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Revision 1.3 - (view) (download) (as text)
| 1 : | golsen | 1.1 | package gjoalign2html; |
| 2 : | |||
| 3 : | use strict; | ||
| 4 : | |||
| 5 : | # Use FIGjs.pm if available: | ||
| 6 : | |||
| 7 : | my $have_FIGjs = eval { require FIGjs; 1 }; | ||
| 8 : | |||
| 9 : | eval { use Data::Dumper }; # Not in all installations | ||
| 10 : | |||
| 11 : | golsen | 1.2 | #------------------------------------------------------------------------------- |
| 12 : | # Prepend and/or append unaligned sequence data to a trimmed alignment: | ||
| 13 : | # | ||
| 14 : | # \@align = add_alignment_context( \@align, \@seqs, \%options ) | ||
| 15 : | # | ||
| 16 : | # ( \@align, $pre_len, $ali_len, $suf_len ) | ||
| 17 : | # = add_alignment_context( \@align, \@seqs, \%options ) | ||
| 18 : | # | ||
| 19 : | # Options: | ||
| 20 : | # | ||
| 21 : | # max_prefix => $limit # limit of residues to be added at beginning | ||
| 22 : | # max_suffix => $limit # limit of residues to be added at end | ||
| 23 : | # pad_char => $char # character to pad beginning and end (D = ' ') | ||
| 24 : | # | ||
| 25 : | #------------------------------------------------------------------------------- | ||
| 26 : | # Change the pad character at the ends of an alignment: | ||
| 27 : | # | ||
| 28 : | # \@align = repad_alignment( \@align, \%options ) | ||
| 29 : | # \@align = repad_alignment( \%options ) | ||
| 30 : | # @align = repad_alignment( \@align, \%options ) | ||
| 31 : | # @align = repad_alignment( \%options ) | ||
| 32 : | # | ||
| 33 : | # Options: | ||
| 34 : | # | ||
| 35 : | # pad_char => $char # character to pad beginning and end (D = ' ') | ||
| 36 : | # old_pad => $regexp # characters to replace at end (D = [^A-Za-z.*]) | ||
| 37 : | # | ||
| 38 : | #------------------------------------------------------------------------------- | ||
| 39 : | # Color an alignment by residue type | ||
| 40 : | # | ||
| 41 : | # \@align = color_alignment_by_residue( \@align, \%options ) | ||
| 42 : | # \@align = color_alignment_by_residue( \%options ) | ||
| 43 : | # ( \@align, \@legend ) = color_alignment_by_residue( \@align, \%options ) | ||
| 44 : | # ( \@align, \@legend ) = color_alignment_by_residue( \%options ) | ||
| 45 : | # | ||
| 46 : | # Options: | ||
| 47 : | # | ||
| 48 : | # align => \@alignment # alignment if not supplied as parameter | ||
| 49 : | # alignment => \@alignment # alignment if not supplied as parameter | ||
| 50 : | # colors => \%colors # character colors (html spec.) | ||
| 51 : | # pallet => $pallet # ale | gde | default | ||
| 52 : | # protein => $bool # indicates a protein alignment | ||
| 53 : | # | ||
| 54 : | #------------------------------------------------------------------------------- | ||
| 55 : | # Color an alignment by consensus | ||
| 56 : | # | ||
| 57 : | # \@align = color_alignment_by_consensus( \@align, \%options ) | ||
| 58 : | # \@align = color_alignment_by_consensus( \%options ) | ||
| 59 : | # ( \@align, \%legend ) = color_alignment_by_consensus( \@align, \%options ) | ||
| 60 : | # ( \@align, \%legend ) = color_alignment_by_consensus( \%options ) | ||
| 61 : | # | ||
| 62 : | # Options: | ||
| 63 : | # | ||
| 64 : | # align => \@alignment # Alignment if not supplied as parameter | ||
| 65 : | # alignment => \@alignment # Alignment if not supplied as parameter | ||
| 66 : | # colors => \%colors # HTML colors for consensus categories | ||
| 67 : | # matrix => \%scr_matrix # Hash of hashes of character align scores | ||
| 68 : | # max_f_diff => $max_f_diff # Maximum fraction exceptions to consensus | ||
| 69 : | # max_n_diff => $max_n_diff # Maximum number of exceptions to consensus | ||
| 70 : | # min_score => $score # Score for conservative change (D=1) | ||
| 71 : | # protein => $is_protein # Indicates a protein alignment | ||
| 72 : | # | ||
| 73 : | #------------------------------------------------------------------------------- | ||
| 74 : | # Make an html table with an alignment: | ||
| 75 : | # | ||
| 76 : | # $html = alignment_2_html_table( \@alignment, \%options ) | ||
| 77 : | # $html = alignment_2_html_table( \%options ) | ||
| 78 : | # ( $html, $javascript ) = alignment_2_html_table( \@alignment, \%options ) | ||
| 79 : | # ( $html, $javascript ) = alignment_2_html_table( \%options ) | ||
| 80 : | # | ||
| 81 : | # In scalar context, the routine returns a single block of html that includes | ||
| 82 : | # the JavaScript followed by the table. In list context, they are returned | ||
| 83 : | # separately. | ||
| 84 : | # | ||
| 85 : | # Options: | ||
| 86 : | # | ||
| 87 : | # align => \@alignment # Alignment, when not a parameter | ||
| 88 : | # alignment => \@alignment # Alignment, when not a parameter | ||
| 89 : | # key => \@legend # Append the supplied legend | ||
| 90 : | # legend => \@legend # Append the supplied legend | ||
| 91 : | # nojavascript => $boolean # Omit the JavaScript for pop-ups | ||
| 92 : | # tooltip => $boolean # Add pop-up tooltip to sequences | ||
| 93 : | # tooltip => \%id2tip # (specify the tip for each id) | ||
| 94 : | # | ||
| 95 : | # Each sequence can be a string, or an array of [ text, color ] pairs. | ||
| 96 : | # @legend is an array of lines of strings and/or [ text, color ] pairs. | ||
| 97 : | # | ||
| 98 : | # Default tooltip is the id and description, but user can supply a | ||
| 99 : | # hash with arrays of alternative mouseover parameters: | ||
| 100 : | # | ||
| 101 : | # mouseover( @{ $tooltip->{ $id } } ) | ||
| 102 : | # mouseover( $ttl, $text, $menu, $parent, $ttl_color, $text_color ) | ||
| 103 : | #------------------------------------------------------------------------------- | ||
| 104 : | # Make an html page with an alignment: | ||
| 105 : | # | ||
| 106 : | # $html = alignment_2_html_page( \@alignment, \%options ) | ||
| 107 : | # $html = alignment_2_html_page( \%options ) | ||
| 108 : | # | ||
| 109 : | # Options: | ||
| 110 : | # | ||
| 111 : | # align => \@alignment | ||
| 112 : | # alignment => \@alignment | ||
| 113 : | # key => \@legend | ||
| 114 : | # legend => \@legend | ||
| 115 : | # title => $page_title | ||
| 116 : | # | ||
| 117 : | # Each sequence can be a string, or an array of character-color pairs. | ||
| 118 : | #------------------------------------------------------------------------------- | ||
| 119 : | |||
| 120 : | golsen | 1.1 | # Some global defaults: |
| 121 : | |||
| 122 : | my $max_n_diff = 1; # Maximum number of exceptions to consensus | ||
| 123 : | my $max_f_diff = 0.10; # Maximum fraction exceptions to consensus | ||
| 124 : | my $minblos = 1; # Minimum score to be called a conservative change | ||
| 125 : | |||
| 126 : | #------------------------------------------------------------------------------- | ||
| 127 : | # Prepend and/or append unaligned sequence data to a trimmed alignment: | ||
| 128 : | # | ||
| 129 : | # \@align = add_alignment_context( \@align, \@seqs, \%options ) | ||
| 130 : | # ( \@align, $pre_len, $ali_len, $suf_len ) = add_alignment_context( \@align, \@seqs, \%options ) | ||
| 131 : | # | ||
| 132 : | # Options: | ||
| 133 : | # | ||
| 134 : | # max_prefix => $limit # limit of residues to be added at beginning | ||
| 135 : | # max_suffix => $limit # limit of residues to be added at end | ||
| 136 : | # pad_char => $char # character to pad beginning and end (D = ' ') | ||
| 137 : | # | ||
| 138 : | #------------------------------------------------------------------------------- | ||
