - -
-
-static Services Services.getService(String servName) - -
-
-static Services Services.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static Services[] Services.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
- -

- - - - - - - - - -
Methods in compbio.ws.client with parameters of type Services
-static - - - - - -<T> MsaWS<T> - Jws2Client.connect(String host, - Services service) - -
- Connects to a web service by the host and the service name
- -

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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
Jws2Client A command line client for JAva Bioinformatics Analysis Web Services
WSTester Class for testing web services
- - -

- - - - - - - - - -
-Enum Summary
Services List 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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- compbio.ws.client.Jws2Client
- compbio.ws.client.WSTester
-

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java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) -
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-Packages that use compbio.ws.client
compbio.ws.client	A 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.*

- -

- - - - - - - - - - - - -
compbio.data.sequence.ClustalAlignmentUtil
-public static final char gapchar 45
- -

- -

- - - - - -
-compbio.metadata.*
- -

- - - - - - - - - - - - -
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-public static final String LOCAL_ENGINE_LIMIT_PRESET "# LocalEngineExecutionLimit #"
- -

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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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-Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.

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-Each annotation type has its own separate page with the following sections:
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Annotation Type declaration
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-Each enum has its own separate page with the following sections:
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Enum declaration
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Enum Constant Summary
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-Use

-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)

-There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with java.lang.Object. The interfaces do not inherit from java.lang.Object.
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When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.
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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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-The Index contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.

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-Constant Field Values

-The Constant Field Values page lists the static final fields and their values. -

- - -This help file applies to API documentation generated using the standard doclet. - -
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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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Limit<T> - Class in compbio.metadata: A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
Limit(int, int, String) - -Constructor for class compbio.metadata.Limit -: Instantiate the limit -
Limit(int, int, String, boolean) - -Constructor for class compbio.metadata.Limit -: -
LimitExceededException - Exception in compbio.metadata: This exception is thrown if the task larger in size that the limit that - applies to the calculation.
LimitExceededException(String) - -Constructor for exception compbio.metadata.LimitExceededException -: -
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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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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-U

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

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-Hierarchy For All Packages

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

-Class Hierarchy -

java.lang.Object
- compbio.data.sequence.Alignment
- compbio.data.sequence.AlignmentMetadata
- compbio.metadata.ChunkHolder
- compbio.data.sequence.ClustalAlignmentUtil
- compbio.data.sequence.FastaSequence
- compbio.ws.client.Jws2Client
- compbio.metadata.Limit<T>
- compbio.metadata.LimitsManager<T>
- compbio.metadata.Option<T> (implements compbio.metadata.Argument<T>) -
  - compbio.metadata.Parameter<T>
  -
- compbio.metadata.Preset<T>
- compbio.metadata.PresetManager<T>
- compbio.metadata.RunnerConfig<T>
- compbio.data.sequence.SequenceUtil
- java.lang.Throwable (implements java.io.Serializable) -
  - java.lang.Exception
    - compbio.metadata.JobExecutionException
    - compbio.metadata.JobSubmissionException
      - compbio.metadata.LimitExceededException
      - compbio.metadata.UnsupportedRuntimeException
      -
    - compbio.metadata.ResultNotAvailableException
    - compbio.data.sequence.UnknownFileFormatException
    - compbio.metadata.WrongParameterException
    -
  -
- compbio.metadata.ValueConstrain
- compbio.ws.client.WSTester
-

-Interface Hierarchy -

compbio.metadata.Argument<T>
compbio.data.msa.MsaWS<T>

-Enum Hierarchy -

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) -
  - compbio.metadata.JobStatus
  - compbio.metadata.ValueConstrain.Type
  - compbio.data.sequence.Program
  - compbio.ws.client.Services
  -
-

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-Class compbio.data.sequence.UnknownFileFormatException extends Exception implements Serializable
- -

-serialVersionUID: 196629543695636854L - -

- - - - - -
-Serialized Fields
- -

-file

-File file

- - -

- - - - - -

-Package compbio.metadata

- -

- - - - - -
-Class compbio.metadata.JobExecutionException extends Exception implements Serializable
- -

