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false.
FASTAWRITERHELPER (BIOJAVA 5.3.0 API) Method which will write your given Sequences to the specified OutputStream.This is a very generic method which writes just the AccessionID of the Sequence as the FASTA header. PARAMETERGUI (BIOJAVA 5.3.0 API) UI for ConfigStrucAligParams, for the AlignmentGUI.Visually parameters are displayed as a label and an input field such as a text box. The following methods are SIMPLELOCATION (BIOJAVA 5.3.0 API) Nested Class Summary. Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.LocationLocation.Tools
DNATOOLS (BIOJAVA-LEGACY 1.9.1 API) Transcribes DNA to RNA. The method more closely represents the biological reality than toRNA(SymbolList syms) does. The presented DNA SymbolList is assumed to be the template strand in the 5' to 3' orientation. The resulting RNA is transcribed from this template effectively a reverse complement in the RNA alphabet. STRUCTUREIOFILE (BIOJAVA 5.3.0 API) Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed. This is generally called only in the constructor of the implementing class. GFF3READER (BIOJAVA 5.0.0 API) Read a file into a FeatureList. Each line of the file becomes oneFeature object.
BIOJAVAHOMEABOUTGET STARTEDDOCUMENTATIONWIKI PAGESGET INVOLVED Protein structures. BioJava provides an API to maintain local installations of the PDB, load and manipulate structures, perform standard analysis such as sequence and structure alignments and visualize them in 3D. WIKI PAGES - BIOJAVA The open-source Java library for bioinformatics. Menu. Home; About; Get started; Documentation; Wiki pages; Get involved OVERVIEW (BIOJAVA-LEGACY 1.9.5 API) The data structures and interfaces included in this package define an interoperable framework for bibliographic searches. FILEDOWNLOADUTILS (BIOJAVA 5.3.0 API) Parameters: url - The HTTP URL to be pinged. timeout - The timeout in millis for both the connection timeout and the response read timeout. Note that the total timeout is effectively two times the given timeout. Returns: true if the given HTTP URL has returned response code 200-399 on a HEAD request within the given timeout, otherwisefalse.
FASTAWRITERHELPER (BIOJAVA 5.3.0 API) Method which will write your given Sequences to the specified OutputStream.This is a very generic method which writes just the AccessionID of the Sequence as the FASTA header. PARAMETERGUI (BIOJAVA 5.3.0 API) UI for ConfigStrucAligParams, for the AlignmentGUI.Visually parameters are displayed as a label and an input field such as a text box. The following methods are SIMPLELOCATION (BIOJAVA 5.3.0 API) Nested Class Summary. Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.LocationLocation.Tools
DNATOOLS (BIOJAVA-LEGACY 1.9.1 API) Transcribes DNA to RNA. The method more closely represents the biological reality than toRNA(SymbolList syms) does. The presented DNA SymbolList is assumed to be the template strand in the 5' to 3' orientation. The resulting RNA is transcribed from this template effectively a reverse complement in the RNA alphabet. STRUCTUREIOFILE (BIOJAVA 5.3.0 API) Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed. This is generally called only in the constructor of the implementing class. GFF3READER (BIOJAVA 5.0.0 API) Read a file into a FeatureList. Each line of the file becomes oneFeature object.
OVERVIEW (BIOJAVA 5.3.0 API) Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of proteinsequences.
INDEX (BIOJAVA 5.2.0 API) aa2CTerminalPka - Static variable in class org.biojava.nbio.aaproperties. Constraints aa2ExtinctionCoefficient - Static variable in class org.biojava.nbio.aaproperties. Constraints aa2Hydrophathicity - Static variable in class org.biojava.nbio.aaproperties. Constraints aa2MolecularWeight - Static variable in class org.biojava.nbio.aaproperties. Constraints BIOJAVA-LEGACY 1.9.1 API The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces. BASEPAIRPARAMETERS (BIOJAVA 5.3.0 API) This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic acid containing structure that has the information about the core base-pair rings. GUIDETREE (BIOJAVA 5.3.0 API) Implements a data structure for a guide tree used during progressive multiple sequence alignment. Leaf GuideTree.Nodes correspond to single Sequences. Internal GuideTree.Nodes correspond to multiple sequence alignments. The root GuideTree.Node corresponds to the full multiplesequence alignment.
MULTIPLEALIGNMENTTOOLS (BIOJAVA 5.3.0 API) Calculate the sequence alignment Strings for the whole alignment. This method creates a sequence alignment where aligned residues are in uppercase and unaligned residues are in lowercase, thus providing a more compact way to represent the alignment. STRUCTUREIOFILE (BIOJAVA 5.3.0 API) Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed. This is generally called only in the constructor of the implementing class. GFF3READER (BIOJAVA 5.0.0 API) Read a file into a FeatureList. Each line of the file becomes oneFeature object.
SOURCE CODE
001 /* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence GENBANKREADER (BIOJAVA 4.2.1 API) This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open. Subsequent calls to the same method continue parsing the rest of the file. This is particularly useful when dealing with very big data files, (e.g. NCBI nr database), which can't fit into memory and will take long time before the first result is available.* Menu
BIOJAVA
The open-source Java library for bioinformatics* Get started
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OPEN SOURCE
The project is hosted, developed, and maintained on GitHub.GitHub project
PROTEIN STRUCTURES
BioJava provides an API to maintain local installations of the PDB, load and manipulate structures, perform standard analysis such as sequence and structure alignments and visualize them in 3D. BIOLOGICAL SEQUENCES BioJava supports reading and writing popular sequence file formats, translating DNA sequences into proteins and other common bioinformatics routines.PLEASE CITE
BIOJAVA 5: A COMMUNITY DRIVEN OPEN-SOURCE BIOINFORMATICS LIBRARY _Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M.Duarte_
PLOS Computational Biology (2019) 15 (2):e1006791.GET IN TOUCH
Questions, comments, and communications regarding BioJava can be done either on GitHub or through the BioJava mailing list. Subscribe to
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TUTORIAL
The tutorial offers an introduction into some of the features providedby BioJava.
Tutorial
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COOKBOOK
The Cookbook provides simple coding recipes to common bioinformatics problems using BioJava.Cookbook
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JAVADOC API
The Javadocs for the current BioJava 5.3.0 release.Javadoc API
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RELEASE 5.3.0
BioJava is available from Maven Central.Maven Central
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WIKI
All pages from the legacy wiki site have been migrated to markdownpages
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LEGACY JAVADOC API
The Javadocs for BioJava legacy 1.x versions.View 1.9.1 API
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