Tag: BioJava

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()            …

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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…

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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…

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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…

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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…

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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:…

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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…

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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…

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