-serialVersionUID: -5477751361755778769L - -

- -

- - - - - -
-Class compbio.metadata.JobSubmissionException extends 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 Exception implements Serializable
- -

-serialVersionUID: -5475613614578761L - -

- -

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

-serialVersionUID: -86624836785110293L - -

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- - - - - -
-Class compbio.metadata.WrongParameterException extends Exception implements Serializable
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- - - diff --git a/website/dm_javadoc/stylesheet.css b/website/dm_javadoc/stylesheet.css deleted file mode 100644 index cbd3428..0000000 --- a/website/dm_javadoc/stylesheet.css +++ /dev/null @@ -1,29 +0,0 @@ -/* Javadoc style sheet */ - -/* Define colors, fonts and other style attributes here to override the defaults */ - -/* Page background color */ -body { background-color: #FFFFFF; color:#000000 } - -/* Headings */ -h1 { font-size: 145% } - -/* Table colors */ -.TableHeadingColor { background: #CCCCFF; color:#000000 } /* Dark mauve */ -.TableSubHeadingColor { background: #EEEEFF; color:#000000 } /* Light mauve */ -.TableRowColor { background: #FFFFFF; color:#000000 } /* White */ - -/* Font used in left-hand frame lists */ -.FrameTitleFont { font-size: 100%; font-family: Helvetica, Arial, sans-serif; color:#000000 } -.FrameHeadingFont { font-size: 90%; font-family: Helvetica, Arial, sans-serif; color:#000000 } -.FrameItemFont { font-size: 90%; font-family: Helvetica, Arial, sans-serif; color:#000000 } - -/* Navigation bar fonts and colors */ -.NavBarCell1 { background-color:#EEEEFF; color:#000000} /* Light mauve */ -.NavBarCell1Rev { background-color:#00008B; color:#FFFFFF} /* Dark Blue */ -.NavBarFont1 { font-family: Arial, Helvetica, sans-serif; color:#000000;color:#000000;} -.NavBarFont1Rev { font-family: Arial, Helvetica, sans-serif; color:#FFFFFF;color:#FFFFFF;} - -.NavBarCell2 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000} -.NavBarCell3 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000} -

-Method Summary
-`static boolean`	`isValidClustalFile(InputStream input)` - - - Please note this method closes the input stream provided as a parameter
-`static Alignment`	`readClustalFile(File file)` - - -
-`static Alignment`	`readClustalFile(InputStream instream)` - - - Read Clustal formatted alignment.
-`static void`	`writeClustalAlignment(OutputStream outStream, - Alignment alignment)` - - - Write Clustal formatted alignment Limitations: does not record the - consensus.

-Method Summary
-`static int`	`countMatchesInSequence(String theString, - String theRegExp)` - - -
- `boolean`	`equals(Object obj)` - - -
- `String`	`getFormatedSequence(int width)` - - - Format sequence per width letter in one string.
- `String`	`getFormattedFasta()` - - -
- `String`	`getId()` - - - Gets the value of id
- `int`	`getLength()` - - -
- `String`	`getOnelineFasta()` - - -
- `String`	`getSequence()` - - - Gets the value of sequence
- `int`	`hashCode()` - - -
- `String`	`toString()` - - - Same as oneLineFasta

-Enum Constant Summary
`CLUSTAL` - - - ClustalW
`MAFFT` - - - Mafft
`MUSCLE` - - - Muscle
`Probcons` - - - Probcons
`Tcoffee` - - - Tcoffee

-Method Summary
-`static Program`	`valueOf(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.

