details: http://www.bx.psu.edu/hg/galaxy/rev/66ea0a1ac929 changeset: 1638:66ea0a1ac929 user: Dan Blankenberg dan@bx.psu.edu date: Mon Nov 24 11:19:48 2008 -0500 description: Update GMAJ to latest beta.
2 file(s) affected in this change:
static/gmaj/gmaj.jar tools/visualization/GMAJ.xml
diffs (30 lines):
diff -r c141cb89aa45 -r 66ea0a1ac929 static/gmaj/gmaj.jar Binary file static/gmaj/gmaj.jar has changed diff -r c141cb89aa45 -r 66ea0a1ac929 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Thu Nov 20 16:15:39 2008 -0500 +++ b/tools/visualization/GMAJ.xml Mon Nov 24 11:19:48 2008 -0500 @@ -46,6 +46,7 @@ <option name="MAF File" value="maf"> <option name="Invalid MAF version (maf_version)" value="maf_version"/> <option name="Skipping unsupported paragraph (maf_paragraph)" value="maf_paragraph"/> + <option name="Unrecognized character found in alignment (bad_char_all)" value="bad_char_all"/> <option name="Skipping all reconstruction scores: no species specified (recon_noseq)" value="recon_noseq"/> <option name="Skipping reconstruction scores in blocks with missing row (recon_missing)" value="recon_missing"/> <option name="The first row in some blocks is not the specified reference sequence (refseq_not_first)" value="refseq_not_first"/> @@ -75,7 +76,7 @@ <option name="Score shading is not yet supported (score_shading)" value="score_shading"/> </option> <option name="Red Flags" value="red"> - <option name="Sequence name in annotation file does not match name in MAF (seqname_mismatch)" value="seqname_mismatch"/> + <option name="Assuming that annotations in file ___ are for species ___ (seqname_fix_all)" value="seqname_fix_all"/> <option name="BED start or end < 0 (bed_coord)" value="bed_coord"/> <option name="GFF start or end < 1 (gff_coord)" value="gff_coord"/> <option name="Missing item name for URL substitution (url_subst)" value="url_subst"/> @@ -87,6 +88,7 @@ <option name="Skipping blocks for export where reference sequence is hidden or all gaps (export_skip)" value="export_skip"/> <option name="Possible parse error: token ends with an escaped quote (escaped_quote)" value="escaped_quote"/> <option name="Draggable panel dividers will not be sticky (no_sticky)" value="no_sticky"/> + <option name="Selecting a large block may be very slow (big_block)" value="big_block"/> </option> </option> </options>