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",
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"},
+ jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
};
};
my @put_first = qw(jalview jvl);
+my @non_primary = qw(mmcif mmcif2 pdb);
+
my $v = ($i4jversion >= 8)?$i4jversion:"";
my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
my $i4jtemplate;
my $i4jautofile = $i4jtemplatefile;
$i4jautofile =~ s/template/auto$1/;
+for my $key (sort keys %$add_associations) {
+ my $a = $add_associations->{$key};
+ warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
+}
+
open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
print MA "<key>CFBundleDocumentTypes</key>\n<array>\n\n";
name => $name,
extensions => \@extensions
};
- warn("Adding file association for $shortname\n");
+ warn("Reading file association for $shortname (".join(",",@extensions).")\n");
}
}
close(IN);
my %all_associations = (%$file_associations, %$add_associations);
-my $num = 0;
-my $i4jcount = 0;
-my @ordered = @put_first;
+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;
- for my $ext (@extensions) {
- $num++;
- }
- #delete $all_associations{$shortname};
- #print "NUM: $num\n";
-}
+my $num = $#ordered + 1;
+warn("--\n");
+my $i4jcount = 0;
for my $shortname (@ordered) {
my $a = $all_associations{$shortname};
next if (ref($a) ne "HASH");
my $extensions = $a->{extensions};
my $mimetype = $mimetypes->{$shortname};
$mimetype = "application/x-$shortname+txt" unless $mimetype;
- #$mimetype = "application/x-$shortname" unless $mimetype;
my $iconfile = $a->{iconfile};
$iconfile = "Jalview-File" unless $iconfile;
+ my $primary = (! grep($_ eq $shortname, @non_primary));
+ my $primarystring = $primary?"true":"false";
+ my $role = $primary?"Editor":"Viewer";
+
my @extensions = @$extensions;
- #warn("LINE: $line\nFound extensions '".join("', '", @extensions)."' for $name Files ($shortname)'n");
my $xname = xml_escape($name);
my $xmimetype = xml_escape($mimetype);
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;
$macentry =~ s/\$\$NAME\$\$/$xname/g;
$macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
$macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
$macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+ $macentry =~ s/\$\$ROLE\$\$/$xrole/g;
+ $macentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
my $pre = $1;
my $post = $2;
$i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
$i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
$i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
-
- my $unixext;
- for my $ext (sort @extensions) {
- if (not defined($unixext)) {
- $unixext = $ext;
- next;
- }
- if (length($ext) < length($unixext)) {
- $unixext = $ext;
- next;
- }
- }
-
- for my $ext (@extensions) {
- $i4jcount++;
- #print "COUNT: $i4jcount\n";
- my $progresspercent = int(($i4jcount/$num)*100);
- #print "PC: $progresspercent\n";
- $progresspercent = 100 if $progresspercent > 100;
- my $xext = xml_escape($ext);
- my $addunixextension = ($ext eq $unixext)?"true":"false";
-
- my $i4jextentry = $i4jentry;
- $i4jextentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
- $i4jextentry =~ s/\$\$EXTENSION\$\$/$xext/g;
- $i4jextentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
- $i4jextentry =~ s/\$\$ID\$\$/$id/g;
- $id++;
- $i4jextentry =~ s/\$\$ID1\$\$/$id/g;
- $id++;
- $i4jextentry =~ s/\$\$ID2\$\$/$id/g;
- $id++;
-
- print IA $i4jextentry;
- }
+ $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+ $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
+
+ my $ext = join(",",sort(@extensions));
+ my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
+ my $progresspercent = int(($i4jcount/$num)*100);
+ $progresspercent = 100 if $progresspercent > 100;
+ $i4jcount++;
+ my $xext = xml_escape($ext);
+ my $addunixextension = "true";
+
+ $i4jentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
+ $i4jentry =~ s/\$\$EXTENSION\$\$/$xext/g;
+ $i4jentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
+ $i4jentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
+ $i4jentry =~ s/\$\$ID\$\$/$id/g;
+ $id++;
+ $i4jentry =~ s/\$\$ID1\$\$/$id/g;
+ $id++;
+ $i4jentry =~ s/\$\$ID2\$\$/$id/g;
+ $id++;
+
+ print IA $i4jentry;
delete $all_associations{$shortname};
+ warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
}
close(IA);
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;
}