[med-svn] r11874 - trunk/packages/strap/trunk/debian
Christoph Gille
christophgil-guest at alioth.debian.org
Mon Jul 23 21:52:07 UTC 2012
Author: christophgil-guest
Date: 2012-07-23 21:52:07 +0000 (Mon, 23 Jul 2012)
New Revision: 11874
Modified:
trunk/packages/strap/trunk/debian/strap.mime
trunk/packages/strap/trunk/debian/strap.sharedmimeinfo
Log:
added file formats to strap.sharedmimeinfo
Modified: trunk/packages/strap/trunk/debian/strap.mime
===================================================================
--- trunk/packages/strap/trunk/debian/strap.mime 2012-07-23 17:41:47 UTC (rev 11873)
+++ trunk/packages/strap/trunk/debian/strap.mime 2012-07-23 21:52:07 UTC (rev 11874)
@@ -6,15 +6,17 @@
chemical/x-pdb; viewer=/usr/bin/strap_protein_alignment; description=Protein DataBank Format; nametemplate=%s.ent;
text/x-msf-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=MSF multiple sequence alignment; nametemplate=%s.msf
-text/x-pfam-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=Multiple sequence alignment from PFAM; nametemplate=PF%s
text/x-stockholm-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=Multiple sequence alignment stockholm format; nametemplate=*.sto
-chemical/seq-aa-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta Amino Acid Sequence; nametemplate=%s.aa
+chemical/seq-aa-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta
+Amino Acid Sequence; nametemplate=%s.aa
chemical/seq-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta Amino Acid Sequence; nametemplate=%s.fa
chemical/seq-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta Amino Acid Sequence; nametemplate=%s.fasta
chemical/seq-aa-genpept; viewer=/usr/bin/strap_protein_alignment '%s'; description=GenPept Flat File; nametemplate=%s.gp
+chemical/x-genbank; viewer=/usr/bin/strap_protein_alignment '%s'; description=Genbank sequence file; nametemplate=%s.gb
+chemical/x-genbank; viewer=/usr/bin/strap_protein_alignment '%s'; description=Genbank sequence file; nametemplate=%s.genbank
chemical/x-swissprot; viewer=/usr/bin/strap_protein_alignment '%s'; description=SWISS-PROT protein sequence; nametemplate=%s.sw
chemical/x-swissprot; viewer=/usr/bin/strap_protein_alignment '%s'; description=SWISS-PROT protein sequence; nametemplate=%s.swiss
Modified: trunk/packages/strap/trunk/debian/strap.sharedmimeinfo
===================================================================
--- trunk/packages/strap/trunk/debian/strap.sharedmimeinfo 2012-07-23 17:41:47 UTC (rev 11873)
+++ trunk/packages/strap/trunk/debian/strap.sharedmimeinfo 2012-07-23 21:52:07 UTC (rev 11874)
@@ -1,12 +1,14 @@
<?xml version="1.0" encoding="UTF-8"?>
<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+
<mime-type type="text/x-strap-script">
<sub-class-of type="text/plain"/>
<comment>Script file for Strap protein alignment package</comment>
<glob pattern="*.strap"/>
- <glob pattern="*.blabla"/>
</mime-type>
+ <!-- Various Alignment format -->
+
<mime-type type="text/x-clustalw-alignment">
<sub-class-of type="text/plain"/>
<comment>Multiple sequence alignment in Clustal W format</comment>
@@ -18,4 +20,88 @@
<glob pattern="*.clustalW"/>
<glob pattern="*.clustalw"/>
</mime-type>
+
+ <mime-type type="text/x-stockholm-alignment">
+ <sub-class-of type="text/plain"/>
+ <comment>Multiple sequence alignment in stockholm format</comment>
+ <magic priority="50">
+ <match type="string" offset="0" value="# STOCKHOLM" offset="0"/>
+ </magic>
+ <glob pattern="PF*"/>
+ </mime-type>
+
+ <mime-type type="text/x-msf-alignment">
+ <sub-class-of type="text/plain"/>
+ <comment>Multiple sequence file format</comment>
+ <glob pattern="*.msf"/>
+ </mime-type>
+
+
+ <!-- Sequence formats -->
+
+ <mime-type type="chemical/x-genbank">
+ <comment>Genbank amino acid or nucleotide sequence format</comment>
+ <glob pattern="*.gb"/>
+ <glob pattern="*.genbank"/>
+ <glob pattern="*.gen"/>
+ <sub-class-of type="text/plain"/>
+ <magic priority="50">
+ <match value="LOCUS" type="string" offset="0"/>
+ </magic>
+ <specification url="ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt"/>
+ <specification url="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html"/>
+ </mime-type>
+
+
+ <mime-type type="chemical/seq-aa-genpept">
+ <comment>GenPept amino acid sequence format</comment>
+ <glob pattern="*.gp"/>
+ <sub-class-of type="text/plain"/>
+ <conflicts type="application/x-gnuplot" fdo="yes"/>
+ <specification url="http://msdlocal.ebi.ac.uk/docs/mimetype.html"/>
+ </mime-type>
+
+ <mime-type type="chemical/x-swissprot">
+ <comment>SWISS-PROT amino acid sequence format</comment>
+ <glob pattern="*.sw"/>
+ <glob pattern="*.swiss"/>
+ <glob pattern="*.swissprot"/>
+ <sub-class-of type="text/plain"/>
+ <magic priority="50">
+ <match value="ID " type="string" offset="0"/>
+ </magic>
+ <specification url="http://www.expasy.ch/cgi-bin/keywlist.pl"/>
+ <specification url="http://ca.expasy.org/sprot/userman.html"/>
+ <specification url="http://www.uniprot.org/manual/"/>
+ </mime-type>
+
+ <mime-type type="chemical/x-embl-dl-nucleotide" support="no">
+ <comment>EMBL nucleotide sequence format</comment>
+ <acronym>EMBL</acronym>
+ <expanded-acronym>European Molecular Biology Laboratory</expanded-acronym>
+ <glob pattern="*.emb"/>
+ <glob pattern="*.embl"/>
+ <magic priority="50">
+ <match value="ID " type="string" offset="0"/>
+ </magic>
+ <specification url="http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#FORMAT"/>
+ <specification url="http://www.biobind.com/faq/emboss/formats.html"/>
+ </mime-type>
+
+
+
+ <mime-type type="chemical/x-fasta">
+ <comment>Fasta amino acid sequence or nucleotide sequence format</comment>
+ <glob pattern="*.fa"/>
+ <glob pattern="*.mfa"/>
+ <glob pattern="*.fasta"/>
+ <sub-class-of type="text/plain"/>
+ <magic priority="50">
+ <match value="<" type="string" offset="0"/>
+ </magic>
+ <alias type="chemical/seq-fasta"/>
+ </mime-type>
+
+
+
</mime-info>
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