-Field Summary
-`static Pattern`	`AA` - - - Valid Amino acids
-`static Pattern`	`AMBIGUOUS_AA` - - - Same as AA pattern but with two additional letters - XU
-`static Pattern`	`AMBIGUOUS_NUCLEOTIDE` - - - Ambiguous nucleotide
-`static Pattern`	`DIGIT` - - - A digit
-`static Pattern`	`NON_AA` - - - inversion of AA pattern
-`static Pattern`	`NON_NUCLEOTIDE` - - - Non nucleotide
-`static Pattern`	`NONWORD` - - - Non word
-`static Pattern`	`NUCLEOTIDE` - - - Nucleotides a, t, g, c, u
-`static Pattern`	`WHITE_SPACE` - - - A whitespace character: [\t\n\x0B\f\r]

-Method Summary
-`static String`	`cleanSequence(String sequence)` - - - Removes all whitespace chars in the sequence string
-`static void`	`closeSilently(Logger log, - Closeable stream)` - - - Closes the Closable and logs the exception if any
-`static String`	`deepCleanSequence(String sequence)` - - - Removes all special characters and digits as well as whitespace chars - from the sequence
-`static boolean`	`isAmbiguosProtein(String sequence)` - - - Check whether the sequence confirms to amboguous protein sequence
-`static boolean`	`isNonAmbNucleotideSequence(String sequence)` - - - Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char
-`static boolean`	`isNucleotideSequence(FastaSequence s)` - - -
-`static boolean`	`isProteinSequence(String sequence)` - - -
-`static List<FastaSequence>`	`readFasta(InputStream inStream)` - - - Reads fasta sequences from inStream into the list of FastaSequence - objects
-`static void`	`writeFasta(OutputStream os, - List<FastaSequence> sequences)` - - - Writes FastaSequence in the file, each sequence will take one line only
-`static void`	`writeFasta(OutputStream outstream, - List<FastaSequence> sequences, - int width)` - - - Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-`static void`	`writeFastaKeepTheStream(OutputStream outstream, - List<FastaSequence> sequences, - int width)` - - -

-Constructor Summary
`UnknownFileFormatException()` - - -
`UnknownFileFormatException(File file, - Throwable cause)` - - -
`UnknownFileFormatException(String message)` - - -
`UnknownFileFormatException(String message, - Throwable cause)` - - -
`UnknownFileFormatException(Throwable cause)` - - -

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

Method parameters in compbio.data.msa with type arguments of type FastaSequence
- `String`	`MsaWS.align(List<FastaSequence> sequences)` - - - Align a list of sequences with default settings.
- `String`	`MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options)` - - - Align a list of sequences with options.
- `String`	`MsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset)` - - - Align a list of sequences with preset.

Methods in compbio.data.sequence that return types with arguments of type FastaSequence
- `List<FastaSequence>`	`Alignment.getSequences()` - - -
-`static List<FastaSequence>`	`SequenceUtil.readFasta(InputStream inStream)` - - - Reads fasta sequences from inStream into the list of FastaSequence - objects

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

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

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

-Class Summary
Alignment	Multiple sequence alignment.
AlignmentMetadata	Alignment metadata e.g.
ClustalAlignmentUtil	Tools to read and write clustal formated files
FastaSequence	A FASTA formatted sequence.
SequenceUtil	Utility class for operations on sequences

-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 - - -

-Method Summary
- `String`	`getDefaultValue()` - - -
- `String`	`getDescription()` - - -
- `URL`	`getFurtherDetails()` - - -
- `String`	`getName()` - - -
- `List<String>`	`getPossibleValues()` - - -
- `void`	`setValue(String defaultValue)` - - - Set default values for the parameter or an option

-Constructor Summary
`JobExecutionException(String message)` - - -
`JobExecutionException(String message, - Throwable cause)` - - -
`JobExecutionException(Throwable cause)` - - -

-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 JobStatus`	`valueOf(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.

