5 my $fileformats = $ARGV[0];
6 $fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
8 # default mimetype will be text/x-$shortname
9 # TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
10 # TODO: look up standard mime type used for BLASTfmt matrices, etc
12 rnaml => "application/rnaml+xml",
13 biojson => "application/x-jalview-biojson+json",
14 jnet => "application/x-jalview-jnet+text",
15 features => "application/x-jalview-features+text",
16 scorematrix => "application/x-jalview-scorematrix+text",
17 pdb => "chemical/x-pdb",
18 mmcif => "chemical/x-cif",
19 mmcif2 => "chemical/x-mmcif",
20 jalview => "application/x-jalview+xml+zip",
21 #jvl => "application/x-jalview-jvl+text",
22 annotations => "application/x-jalview-annotations+text",
25 my @dontaddshortname = qw(features json);
26 my @dontaddextension = qw(html xml json jar mfa fastq);
27 my $add_associations = {
28 biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
29 gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
30 gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
31 features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
32 annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
33 mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
34 mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
35 #jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jalview-launch"},
36 jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
37 scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
39 my $add_extensions = {
42 my @put_first = qw(jalview jvl);
44 my @non_primary = qw(mmcif mmcif2 pdb);
46 my $mailcaptemplatefile = "file_associations_template-mailcap.txt";
48 my $sharedmimeinfotemplatefile = "file_associations_template-shared-mime-info.xml";
49 my $sharedmimeinfotemplate;
51 open(SMT,"<$sharedmimeinfotemplatefile") or die("Could not open '$sharedmimeinfotemplatefile' for reading");
53 $sharedmimeinfotemplate .= $_;
56 open(MCT,"<$mailcaptemplatefile") or die("Could not open '$mailcaptemplatefile' for reading");
58 $mailcaptemplate .= $_;
61 my $sharedmimeinfoauto;
64 # this file should go in /usr/share/mime/packages
65 my $sharedmimeinfoautofile = "debian/jalview-mime.xml";
67 # this file should go in /usr/lib/mime/packages
68 my $mailcapautofile = "debian/jalview-mailcap";
70 # this should be part of the jalview.desktop file that goes in /usr/shares/applications
71 my $desktopfile = "debian/jalview.desktop";
75 for my $key (sort keys %$add_associations) {
76 my $a = $add_associations->{$key};
77 warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
80 open(SMI,">$sharedmimeinfoautofile") or die ("Could not open '$sharedmimeinfoautofile' for writing");
82 open(MCA,">$mailcapautofile") or die ("Could not open '$mailcapautofile' for writing");
84 open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
86 my $file_associations = {};
87 while(my $line = <IN>) {
89 $line =~ s/(^ | $)//g;
90 if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
91 my $shortname = lc($1);
92 next if (grep($_ eq $shortname, @dontaddshortname));
95 $extensions =~ s/\s+//g;
96 my @possextensions = map(lc($_),split(m/,/,$extensions));
98 my $addext = $add_extensions->{$shortname};
99 if (ref($addext) eq "ARRAY") {
100 push(@possextensions, @$addext);
102 for my $possext (@possextensions) {
103 next if grep($_ eq $possext, @extensions);
104 next if grep($_ eq $possext, @dontaddextension);
105 push(@extensions,$possext);
107 next unless scalar(@extensions);
108 $file_associations->{$shortname} = {
109 shortname => $shortname,
111 extensions => \@extensions
113 warn("Reading file association for $shortname (".join(",",@extensions).")\n");
118 my %all_associations = (%$file_associations, %$add_associations);
120 my @ordered = (@put_first, @non_primary);
121 for my $key (sort keys %all_associations) {
122 next if grep($_ eq $key, @ordered);
123 push(@ordered, $key);
