API Specification Errors
Package Summary

For a high-level overview, see Executive Summary
For a statistical breakdown, see Package Statistics 

org.*

  Missing Comments   Minor Errors
Package Number Percent   Number Percent
org.biojava.bibliography -- --   2 1%
org.biojava.bio 6 2%   15 5%
org.biojava.bio.alignment 55 30%   49 27%
org.biojava.bio.annodb 5 8%   2 3%
org.biojava.bio.chromatogram 1 2%   2 4%
org.biojava.bio.chromatogram.graphic -- --   21 27%
org.biojava.bio.dist 3 2%   22 11%
org.biojava.bio.dp 106 37%   42 15%
org.biojava.bio.dp.onehead 23 46%   8 16%
org.biojava.bio.dp.twohead 43 47%   20 22%
org.biojava.bio.gui 42 45%   15 16%
org.biojava.bio.gui.glyph 18 35%   15 29%
org.biojava.bio.gui.sequence 322 34%   143 15%
org.biojava.bio.gui.sequence.tracklayout 12 43%   3 11%
org.biojava.bio.molbio 7 9%   3 4%
org.biojava.bio.program 7 54%   4 31%
org.biojava.bio.program.abi 20 34%   14 24%
org.biojava.bio.program.blast2html 1 2%   6 12%
org.biojava.bio.program.das 41 46%   2 2%
org.biojava.bio.program.das.dasalignment -- --   4 8%
org.biojava.bio.program.das.dasstructure -- --   1 6%
org.biojava.bio.program.formats 9 23%   2 5%
org.biojava.bio.program.gff 34 19%   37 20%
org.biojava.bio.program.gff3 19 44%   7 16%
org.biojava.bio.program.hmmer 16 57%   8 29%
org.biojava.bio.program.homologene 122 41%   58 19%
org.biojava.bio.program.indexdb 2 4%   12 21%
org.biojava.bio.program.phred 2 5%   24 59%
org.biojava.bio.program.sax -- --   9 23%
org.biojava.bio.program.sax.blastxml -- --   8 36%
org.biojava.bio.program.scf 5 25%   4 20%
org.biojava.bio.program.ssaha 18 25%   4 6%
org.biojava.bio.program.ssbind 20 16%   10 8%
org.biojava.bio.program.tagvalue 58 21%   55 20%
org.biojava.bio.program.unigene 3 9%   4 11%
org.biojava.bio.program.xff 34 38%   14 16%
org.biojava.bio.program.xml 11 61%   1 6%
org.biojava.bio.proteomics 50 53%   26 27%
org.biojava.bio.proteomics.aaindex -- --   19 48%
org.biojava.bio.search 59 18%   18 5%
org.biojava.bio.seq 127 18%   145 21%
org.biojava.bio.seq.db 71 30%   29 12%
org.biojava.bio.seq.db.biofetch -- --   1 9%
org.biojava.bio.seq.db.biosql 24 25%   18 19%
org.biojava.bio.seq.db.emblcd 6 15%   4 10%
org.biojava.bio.seq.db.flat 1 9%   1 9%
org.biojava.bio.seq.distributed 9 24%   4 11%
org.biojava.bio.seq.filter 11 85%   -- --
org.biojava.bio.seq.homol 9 19%   5 11%
org.biojava.bio.seq.impl 63 22%   18 6%
org.biojava.bio.seq.io 154 27%   89 15%
org.biojava.bio.seq.io.agave 279 46%   105 17%
org.biojava.bio.seq.io.filterxml 10 20%   21 43%
org.biojava.bio.seq.io.game 40 31%   31 24%
org.biojava.bio.seq.io.game12 2 4%   26 48%
org.biojava.bio.seq.projection 23 22%   8 8%
org.biojava.bio.structure 148 22%   113 17%
org.biojava.bio.structure.align 59 72%   14 17%
org.biojava.bio.structure.align.helper 28 64%   6 14%
org.biojava.bio.structure.align.pairwise 96 62%   26 17%
org.biojava.bio.structure.gui 46 61%   11 15%
org.biojava.bio.structure.gui.events 10 63%   1 6%
org.biojava.bio.structure.gui.util 53 55%   17 18%
org.biojava.bio.structure.io 13 13%   24 24%
org.biojava.bio.structure.io.mmcif 42 37%   18 16%
org.biojava.bio.structure.io.mmcif.chem 37 65%   10 18%
org.biojava.bio.structure.io.mmcif.model 424 93%   7 2%
org.biojava.bio.structure.jama 1 1%   64 62%
org.biojava.bio.structure.secstruc 34 61%   9 16%
org.biojava.bio.structure.server 52 47%   19 17%
org.biojava.bio.symbol 145 19%   108 14%
org.biojava.bio.taxa 24 29%   9 11%
org.biojava.directory 7 18%   2 5%
org.biojava.naming 18 28%   2 3%
org.biojava.ontology 73 35%   22 10%
org.biojava.ontology.io 1 10%   2 20%
org.biojava.ontology.obo 52 75%   9 13%
org.biojava.stats.svm 99 50%   9 5%
org.biojava.stats.svm.tools 23 37%   10 16%
org.biojava.utils 150 35%   50 12%
org.biojava.utils.automata 45 62%   6 8%
org.biojava.utils.cache 13 30%   3 7%
org.biojava.utils.candy 4 9%   12 28%
org.biojava.utils.io 43 49%   8 9%
org.biojava.utils.lsid -- --   9 53%
org.biojava.utils.math -- --   3 50%
org.biojava.utils.net -- --   1 33%
org.biojava.utils.process -- --   36 57%
org.biojava.utils.regex 8 19%   16 38%
org.biojava.utils.stax 12 13%   4 4%
org.biojava.utils.walker 4 36%   2 18%
org.biojava.utils.xml 26 41%   18 29%
org.biojavax 23 8%   148 53%
org.biojavax.bio 13 14%   55 59%
org.biojavax.bio.alignment 2 13%   5 31%
org.biojavax.bio.alignment.blast 13 29%   17 38%
org.biojavax.bio.db 4 6%   8 12%
org.biojavax.bio.db.biosql 45 21%   20 9%
org.biojavax.bio.db.ncbi 4 13%   19 61%
org.biojavax.bio.phylo 8 67%   1 8%
org.biojavax.bio.phylo.io.nexus 105 26%   19 5%
org.biojavax.bio.phylo.io.phylip 5 20%   3 12%
org.biojavax.bio.seq 48 9%   241 48%
org.biojavax.bio.seq.io 367 47%   143 18%
org.biojavax.bio.taxa 13 16%   46 55%
org.biojavax.bio.taxa.io 2 22%   4 44%
org.biojavax.ga 17 31%   36 67%
org.biojavax.ga.exception 2 50%   2 50%
org.biojavax.ga.functions 25 25%   23 23%
org.biojavax.ga.impl 21 32%   5 8%
org.biojavax.ga.util 2 7%   6 22%
org.biojavax.ontology 9 8%   76 69%
org.biojavax.utils 1 5%   8 38%
Note:
The Minor Errors table shows the number of items that, have a minor error, rather than the number of errors. (If there was one method missing 4 tags, this table would show "1" in the Tags column.)