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-mcif",
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 my @dontaddextension = qw(html xml json jar mfa fastq);
34 my $add_associations = {
35 biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
36 gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
37 gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
38 features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
39 annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
40 mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
41 jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"Jalview-Launch"},
42 jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
43 scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
45 my $add_extensions = {
48 my @put_first = qw(jalview jvl);
50 my $v = ($i4jversion >= 8)?$i4jversion:"";
51 my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
53 my $mactemplatefile = "file_associations_template-Info_plist.xml";
56 open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
61 open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
69 my $macautofile = $mactemplatefile;
70 $macautofile =~ s/template/auto$1/;
72 my $i4jautofile = $i4jtemplatefile;
73 $i4jautofile =~ s/template/auto$1/;
75 open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
76 print MA "<key>CFBundleDocumentTypes</key>\n<array>\n\n";
78 open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
80 open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
82 my $file_associations = {};
83 while(my $line = <IN>) {
85 $line =~ s/(^ | $)//g;
86 if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
87 my $shortname = lc($1);
88 next if (grep($_ eq $shortname, @dontaddshortname));
91 $extensions =~ s/\s+//g;
92 my @possextensions = map(lc($_),split(m/,/,$extensions));
94 my $addext = $add_extensions->{$shortname};
95 if (ref($addext) eq "ARRAY") {
96 push(@possextensions, @$addext);
98 for my $possext (@possextensions) {
99 next if grep($_ eq $possext, @extensions);
100 next if grep($_ eq $possext, @dontaddextension);
101 push(@extensions,$possext);
103 next unless scalar(@extensions);
104 $file_associations->{$shortname} = {
105 shortname => $shortname,
107 extensions => \@extensions
109 warn("Adding file association for $shortname (".join(",",@extensions).")\n");
114 my %all_associations = (%$file_associations, %$add_associations);
118 my @ordered = @put_first;
119 for my $key (sort keys %all_associations) {
120 next if grep($_ eq $key, @ordered);
121 push(@ordered, $key);
123 for my $key (@ordered) {
124 my $a = $all_associations{$key};
125 next if (ref($a) ne "HASH");
127 my $extensions = $a->{extensions};
128 my @extensions = @$extensions;
130 # multiple extensions now all dealt with together since i4j 8.0.1
131 #for my $ext (@extensions) {
136 #delete $all_associations{$shortname};
137 #print "NUM: $num\n";
141 for my $shortname (@ordered) {
142 my $a = $all_associations{$shortname};
143 next if (ref($a) ne "HASH");
145 my $name = $a->{name};
146 my $extensions = $a->{extensions};
147 my $mimetype = $mimetypes->{$shortname};
148 $mimetype = "application/x-$shortname+txt" unless $mimetype;
149 #$mimetype = "application/x-$shortname" unless $mimetype;
151 my $iconfile = $a->{iconfile};
152 $iconfile = "Jalview-File" unless $iconfile;
154 my @extensions = @$extensions;
155 #warn("LINE: $line\nFound extensions '".join("', '", @extensions)."' for $name Files ($shortname)'n");
157 my $xname = xml_escape($name);
158 my $xmimetype = xml_escape($mimetype);
159 my $xshortname = xml_escape($shortname);
160 my $xiconfile = xml_escape($iconfile);
162 my $macentry = $mactemplate;
163 $macentry =~ s/\$\$NAME\$\$/$xname/g;
164 $macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
165 $macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
166 $macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
167 while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
171 for my $ext (@extensions) {
172 my $xext = xml_escape($ext);
173 $macextensions .= $pre.$xext.$post;
175 $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
179 my $i4jentry = $i4jtemplate;
180 $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
181 $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
182 $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
183 $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
185 # multiple extensions now all dealt with together since i4j 8.0.1
187 # for my $ext (sort @extensions) {
188 # if (not defined($unixext)) {
192 # if (length($ext) < length($unixext)) {
197 # for my $ext (@extensions) {
199 # #print "COUNT: $i4jcount\n";
200 # my $progresspercent = int(($i4jcount/$num)*100);
201 # #print "PC: $progresspercent\n";
202 # $progresspercent = 100 if $progresspercent > 100;
203 # my $xext = xml_escape($ext);
204 # my $addunixextension = ($ext eq $unixext)?"true":"false";
206 # my $i4jextentry = $i4jentry;
207 # $i4jextentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
208 # $i4jextentry =~ s/\$\$EXTENSION\$\$/$xext/g;
209 # $i4jextentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
210 # $i4jextentry =~ s/\$\$ID\$\$/$id/g;
212 # $i4jextentry =~ s/\$\$ID1\$\$/$id/g;
214 # $i4jextentry =~ s/\$\$ID2\$\$/$id/g;
217 # print IA $i4jextentry;
220 my $ext = join(",",sort(@extensions));
221 my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
223 #print "COUNT: $i4jcount\n";
224 my $progresspercent = int(($i4jcount/$num)*100);
225 #print "PC: $progresspercent\n";
226 $progresspercent = 100 if $progresspercent > 100;
227 my $xext = xml_escape($ext);
228 #my $addunixextension = ($ext eq $unixext)?"true":"false";
229 my $addunixextension = "true";
231 my $i4jextentry = $i4jentry;
232 $i4jextentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
233 $i4jextentry =~ s/\$\$EXTENSION\$\$/$xext/g;
234 $i4jextentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
235 $i4jextentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
236 $i4jextentry =~ s/\$\$ID\$\$/$id/g;
238 $i4jextentry =~ s/\$\$ID1\$\$/$id/g;
240 $i4jextentry =~ s/\$\$ID2\$\$/$id/g;
243 print IA $i4jextentry;
246 delete $all_associations{$shortname};
250 print MA "</array>\n";
255 # stolen from Pod::Simple::XMLOutStream in base distro
256 $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789])/'&#'.(ord($1)).';'/eg;