Package | Description |
---|---|
compbio.data.msa |
Web Service interfaces for JAva Bioinformatics Analysis Web Services.
|
compbio.data.msa.jaxws | |
compbio.data.sequence |
A data model for multiple sequence alignment web services and utility methods
that work on the objects of this model.
|
compbio.engine | |
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.runner |
Utilities commonly used by all runners.
|
compbio.ws.client |
A command line client and web services testing client for
JAva Bioinformatics Analysis Web Services.
|
compbio.ws.server |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
MsaWS.align(java.util.List<FastaSequence> sequences)
Align a list of sequences with default settings.
|
java.lang.String |
SequenceAnnotation.analize(java.util.List<FastaSequence> sequences)
Analyse the sequences.
|
java.lang.String |
MsaWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options)
Align a list of sequences with options.
|
java.lang.String |
SequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options)
Analyse the sequences according to custom settings defined in options
list.
|
java.lang.String |
MsaWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<T> preset)
Align a list of sequences with preset.
|
java.lang.String |
SequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<T> preset)
Analyse the sequences according to the preset settings.
|
Modifier and Type | Field and Description |
---|---|
private java.util.List<FastaSequence> |
PresetAnalize.fastaSequences |
private java.util.List<FastaSequence> |
PresetAlign.fastaSequences |
private java.util.List<FastaSequence> |
CustomAnalize.fastaSequences |
private java.util.List<FastaSequence> |
CustomAlign.fastaSequences |
private java.util.List<FastaSequence> |
Analize.fastaSequences |
private java.util.List<FastaSequence> |
Align.fastaSequences |
Modifier and Type | Method and Description |
---|---|
java.util.List<FastaSequence> |
PresetAnalize.getFastaSequences() |
java.util.List<FastaSequence> |
PresetAlign.getFastaSequences() |
java.util.List<FastaSequence> |
CustomAnalize.getFastaSequences() |
java.util.List<FastaSequence> |
CustomAlign.getFastaSequences() |
java.util.List<FastaSequence> |
Analize.getFastaSequences() |
java.util.List<FastaSequence> |
Align.getFastaSequences() |
Modifier and Type | Method and Description |
---|---|
void |
PresetAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences) |
void |
PresetAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) |
void |
CustomAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences) |
void |
CustomAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) |
void |
Analize.setFastaSequences(java.util.List<FastaSequence> fastaSequences) |
void |
Align.setFastaSequences(java.util.List<FastaSequence> fastaSequences) |
Modifier and Type | Field and Description |
---|---|
protected java.util.List<FastaSequence> |
Alignment.sequences |
Modifier and Type | Method and Description |
---|---|
FastaSequence |
FastaReader.next()
Reads the next FastaSequence from the input
|
private static FastaSequence |
FastaReader.toFastaSequence(java.lang.String singleFastaEntry) |
Modifier and Type | Method and Description |
---|---|
java.util.List<FastaSequence> |
Alignment.getSequences() |
static java.util.List<FastaSequence> |
SequenceUtil.openInputStream(java.lang.String inFilePath)
Reads and parses Fasta or Clustal formatted file into a list of
FastaSequence objects
|
static java.util.List<FastaSequence> |
SequenceUtil.readFasta(java.io.InputStream inStream)
Reads fasta sequences from inStream into the list of FastaSequence
objects
|
Modifier and Type | Method and Description |
---|---|
static boolean |
SequenceUtil.isNucleotideSequence(FastaSequence s) |
Modifier and Type | Method and Description |
---|---|
static void |
SequenceUtil.writeClustal(java.io.OutputStream outStream,
java.util.List<FastaSequence> sequences,
char gapChar) |
static void |
SequenceUtil.writeFasta(java.io.OutputStream os,
java.util.List<FastaSequence> sequences)
Writes FastaSequence in the file, each sequence will take one line only
|
static void |
SequenceUtil.writeFasta(java.io.OutputStream outstream,
java.util.List<FastaSequence> sequences,
int width)
Writes list of FastaSequeces into the outstream formatting the sequence
so that it contains width chars on each line
|
static void |
SequenceUtil.writeFastaKeepTheStream(java.io.OutputStream outstream,
java.util.List<FastaSequence> sequences,
int width) |
Constructor and Description |
---|
Alignment(java.util.List<FastaSequence> sequences,
AlignmentMetadata metadata) |
Alignment(java.util.List<FastaSequence> sequences,
Program program,
char gapchar) |
Modifier and Type | Method and Description |
---|---|
static <T> ConfiguredExecutable<T> |
Configurator.configureExecutable(Executable<T> executable,
java.util.List<FastaSequence> dataSet) |
static <T,V> Executable.ExecProvider |
LoadBalancer.getEngine(Executable<V> executable,
java.util.List<FastaSequence> dataSet) |
(package private) static Executable.ExecProvider |
Configurator.getExecProvider(ConfiguredExecutable<?> executable,
java.util.List<FastaSequence> dataSet)
Depending on the values defined in the properties
(engine.cluster.enable=true and engine.local.enable=true) return either
Cluster job submission engine
#JobRunner or local job submission
engine #LocalRunner If both engines enabled than ask
LoadBalancer for an engine. |
Modifier and Type | Method and Description |
---|---|
static int |
Limit.getAvgSequenceLength(java.util.List<FastaSequence> data)
Calculates an average sequence length of the dataset
|
boolean |
Limit.isExceeded(java.util.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,
java.util.List<FastaSequence> seqs) |
Modifier and Type | Method and Description |
---|---|
static void |
RunnerUtil.writeClustalInput(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<?> exec,
char gapChar) |
static void |
Util.writeInput(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<?> exec) |
static void |
RunnerUtil.writeInput(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<?> exec) |
Modifier and Type | Method and Description |
