Categories
Tag: BioJava
Central Repository: org/biojava/biojava-structure/6.0.5
../ biojava-structure-6.0.5-javadoc.jar 2022-02-01 17:49 3997549 biojava-structure-6.0.5-javadoc.jar.asc 2022-02-01 17:49 488 biojava-structure-6.0.5-javadoc.jar.md5 2022-02-01 17:49 32 biojava-structure-6.0.5-javadoc.jar.sha1 2022-02-01 17:49 40 biojava-structure-6.0.5-sources.jar 2022-02-01 17:49 1204756 biojava-structure-6.0.5-sources.jar.asc 2022-02-01 17:49 488 biojava-structure-6.0.5-sources.jar.md5 2022-02-01 17:49 32 biojava-structure-6.0.5-sources.jar.sha1 2022-02-01 17:49 40 biojava-structure-6.0.5.jar 2022-02-01 17:49 1431808 biojava-structure-6.0.5.jar.asc 2022-02-01 17:49 488 biojava-structure-6.0.5.jar.md5 2022-02-01 17:49 32 biojava-structure-6.0.5.jar.sha1 2022-02-01 17:49 40 biojava-structure-6.0.5.pom…
Central Repository: org/biojava/biojava-structure/5.1.0
../ biojava-structure-5.1.0-javadoc.jar 2018-08-29 23:51 3942372 biojava-structure-5.1.0-javadoc.jar.asc 2018-08-29 23:51 488 biojava-structure-5.1.0-javadoc.jar.md5 2018-08-29 23:51 32 biojava-structure-5.1.0-javadoc.jar.sha1 2018-08-29 23:51 40 biojava-structure-5.1.0-sources.jar 2018-08-29 23:51 1357544 biojava-structure-5.1.0-sources.jar.asc 2018-08-29 23:51 488 biojava-structure-5.1.0-sources.jar.md5 2018-08-29 23:51 32 biojava-structure-5.1.0-sources.jar.sha1 2018-08-29 23:51 40 biojava-structure-5.1.0.jar 2018-08-29 23:51 1605196 biojava-structure-5.1.0.jar.asc 2018-08-29 23:51 488 biojava-structure-5.1.0.jar.md5 2018-08-29 23:51 32 biojava-structure-5.1.0.jar.sha1 2018-08-29 23:51 40 biojava-structure-5.1.0.pom…
Bioinformatics Trainer Part Time Job Opening at Biotecnika
Bioinformatics Trainer Part Time Job Opening at Biotecnika Bangalore Biotecnika Info Labs Pvt Ltd is a leading Bio-IT Company with a diversified portfolio in Information technology and biotechnology. We seek a highly motivated and experienced individual to join our team as a Part-Time Bioinformatics Trainer & Researcher. The successful candidate…
Uses of Interface org.biojava.bio.gui.sequence.ImageMap (BioJava-1.7 API)
Constructors in org.biojava.bio.gui.sequence with parameters of type ImageMap BasicImapRenderer(BasicFeatureRenderer renderer, ImageMap imageMap, URLFactory urlFactory) Creates a new BasicImapRenderer. RectangularImapRenderer(RectangularBeadRenderer renderer, ImageMap imageMap, URLFactory urlFactory) Creates a new RectangularImapRenderer. ZiggyImapRenderer(ZiggyFeatureRenderer renderer, ImageMap imageMap, URLFactory urlFactory) Creates a new ZiggyImapRenderer. Read more here: Source link
How to install or uninstall “python3-biopython-sql” on Kali Linux ?