| 139 : | sub add_alignment_context | ||
| 140 : | { | ||
| 141 : | my ( $align, $seqs, $options ) = @_; | ||
| 142 : | |||
| 143 : | $align && ( ref( $align ) eq 'ARRAY' ) | ||
| 144 : | && ( @$align > 0 ) | ||
| 145 : | or print STDERR "add_alignment_context called without valid alignment\n" | ||
| 146 : | and return undef; | ||
| 147 : | |||
| 148 : | $seqs && ( ref( $seqs ) eq 'ARRAY' ) | ||
| 149 : | && ( @$seqs > 0 ) | ||
| 150 : | or print STDERR "add_alignment_context called without valid sequences\n" | ||
| 151 : | and return undef; | ||
| 152 : | |||
| 153 : | my %index = map { $_->[0], $_ } @$seqs; | ||
| 154 : | |||
| 155 : | my %options = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 156 : | foreach ( keys %options ) { $options{ canonical_key( $_ ) } = $options{ $_ } } | ||
| 157 : | |||
| 158 : | my $max_prefix = defined( $options{ maxprefix } ) ? $options{ maxprefix } : 1e100; | ||
| 159 : | my $max_suffix = defined( $options{ maxsuffix } ) ? $options{ maxsuffix } : 1e100; | ||
| 160 : | my $pad_char = $options{ padchar } ? substr( $options{ padchar }, 0, 1 ) : ' '; | ||
| 161 : | |||
| 162 : | my $pre_len = 0; | ||
| 163 : | my $ali_len = length( $align->[0]->[2] ); | ||
| 164 : | my $suf_len = 0; | ||
| 165 : | |||
| 166 : | my %fix_data = (); | ||
| 167 : | my ( $id, $def, $aln_seq ); | ||
| 168 : | my ( $pre0, $npre, $suf0, $nsuf ); | ||
| 169 : | my ( $aligned, $full, $pos ); | ||
| 170 : | |||
| 171 : | foreach ( @$align ) | ||
| 172 : | { | ||
| 173 : | ( $id, $def, $aln_seq ) = @$_; | ||
| 174 : | if ( $index{$id} ) | ||
| 175 : | { | ||
| 176 : | $aligned = lc $aln_seq; | ||
| 177 : | $aligned =~ tr/a-z//cd; | ||
| 178 : | $full = lc $index{$id}->[2]; | ||
| 179 : | $pos = index( $full, $aligned ); | ||
| 180 : | if ( $pos > -1 ) | ||
| 181 : | { | ||
| 182 : | $npre = ( $pos <= $max_prefix ) ? $pos : $max_prefix; | ||
| 183 : | $pre0 = $pos - $npre; | ||
| 184 : | if ( $npre > $pre_len ) { $pre_len = $npre } | ||
| 185 : | $suf0 = $pos + length( $aligned ); | ||
| 186 : | $nsuf = length( $full ) - $suf0; | ||
| 187 : | $nsuf = $max_suffix if $nsuf > $max_suffix; | ||
| 188 : | if ( $nsuf > $suf_len ) { $suf_len = $nsuf } | ||
| 189 : | } | ||
| 190 : | else | ||
| 191 : | { | ||
| 192 : | $npre = 0; | ||
| 193 : | $nsuf = 0; | ||
| 194 : | } | ||
| 195 : | } | ||
| 196 : | $fix_data{ $id } = [ $pre0, $npre, $suf0, $nsuf, $index{$id} ]; | ||
| 197 : | } | ||
| 198 : | |||
| 199 : | my @align2; | ||
| 200 : | my ( @parts, $seq_entry ); | ||
| 201 : | foreach ( @$align ) | ||
| 202 : | { | ||
| 203 : | ( $id, $def, $aln_seq ) = @$_; | ||
| 204 : | ( $pre0, $npre, $suf0, $nsuf, $seq_entry ) = @{ $fix_data{ $id } }; | ||
| 205 : | |||
| 206 : | @parts = (); | ||
| 207 : | push @parts, $pad_char x ( $pre_len - $npre ) if ( $npre < $pre_len ); | ||
| 208 : | push @parts, lc substr( $seq_entry->[2], $pre0, $npre ) if $npre; | ||
| 209 : | $aln_seq =~ s/^([^A-Za-z.]+)/$pad_char x length($1)/e if ( $pre_len && ! $npre ); | ||
| 210 : | $aln_seq =~ s/([^A-Za-z.]+)$/$pad_char x length($1)/e if ( $suf_len && ! $nsuf ); | ||
| 211 : | push @parts, uc $aln_seq; | ||
| 212 : | push @parts, lc substr( $seq_entry->[2], $suf0, $nsuf ) if $nsuf; | ||
| 213 : | push @parts, $pad_char x ( $suf_len - $nsuf ) if ( $nsuf < $suf_len ); | ||
| 214 : | |||
| 215 : | push @align2, [ $id, $def, join( '', @parts ) ]; | ||
| 216 : | } | ||
| 217 : | |||
| 218 : | wantarray ? ( \@align2, $pre_len, $ali_len, $suf_len ) : \@align2; | ||
| 219 : | } | ||
| 220 : | |||
| 221 : | |||
| 222 : | #------------------------------------------------------------------------------- | ||
| 223 : | # Change the pad character at the ends of an alignment: | ||
| 224 : | # | ||
| 225 : | # \@align = repad_alignment( \@align, \%options ) | ||
| 226 : | # \@align = repad_alignment( \%options ) | ||
| 227 : | # @align = repad_alignment( \@align, \%options ) | ||
| 228 : | # @align = repad_alignment( \%options ) | ||
| 229 : | # | ||
| 230 : | # Options: | ||
| 231 : | # | ||
| 232 : | # pad_char => $char # character to pad beginning and end (D = ' ') | ||
| 233 : | # old_pad => $regexp # characters to replace at end (D = [^A-Za-z.*]) | ||
| 234 : | # | ||
| 235 : | #------------------------------------------------------------------------------- | ||
| 236 : | sub repad_alignment | ||
| 237 : | { | ||
| 238 : | my $align; | ||
| 239 : | $align = shift if ( ref($_[0]) eq 'ARRAY' ); | ||
| 240 : | |||
| 241 : | my %data = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 242 : | foreach ( keys %data ) { $data{ canonical_key( $_ ) } = $data{ $_ } } | ||
| 243 : | |||
| 244 : | $align ||= $data{ align } || $data{ alignment }; | ||
| 245 : | if ( ! $align || ( ref( $align ) ne 'ARRAY' ) ) | ||
| 246 : | { | ||
| 247 : | print STDERR "repad_alignment called without alignment\n"; | ||
| 248 : | return (); | ||
| 249 : | } | ||
| 250 : | |||
| 251 : | $data{ padchar } ||= $data{ pad }; # Make this a fallback synonym; | ||
| 252 : | my $pad_char = $data{ padchar } ? substr( $data{ padchar }, 0, 1 ) : ' '; | ||
| 253 : | |||
| 254 : | $data{ oldpad } ||= $data{ old }; # Make this a fallback synonym; | ||
| 255 : | my $old_pad = $data{ oldpad } ? $data{ padchar } : '[^A-Za-z.*]'; | ||
| 256 : | my $reg1 = qr/^($old_pad+)/; | ||
| 257 : | my $reg2 = qr/($old_pad+)$/; | ||
| 258 : | |||
| 259 : | my ( $id, $def, $seq ); | ||
| 260 : | my @align2 = (); | ||
| 261 : | |||
| 262 : | foreach ( @$align ) | ||
| 263 : | { | ||
| 264 : | ( $id, $def, $seq ) = @$_; | ||
| 265 : | $seq =~ s/$reg1/$pad_char x length($1)/e; | ||
| 266 : | $seq =~ s/$reg2/$pad_char x length($1)/e; | ||
| 267 : | push @align2, [ $id, $def, $seq ]; | ||
| 268 : | } | ||
| 269 : | |||
| 270 : | wantarray ? @align2 : \@align2; | ||
| 271 : | } | ||
| 272 : | |||
| 273 : | |||
| 274 : | #------------------------------------------------------------------------------- | ||
| 275 : | # Color an alignment by residue type | ||
| 276 : | # | ||
| 277 : | # \@align = color_alignment_by_residue( \@align, \%options ) | ||
| 278 : | # \@align = color_alignment_by_residue( \%options ) | ||
| 279 : | # ( \@align, \@legend ) = color_alignment_by_residue( \@align, \%options ) | ||
| 280 : | # ( \@align, \@legend ) = color_alignment_by_residue( \%options ) | ||
| 281 : | # | ||
| 282 : | # Options: | ||
| 283 : | # | ||
| 284 : | # align => \@alignment # alignment if not supplied as parameter | ||
| 285 : | # alignment => \@alignment # alignment if not supplied as parameter | ||
| 286 : | # colors => \%colors # character colors (html spec.) | ||
| 287 : | # pallet => $pallet # ale | gde | default | ||
| 288 : | # protein => $bool # indicates a protein alignment | ||
| 289 : | # | ||
| 290 : | #------------------------------------------------------------------------------- | ||
| 291 : | sub color_alignment_by_residue | ||
| 292 : | { | ||
| 293 : | my $align; | ||
| 294 : | $align = shift if ( ref($_[0]) eq 'ARRAY' ); | ||
| 295 : | |||
| 296 : | my %data = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 297 : | foreach ( keys %data ) { $data{ canonical_key( $_ ) } = $data{ $_ } } | ||
| 298 : | |||
| 299 : | $align ||= $data{ align } || $data{ alignment }; | ||
| 300 : | if ( ! $align || ( ref( $align ) ne 'ARRAY' ) ) | ||
| 301 : | { | ||
| 302 : | print STDERR "color_alignment_by_residue called without alignment\n"; | ||
| 303 : | return (); | ||
| 304 : | } | ||
