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

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FFastaSequence.html;fp=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FFastaSequence.html;h=b77ae86bcf7f8d2e6c5eed0557c088e5d24ee803;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html new file mode 100644 index 0000000..b77ae86 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,539 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +

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

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+Uses of Class
compbio.data.sequence.FastaSequence

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

+Packages that use FastaSequence
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.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
+ 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.
+ +

Method parameters in compbio.data.msa with type arguments of type FastaSequence
+ `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.

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

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

Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
+ `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()` + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
+ 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) + +
+
+ +

Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
+ `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)` + + +

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

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

Methods in compbio.data.sequence that return FastaSequence
+ `FastaSequence`	`FastaReader.next()` + + + Reads the next FastaSequence from the input

+ + + + + + + + + + + + + + + + + +
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
+ java.util.List<FastaSequence> Alignment.getSequences() + +
+
+static java.util.List<FastaSequence> SequenceUtil.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
+ +

Methods in compbio.data.sequence that return types with arguments of type FastaSequence
+ `java.util.List<FastaSequence>`	`Alignment.getSequences()` + + +
+`static java.util.List<FastaSequence>`	`SequenceUtil.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

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

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(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) + +
+
+ +

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

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

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

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.metadata with type arguments of type FastaSequence
+static 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) + +
+
+ +

Method parameters in compbio.metadata with type arguments of type FastaSequence
+`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)` + + +