+++ /dev/null
-#!/usr/bin/env perl
-
-use strict;
-
-my $i4jversion = 8;
-if ($ARGV[0] eq "-v") {
- shift @ARGV;
- $i4jversion = shift @ARGV;
- die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
-}
-
-my $fileformats = $ARGV[0];
-$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-mmcif",
- 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"]},
- mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
- mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
- jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
- 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 @non_primary = qw(mmcif mmcif2 pdb);
-
-my $v = ($i4jversion >= 8)?$i4jversion:"";
-my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
-my $i4jtemplate;
-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 $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;
- $extensions =~ s/\s+//g;
- my @possextensions = map(lc($_),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);
- }
- next unless scalar(@extensions);
- $file_associations->{$shortname} = {
- shortname => $shortname,
- name => $name,
- extensions => \@extensions
- };
- warn("Reading file association for $shortname (".join(",",@extensions).")\n");
- }
-}
-close(IN);
-
-my %all_associations = (%$file_associations, %$add_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};
- next if (ref($a) ne "HASH");
-
- my $name = $a->{name};
- my $extensions = $a->{extensions};
- my $mimetype = $mimetypes->{$shortname};
- $mimetype = "application/x-$shortname+txt" unless $mimetype;
-
- my $iconfile = $a->{iconfile};
- $iconfile = "Jalview-File" unless $iconfile;
-
- my $primary = (! grep($_ eq $shortname, @non_primary));
- my $primarystring = $primary?"true":"false";
- my $role = $primary?"Editor":"Viewer";
-
- my @extensions = @$extensions;
-
- 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;
-}
git://source.jalview.org / jalview.git / blobdiff