1. Install python3-biopython-sql package Please follow the steps below to install python3-biopython-sql package: sudo apt install python3-biopython-sql Copy 2. Uninstall / Remove python3-biopython-sql package Please follow the steps below to uninstall python3-biopython-sql package: sudo apt remove python3-biopython-sql Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of python3-biopython-sql…
Uses of Package org.biojava.bio.structure.io.mmcif.model (BioJava-1.7 API)
Classes in org.biojava.bio.structure.io.mmcif.model used by org.biojava.bio.structure.io.mmcif AtomSite ChemComp DatabasePDBremark DatabasePDBrev Entity A simple class to represent Entity records in mmCif files EntityPolySeq Container for _entity_poly_seq records Exptl PdbxEntityNonPoly A bean for the Pdbx_entity_nonpoly category. PdbxNonPolyScheme A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level…
Maven Central: org.biojava:gui
<dependency> <groupId>org.biojava</groupId> <artifactId>gui</artifactId> <version>1.9.7</version> </dependency> <?xml version=”1.0″ encoding=”UTF-8″?> <project xmlns=”http://maven.apache.org/POM/4.0.0″ xmlns:xsi=”http://www.w3.org/2001/XMLSchema-instance” xsi:schemaLocation=”http://maven.apache.org/POM/4.0.0 maven.apache.org/maven-v4_0_0.xsd“> <modelVersion>4.0.0</modelVersion> <parent> <artifactId>biojava-legacy</artifactId> <groupId>org.biojava</groupId> <version>1.9.7</version> </parent> <artifactId>gui</artifactId> <packaging>jar</packaging> <version>1.9.7</version> <name>gui</name> <description>BioJava gui module</description> <dependencies> <dependency> <groupId>junit</groupId> <artifactId>junit</artifactId> <scope>test</scope> </dependency> <dependency> <groupId>org.biojava</groupId> <artifactId>core</artifactId> <version>${project.version}</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.biojava</groupId> <artifactId>sequencing</artifactId> <version>${project.version}</version> <scope>compile</scope> </dependency> </dependencies> </project> Read more here: Source…
Uses of Package org.biojava.bio.structure.jama (BioJava-1.7 API)
Packages that use org.biojava.bio.structure.jama org.biojava.bio.structure Interfaces and classes for protein structure (PDB). org.biojava.bio.structure.align Classes for the super-imposition of structures. org.biojava.bio.structure.align.helper Helper classes for structural alignment. org.biojava.bio.structure.align.pairwise Classes for the pairwise alignment of structures. org.biojava.bio.structure.gui A few convenience classes to view protein structures with Jmol (if it is on the classpath),…
Sequence (BioJava-1.7 API)
Sequence (BioJava-1.7 API) PREV CLASS NEXT CLASS FRAMES NO FRAMES All Classes SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD org.biojava.bio.seq Interface Sequence All Superinterfaces: Annotatable, Changeable, FeatureHolder, SymbolList All Known Subinterfaces: GappedSequence, RichSequence All Known Implementing Classes: CircularView, DummySequence, NewSimpleAssembly, PhredSequence, RevCompSequence, SimpleAssembly, SimpleGappedSequence, SimpleRichSequence, SimpleSequence, SubSequence, ThinRichSequence, ViewSequence public interface Sequence…
ElementRecognizer.ByLocalName (BioJava-1.7 API)
ElementRecognizer.ByLocalName (BioJava-1.7 API) org.biojava.bio.program.xff Class ElementRecognizer.ByLocalName java.lang.Object org.biojava.bio.program.xff.ElementRecognizer.ByLocalName All Implemented Interfaces: ElementRecognizer Enclosing interface: ElementRecognizer public static class ElementRecognizer.ByLocalName extends Object implements ElementRecognizer Filter elements by local name (not recommended). ElementRecognizer.ByLocalName public ElementRecognizer.ByLocalName(String localName) filterStartElement public boolean filterStartElement(String nsURI, String localName, String qName, Attributes attrs) Description copied from…
Uses of Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter (BioJava-1.7 API)
Subclasses of BioSQLFeatureFilter.HibernateFeatureFilter in org.biojavax.bio.db.biosql static class BioSQLFeatureFilter.And A filter that returns all features accepted by both child filter. static class BioSQLFeatureFilter.ByName Construct one of these to filter features by display name. static class BioSQLFeatureFilter.ByNote A filter that returns all features that have the given note, and the value and rank is checked…
