use strict;
+my $i4jversion = 7;
+if ($ARGV[0] eq "-v") {
+ shift @ARGV;
+ $i4jversion = shift @ARGV;
+ die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
+}
+# backwards compatibility
+$i4jversion = "" if $i4jversion < 8;
+
my $fileformats = $ARGV[0];
-$fileformats = "./src/jalview/io/FileFormats.java" unless $fileformats;
+$fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
+
+# default mimetype will be text/x-$shortname
+# TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
+# TODO: look up standard mime type used for BLASTfmt matrices, etc
+my $mimetypes = {
+ rnaml => "application/rnaml+xml",
+ biojson => "application/x-jalview-biojson+json",
+ jnet => "application/x-jalview-jnet+text",
+ features => "application/x-jalview-features+text",
+ scorematrix => "application/x-jalview-scorematrix+text",
+ pdb => "chemical/x-pdb",
+ mmcif => "chemical/x-cif",
+ mmcif2 => "chemical/x-mcif",
+ jalview => "application/x-jalview+xml+zip",
+ jvl => "application/x-jalview-jvl+text",
+ annotations => "application/x-jalview-annotations+text",
+};
+
+my @dontaddshortname = qw(features json);
+my @dontaddextension = qw(html xml json jar mfa fastq);
+my $add_associations = {
+ biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
+ gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
+ 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"]},
+ mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
+ jvl => {shortname=>"jvl",name=>"Jalview Version Locator",extensions=>["jvl"],iconfile=>"Jalview-Version-Locator"},
+ jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
+ scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
+};
+my $add_extensions = {
+ blc => ["blc"],
+};
+my @put_first = qw(jalview jvl);
my $mactemplatefile = "file_associations_template-Info_plist.xml";
-my $i4jtemplatefile = "file_associations_template-install4j.xml";
+my $i4jtemplatefile = ($i4jversion >= 8)?"file_associations_template-install4j${i4jversion}.xml";
my $mactemplate;
my $i4jtemplate;
open(MT,"<$mactemplatefile") or dir("Could not open '$mactemplatefile' for reading");
open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
my $id = 10000;
+my $file_associations = {};
while(my $line = <IN>) {
$line =~ s/\s+/ /g;
$line =~ s/(^ | $)//g;
if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
my $shortname = lc($1);
+ next if (grep($_ eq $shortname, @dontaddshortname));
my $name = $2;
my $extensions = $3;
$extensions =~ s/\s+//g;
- my @extensions = split(m/,/,$extensions);
- #warn("LINE: $line\nFound extensions '".join("', '", @extensions)."' for $name Files ($shortname)'n");
-
- my $macentry = $mactemplate;
- my $i4jentry = $i4jtemplate;
-
- $macentry =~ s/\$\$NAME\$\$/$name/g;
- $macentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
-
- $i4jentry =~ s/\$\$NAME\$\$/$name/g;
- $i4jentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
-
- while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
- my $pre = $1;
- my $post = $2;
- my $macextensions;
- for my $ext (@extensions) {
- $macextensions .= $pre.$ext.$post;
- }
- $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
+ my @possextensions = split(m/,/,$extensions);
+ my @extensions;
+ my $addext = $add_extensions->{$shortname};
+ if (ref($addext) eq "ARRAY") {
+ push(@possextensions, @$addext);
+ }
+ for my $possext (@possextensions) {
+ next if grep($_ eq $possext, @extensions);
+ next if grep($_ eq $possext, @dontaddextension);
+ push(@extensions,$possext);
}
- print MA $macentry;
+ next unless scalar(@extensions);
+ $file_associations->{$shortname} = {
+ shortname => $shortname,
+ name => $name,
+ extensions => \@extensions
+ };
+ warn("Adding file association for $shortname\n");
+ }
+}
+close(IN);
- for my $ext (@extensions) {
- my $i4jextentry = $i4jentry;
- $i4jextentry =~ s/\$\$EXTENSION\$\$/$ext/g;
- $i4jextentry =~ s/\$\$ID\$\$/$id/g;
- $id++;
+my %all_associations = (%$file_associations, %$add_associations);
+
+for my $shortname (@put_first, sort keys %all_associations) {
+ my $a = $all_associations{$shortname};
+ if (ref($a) ne "HASH") {
+ next;
+ }
+
+ my $name = $a->{name};
+ my $extensions = $a->{extensions};
+ my $mimetype = $mimetypes->{$shortname};
+ $mimetype = "text/x-$shortname" unless $mimetype;
- print IA $i4jextentry;
+ 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 $macentry = $mactemplate;
+ my $i4jentry = $i4jtemplate;
+
+ $macentry =~ s/\$\$NAME\$\$/$name/g;
+ $macentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
+ $macentry =~ s/\$\$MIMETYPE\$\$/$mimetype/g;
+ $macentry =~ s/\$\$ICONFILE\$\$/$iconfile/g;
+
+ $i4jentry =~ s/\$\$NAME\$\$/$name/g;
+ $i4jentry =~ s/\$\$SHORTNAME\$\$/$shortname/g;
+ $i4jentry =~ s/\$\$MIMETYPE\$\$/$mimetype/g;
+ $i4jentry =~ s/\$\$ICONFILE\$\$/$iconfile/g;
+
+ while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
+ my $pre = $1;
+ my $post = $2;
+ my $macextensions;
+ for my $ext (@extensions) {
+ $macextensions .= $pre.$ext.$post;
}
+ $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
+ }
+ print MA $macentry;
+
+ for my $ext (@extensions) {
+ my $i4jextentry = $i4jentry;
+ $i4jextentry =~ s/\$\$EXTENSION\$\$/$ext/g;
+ $i4jextentry =~ s/\$\$ID\$\$/$id/g;
+ $id++;
+ print IA $i4jextentry;
}
+
+ delete $all_associations{$shortname};
}
-close(IN);
+
close(IA);
print MA "</array>\n";
close(MA);
git://source.jalview.org / jalview.git / blobdiff