my $m = $c->model('Directory');
my $tradition = $m->tradition( $c->request->params->{'textid'} );
my $table = $tradition->collation->make_alignment_table();
- my $witlist = shift @$table;
- $c->stash->{witnesses} = $wits;
+ my $witlist = map { $_->{'witness'} } @{$table->{'alignment'}};
+ $c->stash->{witnesses} = $witlist;
$c->stash->{alignment} = $table;
$c->stash->{template} = 'relate.tt';
}
my $m = $c->model( 'Directory' );
my $tradition = $m->tradition( $c->request->params->{'textid'} );
my $table = $tradition->collation->make_alignment_table();
- $c->stash->{'result'} => $table;
+ $c->stash->{'result'} = $table;
$c->forward-( 'View::JSON' );
}
use Moose;
use namespace::autoclean;
use File::Temp;
+use JSON;
use Text::Tradition::Collation;
-use Text::Tradition::Stemma;
+use Text::Tradition::StemmaUtil qw/ phylip_pars_input /;
BEGIN { extends 'Catalyst::Controller' }
$c->forward( "View::SVG" );
}
+=head2 character_matrix
+
+Given an alignment table in JSON form, in the parameter 'alignment', returns a
+character matrix suitable for input to Phylip PARS.
+
+=cut
+
+sub character_matrix :Local {
+ my( $self, $c ) = @_;
+ my $json = $c->request->params->{'alignment'};
+ $c->log->debug( $json );
+ my $table = from_json( $json );
+ my $matrix = phylip_pars_input( $table );
+ $c->stash->{'result'} = { 'matrix' => $matrix };
+ $c->forward( 'View::JSON' );
+}
=head2 end
Attempt to render a view, if needed.
}
my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
my @all_pos = ( 1 .. $self->end->rank - 1 );
- foreach my $wit ( $self->tradition->witnesses ) {
+ foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
if( $include ) {
next unless $include->{$wit->sigil};
}
use Graph;
use Graph::Reader::Dot;
use IPC::Run qw/ run binary /;
+use Text::Tradition::StemmaUtil qw/ phylip_pars_input /;
use Moose;
has collation => (
}
}
};
-
-sub make_character_matrix {
- my $self = shift;
- unless( $self->collation->linear ) {
- warn "Need a linear graph in order to make an alignment table";
- return;
- }
- my $table = $self->collation->make_alignment_table;
- # Push the names of the witnesses to initialize the rows of the matrix.
- my @matrix = map { [ $self->_normalize_ac( $_->{'witness'} ) ] }
- @{$table->{'alignment'}};
- foreach my $token_index ( 0 .. $table->{'length'} - 1) {
- # First implementation: make dumb alignment table, caring about
- # nothing except which reading is in which position.
- my @pos_readings = map { $_->{'tokens'}->[$token_index] }
- @{$table->{'alignment'}};
- my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings;
- my @chars = convert_characters( \@pos_text );
- foreach my $idx ( 0 .. $#matrix ) {
- push( @{$matrix[$idx]}, $chars[$idx] );
- }
- }
- return \@matrix;
-}
-
-sub _normalize_ac {
- my( $self, $witname ) = @_;
- my $ac = $self->collation->ac_label;
- if( $witname =~ /(.*)\Q$ac\E$/ ) {
- $witname = $1 . '_ac';
- }
- return sprintf( "%-10s", $witname );
-}
-
-sub convert_characters {
- my $row = shift;
- # This is a simple algorithm that treats every reading as different.
- # Eventually we will want to be able to specify how relationships
- # affect the character matrix.
- my %unique = ( '__UNDEF__' => 'X',
- '#LACUNA#' => '?',
- );
- my %count;
- my $ctr = 0;
- foreach my $word ( @$row ) {
- if( $word && !exists $unique{$word} ) {
- $unique{$word} = chr( 65 + $ctr );
- $ctr++;
- }
- $count{$word}++ if $word;
- }
- # Try to keep variants under 8 by lacunizing any singletons.
- if( scalar( keys %unique ) > 8 ) {
- foreach my $word ( keys %count ) {
- if( $count{$word} == 1 ) {
- $unique{$word} = '?';
- }
- }
- }
- my %u = reverse %unique;
- if( scalar( keys %u ) > 8 ) {
- warn "Have more than 8 variants on this location; phylip will break";
- }
- my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
- return @chars;
-}
-
-sub phylip_pars_input {
- my $self = shift;
- my $character_matrix = $self->make_character_matrix;
- my $input = '';
- my $rows = scalar @{$character_matrix};
- my $columns = scalar @{$character_matrix->[0]} - 1;
- $input .= "\t$rows\t$columns\n";
- foreach my $row ( @{$character_matrix} ) {
- $input .= join( '', @$row ) . "\n";
- }
- return $input;
-}
sub run_phylip_pars {
my $self = shift;
# $phylip_dir->unlink_on_destroy(0);
# We need an infile, and we need a command input file.
open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
- print MATRIX $self->phylip_pars_input();
+ print MATRIX phylip_pars_input( $self->collation->make_alignment_table() );
close MATRIX;
open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
--- /dev/null
+package Text::Tradition::StemmaUtil;
+
+use strict;
+use warnings;
+use Exporter 'import';
+use vars qw/ @EXPORT_OK /;
+@EXPORT_OK = qw/ phylip_pars_input /;
+
+sub make_character_matrix {
+ my( $table ) = @_;
+ # Push the names of the witnesses to initialize the rows of the matrix.
