6 if ($ARGV[0] eq "-v") {
8 $i4jversion = shift @ARGV;
9 die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
12 my $fileformats = $ARGV[0];
13 $fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
15 # default mimetype will be text/x-$shortname
16 # TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
17 # TODO: look up standard mime type used for BLASTfmt matrices, etc
19 rnaml => "application/rnaml+xml",
20 biojson => "application/x-jalview-biojson+json",
21 jnet => "application/x-jalview-jnet+text",
22 features => "application/x-jalview-features+text",
23 scorematrix => "application/x-jalview-scorematrix+text",
24 pdb => "chemical/x-pdb",
25 mmcif => "chemical/x-cif",
26 mmcif2 => "chemical/x-mmcif",
27 jalview => "application/x-jalview+xml+zip",
28 jvl => "application/x-jalview-jvl+text",
29 annotations => "application/x-jalview-annotations+text",
32 my @dontaddshortname = qw(features json);
33 # mfa and fastq not properly supported in Jalview (but enough to be in the application extensions)
34 # ENA flatfile extension txt is too generic, as well as html xml json jar
35 my @dontaddextension = qw(txt html xml json jar mfa fastq);
36 my $add_associations = {
37 biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
38 gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
39 gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
40 features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
41 annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
42 mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
43 mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
44 jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
45 jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
46 scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
48 my $add_extensions = {
51 my @put_first = qw(jalview jvl);
52 my @owner = @put_first;
54 my @non_primary = qw(mmcif mmcif2 pdb txt);
56 my $v = ($i4jversion >= 8)?$i4jversion:"";
57 my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
59 my $mactemplatefile = "file_associations_template-Info_plist.xml";
62 open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
67 open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
75 my $macautofile = $mactemplatefile;
76 $macautofile =~ s/template/auto$1/;
78 my $i4jautofile = $i4jtemplatefile;
79 $i4jautofile =~ s/template/auto$1/;
81 for my $key (sort keys %$add_associations) {
82 my $a = $add_associations->{$key};
83 warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
86 open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
87 print MA "<key>CFBundleDocumentTypes</key>\n<array>\n\n";
89 open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
91 open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
93 my $file_associations = {};
94 while(my $line = <IN>) {
96 $line =~ s/(^ | $)//g;
97 if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
98 my $shortname = lc($1);
99 next if (grep($_ eq $shortname, @dontaddshortname));
102 $extensions =~ s/\s+//g;
103 my @possextensions = map(lc($_),split(m/,/,$extensions));
105 my $addext = $add_extensions->{$shortname};
106 if (ref($addext) eq "ARRAY") {
107 push(@possextensions, @$addext);
109 for my $possext (@possextensions) {
110 next if grep($_ eq $possext, @extensions);
111 next if grep($_ eq $possext, @dontaddextension);
112 push(@extensions,$possext);
114 next unless scalar(@extensions);
115 $file_associations->{$shortname} = {
116 shortname => $shortname,
118 extensions => \@extensions
120 warn("Reading file association for $shortname (".join(",",@extensions).")\n");
125 my %all_associations = (%$file_associations, %$add_associations);
127 my @ordered = (@put_first, @non_primary);
128 for my $key (sort keys %all_associations) {
129 next if grep($_ eq $key, @ordered);
130 push(@ordered, $key);
132 my $num = $#ordered + 1;
137 for my $shortname (@ordered) {
138 my $a = $all_associations{$shortname};
139 next if (ref($a) ne "HASH");
141 my $name = $a->{name};
142 my $extensions = $a->{extensions};
143 my $mimetype = $mimetypes->{$shortname};
144 $mimetype = "application/x-$shortname+txt" unless $mimetype;
146 my $iconfile = $a->{iconfile};
147 $iconfile = "Jalview-File" unless $iconfile;
149 my $owner = grep($_ eq $shortname, @owner);
150 my $primary = (! grep($_ eq $shortname, @non_primary));
151 my $primarystring = $primary?"true":"false";
152 #my $role = $owner?"Owner":($primary?"Editor":"Viewer");
153 my $role = $primary?"Editor":"Viewer";
154 my $rank = $owner?"Owner":($primary?"Default":"Alternate");
156 my @extensions = @$extensions;
158 my $xname = xml_escape($name);
159 my $xmimetype = xml_escape($mimetype);
160 my $xshortname = xml_escape($shortname);
161 my $xiconfile = xml_escape($iconfile);
162 my $xrole = xml_escape($role);
163 my $xROLE = xml_escape(uc($role));
164 my $xrank = xml_escape($rank);
165 my $xprimarystring = xml_escape($primarystring);
167 my $macentry = $mactemplate;
168 $macentry =~ s/\$\$NAME\$\$/$xname/g;
169 $macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
170 $macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
171 $macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
172 $macentry =~ s/\$\$ROLE\$\$/$xrole/g;
173 $macentry =~ s/\$\$RANK\$\$/$xrank/g;
174 $macentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
175 while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
179 for my $ext (@extensions) {
180 my $xext = xml_escape($ext);
181 $macextensions .= $pre.$xext.$post;
183 $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
187 my $i4jentry = $i4jtemplate;
188 $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
189 $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
190 $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
191 $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
192 $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
193 $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
195 my $ext = join(",",sort(@extensions));
196 my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
197 my $progresspercent = int(($i4jcount/$num)*100);
198 $progresspercent = 100 if $progresspercent > 100;
200 my $xext = xml_escape($ext);
201 my $addunixextension = "true";
203 $i4jentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
204 $i4jentry =~ s/\$\$EXTENSION\$\$/$xext/g;
205 $i4jentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
206 $i4jentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
207 $i4jentry =~ s/\$\$ID\$\$/$id/g;
209 $i4jentry =~ s/\$\$ID1\$\$/$id/g;
211 $i4jentry =~ s/\$\$ID2\$\$/$id/g;
216 delete $all_associations{$shortname};
217 warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
221 print MA "</array>\n";
226 # stolen from Pod::Simple::XMLOutStream in base distro
227 $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;