X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FFastaSequence.html;h=4b3182174422ce8010c77750fccbfcfab24e677e;hb=5ca8c6a56369ea884670666cddcc5f1d3a09bc10;hp=763d6483185ab707a55d35ddef3b88cb08e2b822;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;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 index 763d648..4b31821 100644 --- a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html +++ b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -2,12 +2,12 @@ - + Uses of Class compbio.data.sequence.FastaSequence - + @@ -90,9 +90,13 @@ function windowTitle() 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 - Classes in this package have no dependencies to other sources in the project.  +A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.  compbio.metadata @@ -102,6 +106,49 @@ Packages that use  

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

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

@@ -118,7 +165,7 @@ Uses of + List<FastaSequence> - + - @@ -169,14 +216,24 @@ Uses of - + + + +
- java.util.List<FastaSequence> Alignment.getSequences()
@@ -126,8 +173,8 @@ Uses of 		-static java.util.List<FastaSequence>SequenceUtil.readFasta(java.io.InputStream inStream) +static List<FastaSequence>SequenceUtil.readFasta(InputStream inStream)
          Reads fasta sequences from inStream into the list of FastaSequence @@ -160,8 +207,8 @@ Uses of 		static voidSequenceUtil.writeFasta(java.io.OutputStream os, - java.util.List<FastaSequence> sequences) +SequenceUtil.writeFasta(OutputStream os, + List<FastaSequence> sequences)
          Writes FastaSequence in the file, each sequence will take one line only		 static voidSequenceUtil.writeFasta(java.io.OutputStream outstream, - java.util.List<FastaSequence> sequences, +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 voidSequenceUtil.writeFastaKeepTheStream(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+           
 

@@ -186,14 +243,14 @@ Uses of Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence -Alignment(java.util.List<FastaSequence> sequences, +Alignment(List<FastaSequence> sequences, AlignmentMetadata metadata)
            -Alignment(java.util.List<FastaSequence> sequences, +Alignment(List<FastaSequence> sequences, Program program, char gapchar) @@ -220,7 +277,7 @@ Uses of static int -Limit.getAvgSequenceLength(java.util.List<FastaSequence> data) +Limit.getAvgSequenceLength(List<FastaSequence> data)
          Calculates an average sequence length of the dataset @@ -228,17 +285,17 @@ Uses of  boolean -Limit.isExceeded(java.util.List<FastaSequence> data) +Limit.isExceeded(List<FastaSequence> data)
          Checks if the number of sequences or their average length in the dataset - exceeds limits the values defined by this Limit + exceeds this limit. static LimitExceededException LimitExceededException.newLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) + List<FastaSequence> seqs)