| 305 : | |||
| 306 : | my $colors = $data{ color }; | ||
| 307 : | if ( $colors && ( ref( $colors ) eq 'HASH' ) ) | ||
| 308 : | { | ||
| 309 : | print STDERR "color_alignment_by_residue called without invalid colors hash\n"; | ||
| 310 : | return (); | ||
| 311 : | } | ||
| 312 : | |||
| 313 : | if ( ! $colors ) | ||
| 314 : | { | ||
| 315 : | my $is_prot = defined( $data{ protein } ) ? $data{ protein } : &guess_prot( $align ); | ||
| 316 : | my $pallet = $data{ pallet }; | ||
| 317 : | $colors = $is_prot ? aa_colors( $pallet ) : nt_colors( $pallet ); | ||
| 318 : | } | ||
| 319 : | |||
| 320 : | my ( $id, $def, $seq ); | ||
| 321 : | my $pad_char = $data{ padchar } || $data{ pad } || ' '; | ||
| 322 : | my $reg1 = qr/^([^A-Za-z.*]+)/; | ||
| 323 : | my $reg2 = qr/([^A-Za-z.*]+)$/; | ||
| 324 : | my @colored_align = (); | ||
| 325 : | |||
| 326 : | foreach ( @$align ) | ||
| 327 : | { | ||
| 328 : | ( $id, $def, $seq ) = @$_; | ||
| 329 : | $seq =~ s/$reg1/$pad_char x length($1)/e; | ||
| 330 : | $seq =~ s/$reg2/$pad_char x length($1)/e; | ||
| 331 : | push @colored_align, [ $id, $def, scalar color_sequence( $seq, $colors ) ]; | ||
| 332 : | } | ||
| 333 : | |||
| 334 : | my @legend = (); # Need to create this still | ||
| 335 : | if ( wantarray ) | ||
| 336 : | { | ||
| 337 : | my ( $i, $chr ); | ||
| 338 : | my @row = (); | ||
| 339 : | foreach ( $i = 32; $i < 127; $i++ ) | ||
| 340 : | { | ||
| 341 : | $chr = chr( $i ); | ||
| 342 : | push @row, [ $chr, $colors->{$chr} || '#fff' ]; | ||
| 343 : | if ( $i % 32 == 31 ) { push @legend, [ @row ]; @row = () } | ||
| 344 : | } | ||
| 345 : | push @legend, [ @row ]; | ||
| 346 : | } | ||
| 347 : | |||
| 348 : | wantarray ? ( \@colored_align, \@legend ) : \@colored_align; | ||
| 349 : | } | ||
| 350 : | |||
| 351 : | |||
| 352 : | #------------------------------------------------------------------------------- | ||
| 353 : | # Convert sequence to list of character-color pairs: | ||
| 354 : | # | ||
| 355 : | # \@colored_sequence = color_sequence( $sequence, \%colors ) | ||
| 356 : | # @colored_sequence = color_sequence( $sequence, \%colors ) | ||
| 357 : | #------------------------------------------------------------------------------- | ||
| 358 : | sub color_sequence | ||
| 359 : | { | ||
| 360 : | my ( $seq, $colors ) = @_; | ||
| 361 : | my %colors = ref($colors) eq 'HASH' ? %$colors : (); | ||
| 362 : | my @colored_seq = map { [ $_, $colors{ $_ } || '#fff' ] } split //, $seq; | ||
| 363 : | wantarray ? @colored_seq : \@colored_seq; | ||
| 364 : | } | ||
| 365 : | |||
| 366 : | |||
| 367 : | #------------------------------------------------------------------------------- | ||
| 368 : | # Color an alignment by consensus | ||
| 369 : | # | ||
| 370 : | # \@align = color_alignment_by_consensus( \@align, \%options ) | ||
| 371 : | # \@align = color_alignment_by_consensus( \%options ) | ||
| 372 : | # ( \@align, \%legend ) = color_alignment_by_consensus( \@align, \%options ) | ||
| 373 : | # ( \@align, \%legend ) = color_alignment_by_consensus( \%options ) | ||
| 374 : | # | ||
| 375 : | # Options: | ||
| 376 : | # | ||
| 377 : | # align => \@alignment # Alignment if not supplied as parameter | ||
| 378 : | # alignment => \@alignment # Alignment if not supplied as parameter | ||
| 379 : | # colors => \%colors # HTML colors for consensus categories | ||
| 380 : | # matrix => \%scr_matrix # Hash of hashes of character align scores | ||
| 381 : | # max_f_diff => $max_f_diff # Maximum fraction exceptions to consensus | ||
| 382 : | # max_n_diff => $max_n_diff # Maximum number of exceptions to consensus | ||
| 383 : | # min_score => $score # Score for conservative change (D=1) | ||
| 384 : | # protein => $is_protein # Indicates a protein alignment | ||
| 385 : | # | ||
| 386 : | #------------------------------------------------------------------------------- | ||
| 387 : | sub color_alignment_by_consensus | ||
| 388 : | { | ||
| 389 : | my $align; | ||
| 390 : | $align = shift if ( ref($_[0]) eq 'ARRAY' ); | ||
| 391 : | |||
| 392 : | # Options, with canonical form of keys | ||
| 393 : | |||
| 394 : | my %data = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 395 : | foreach ( keys %data ) { $data{ canonical_key( $_ ) } = $data{ $_ } } | ||
| 396 : | |||
| 397 : | $align ||= $data{ align } || $data{ alignment }; | ||
| 398 : | if ( ! $align || ( ref( $align ) ne 'ARRAY' ) ) | ||
| 399 : | { | ||
| 400 : | print STDERR "color_alignment_by_consensus called without alignment\n"; | ||
| 401 : | return (); | ||
| 402 : | } | ||
| 403 : | |||
| 404 : | my ( $pallet, $legend ) = consensus_pallet( $data{ color } ); | ||
| 405 : | |||
| 406 : | my $conserve_list = conservative_change_list( \%data ); | ||
| 407 : | my $conserve_hash = conservative_change_hash( \%data ); | ||
| 408 : | |||
| 409 : | my $chars = qr/^[-*A-Za-z]$/; | ||
| 410 : | |||
| 411 : | my $s; | ||
| 412 : | my $pad_char = $data{ padchar } || $data{ pad } || ' '; | ||
| 413 : | my $reg1 = qr/^([^A-Za-z.*]+)/; | ||
| 414 : | my $reg2 = qr/([^A-Za-z.*]+)$/; | ||
| 415 : | |||
| 416 : | my @seq = map { $s = uc $_->[2]; | ||
| 417 : | $s =~ s/$reg1/$pad_char x length($1)/e; | ||
| 418 : | $s =~ s/$reg2/$pad_char x length($1)/e; | ||
| 419 : | $s | ||
| 420 : | } | ||
| 421 : | @$align; | ||
| 422 : | |||
| 423 : | # Define the consensus type(s) for each site. There are a 3 options: | ||
| 424 : | # 1. There is a single consensus nucleotide. | ||
| 425 : | # 2. Two residue types are sufficient to describe the position. | ||
| 426 : | # 3. A residue and conservative changes are sufficient. | ||
| 427 : | |||
| 428 : | my $len = length( $seq[0] ); | ||
| 429 : | |||
| 430 : | $max_n_diff = $data{ maxndiff } if defined( $data{ maxndiff } ); | ||
| 431 : | $max_f_diff = $data{ maxfdiff } if defined( $data{ maxfdiff } ); | ||
| 432 : | |||
| 433 : | my @col_clr; # An array of hashes, one for each column | ||
| 434 : | my $cons1 = ' ' x $len; # Primary consensus characters | ||
| 435 : | my $cons2 = ' ' x $len; # Secondary consensus characters | ||
| 436 : | |||
| 437 : | my ( $i, %cnt, $chr, @c, $n_signif, $min_consen, $c1, $c2, $clr ); | ||
| 438 : | |||
| 439 : | for ( $i = 0; $i < $len; $i++) | ||
| 440 : | { | ||
| 441 : | # Count the number of each residue type in the column | ||
| 442 : | |||
| 443 : | %cnt = (); | ||
| 444 : | foreach ( @seq ) { $chr = substr($_,$i,1); $cnt{$chr}++ if $chr =~ /$chars/ } | ||
| 445 : | |||
| 446 : | $n_signif = sum( map { $cnt{$_} } keys %cnt ); | ||
| 447 : | $min_consen = $n_signif - max( $max_n_diff, int( $max_f_diff * $n_signif ) ); | ||
| 448 : | |||
| 449 : | ( $c1, $c2, @c ) = consensus_residues( \%cnt, $min_consen, $conserve_hash ); | ||
| 450 : | |||
| 451 : | substr( $cons1, $i, 1 ) = $c1 if $c1; | ||
| 452 : | substr( $cons2, $i, 1 ) = $c2 if $c2; | ||
| 453 : | push @col_clr, consensus_colors( $pallet, $conserve_list, $c1, $c2, @c ); | ||
| 454 : | } | ||
| 455 : | |||
| 456 : | my @color_align = (); | ||
| 457 : | golsen | 1.3 | my ( $id, $def, $seq ); |
| 458 : | golsen | 1.1 | foreach ( @$align, [ 'Consen1', 'Primary consensus', $cons1 ], |
| 459 : | [ 'Consen2', 'Secondary consensus', $cons2 ] | ||
| 460 : | ) | ||
| 461 : | { | ||
| 462 : | ( $id, $def, $seq ) = @$_; | ||
| 463 : | $seq =~ s/^([^A-Za-z.]+)/$pad_char x length($1)/e; | ||
| 464 : | $seq =~ s/([^A-Za-z.]+)$/$pad_char x length($1)/e; | ||
| 465 : | |||
| 466 : | $i = 0; | ||