125 my $num = $#ordered + 1;
128 print SMI qq(<?xml version="1.0" encoding="UTF-8"?>\n<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">\n\n);
130 my $mailcapcount = 0;
131 for my $shortname (@ordered) {
132 my $a = $all_associations{$shortname};
133 next if (ref($a) ne "HASH");
135 my $name = $a->{name};
136 my $extensions = $a->{extensions};
137 my $mimetype = $mimetypes->{$shortname};
138 $mimetype = "application/x-$shortname+txt" unless $mimetype;
140 $MimeType .= $MimeType?";":"";
141 $MimeType .= $mimetype;
143 my $iconfile = $a->{iconfile};
144 $iconfile = "x-jalview-file" unless $iconfile;
146 my $primary = (! grep($_ eq $shortname, @non_primary));
147 my $primarystring = $primary?"true":"false";
148 my $role = $primary?"Editor":"Viewer";
149 my $priority = $primary?9:4;
150 $priority = 10 if $mimetype =~ m/\bjalview\b/;
152 my @extensions = @$extensions;
153 my $extension0 = $extensions[0];
155 my $xname = xml_escape($name);
156 my $xmimetype = xml_escape($mimetype);
157 my $xshortname = xml_escape($shortname);
158 my $xiconfile = xml_escape($iconfile);
159 my $xrole = xml_escape($role);
160 my $xROLE = xml_escape(uc($role));
161 my $xprimarystring = xml_escape($primarystring);
163 my $sharedmimeinfoentry = $sharedmimeinfotemplate;
164 $sharedmimeinfoentry =~ s/\$\$NAME\$\$/$xname/g;
165 $sharedmimeinfoentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
166 $sharedmimeinfoentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
167 $sharedmimeinfoentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
168 $sharedmimeinfoentry =~ s/\$\$ROLE\$\$/$xrole/g;
169 $sharedmimeinfoentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
170 $sharedmimeinfoentry =~ s/\$\$PRIORITY\$\$/$priority/g;
171 while ($sharedmimeinfoentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
174 my $sharedmimeinfoextensions;
175 for my $ext (@extensions) {
176 my $xext = xml_escape($ext);
177 $sharedmimeinfoextensions .= $pre.$xext.$post;
180 $prere =~ s/([\*\.])/\\\1/g;
182 $postre =~ s/([\*\.])/\\\1/g;
183 $sharedmimeinfoentry =~ s/\$\$${prere}EXTENSIONS${postre}\$\$/$sharedmimeinfoextensions/gs;
185 print SMI $sharedmimeinfoentry;
187 my $mailcapentry = $mailcaptemplate;
188 $mailcapentry =~ s/\$\$NAME\$\$/$xname/g;
189 $mailcapentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
190 $mailcapentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
191 $mailcapentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
192 $mailcapentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
193 $mailcapentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
194 $mailcapentry =~ s/\$\$EXTENSION\$\$/$extension0/g;
195 $mailcapentry =~ s/\$\$PRIORITY\$\$/$priority/g;
197 my $ext = join(",",sort(@extensions));
198 my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
199 my $progresspercent = int(($mailcapcount/$num)*100);
200 $progresspercent = 100 if $progresspercent > 100;
202 my $xext = xml_escape($ext);
203 my $addunixextension = "true";
205 $mailcapentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
206 $mailcapentry =~ s/\$\$EXTENSION\$\$/$xext/g;
207 $mailcapentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
208 $mailcapentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
209 $mailcapentry =~ s/\$\$ID\$\$/$id/g;
211 $mailcapentry =~ s/\$\$ID1\$\$/$id/g;
213 $mailcapentry =~ s/\$\$ID2\$\$/$id/g;
216 print MCA $mailcapentry;
218 delete $all_associations{$shortname};
219 warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
222 print SMI "</mime-info>\n";
227 open(D,">$desktopfile") or die ("Could not open '$desktopfile' for writing");
228 print D qq([Desktop Entry]
232 Comment=Multiple Sequence Alignment Editor
238 Categories=Science;Biology;
239 Keywords=alignment;sequence;
246 # stolen from Pod::Simple::XMLOutStream in base distro
247 $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;