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

-align

-customAlign

-presetAlign

-getResult

-cancelJob

-getJobStatus

-pullExecStatistics

-getRunnerOptions

-getPresets

-getLimit

-getLimits

-Uses of Interfacecompbio.data.msa.MsaWS

-Package compbio.data.msa -

-Package compbio.data.msa Description -

-Hierarchy For Package compbio.data.msa -

-Interface Hierarchy -

-Uses of Packagecompbio.data.msa

- -compbio.data.sequence - -Class Alignment

-Alignment

-Alignment

-getSequences

-getSize

-getMetadata

-toString

-hashCode

-equals

- -compbio.data.sequence - -Class AlignmentMetadata

-AlignmentMetadata

-getProgram

-getGapchar

-equals

-hashCode

- -compbio.data.sequence - -Class ClustalAlignmentUtil

-gapchar

-ClustalAlignmentUtil

-readClustalFile

-isValidClustalFile

-writeClustalAlignment

-readClustalFile

- -compbio.data.sequence - -Class FastaSequence

-FastaSequence

-getId

-getSequence

-countMatchesInSequence

-getFormattedFasta

-getOnelineFasta

-getFormatedSequence

-getLength

-toString

-hashCode

-equals

- -compbio.data.sequence - -Enum Program

-CLUSTAL

-MAFFT

-MUSCLE

-Tcoffee

-Probcons

-values

-valueOf

- -compbio.data.sequence - -Class SequenceUtil

-WHITE_SPACE

-DIGIT

-NONWORD

-AA

-NON_AA

-AMBIGUOUS_AA

-NUCLEOTIDE

-AMBIGUOUS_NUCLEOTIDE

-NON_NUCLEOTIDE

-isNucleotideSequence

-isNonAmbNucleotideSequence

-cleanSequence

-deepCleanSequence

-isProteinSequence

-isAmbiguosProtein

-writeFasta

-writeFastaKeepTheStream

-readFasta

-writeFasta

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

-Uses of Interface
compbio.data.msa.MsaWS

-Uses of Package
compbio.data.msa

- -compbio.data.sequence -
-Class Alignment

- -compbio.data.sequence -
-Class AlignmentMetadata

- -compbio.data.sequence -
-Class ClustalAlignmentUtil

- -compbio.data.sequence -
-Class FastaSequence

- -compbio.data.sequence -
-Enum Program

- -compbio.data.sequence -
-Class SequenceUtil

- -compbio.data.sequence -
-Class UnknownFileFormatException

-Uses of Class
compbio.data.sequence.Alignment

-Uses of Class
compbio.data.sequence.AlignmentMetadata

-Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

-Uses of Class
compbio.data.sequence.FastaSequence

-Uses of Class
compbio.data.sequence.Program

-Uses of Class
compbio.data.sequence.SequenceUtil

-Uses of Class
compbio.data.sequence.UnknownFileFormatException

-Uses of Package
compbio.data.sequence

- -compbio.metadata -
-Interface Argument<T>

- -compbio.metadata -
-Class ChunkHolder

- -compbio.metadata -
-Class JobExecutionException

- -compbio.metadata -
-Enum JobStatus

- -compbio.metadata -
-Class JobSubmissionException

- -compbio.metadata -
-Class Limit<T>

- -compbio.metadata -
-Class LimitExceededException

-Constructor Summary
`JobSubmissionException(String message)` - - -
`JobSubmissionException(String message, - Throwable cause)` - - -
`JobSubmissionException(Throwable cause)` - - -

-Constructor Summary
`Limit(int seqNumber, - int seqLength, - String preset)` - - - Instantiate the limit
`Limit(int seqNumber, - int seqLength, - String preset, - boolean isDefault)` - - -

-Method Summary
- `int`	`getActualNumberofSequences()` - - -
- `int`	`getNumberOfSequencesAllowed()` - - -
- `int`	`getSequenceLenghtActual()` - - -
- `int`	`getSequenceLenghtAllowed()` - - -
-`static LimitExceededException`	`newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs)` - - -

-Method Summary
- `Limit<T>`	`getDefaultLimit()` - - -
- `Limit<T>`	`getLimitByName(String presetName)` - - -
- `List<Limit<T>>`	`getLimits()` - - -
- `String`	`toString()` - - -
- `void`	`validate(PresetManager<T> presets)` - - - Validate Limits

-Field Summary
-`protected String`	`defaultValue` - - -
-`protected String`	`description` - - -
-`protected URL`	`furtherDetails` - - -
-`protected boolean`	`isRequired` - - -
-`protected String`	`name` - - -