| 467 : | my @clr_seq = map { [ $_, $col_clr[$i++]->{$_} || '#fff' ] } | ||
| 468 : | split //, $seq; | ||
| 469 : | push @color_align, [ $id, $def, \@clr_seq ]; | ||
| 470 : | } | ||
| 471 : | |||
| 472 : | wantarray ? ( \@color_align, $legend ) : \@color_align; | ||
| 473 : | } | ||
| 474 : | |||
| 475 : | |||
| 476 : | #------------------------------------------------------------------------------- | ||
| 477 : | # Work out the consensus residues at a site: | ||
| 478 : | # | ||
| 479 : | # ( $consen1, $consen2, @chars ) = consensus_residues( $counts, $min_match, | ||
| 480 : | # $conserve_hash ) | ||
| 481 : | #------------------------------------------------------------------------------- | ||
| 482 : | sub consensus_residues | ||
| 483 : | { | ||
| 484 : | my ( $cnt_hash, $min_match, $conserve_hash ) = @_; | ||
| 485 : | |||
| 486 : | # Sort the residues from most to least frequent, and note first 2: | ||
| 487 : | |||
| 488 : | my %cnt = %$cnt_hash; | ||
| 489 : | my ( $c1, $c2, @c ); | ||
| 490 : | |||
| 491 : | ( $c1, $c2 ) = @c = sort { $cnt{$b} <=> $cnt{$a} } keys %cnt; | ||
| 492 : | ( $cnt{$c1} >= 2 ) or return ( '', '' ); | ||
| 493 : | |||
| 494 : | # Are there at least $min_match of the most abundant? | ||
| 495 : | |||
| 496 : | if ( $cnt{$c1} >= $min_match ) | ||
| 497 : | { | ||
| 498 : | $c2 = ''; | ||
| 499 : | } | ||
| 500 : | |||
| 501 : | # Are there at least $min_match of the two most abundant? | ||
| 502 : | |||
| 503 : | elsif ( ( $cnt{$c2} >= 2 ) && ( ( $cnt{$c1} + $cnt{$c2} ) >= $min_match ) ) | ||
| 504 : | { | ||
| 505 : | $c1 = lc $c1; | ||
| 506 : | $c2 = lc $c2; | ||
| 507 : | } | ||
| 508 : | |||
| 509 : | # Can we make a consensus of conservative changes? | ||
| 510 : | |||
| 511 : | else | ||
| 512 : | { | ||
| 513 : | $c2 = ''; | ||
| 514 : | my ( $is_conservative, @pos, $total ); | ||
| 515 : | my $found = 0; | ||
| 516 : | foreach $c1 ( grep { /^[AC-IK-NP-TVWY]$/ } @c ) | ||
| 517 : | { | ||
| 518 : | ( $is_conservative = $conserve_hash->{ $c1 } ) or next; | ||
| 519 : | @pos = grep { $is_conservative->{ $_ } } @c; | ||
| 520 : | $total = sum( map { $cnt{ $_ } } @pos ); | ||
| 521 : | if ( $total >= $min_match ) { $found = 1; last } | ||
| 522 : | } | ||
| 523 : | $c1 = $found ? lc $c1 : ''; | ||
| 524 : | } | ||
| 525 : | |||
| 526 : | return ( $c1, $c2, @c ); | ||
| 527 : | } | ||
| 528 : | |||
| 529 : | |||
| 530 : | #------------------------------------------------------------------------------- | ||
| 531 : | # Work out the residue colors for the consensus at a site: | ||
| 532 : | # | ||
| 533 : | # \%color = consensus_colors( $pallet, $consevative, $cons1, $cons2, @chars ) | ||
| 534 : | #------------------------------------------------------------------------------- | ||
| 535 : | sub consensus_colors | ||
| 536 : | { | ||
| 537 : | my ( $pallet, $conservative, $c1, $c2, @c ) = @_; | ||
| 538 : | # print STDERR Dumper( $c1, $c2, \@c ); exit; | ||
| 539 : | return {} if ! $c1; | ||
| 540 : | |||
| 541 : | my %pallet = ( ref($pallet) eq 'HASH' ) ? %$pallet | ||
| 542 : | : @{ scalar consensus_pallet() }; | ||
| 543 : | |||
| 544 : | $conservative = {} if ref( $conservative ) ne 'HASH'; | ||
| 545 : | |||
| 546 : | # Mark everything but ' ' and . as mismatch, then overwrite exceptions: | ||
| 547 : | |||
| 548 : | my %color = map { $_ => $pallet{ mismatch } } | ||
| 549 : | grep { ! /^[ .]$/ } | ||
| 550 : | @c; | ||
| 551 : | |||
| 552 : | if ( $c1 ne '-' ) | ||
| 553 : | { | ||
| 554 : | $c1 = uc $c1; | ||
| 555 : | foreach ( @{ $conservative->{$c1} || [] } ) | ||
| 556 : | { | ||
| 557 : | $color{ $_ } = $pallet{ positive } | ||
| 558 : | } | ||
| 559 : | $color{ $c1 } = $pallet{ consen1 }; | ||
| 560 : | if ( $c2 ) | ||
| 561 : | { | ||
| 562 : | $color{ uc $c2 } = ( $c2 ne '-' ) ? $pallet{ consen2 } : $pallet{ consen2g }; | ||
| 563 : | } | ||
| 564 : | } | ||
| 565 : | else | ||
| 566 : | { | ||
| 567 : | $color{ $c1 } = $pallet{ consen1g }; | ||
| 568 : | if ( $c2 ) { $color{ uc $c2 } = $pallet{ consen2 } } | ||
| 569 : | } | ||
| 570 : | |||
| 571 : | # Copy colors to lowercase letters: | ||
| 572 : | |||
| 573 : | foreach ( grep { /^[A-Z]$/ } keys %color ) | ||
| 574 : | { | ||
| 575 : | $color{ lc $_ } = $color{ $_ } | ||
| 576 : | } | ||
| 577 : | |||
| 578 : | return \%color; | ||
| 579 : | } | ||
| 580 : | |||
| 581 : | |||
| 582 : | #------------------------------------------------------------------------------- | ||
| 583 : | # Numerical maximum: | ||
| 584 : | # | ||
| 585 : | # $max = max( $a, $b ) | ||
| 586 : | #------------------------------------------------------------------------------- | ||
| 587 : | sub max { $_[0] > $_[1] ? $_[0] : $_[1] } | ||
| 588 : | |||
| 589 : | |||
| 590 : | #------------------------------------------------------------------------------- | ||
| 591 : | # Define the colors used to color by consensus: | ||
| 592 : | # | ||
| 593 : | # \%color_pallet = consensus_pallet() | ||
| 594 : | # \%color_pallet = consensus_pallet( \%user_pallet ) | ||
| 595 : | # ( \%color_pallet, \@legend ) = consensus_pallet() | ||
| 596 : | # ( \%color_pallet, \@legend ) = consensus_pallet( \%user_pallet ) | ||
| 597 : | # | ||
| 598 : | # \%color_pallet is key/color pairs, where key is a residue category | ||
| 599 : | # \@legend is lines of text/color pairs | ||
| 600 : | #------------------------------------------------------------------------------- | ||
| 601 : | sub consensus_pallet | ||
| 602 : | { | ||
| 603 : | # Initialize with a standard set, ensuring that all keys are covered: | ||
| 604 : | |||
| 605 : | my %pallet = ( '' => '#fff', | ||
| 606 : | other => '#fff', | ||
| 607 : | consen1 => '#bdf', consen1g => '#def', | ||
| 608 : | positive => '#6e9', | ||
| 609 : | consen2 => '#ee4', consen2g => '#eea', | ||
| 610 : | mismatch => '#f9f' | ||
| 611 : | ); | ||
| 612 : | |||
| 613 : | # Overwrite defaults with user-supplied colors | ||
| 614 : | |||
| 615 : | if ( ref($_[0]) eq 'HASH' ) | ||
| 616 : | { | ||
| 617 : | my %user_pallet = %{ $_[0] }; | ||
| 618 : | foreach ( keys %user_pallet ) { $pallet{ $_ } = $user_pallet{ $_ } } | ||
| 619 : | } | ||
| 620 : | |||
| 621 : | my @legend; | ||
| 622 : | if ( wantarray ) | ||
| 623 : | { | ||
| 624 : | @legend = ( [ [ 'Consensus 1' => $pallet{ consen1 } ], | ||
| 625 : | [ ' (when a gap)' => $pallet{ consen1g } ] ], | ||
| 626 : | |||
| 627 : | [ [ 'Conservative difference' => $pallet{ positive } ] ], | ||
| 628 : | |||
| 629 : | [ [ 'Consensus 2' => $pallet{ consen2 } ], | ||
| 630 : | [ ' (when a gap)' => $pallet{ consen2g } ] ], | ||
| 631 : | |||
| 632 : | [ [ 'Nonconservative diff.' => $pallet{ mismatch } ] ], | ||
| 633 : | |||
| 634 : | [ [ 'Other character' => $pallet{ '' } ] ], | ||
| 635 : | ); | ||
| 636 : | } | ||
| 637 : | |||
| 638 : | wantarray ? ( \%pallet, \@legend ) : \%pallet; | ||
| 639 : | } | ||
| 640 : | |||
| 641 : | |||
| 642 : | #------------------------------------------------------------------------------- | ||
| 643 : | # Define the list of conserved amino acid replacements for each amino acid: | ||
| 644 : | # | ||
| 645 : | # \%conserve_change_lists = conservative_change_list( \%options ) | ||
| 646 : | # \%conserve_change_lists = conservative_change_list( %options ) | ||
| 647 : | # | ||
| 648 : | # \@conserve_changes = $conserve_change_lists->{ $aa }; | ||
| 649 : | # | ||
| 650 : | # Options: | ||
| 651 : | # | ||
| 652 : | # min_score => $score # Minimum score for conservative designation | ||
