Tag: BioJava

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 =…

/** * 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() {…

/** * 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,…

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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…

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…

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…

—–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) 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) 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…

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

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) 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) 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)  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…

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…

$ 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…

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? 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:…

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…

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…