SoftMaskedAlphabet.CaseSensitiveTokenization (BioJava-1.7 API)
SoftMaskedAlphabet.CaseSensitiveTokenization (BioJava-1.7 API) PREV CLASS NEXT CLASS FRAMES NO FRAMES All Classes SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD org.biojava.bio.symbol Class SoftMaskedAlphabet.CaseSensitiveTokenization java.lang.Object org.biojava.utils.Unchangeable org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization All Implemented Interfaces: Annotatable, SymbolTokenization, Changeable Enclosing class: SoftMaskedAlphabet public class SoftMaskedAlphabet.CaseSensitiveTokenization extends Unchangeable implements SymbolTokenization This SymbolTokenizer works with a delegate to softmask symbol tokenization as…
ABITools (BioJava-1.7 API)
ABITools (BioJava-1.7 API) org.biojava.bio.program.abi Class ABITools java.lang.Object org.biojava.bio.program.abi.ABITools public class ABITools extends Object Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters. Author: Matthew Pocock Field Summary static AtomicSymbol _0 The poorly supported symbol. static AtomicSymbol _1 The well…
ProteaseManager (BioJava-1.7 API)
ProteaseManager (BioJava-1.7 API) org.biojava.bio.proteomics Class ProteaseManager java.lang.Object org.biojava.bio.proteomics.ProteaseManager public final class ProteaseManager extends Object Registry and utility methods for Proteases. Author: Mark Schreiber Method Summary static Protease createProtease(String cleaveRes, boolean endoProtease, String name) static Protease createProtease(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, String name) static Protease createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and…
BIOJAVA FACULTY – Synteny lifesciences private limited
BIOJAVA FACULTYType of Job: Part / FulltimeLocality: New NallakuntaCompany Name: SyntenyLifesciences Pvt. Ltd.Designation: BIOJAVA TrainerEducation: Post-Graduate Experience: Less Than 1 YrAnnual Compensation: Rs. 1L – Rs. 2L Wanted Experienced BIOJAVA Faculty With Immediate Appointment. Excellent knowledge of English, communication and teaching skills and the ability to interact proactively with Students…
OmicsSuite: Tailored Pipeline for Multi-Omics Big Data Analysis
Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging…
BIOJAVA SDN BHD | 200601014420 (734171-H)
BIOJAVA SDN BHD | 200601014420 (734171-H) – Get Latest Business Report Back to Business Directory Registration Number 200601014420 (734171-H) Business Nature TRADING OF SOLUBLE AND LIQUID ANIMAL HEALTH AND NUTRITION PRODUCTS AND EXPORT ACTIVITIES Date of Incorporation 19/05/2006 #1 Click “Purchase SSM Report” button and you will be redirected to…
broken symlink /usr/share/logol/lib/biojava.jar -> ../../java/biojava.jar
Package: logol Version: 1.7.9+dfsg-6 Severity: serious User: debian…@lists.debian.org Usertags: piuparts Hi, during a test with piuparts I noticed your package ships (or creates) a broken symlink: 0m42.9s ERROR: FAIL: Broken symlinks: /usr/share/logol/lib/biojava.jar -> ../../java/biojava.jar (logol) libbiojava-java (which is not in the dependencies) does no longer provide a jar file with…
MergeLocation (biojava-legacy 1.9.5 API)
Produced by LocationTools as a result of union operations. It’s a RangeLocation and can be used as such but it also retains knowledge of which individual components made it up. None of the methods of RangeLocation are overridden only new methods have been added to get the subcomponents. For example…
SwissprotProcessor (biojava-legacy 1.9.4 API)
SwissprotProcessor (biojava-legacy 1.9.4 API) JavaScript is disabled on your browser. Nested Class Summary Nested Classes Modifier and Type Class and Description static class SwissprotProcessor.Factory Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor Method Summary Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait Constructor…
org.biojava.nbio.structure.align.util.URLConnectionTools.doPOST java code examples | Tabnine
