X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=utils%2Finstall4j%2Fauto_file_associations-i4j8.pl;h=f2814696f1be0e5ab0539376b6f23699fb4a9f5e;hb=876d4a91fbe3c15d7cc7cf54ee477a79ce16a706;hp=e0916818de6e1f77bb9ba3fb71720bc388d68f61;hpb=647ab2685d475e3f0c89d0a8f06f80358d7d4ea6;p=jalview.git

diff --git a/utils/install4j/auto_file_associations-i4j8.pl b/utils/install4j/auto_file_associations-i4j8.pl
index e091681..f281469 100755
--- 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"]},
@@ -120,25 +121,16 @@ close(IN);
 
 my %all_associations = (%$file_associations, %$add_associations);
 
-my $num = 0;
-my $i4jcount = 0;
 my @ordered = (@put_first, @non_primary);
 for my $key (sort keys %all_associations) {
   next if grep($_ eq $key, @ordered);
   push(@ordered, $key);
 }
-for my $key (@ordered) {
-  my $a = $all_associations{$key};
-  next if (ref($a) ne "HASH");
-
-  my $extensions = $a->{extensions};
-  my @extensions = @$extensions;
-
-  $num++
-}
+my $num = $#ordered + 1;
 
 warn("--\n");
 
+my $i4jcount = 0;
 for my $shortname (@ordered) {
   my $a = $all_associations{$shortname};
   next if (ref($a) ne "HASH");
@@ -162,6 +154,7 @@ for my $shortname (@ordered) {
   my $xshortname = xml_escape($shortname);
   my $xiconfile = xml_escape($iconfile);
   my $xrole = xml_escape($role);
+  my $xROLE = xml_escape(uc($role));
   my $xprimarystring = xml_escape($primarystring);
 
   my $macentry = $mactemplate;
@@ -189,12 +182,13 @@ for my $shortname (@ordered) {
   $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
   $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
   $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+  $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
 
   my $ext = join(",",sort(@extensions));
   my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
-  $i4jcount++;
   my $progresspercent = int(($i4jcount/$num)*100);
   $progresspercent = 100 if $progresspercent > 100;
+  $i4jcount++;
   my $xext = xml_escape($ext);
   my $addunixextension = "true";
 
@@ -222,6 +216,6 @@ 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;
 }