JAL-3447 minor corrections to cif and mmcif file associations

[jalview.git] / utils / install4j / auto_file_associations-i4j8.pl

diff --git a/utils/install4j/auto_file_associations-i4j8.pl b/utils/install4j/auto_file_associations-i4j8.pl
index bf24b11..9b26f22 100755 (executable)
--- a/utils/install4j/auto_file_associations-i4j8.pl
+++ b/utils/install4j/auto_file_associations-i4j8.pl
@@ -23,7 +23,7 @@ my $mimetypes = {
   scorematrix => "application/x-jalview-scorematrix+text",
   pdb => "chemical/x-pdb",
   mmcif => "chemical/x-cif",
-  mmcif2 => "chemical/x-mcif",
+  mmcif2 => "chemical/x-mmcif",
   jalview => "application/x-jalview+xml+zip",
   jvl => "application/x-jalview-jvl+text",
   annotations => "application/x-jalview-annotations+text",
@@ -37,6 +37,7 @@ my $add_associations = {
   gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
   features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
   annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
+  mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
   mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
   jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"Jalview-Launch"},
   jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
@@ -213,6 +214,6 @@ close(MA);
 sub xml_escape {
   my $x = shift;
   # stolen from Pod::Simple::XMLOutStream in base distro
-  $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789])/'&#'.(ord($1)).';'/eg;
+  $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
   return $x;
 }