-Method Summary
- `Set<String>`	`addOptionNames(String... value)` - - - Adds an option to the optionName list
- `boolean`	`equals(Object obj)` - - -
- `String`	`getDefaultValue()` - - - A default value of the option.
- `String`	`getDescription()` - - - A long description of the Option
- `URL`	`getFurtherDetails()` - - - The URL where further details about the option can be found
- `String`	`getName()` - - - Human readable name of the option
- `List<String>`	`getOptionNames()` - - -
- `List<String>`	`getPossibleValues()` - - - List of possible optionNames
- `int`	`hashCode()` - - -
- `boolean`	`isRequired()` - - - Flag that indicated that this option must be specified in the command - line for an executable to run
- `void`	`setDefaultValue(String defaultVal)` - - - Sets one of the values defined in optionList as default.
- `void`	`setDescription(String description)` - - -
- `void`	`setFurtherDetails(URL furtherDetails)` - - -
- `void`	`setName(String name)` - - -
- `void`	`setOptionNames(Set<String> optionNames)` - - -
- `void`	`setRequired(boolean isRequired)` - - -
- `void`	`setValue(String dValue)` - - - Set default values for the parameter or an option
- `String`	`toCommand(String nameValueSeparator)` - - - Convert the option to the command string.
- `String`	`toString()` - - -

-Method Summary
- `boolean`	`equals(Object obj)` - - -
- `List<Option<T>>`	`getArguments(RunnerConfig<T> rconfig)` - - - Converts list of options as String to type Option
- `String`	`getDescription()` - - -
- `String`	`getName()` - - -
- `List<String>`	`getOptions()` - - -
- `int`	`hashCode()` - - -
- `void`	`setDescription(String description)` - - -
- `void`	`setName(String name)` - - -
- `void`	`setOptions(List<String> option)` - - -
- `String`	`toString()` - - -

-Method Summary
- `Preset<T>`	`getPresetByName(String presetName)` - - -
- `List<Preset<T>>`	`getPresets()` - - -
- `String`	`getRunnerClassName()` - - -
- `void`	`setPresets(List<Preset<T>> presets)` - - -
- `void`	`setRunnerClassName(String runnerClassName)` - - -
- `String`	`toString()` - - -
- `void`	`validate(RunnerConfig<T> options)` - - - Checks whether preset option and parameter are defined in RunnerConfig - object.

-Constructor Summary
`ResultNotAvailableException(String message)` - - -
`ResultNotAvailableException(String message, - Throwable cause)` - - -
`ResultNotAvailableException(Throwable cause)` - - -

-Method Summary
- `void`	`addOption(Option<T> option)` - - - Adds Option to the internal list of options
- `void`	`addParameter(Parameter<T> param)` - - - Adds parameter to the internal parameter list
- `RunnerConfig<T>`	`copyAndValidateRConfig(RunnerConfig<?> runnerConf)` - - -
- `boolean`	`equals(Object obj)` - - -
- `Option<T>`	`getArgument(String name)` - - - Returns the argument by its name if found, NULL otherwise.
- `Option<T>`	`getArgumentByOptionName(String optionName)` - - - Returns the argument by option name, NULL if the argument is not found
- `List<Option<T>>`	`getArguments()` - - - Returns list of `Parameter` and `Option` supported by current - runner
- `List<Option<T>>`	`getOptions()` - - - Returns the list of the Options supported by the executable of type T
- `List<Parameter<T>>`	`getParameters()` - - - Returns the list of parameters supported executable of type T.
- `String`	`getPrmSeparator()` - - -
- `String`	`getRunnerClassName()` - - -
- `boolean`	`removeArgument(String name)` - - - Removes the argument `Argument` if found.
- `boolean`	`removeArgumentByOptionName(String optionName)` - - - Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor.
- `void`	`setOptions(List<Option<T>> parameters)` - - - Adds the list of options or parameters to the internal list of options
- `void`	`setParameters(List<Parameter<T>> parameters)` - - - Sets the list of parameters as internal list
- `void`	`setPrmSeparator(String prmSeparator)` - - - Sets name value separator character
- `void`	`setRunnerClassName(String runnerClassName)` - - - Set the name of a runner class
- `String`	`toString()` - - -
- `void`	`validate()` - - - Validate the value of the argument.