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 Version Locator",extensions=>["jvl"],iconfile=>"Jalview-Version-Locator"},
+ jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"Jalview-Launch"},
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 $i4jtemplate;
-open(IT,"<$i4jtemplatefile") or dir("Could not open '$i4jtemplatefile' for reading");
+my $mactemplatefile = "file_associations_template-Info_plist.xml";
+my $mactemplate;
+
+open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
+while(<MT>){
+ $mactemplate .= $_;
+}
+close(MT);
+open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
while(<IT>){
$i4jtemplate .= $_;
}
close(IT);
+my $macauto;
my $i4jauto;
+my $macautofile = $mactemplatefile;
+$macautofile =~ s/template/auto$1/;
+
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";
+
open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
my $name = $2;
my $extensions = $3;
$extensions =~ s/\s+//g;
- my @possextensions = split(m/,/,$extensions);
+ my @possextensions = map(lc($_),split(m/,/,$extensions));
my @extensions;
my $addext = $add_extensions->{$shortname};
if (ref($addext) eq "ARRAY") {
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);
-for my $shortname (@put_first, sort keys %all_associations) {
+my @ordered = (@put_first, @non_primary);
+for my $key (sort keys %all_associations) {
+ next if grep($_ eq $key, @ordered);
+ push(@ordered, $key);
+}
+my $num = $#ordered + 1;
+
+warn("--\n");
+
+my $i4jcount = 0;
+for my $shortname (@ordered) {
my $a = $all_associations{$shortname};
- if (ref($a) ne "HASH") {
- next;
- }
+ next if (ref($a) ne "HASH");
my $name = $a->{name};
my $extensions = $a->{extensions};
my $mimetype = $mimetypes->{$shortname};
- $mimetype = "text/x-$shortname" unless $mimetype;
+ $mimetype = "application/x-$shortname+txt" unless $mimetype;
my $iconfile = $a->{iconfile};
$iconfile = "Jalview-File" unless $iconfile;
- my @extensions = @$extensions;
- #warn("LINE: $line\nFound extensions '".join("', '", @extensions)."' for $name Files ($shortname)'n");
-
- my $i4jentry = $i4jtemplate;
-
- $i4jentry =~ s/\$\$NAME\$\$/$name/g;
- $i4jentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
- $i4jentry =~ s/\$\$MIMETYPE\$\$/$mimetype/g;
- $i4jentry =~ s/\$\$ICONFILE\$\$/$iconfile/g;
+ my $primary = (! grep($_ eq $shortname, @non_primary));
+ my $primarystring = $primary?"true":"false";
+ my $role = $primary?"Editor":"Viewer";
- for my $ext (@extensions) {
- my $i4jextentry = $i4jentry;
- $i4jextentry =~ s/\$\$EXTENSION\$\$/$ext/g;
- $i4jextentry =~ s/\$\$ID\$\$/$id/g;
- $id++;
+ my @extensions = @$extensions;
- print IA $i4jextentry;
+ 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;
+ my $macextensions;
+ for my $ext (@extensions) {
+ my $xext = xml_escape($ext);
+ $macextensions .= $pre.$xext.$post;
+ }
+ $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
}
+ print MA $macentry;
+
+ my $i4jentry = $i4jtemplate;
+ $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
+ $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+ $i4jentry =~ s/\$\$MIMETYPE\$\$/$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))));
+ 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);
+print MA "</array>\n";
+close(MA);
+
+sub xml_escape {
+ my $x = shift;
+ # stolen from Pod::Simple::XMLOutStream in base distro
+ $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
+ return $x;
+}