+ my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] }
+ @{$table->{'alignment'}};
+ foreach my $token_index ( 0 .. $table->{'length'} - 1) {
+ # First implementation: make dumb alignment table, caring about
+ # nothing except which reading is in which position.
+ my @pos_readings = map { $_->{'tokens'}->[$token_index] }
+ @{$table->{'alignment'}};
+ my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings;
+ my @chars = convert_characters( \@pos_text );
+ foreach my $idx ( 0 .. $#matrix ) {
+ push( @{$matrix[$idx]}, $chars[$idx] );
+ }
+ }
+ return \@matrix;
+}
+
+# Helper function to make the witness name something legal for pars
+
+sub _normalize_witname {
+ my( $witname ) = @_;
+ $witname =~ s/\s+/ /g;
+ $witname =~ s/[\[\]\(\)\:;,]//g;
+ $witname = substr( $witname, 0, 10 );
+ return sprintf( "%-10s", $witname );
+}
+
+sub convert_characters {
+ my $row = shift;
+ # This is a simple algorithm that treats every reading as different.
+ # Eventually we will want to be able to specify how relationships
+ # affect the character matrix.
+ my %unique = ( '__UNDEF__' => 'X',
+ '#LACUNA#' => '?',
+ );
+ my %count;
+ my $ctr = 0;
+ foreach my $word ( @$row ) {
+ if( $word && !exists $unique{$word} ) {
+ $unique{$word} = chr( 65 + $ctr );
+ $ctr++;
+ }
+ $count{$word}++ if $word;
+ }
+ # Try to keep variants under 8 by lacunizing any singletons.
+ if( scalar( keys %unique ) > 8 ) {
+ foreach my $word ( keys %count ) {
+ if( $count{$word} == 1 ) {
+ $unique{$word} = '?';
+ }
+ }
+ }
+ my %u = reverse %unique;
+ if( scalar( keys %u ) > 8 ) {
+ warn "Have more than 8 variants on this location; phylip will break";
+ }
+ my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
+ return @chars;
+}
+
+sub phylip_pars_input {
+ my $table = shift;
+ my $character_matrix = make_character_matrix( $table );
+ my $input = '';
+ my $rows = scalar @{$character_matrix};
+ my $columns = scalar @{$character_matrix->[0]} - 1;
+ $input .= "\t$rows\t$columns\n";
+ foreach my $row ( @{$character_matrix} ) {
+ $input .= join( '', @$row ) . "\n";
+ }
+ return $input;
+}
+
use Test::More;
use lib 'lib';
use Text::Tradition;
+use Text::Tradition::StemmaUtil qw/ phylip_pars_input /;
use XML::LibXML;
use XML::LibXML::XPathContext;
is( $stemma->graph, '1-2,1-A,2-B,2-C', "Got the correct graph" );
# Test for character matrix creation
-my $m = $stemma->make_character_matrix();
+my $m = phylip_pars_input( $c->make_alignment_table() );
## check number of rows
-is( scalar @$m, 3, "Found three witnesses in char matrix" );
- ## check number of columns
-is( scalar( @{$m->[0]} ), 19, "Found 18 rows plus sigla in char matrix" );
- ## check matrix
-my %expected = (
- 'A' => 'AAAAAAAXAAAAAAAAAA',
- 'B' => 'AXXXAAAAAABABAABAA',
- 'C' => 'AXXXAAAAABAAAAAXBB',
- );
-my @wits = map { shift @$_; } @$m;
-map { s/\s+//g } @wits;
-foreach my $i ( 0 .. $#wits ) {
- my $w = $wits[$i];
- is( join( '', @{$m->[$i]} ), $expected{$w}, "Row for witness $w is correct" );
-}
+my $expected = "\t3\t18\n";
+$expected .= 'A AAAAAAAXAAAAAAAAAA
+B AXXXAAAAAABABAABAA
+C AXXXAAAAABAAAAAXBB';
+$expected .= "\n";
+is( $m, $expected, "Got the right pars input" );
+# is( scalar @$m, 3, "Found three witnesses in char matrix" );
+# ## check number of columns
+# is( scalar( @{$m->[0]} ), 19, "Found 18 rows plus sigla in char matrix" );
+# ## check matrix
+# my %expected = (
+# 'A' => 'AAAAAAAXAAAAAAAAAA',
+# 'B' => 'AXXXAAAAAABABAABAA',
+# 'C' => 'AXXXAAAAABAAAAAXBB',
+# );
+# my @wits = map { shift @$_; } @$m;
+# map { s/\s+//g } @wits;
+# foreach my $i ( 0 .. $#wits ) {
+# my $w = $wits[$i];
+# is( join( '', @{$m->[$i]} ), $expected{$w}, "Row for witness $w is correct" );
+# }
# Test that pars runs
SKIP: {
projects / scpubgit/stemmatology.git / commitdiff