| 653 : | # matrix => \%score_hash # Score matrix as hash of hashes | ||
| 654 : | #------------------------------------------------------------------------------- | ||
| 655 : | sub conservative_change_list | ||
| 656 : | { | ||
| 657 : | my %options = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 658 : | foreach ( keys %options ) { $options{ canonical_key( $_ ) } = $options{ $_ } } | ||
| 659 : | |||
| 660 : | my $min_score = defined( $options{ minscore } ) ? $options{ minscore } : 1; | ||
| 661 : | |||
| 662 : | my $matrix = ( ref( $options{ matrix } ) eq 'HASH' ) ? $options{ matrix } | ||
| 663 : | : blosum62_hash_hash(); | ||
| 664 : | |||
| 665 : | my %hash; | ||
| 666 : | foreach ( keys %$matrix ) | ||
| 667 : | { | ||
| 668 : | my $score = $matrix->{ $_ }; | ||
| 669 : | $hash{ $_ } = [ grep { $score->{ $_ } >= $min_score } keys %$score ]; | ||
| 670 : | } | ||
| 671 : | return \%hash; | ||
| 672 : | } | ||
| 673 : | |||
| 674 : | |||
| 675 : | #------------------------------------------------------------------------------- | ||
| 676 : | # Define a hash of conserved amino acid replacements for each amino acid: | ||
| 677 : | # | ||
| 678 : | # \%conserve_change_hashes = conservative_change_hash( \%options ) | ||
| 679 : | # \%conserve_change_hashes = conservative_change_hash( %options ) | ||
| 680 : | # | ||
| 681 : | # \%conserve_changes = $conserve_change_hashes->{ $aa }; | ||
| 682 : | # | ||
| 683 : | # Options: | ||
| 684 : | # | ||
| 685 : | # min_score => $score # Minimum score for conservative designation | ||
| 686 : | # matrix => \%score_hash # Score matrix as hash of hashes | ||
| 687 : | #------------------------------------------------------------------------------- | ||
| 688 : | sub conservative_change_hash | ||
| 689 : | { | ||
| 690 : | my %options = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 691 : | foreach ( keys %options ) { $options{ canonical_key( $_ ) } = $options{ $_ } } | ||
| 692 : | |||
| 693 : | my $min_score = defined( $options{ minscore } ) ? $options{ minscore } : 1; | ||
| 694 : | |||
| 695 : | my $matrix = ( ref( $options{ matrix } ) eq 'HASH' ) ? $options{ matrix } | ||
| 696 : | : blosum62_hash_hash(); | ||
| 697 : | |||
| 698 : | my %hash; | ||
| 699 : | foreach ( keys %$matrix ) | ||
| 700 : | { | ||
| 701 : | my $score = $matrix->{ $_ }; | ||
| 702 : | $hash{ $_ } = { map { $_ => 1 } | ||
| 703 : | grep { $score->{ $_ } >= $min_score } | ||
| 704 : | keys %$score | ||
| 705 : | }; | ||
| 706 : | } | ||
| 707 : | |||
| 708 : | return \%hash; | ||
| 709 : | } | ||
| 710 : | |||
| 711 : | |||
| 712 : | #------------------------------------------------------------------------------- | ||
| 713 : | # Define a hash of hashes with the blosum62 scores for each amino acid: | ||
| 714 : | # | ||
| 715 : | # \%blosum62 = blosum62_hash_hash() | ||
| 716 : | # $score = $blosum62->{$aa1}->{$aa2}; | ||
| 717 : | # | ||
| 718 : | #------------------------------------------------------------------------------- | ||
| 719 : | sub blosum62_hash_hash | ||
| 720 : | { | ||
| 721 : | my ( $aa_list, $raw_scores ) = raw_blosum62(); | ||
| 722 : | my %hash; | ||
| 723 : | my @scores = @$raw_scores; | ||
| 724 : | foreach ( @$aa_list ) | ||
| 725 : | { | ||
| 726 : | my @scr = @{ shift @scores }; | ||
| 727 : | $hash{ $_ } = { map { $_ => shift @scr } @$aa_list }; | ||
| 728 : | } | ||
| 729 : | return \%hash; | ||
| 730 : | } | ||
| 731 : | |||
| 732 : | |||
| 733 : | #------------------------------------------------------------------------------- | ||
| 734 : | # Define an ordered list of aminoacids and lists of each of their blosum scores | ||
| 735 : | # | ||
| 736 : | # ( \@aa_list, \@scores ) = raw_blosum62() | ||
| 737 : | # | ||
| 738 : | #------------------------------------------------------------------------------- | ||
| 739 : | sub raw_blosum62 | ||
| 740 : | { | ||
| 741 : | return ( [ qw( A R N D C Q E G H I L K M F P S T W Y V B Z X * ) ], | ||
| 742 : | [ map { shift @$_; $_ } | ||
| 743 : | ( | ||
| 744 : | # A R N D C Q E G H I L K M F P S T W Y V B Z X * # | ||
| 745 : | [ qw( A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 ) ], | ||
| 746 : | [ qw( R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 ) ], | ||
| 747 : | [ qw( N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 ) ], | ||
| 748 : | [ qw( D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 ) ], | ||
| 749 : | [ qw( C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 ) ], | ||
| 750 : | [ qw( Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 ) ], | ||
| 751 : | [ qw( E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 ) ], | ||
| 752 : | [ qw( G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 ) ], | ||
| 753 : | [ qw( H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 ) ], | ||
| 754 : | [ qw( I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 ) ], | ||
| 755 : | [ qw( L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 ) ], | ||
| 756 : | [ qw( K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 ) ], | ||
| 757 : | [ qw( M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 ) ], | ||
| 758 : | [ qw( F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 ) ], | ||
| 759 : | [ qw( P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 ) ], | ||
| 760 : | [ qw( S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 ) ], | ||
| 761 : | [ qw( T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 ) ], | ||
| 762 : | [ qw( W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 ) ], | ||
| 763 : | [ qw( Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 ) ], | ||
| 764 : | [ qw( V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 ) ], | ||
| 765 : | [ qw( B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 ) ], | ||
| 766 : | [ qw( Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 ) ], | ||
| 767 : | [ qw( X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 ) ], | ||
| 768 : | [ qw( * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 ) ] | ||
| 769 : | ) | ||
| 770 : | ] | ||
| 771 : | ) | ||
| 772 : | } | ||
| 773 : | |||
| 774 : | |||
| 775 : | #------------------------------------------------------------------------------- | ||
| 776 : | # Make an html table with an alignment: | ||
| 777 : | # | ||
| 778 : | # $html = alignment_2_html_table( \@alignment, \%options ) | ||
| 779 : | # $html = alignment_2_html_table( \%options ) | ||
| 780 : | # ( $html, $javascript ) = alignment_2_html_table( \@alignment, \%options ) | ||
| 781 : | # ( $html, $javascript ) = alignment_2_html_table( \%options ) | ||
| 782 : | # | ||
| 783 : | # In scalar context, the routine returns a single block of html that includes | ||
| 784 : | # the JavaScript followed by the table. In list context, they are returned | ||
| 785 : | # separately. | ||
| 786 : | # | ||
| 787 : | # Options: | ||
| 788 : | # | ||
| 789 : | # align => \@alignment # Alignment, when not a parameter | ||
| 790 : | # alignment => \@alignment # Alignment, when not a parameter | ||
| 791 : | # key => \@legend # Append the supplied legend | ||
| 792 : | # legend => \@legend # Append the supplied legend | ||
| 793 : | # nojavascript => $boolean # Omit the JavaScript for pop-ups | ||
| 794 : | # tooltip => $boolean # Add pop-up tooltip to sequences | ||
| 795 : | golsen | 1.2 | # tooltip => \%id2tip # (specify the tip for each id) |
| 796 : | golsen | 1.1 | # |