public static final void sendAFPChainToServer(String serverLocation, AFPChain afpChain,Atom[] ca1, Atom[] ca2) throws JobKillException { String sendURL = serverLocation + sendAPPEND; String version = resourceManager.getString(“jfatcat.version”); int timeout = getTimeout(); try { // just to make sure that similarity has been calculated! afpChain.getSimilarity(); String xml = AFPChainXMLConverter.toXML(afpChain, ca1, ca2); String u =…
org.biojava.nbio.core.sequence.CDSSequence.getSequenceAsString java code examples | Tabnine
/** * A CDS sequence if negative stranded needs to be reverse complement * to represent the actual coding sequence. When getting a ProteinSequence * from a TranscriptSequence this method is callled for each CDSSequence * {@link www.sequenceontology.org/gff3.shtml} * {@link biowiki.org/~yam/bioe131/GFF.ppt} * @return coding sequence */ public String getCodingSequence() {…
org.biojava.nbio.structure.Calc.subtract java code examples | Tabnine
/** * Use unit vectors NC and NCalpha Add them. Calc unit vector and * substract it from N. * C coordinates are from amino acid i-1 * N, CA atoms from amino acid i * * @link openbioinformatics.blogspot.com/ * 2009/08/how-to-calculate-h-atoms-for-nitrogens.html */ @SuppressWarnings(“unused”) private static Atom calc_H(Atom C, Atom N,…
Talk:BioJava – Wikiwand
This article is within the scope of WikiProject Java, a collaborative effort to improve the coverage of Java on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.JavaWikipedia:WikiProject JavaTemplate:WikiProject JavaJava articles Start This article…
Difference between python and biopython
Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…
Answered: Java code with biojava
Java code with biojava alter program to be able to translate three forwarding open reading frames.its possible to transcribe() method of the GeneticCodes class to transcribe the DNA sequence into a RNA sequence, and then use the translate() method to translate it into a protein sequence. import org.biojava.bio.BioException;import org.biojavax.bio.seq.RichSequence;import org.biojavax.bio.seq.RichSequenceIterator;import…
java – Calculating physico-chemical properties of amino acids in Biojava
I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava. I have found in the BioJava tutorial how to read the Fasta files and implemented this code. But I have no ideas how to solve this…
Accepted biojava-live 1:1.9.5+dfsg-1 (source all) into experimental, experimental
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 08 Apr 2022 21:21:13 +0200 Source: biojava-live Binary: libbiojava-java libbiojava-java-doc libbiojava1.9-java Architecture: source all Version: 1:1.9.5+dfsg-1 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Pierre Gruet <p…@debian.org> Description: libbiojava-java – Java API to biological data and applications…
ChromatogramNonlinearScaler.Identity (biojava-legacy 1.9.2 API)
ChromatogramNonlinearScaler.Identity (biojava-legacy 1.9.2 API) JavaScript is disabled on your browser. Summary: Nested | Field | Constr | Method Detail: Field | Constr | Method java.lang.Object org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity Method Summary Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait Summary: Nested | Field | Constr | Method Detail: Field | Constr | Method Copyright © 2020…
FeatureTypes.RepositoryImpl (biojava-legacy 1.9.2 API)
FeatureTypes.RepositoryImpl (biojava-legacy 1.9.2 API) JavaScript is disabled on your browser. Method Summary Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait Constructor Detail RepositoryImpl public RepositoryImpl(String name) Create a named repository. Parameters: name – the name of this repository Method Detail createType public FeatureTypes.Type createType(String name, FeatureFilter schema, Set parents) Create…
org.biojava.nbio.structure.PDBHeader.getRfree java code examples | Tabnine
mmtfDecoderInterface.setHeaderInfo(pdbHeader.getRfree(), pdbHeader.getRwork(), pdbHeader.getResolution(), pdbHeader.getTitle(), MmtfUtils.dateToIsoString(pdbHeader.getDepDate()), MmtfUtils.dateToIsoString(pdbHeader.getRelDate()), MmtfUtils.techniquesToStringArray(pdbHeader.getExperimentalTechniques())); mmtfDecoderInterface.setXtalInfo(MmtfUtils.getSpaceGroupAsString(xtalInfo.getSpaceGroup()), MmtfUtils.getUnitCellAsArray(xtalInfo), MmtfUtils.getNcsAsArray(xtalInfo.getNcsOperators())); Read more here: Source link
File: reproducible.patch | Debian Sources