---|---|
private static java.util.List<FastaSequence> |
WSTester.loadAlignment()
Converting input to a form accepted by WS
|
private static java.util.List<FastaSequence> |
WSTester.loadRNAAlignment()
Converting input to a form accepted by WS
|
private static java.util.List<FastaSequence> |
WSTester.loadSeqs(int nLines)
Converting input to a form accepted by WS
|
Modifier and Type | Method and Description |
---|---|
(package private) static <T> ScoreManager |
Jws2Client.analize(java.util.List<FastaSequence> fastalist,
SequenceAnnotation<T> wsproxy,
Preset<T> preset,
java.util.List<Option<T>> customOptions)
Calculate conservation for sequences loaded from a FASTA record list structure
|
private <T> boolean |
WSTester.testDefaultAnalyse(java.util.List<FastaSequence> fastalist,
SequenceAnnotation<T> wsproxy,
Preset<T> preset,
java.util.List<Option<T>> customOptions) |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
GLprobsWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
MafftWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
ClustalOWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
MSAprobsWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
MuscleWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
ClustalWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
TcoffeeWS.align(java.util.List<FastaSequence> sequences) |
java.lang.String |
ProbconsWS.align(java.util.List<FastaSequence> sequences) |
static <T> java.lang.String |
WSUtil.align(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<T> confExec,
org.apache.log4j.Logger logger,
java.lang.String callingMethod,
Limit<T> limit) |
java.lang.String |
SequenceAnnotationService.analize(java.util.List<FastaSequence> sequences) |
java.lang.String |
AAConWS.analize(java.util.List<FastaSequence> sequences) |
java.lang.String |
RNAalifoldWS.analize(java.util.List<FastaSequence> sequences) |
static <T> java.lang.String |
WSUtil.analize(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<T> confExec,
org.apache.log4j.Logger log,
java.lang.String method,
Limit<T> limit) |
java.lang.String |
ClustalOWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<ClustalO>> options) |
java.lang.String |
ClustalWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<ClustalW>> options) |
java.lang.String |
GLprobsWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<GLprobs>> options) |
java.lang.String |
MafftWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Mafft>> options) |
java.lang.String |
MSAprobsWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<MSAprobs>> options) |
java.lang.String |
MuscleWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Muscle>> options) |
java.lang.String |
ProbconsWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Probcons>> options) |
java.lang.String |
TcoffeeWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Tcoffee>> options) |
java.lang.String |
AAConWS.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<AACon>> options) |
java.lang.String |
DisemblWS.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<Disembl>> options) |
java.lang.String |
GlobPlotWS.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<GlobPlot>> options) |
java.lang.String |
RNAalifoldWS.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<RNAalifold>> options) |
java.lang.String |
SequenceAnnotationService.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options) |
static <T> java.lang.String |
WSUtil.fold(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<T> confExec,
org.apache.log4j.Logger log,
java.lang.String method,
Limit<T> limit) |
(package private) ConfiguredExecutable<T> |
GenericMetadataService.init(java.util.List<FastaSequence> sequences) |
(package private) ConfiguredExecutable<GLprobs> |
GLprobsWS.init(java.util.List<FastaSequence> dataSet) |
(package private) ConfiguredExecutable<Mafft> |
MafftWS.init(java.util.List<FastaSequence> dataSet) |
(package private) ConfiguredExecutable<ClustalO> |
ClustalOWS.init(java.util.List<FastaSequence> dataSet) |
(package private) ConfiguredExecutable<MSAprobs> |
MSAprobsWS.init(java.util.List<FastaSequence> dataSet) |
(package private) ConfiguredExecutable<Muscle> |
MuscleWS.init(java.util.List<FastaSequence> sequences) |
(package private) ConfiguredExecutable<ClustalW> |
ClustalWS.init(java.util.List<FastaSequence> dataSet) |
(package private) ConfiguredExecutable<Tcoffee> |
TcoffeeWS.init(java.util.List<FastaSequence> sequences) |
(package private) ConfiguredExecutable<Probcons> |
ProbconsWS.init(java.util.List<FastaSequence> dataSet) |
java.lang.String |
ClustalOWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<ClustalO> preset) |
java.lang.String |
ClustalWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<ClustalW> preset) |
java.lang.String |
GLprobsWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<GLprobs> preset) |
java.lang.String |
MafftWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Mafft> preset) |
java.lang.String |
MSAprobsWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<MSAprobs> preset) |
java.lang.String |
MuscleWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Muscle> preset) |
java.lang.String |
ProbconsWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Probcons> preset) |
java.lang.String |
TcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Tcoffee> preset) |
java.lang.String |
AAConWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<AACon> preset) |
java.lang.String |
DisemblWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<Disembl> preset) |
java.lang.String |
GlobPlotWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<GlobPlot> preset) |
java.lang.String |
IUPredWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<IUPred> preset) |
java.lang.String |
RNAalifoldWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<RNAalifold> preset) |
java.lang.String |
SequenceAnnotationService.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<T> preset) |
static void |
WSUtil.validateAAConInput(java.util.List<FastaSequence> sequences) |
static void |
WSUtil.validateFastaInput(java.util.List<FastaSequence> sequences) |