| 797 : | # Each sequence can be a string, or an array of [ text, color ] pairs. | ||
| 798 : | # @legend is an array of lines of strings and/or [ text, color ] pairs. | ||
| 799 : | golsen | 1.2 | # |
| 800 : | # Default tooltip is the id and description, but user can supply a | ||
| 801 : | # hash with arrays of alternative mouseover parameters: | ||
| 802 : | # | ||
| 803 : | # mouseover( @{ $tooltip->{ $id } } ) | ||
| 804 : | # mouseover( $ttl, $text, $menu, $parent, $ttl_color, $text_color ) | ||
| 805 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 806 : | sub alignment_2_html_table | ||
| 807 : | { | ||
| 808 : | my $align; | ||
| 809 : | $align = shift if ( ref($_[0]) eq 'ARRAY' ); | ||
| 810 : | |||
| 811 : | # Options, with canonical form of keys | ||
| 812 : | |||
| 813 : | my %options = ( ref( $_[0] ) eq 'HASH' ) ? %{ $_[0] } : @_; | ||
| 814 : | foreach ( keys %options ) { $options{ canonical_key( $_ ) } = $options{ $_ } } | ||
| 815 : | |||
| 816 : | $align ||= $options{ align } || $options{ alignment }; | ||
| 817 : | if ( ! $align || ( ref( $align ) ne 'ARRAY' ) ) | ||
| 818 : | { | ||
| 819 : | print STDERR "alignment_2_html_table called without alignment\n"; | ||
| 820 : | return ''; | ||
| 821 : | } | ||
| 822 : | |||
| 823 : | my $tooltip = $options{ tooltip } || $options{ popup } || 0; | ||
| 824 : | my $tiplink = ''; | ||
| 825 : | |||
| 826 : | my $nojavascript = $options{ nojavascript } || ( $tooltip ? 0 : 1 ); | ||
| 827 : | |||
| 828 : | my @html; | ||
| 829 : | golsen | 1.3 | push @html, "<TABLE Col=5 CellPadding=0 CellSpacing=0>\n"; |
| 830 : | golsen | 1.1 | foreach ( @$align ) |
| 831 : | { | ||
| 832 : | if ( $tooltip ) | ||
| 833 : | { | ||
| 834 : | golsen | 1.2 | # Default tooltip is the id and description, but user can supply a |
| 835 : | # hash with alternative mouseover parameters: | ||
| 836 : | # | ||
| 837 : | # mouseover( $ttl, $text, $menu, $parent, $ttl_color, $text_color ) | ||
| 838 : | # | ||
| 839 : | my @args; | ||
| 840 : | if ( ( ref( $tooltip ) eq 'HASH' ) | ||
| 841 : | && ( ref( $tooltip->{ $_->[0] } ) eq 'ARRAY' ) | ||
| 842 : | ) | ||
| 843 : | { | ||
| 844 : | @args = @{ $tooltip->{ $_->[0] } } | ||
| 845 : | } | ||
| 846 : | else | ||
| 847 : | { | ||
| 848 : | @args = ( $_->[0], ( $_->[1] || ' ' ) ); | ||
| 849 : | } | ||
| 850 : | golsen | 1.1 | $tiplink = '<A' . &mouseover( @args ) . '>'; |
| 851 : | } | ||
| 852 : | |||
| 853 : | push @html, " <TR>\n", | ||
| 854 : | " <TD NoWrap>$_->[0]</TD>\n", | ||
| 855 : | golsen | 1.3 | " <TD NoWrap> </TD>\n", # Getting rid of padding, so ... |
| 856 : | golsen | 1.1 | " <TD NoWrap>$_->[1]</TD>\n", |
| 857 : | golsen | 1.3 | " <TD NoWrap> </TD>\n", # Getting rid of padding, so ... |
| 858 : | " <TD NoWrap> </TD>\n", | ||
| 859 : | " <TD><TT><Big>", | ||
| 860 : | golsen | 1.1 | ( $tooltip ? $tiplink : () ), |
| 861 : | sequence_2_html( $_->[2] ), | ||
| 862 : | ( $tooltip ? '</A>' : () ), | ||
| 863 : | golsen | 1.3 | "</Big></TT></TD>\n", |
| 864 : | golsen | 1.1 | " </TR>\n"; |
| 865 : | } | ||
| 866 : | push @html, "</TABLE>\n"; | ||
| 867 : | |||
| 868 : | my $legend = $options{ key } || $options{ legend }; | ||
| 869 : | if ( ref( $legend ) eq 'ARRAY' ) | ||
| 870 : | { | ||
| 871 : | golsen | 1.3 | push @html, "<BR />\n", "<TABLE Col=1 CellPadding=0 CellSpacing=0>\n"; |
| 872 : | golsen | 1.1 | foreach ( @$legend ) |
| 873 : | { | ||
| 874 : | golsen | 1.3 | push @html, " <TR><TD><TT><Big>", |
| 875 : | golsen | 1.1 | sequence_2_html( $_ ), |
| 876 : | golsen | 1.3 | "</Big></TT></TD></TR>\n"; |
| 877 : | golsen | 1.1 | } |
| 878 : | push @html, "</TABLE>\n"; | ||
| 879 : | } | ||
| 880 : | |||
| 881 : | my $javascript = $nojavascript ? '' : &mouseover_JavaScript(); | ||
| 882 : | |||
| 883 : | wantarray && $javascript ? ( join( '', @html ), $javascript ) # ( $html, $script ) | ||
| 884 : | : join( '', $javascript, @html ); # $html | ||
| 885 : | } | ||
| 886 : | |||
| 887 : | |||
| 888 : | #------------------------------------------------------------------------------- | ||
| 889 : | # Make html to display a possibly colored sequence: | ||
| 890 : | # | ||
| 891 : | # $html = sequence_2_html( $string ) | ||
| 892 : | # $html = sequence_2_html( \@character_color_pairs ) | ||
| 893 : | # | ||
| 894 : | # Each sequence can be a string, or an array of character-color pairs. | ||
| 895 : | #------------------------------------------------------------------------------- | ||
| 896 : | sub sequence_2_html | ||
| 897 : | { | ||
| 898 : | return $_[0] if ref( $_[0] ) ne 'ARRAY'; | ||
| 899 : | |||
| 900 : | my $string = shift; | ||
| 901 : | my @html = (); | ||
| 902 : | my ( $txt, $clr ); | ||
| 903 : | foreach ( @{ merge_common_color( $string ) } ) | ||
| 904 : | { | ||
| 905 : | $txt = html_esc( $_->[0] ); | ||
| 906 : | $txt or next; | ||
| 907 : | golsen | 1.3 | $txt =~ s/ / /g; # 2009-03-02 -- Change from <Pre> to <TT> wrapper |
| 908 : | golsen | 1.1 | $clr = $_->[1]; |
| 909 : | push @html, ( $clr ? qq(<span style="background-color:$clr">$txt</span>) | ||
| 910 : | : $txt | ||
| 911 : | ) | ||
| 912 : | } | ||
| 913 : | join '', @html; | ||
| 914 : | } | ||
| 915 : | |||
| 916 : | |||
| 917 : | #------------------------------------------------------------------------------- | ||
| 918 : | # Merge adjacent strings with same color to cut amount of html: | ||
| 919 : | # | ||
| 920 : | # \@character_color_pairs = merge_common_color( \@character_color_pairs ) | ||
| 921 : | # | ||
| 922 : | #------------------------------------------------------------------------------- | ||
| 923 : | sub merge_common_color | ||
| 924 : | { | ||
| 925 : | return $_[0] if ref( $_[0] ) ne 'ARRAY'; | ||
| 926 : | |||
| 927 : | my @string = (); | ||
| 928 : | my $color = ''; | ||
| 929 : | my @common_color = (); | ||
| 930 : | foreach ( @{ $_[0] }, [ '', 0 ] ) # One bogus empty string to flush it | ||
| 931 : | { | ||
| 932 : | if ( $_->[1] ne $color ) | ||
| 933 : | { | ||
| 934 : | push @string, [ join( '', @common_color ), $color ], | ||
| 935 : | @common_color = (); | ||
| 936 : | $color = $_->[1] | ||
| 937 : | } | ||
| 938 : | push @common_color, $_->[0]; | ||
| 939 : | } | ||
| 940 : | return \@string; | ||
| 941 : | } | ||
| 942 : | |||
| 943 : | |||
| 944 : | #------------------------------------------------------------------------------- | ||
| 945 : | # Make an html page with an alignment: | ||
| 946 : | # | ||
| 947 : | # $html = alignment_2_html_page( \@alignment, \%options ) | ||
| 948 : | # $html = alignment_2_html_page( \%options ) | ||
| 949 : | # | ||
| 950 : | # Options: | ||
| 951 : | # | ||
| 952 : | # align => \@alignment | ||
| 953 : | # alignment => \@alignment | ||
| 954 : | # key => \@legend | ||
| 955 : | # legend => \@legend | ||
| 956 : | # title => $page_title | ||
| 957 : | # | ||
| 958 : | # Each sequence can be a string, or an array of character-color pairs. | ||
| 959 : | #------------------------------------------------------------------------------- | ||
| 960 : | sub alignment_2_html_page | ||
| 961 : | { | ||
| 962 : | my $options = ref( $_[0] ) eq 'HASH' ? $_[0] : | ||
| 963 : | ref( $_[1] ) eq 'HASH' ? $_[1] : {}; | ||
| 964 : | |||
| 965 : | join '', html_prefix( $options ), | ||
| 966 : | ( alignment_2_html_table( @_ ) )[1,0], | ||
| 967 : | html_suffix( $options ); | ||
| 968 : | } | ||
| 969 : | |||
| 970 : | |||
| 971 : | #------------------------------------------------------------------------------- | ||