123456789101112131415 Author: Chris West <solo-debianbugs@goeswhere.com> Last-Update: Sun, 9 Apr 2017 17:36:01 UTC Bug-Debian: bugs.debian.org/859958 Description: make build reproducible — a/build.xml +++ b/build.xml @@ -403,6 +403,7 @@ doctitle=”${Name.biojava}-${version}” maxmemory=”512m”> <link href=”http://java.sun.com/j2se/1.5.0/docs/api/” offline=”false”/> + <arg value=”-notimestamp”/> <group title=”Core biological packages” packages=”org.biojava.bio:org.biojava.bio.dist:org.biojava.bio.search:org.biojava.bio.seq:org.biojava.bio.seq.db:org.biojava.bio.seq.genomic:org.biojava.bio.seq.io:org.biojava.bio.symbol:org.biojava.bio.alignment:org.biojava.directory:org.biojava.bibliography:org.biojava.bio.taxa:org.biojava.bio.seq.filter” /> Read more here: Source link
BlockPainter (biojava-legacy 1.9.5 API)
BlockPainter (biojava-legacy 1.9.5 API) JavaScript is disabled on your browser. JavaScript is disabled on your browser. Summary: Nested | Field | Constr | Method Detail: Field | Constr | Method JavaScript is disabled on your browser. Summary: Nested | Field | Constr | Method Detail: Field | Constr | Method Copyright © 2021 BioJava. All rights reserved. Read more…
LargeBuffer (BioJava-1.4 API)
LargeBuffer (BioJava-1.4 API) org.biojava.utils.io Class LargeBuffer java.lang.Object org.biojava.utils.io.LargeBuffer public class LargeBuffer extends Object Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs. Author: Matthews Pocock Method Summary void force() byte get() byte get(long pos) char getChar() char getChar(long pos) double getDouble() …
FilterTest (BioJava-1.4 API)
FilterTest (BioJava-1.4 API) PREV CLASS NEXT CLASS FRAMES NO FRAMES All Classes SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD org.biojava.bio.search Interface FilterTest All Known Implementing Classes: FilterTest.Equals, FilterTest.GreaterThan, FilterTest.LessThan public interface FilterTest Class for implementing tests with BlastLikeSearchFilter objects. Several precanned tests are included. Author: David Huen Nested Class Summary static class FilterTest.Equals…
biojava-modfinder requires external resources that are no longer freely available
All files needed are from phosphosite resource, e.g.: www.phosphosite.org/downloads/Acetylation_site_dataset.gz , They give a 403 error code on download (forbidden). The only way to download it now seems to be by going to the website and logging in. I contacted the phosphosite resource a few weeks ago when I first saw…
Add module descriptors for javadoc
$ mvn javadoc:aggregate … [INFO] — maven-javadoc-plugin:3.0.1:aggregate (default-cli) @ biojava-legacy — [ERROR] no module descriptor for org.biojava:biojava-legacy [ERROR] no module descriptor for org.biojava:bytecode [ERROR] no module descriptor for org.biojava:core [ERROR] no module descriptor for org.biojava:alignment [ERROR] no module descriptor for org.biojava:biosql [ERROR] no module descriptor for org.biojava:blast [ERROR] no module…
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. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008…
How to compile Java files in bash?
How to compile Java files in bash? 0 Hi everyone, Am very brand new dealing with java and biojava. Am working on a project to calculate codon adaptation index CAI using java and biojava following this tutorial “www.ihes.fr/~carbone/materials/description.html“. but errors are arising while trying to compile the two java files:…
There is a problem with the BLASTN xml output
Based on biojava, I personally made and am using something that works with blastN. I was using the NR and NT DB of v4 locally. However, there was one problem after updating this v5. I tried to read and xml the pasta file with version 2.11.0 of BLAST+. (This is…
biojava5-live — Java API to biological data and applications (version 5)
Package: wnpp Severity: wishlist Owner: Debian-med team <debian-…@lists.debian.org> X-Debbugs-Cc: debian-de…@lists.debian.org, debian-…@lists.debian.org * Package name : biojava5-live Version : 5.4.0 Upstream Author : BioJava Developers <biojav…@biojava.org> * URL : www.biojava.org/ * License : LGPL-2.1 Programming Lang: Java Description : Java API to biological data and applications (version 5) This package presents…