| 972 : | # $html_page_start = html_prefix() | ||
| 973 : | #------------------------------------------------------------------------------- | ||
| 974 : | sub html_prefix | ||
| 975 : | { | ||
| 976 : | my $options = ref( $_[0] ) eq 'HASH' ? $_[0] : {}; | ||
| 977 : | |||
| 978 : | my $title = $options->{ title } || 'Alignment'; | ||
| 979 : | |||
| 980 : | return <<"End_of_Prefix"; | ||
| 981 : | <HTML> | ||
| 982 : | <HEAD> | ||
| 983 : | <TITLE>$title</TITLE> | ||
| 984 : | </HEAD> | ||
| 985 : | <BODY> | ||
| 986 : | End_of_Prefix | ||
| 987 : | } | ||
| 988 : | |||
| 989 : | |||
| 990 : | #------------------------------------------------------------------------------- | ||
| 991 : | # $html_page_end = html_suffix() | ||
| 992 : | #------------------------------------------------------------------------------- | ||
| 993 : | sub html_suffix | ||
| 994 : | { | ||
| 995 : | return <<"End_of_Suffix"; | ||
| 996 : | </BODY> | ||
| 997 : | </HTML> | ||
| 998 : | End_of_Suffix | ||
| 999 : | } | ||
| 1000 : | |||
| 1001 : | |||
| 1002 : | #------------------------------------------------------------------------------- | ||
| 1003 : | # $html_text = html_esc{ $text ) | ||
| 1004 : | #------------------------------------------------------------------------------- | ||
| 1005 : | sub html_esc | ||
| 1006 : | { | ||
| 1007 : | my $txt = shift; | ||
| 1008 : | $txt =~ s/\&/&/g; | ||
| 1009 : | $txt =~ s/\</</g; | ||
| 1010 : | $txt =~ s/\>/>/g; | ||
| 1011 : | return $txt; | ||
| 1012 : | } | ||
| 1013 : | |||
| 1014 : | |||
| 1015 : | sub sum | ||
| 1016 : | { | ||
| 1017 : | my $cnt = 0; | ||
| 1018 : | while ( defined( $_[0] ) ) { $cnt += shift } | ||
| 1019 : | $cnt | ||
| 1020 : | } | ||
| 1021 : | |||
| 1022 : | |||
| 1023 : | #------------------------------------------------------------------------------- | ||
| 1024 : | # A canonical key is lower case, has no underscores, and no terminal s | ||
| 1025 : | # | ||
| 1026 : | # $key = canonical_key( $key ) | ||
| 1027 : | #------------------------------------------------------------------------------- | ||
| 1028 : | sub canonical_key { my $key = lc shift; $key =~ s/_//g; $key =~ s/s$//; $key } | ||
| 1029 : | |||
| 1030 : | |||
| 1031 : | #------------------------------------------------------------------------------- | ||
| 1032 : | # $is_protein_alignment = guess_prot( \@alignment ) | ||
| 1033 : | #------------------------------------------------------------------------------- | ||
| 1034 : | sub guess_prot | ||
| 1035 : | { | ||
| 1036 : | my $align = shift; | ||
| 1037 : | my $seq = uc $align->[0]->[-1]; # First sequence | ||
| 1038 : | my $nt = $seq =~ tr/ACGTU//; # Nucleotides | ||
| 1039 : | my $res = $seq =~ tr/ACDEFGHIKLMNPQRSTUVWY//; # Total residues | ||
| 1040 : | return ( $nt > 0.7 * $res ) ? 0 : 1; # >70% of total? | ||
| 1041 : | } | ||
| 1042 : | |||
| 1043 : | |||
| 1044 : | |||
| 1045 : | #------------------------------------------------------------------------------- | ||
| 1046 : | # \%character_color_pallet = aa_colors() # Default | ||
| 1047 : | # \%character_color_pallet = aa_colors( $set_name ) # ale | ||
| 1048 : | #------------------------------------------------------------------------------- | ||
| 1049 : | sub aa_colors | ||
| 1050 : | { | ||
| 1051 : | my $pallet = shift || ''; | ||
| 1052 : | my %colors; | ||
| 1053 : | |||
| 1054 : | if ( $pallet =~ /ale/i ) | ||
| 1055 : | { | ||
| 1056 : | %colors = ( | ||
| 1057 : | ' ' => '#bebebe', # Grey | ||
| 1058 : | '~' => '#bebebe', # Grey | ||
| 1059 : | '-' => '#696969', # DimGray | ||
| 1060 : | '.' => '#828282', # Grey51 | ||
| 1061 : | '*' => '#ff0000', # Red | ||
| 1062 : | |||
| 1063 : | G => '#ffffff', # White | ||
| 1064 : | |||
| 1065 : | A => '#d3d3d3', # LightGray | ||
| 1066 : | V => '#d3d3d3', # LightGray | ||
| 1067 : | L => '#d3d3d3', # LightGray | ||
| 1068 : | I => '#d3d3d3', # LightGray | ||
| 1069 : | M => '#d3d3d3', # LightGray | ||
| 1070 : | C => '#d3d3d3', # LightGray | ||
| 1071 : | U => '#d3d3d3', # LightGray | ||
| 1072 : | |||
| 1073 : | W => '#ffd700', # Gold | ||
| 1074 : | F => '#ffd700', # Gold | ||
| 1075 : | Y => '#ffd700', # Gold | ||
| 1076 : | |||
| 1077 : | K => '#00bfff', # DeepSkyBlue | ||
| 1078 : | R => '#00bfff', # DeepSkyBlue | ||
| 1079 : | H => '#40e0d0', # Turquoise | ||
| 1080 : | |||
| 1081 : | N => '#98fb98', # PaleGreen | ||
| 1082 : | Q => '#98fb98', # PaleGreen | ||
| 1083 : | S => '#98fb98', # PaleGreen | ||
| 1084 : | T => '#98fb98', # PaleGreen | ||
| 1085 : | P => '#98fb98', # PaleGreen | ||
| 1086 : | |||
| 1087 : | D => '#fa8072', # Salmon | ||
| 1088 : | E => '#fa8072', # Salmon | ||
| 1089 : | ); | ||
| 1090 : | } | ||
| 1091 : | else | ||
| 1092 : | { | ||
| 1093 : | %colors = ( | ||
| 1094 : | ' ' => '#fff', # White | ||
| 1095 : | '~' => '#fff', # White | ||
| 1096 : | '.' => '#fff', # White | ||
| 1097 : | '-' => '#888', # Gray | ||
| 1098 : | '*' => '#f00', # Red | ||
| 1099 : | |||
| 1100 : | G => '#d8d', # DullMagenta | ||
| 1101 : | |||
| 1102 : | A => '#ddd', # LightGray | ||
| 1103 : | V => '#ddd', # LightGray | ||
| 1104 : | L => '#ddd', # LightGray | ||
| 1105 : | I => '#ddd', # LightGray | ||
| 1106 : | M => '#ddd', # LightGray | ||
| 1107 : | |||
| 1108 : | C => '#ff0', # Yellow | ||
| 1109 : | U => '#ff0', # Yellow | ||
| 1110 : | |||
| 1111 : | W => '#da2', # Goldenrod | ||
| 1112 : | F => '#da2', # Goldenrod | ||
| 1113 : | Y => '#da2', # Goldenrod | ||
| 1114 : | |||
| 1115 : | K => '#0bf', # DeepSkyBlue | ||
| 1116 : | R => '#0bf', # DeepSkyBlue | ||
| 1117 : | H => '#4ed', # Turquoise | ||
| 1118 : | |||
| 1119 : | N => '#9f9', # PaleGreen | ||
| 1120 : | Q => '#9f9', # PaleGreen | ||
| 1121 : | S => '#9f9', # PaleGreen | ||
| 1122 : | T => '#9f9', # PaleGreen | ||
| 1123 : | |||
| 1124 : | P => '#ada', # DullGreen | ||
| 1125 : | |||
| 1126 : | D => '#f87', # Salmon | ||
| 1127 : | E => '#f87', # Salmon | ||
| 1128 : | ); | ||
| 1129 : | } | ||
| 1130 : | |||
| 1131 : | foreach ( keys %colors ) { $colors{ lc $_ } = $colors{ $_ } } | ||
| 1132 : | |||
| 1133 : | return \%colors; | ||
| 1134 : | } | ||
| 1135 : | |||
| 1136 : | |||
| 1137 : | #------------------------------------------------------------------------------- | ||
| 1138 : | # \%character_color_pallet = nt_colors() # Default | ||
| 1139 : | # \%character_color_pallet = nt_colors( $set_name ) # ale | gde | ||
| 1140 : | #------------------------------------------------------------------------------- | ||
| 1141 : | sub nt_colors | ||
| 1142 : | { | ||
| 1143 : | my $pallet = shift || ''; | ||
| 1144 : | my %colors; | ||
| 1145 : | |||
| 1146 : | if ( $pallet =~ /ale/i ) | ||
| 1147 : | { | ||
| 1148 : | %colors = ( | ||
| 1149 : | ' ' => '#666', # DimGray | ||
| 1150 : | '~' => '#666', # DimGray | ||
| 1151 : | '-' => '#bbb', # Gray | ||
| 1152 : | '.' => '#888', # Gray51 | ||
| 1153 : | |||
| 1154 : | A => '#fd0', # Gold | ||
| 1155 : | C => '#0ff', # Cyan | ||
| 1156 : | G => '#ff0', # Yellow | ||
| 1157 : | T => '#9f9', # PaleGreen | ||
| 1158 : | U => '#9f9', # PaleGreen | ||
| 1159 : | ); | ||
| 1160 : | } | ||
| 1161 : | elsif ( $pallet =~ /gde/i ) | ||
| 1162 : | { | ||
| 1163 : | %colors = ( | ||
| 1164 : | ' ' => '#666', # DimGray | ||
| 1165 : | '~' => '#666', # DimGray | ||
| 1166 : | '-' => '#bbb', # Gray | ||
| 1167 : | '.' => '#888', # Gray51 | ||
| 1168 : | |||
| 1169 : | A => '#f00', # Red | ||
| 1170 : | C => '#00f', # Blue | ||
| 1171 : | G => '#ff8', # PaleYellow | ||
| 1172 : | T => '#0f0', # Green | ||
| 1173 : | U => '#0f0', # Green | ||
| 1174 : | ); | ||
| 1175 : | } | ||
| 1176 : | else | ||
| 1177 : | { | ||
| 1178 : | %colors = ( | ||
| 1179 : | ' ' => '#777', | ||
| 1180 : | '~' => '#777', | ||
| 1181 : | '-' => '#bbb', | ||
| 1182 : | '.' => '#888', | ||
| 1183 : | |||
| 1184 : | A => '#f66', | ||
| 1185 : | G => '#ff0', | ||
| 1186 : | C => '#0f0', | ||
| 1187 : | T => '#88f', | ||
| 1188 : | U => '#88f', | ||
| 1189 : | |||
| 1190 : | R => '#fa4', | ||
| 1191 : | Y => '#4d8', | ||
| 1192 : | K => '#bb9', | ||
| 1193 : | M => '#ee6', | ||
| 1194 : | S => '#af5', | ||
| 1195 : | W => '#c8c', | ||
| 1196 : | |||
| 1197 : | B => '#bdd', | ||
| 1198 : | H => '#bbd', | ||
| 1199 : | D => '#dbd', | ||
| 1200 : | V => '#dda', | ||
| 1201 : | |||
| 1202 : | N => '#ddd', | ||
| 1203 : | ); | ||
| 1204 : | } | ||
| 1205 : | |||
| 1206 : | foreach ( keys %colors ) { $colors{ lc $_ } = $colors{ $_ } } | ||
| 1207 : | |||
| 1208 : | return \%colors; | ||
| 1209 : | } | ||
| 1210 : | |||
| 1211 : | |||
| 1212 : | #------------------------------------------------------------------------------- | ||
| 1213 : | # Return a string for adding an onMouseover tooltip handler: | ||
| 1214 : | # | ||
| 1215 : | # mouseover( $title, $text, $menu, $parent, $titlecolor, $bodycolor) | ||
| 1216 : | # | ||
| 1217 : | # The code here is virtually identical to that in FIGjs.pm, but makes this | ||
| 1218 : | # SEED independent. | ||
| 1219 : | #------------------------------------------------------------------------------- | ||
| 1220 : | sub mouseover | ||
| 1221 : | { | ||
| 1222 : | if ( $have_FIGjs ) { return &FIGjs::mouseover( @_ ) } | ||
| 1223 : | |||
| 1224 : | golsen | 1.3 | my ( $title, $text, $menu, $parent, $titlecolor, $bodycolor ) = @_; |
| 1225 : | golsen | 1.1 | |
| 1226 : | defined( $title ) or $title = ''; | ||
| 1227 : | $title =~ s/'/\\'/g; # escape ' | ||
| 1228 : | $title =~ s/"/"/g; # escape " | ||
| 1229 : | |||
| 1230 : | defined( $text ) or $text = ''; | ||
| 1231 : | $text =~ s/'/\\'/g; # escape ' | ||
| 1232 : | $text =~ s/"/"/g; # escape " | ||
| 1233 : | |||
| 1234 : | defined( $menu ) or $menu = ''; | ||
| 1235 : | $menu =~ s/'/\\'/g; # escape ' | ||
| 1236 : | $menu =~ s/"/"/g; # escape " | ||
| 1237 : | |||
| 1238 : | golsen | 1.3 | $parent = '' if ! defined $parent; |
| 1239 : | $titlecolor = '' if ! defined $titlecolor; | ||
| 1240 : | $bodycolor = '' if ! defined $bodycolor; | ||
| 1241 : | |||
| 1242 : | golsen | 1.1 | qq( onMouseover="javascript:if(!this.tooltip) this.tooltip=new Popup_Tooltip(this,'$title','$text','$menu','$parent','$titlecolor','$bodycolor');this.tooltip.addHandler(); return false;" ); |
| 1243 : | } | ||
| 1244 : | |||
| 1245 : | |||
| 1246 : | #------------------------------------------------------------------------------- | ||
| 1247 : | # Return a text string with the necessary JavaScript for the mouseover | ||
| 1248 : | # tooltips. | ||
| 1249 : | # | ||
| 1250 : | # $html = mouseover_JavaScript() | ||
| 1251 : | # | ||
| 1252 : | # The code here is virtually identical to that in FIGjs.pm, but makes this | ||
| 1253 : | # SEED independent. | ||
| 1254 : | #------------------------------------------------------------------------------- | ||
| 1255 : | sub mouseover_JavaScript | ||
| 1256 : | { | ||
| 1257 : | if ( $have_FIGjs ) { return &FIGjs::toolTipScript( ) } | ||
| 1258 : | |||
| 1259 : | return <<'End_of_JavaScript'; | ||
| 1260 : | <SCRIPT Language='JavaScript'> | ||
| 1261 : | // | ||
| 1262 : | // javascript class for tooltips and popup menus | ||
| 1263 : | // | ||
| 1264 : | // This class manages the information, creating area to draw tooltips and | ||
| 1265 : | // popup menus and provides the event handlers to handle them | ||
| 1266 : | // | ||
| 1267 : | var DIV_WIDTH=250; | ||
| 1268 : | var px; // position suffix with "px" in some cases | ||
| 1269 : | var initialized = false; | ||
| 1270 : | var ns4 = false; | ||
| 1271 : | var ie4 = false; | ||
| 1272 : | var ie5 = false; | ||
| 1273 : | var kon = false; | ||
| 1274 : | var iemac = false; | ||
| 1275 : | var tooltip_name='popup_tooltip_div'; | ||
| 1276 : | |||
| 1277 : | function Popup_Tooltip(object, tooltip_title, tooltip_text, | ||
| 1278 : | popup_menu, use_parent_pos, head_color, | ||
| 1279 : | body_color) { | ||
| 1280 : | // The first time an object of this class is instantiated, | ||
| 1281 : | // we have to setup some browser specific settings | ||
| 1282 : | |||
| 1283 : | if (!initialized) { | ||
| 1284 : | ns4 = (document.layers) ? true : false; | ||
| 1285 : | ie4 = (document.all) ? true : false; | ||
| 1286 : | ie5 = ((ie4) && ((navigator.userAgent.indexOf('MSIE 5') > 0) || | ||
| 1287 : | (navigator.userAgent.indexOf('MSIE 6') > 0))) ? true : false; | ||
| 1288 : | kon = (navigator.userAgent.indexOf('konqueror') > 0) ? true : false; | ||
| 1289 : | if(ns4||kon) { | ||
| 1290 : | //setTimeout("window.onresize = function () {window.location.reload();};", 2000); | ||
| 1291 : | } | ||
| 1292 : | ns4 ? px="" : px="px"; | ||
| 1293 : | iemac = ((ie4 || ie5) && (navigator.userAgent.indexOf('Mac') > 0)) ? true : false; | ||
| 1294 : | |||
| 1295 : | initialized=true; | ||
| 1296 : | } | ||
| 1297 : | |||
| 1298 : | if (iemac) { return; } // Give up | ||
| 1299 : | |||
| 1300 : | this.tooltip_title = tooltip_title; | ||
| 1301 : | this.tooltip_text = tooltip_text; | ||
| 1302 : | |||
| 1303 : | if (head_color) { this.head_color = head_color; } | ||
| 1304 : | else { this.head_color = "#333399"; } | ||
| 1305 : | |||
| 1306 : | if (body_color) { this.body_color = body_color; } | ||
| 1307 : | else { this.body_color = "#CCCCFF"; } | ||
| 1308 : | |||
| 1309 : | this.popup_menu = popup_menu; | ||
| 1310 : | if (use_parent_pos) { | ||
| 1311 : | this.popup_menu_x = object.offsetLeft; | ||
| 1312 : | this.popup_menu_y = object.offsetTop + object.offsetHeight + 3; | ||
| 1313 : | } | ||
| 1314 : | else { | ||
| 1315 : | this.popup_menu_x = -1; | ||
| 1316 : | this.popup_menu_y = -1; | ||
| 1317 : | } | ||
| 1318 : | |||
| 1319 : | // create the div if necessary | ||
| 1320 : | // the div may be shared between several instances | ||
| 1321 : | // of this class | ||
| 1322 : | |||
| 1323 : | this.div = getDiv(tooltip_name); | ||
| 1324 : | if (! this.div) { | ||
| 1325 : | // create a hidden div to contain the information | ||
| 1326 : | this.div = document.createElement("div"); | ||
| 1327 : | this.div.id=tooltip_name; | ||
| 1328 : | this.div.style.position="absolute"; | ||
| 1329 : | this.div.style.zIndex=0; | ||
| 1330 : | this.div.style.top="0"+px; | ||
| 1331 : | this.div.style.left="0"+px; | ||
| 1332 : | this.div.style.visibility=ns4?"hide":"hidden"; | ||
| 1333 : | this.div.tooltip_visible=0; | ||
| 1334 : | this.div.menu_visible=0 | ||
| 1335 : | document.body.appendChild(this.div); | ||
| 1336 : | } | ||
| 1337 : | |||
| 1338 : | // register methods | ||
| 1339 : | |||
| 1340 : | this.showTip = showTip; | ||
| 1341 : | this.hideTip = hideTip; | ||
| 1342 : | this.fillTip = fillTip; | ||
| 1343 : | this.showMenu = showMenu; | ||
| 1344 : | this.hideMenu = hideMenu; | ||
| 1345 : | this.fillMenu = fillMenu; | ||
| 1346 : | this.addHandler = addHandler; | ||
| 1347 : | this.delHandler = delHandler; | ||
| 1348 : | this.mousemove = mousemove; | ||
| 1349 : | this.showDiv = showDiv; | ||
| 1350 : | |||
| 1351 : | // object state | ||
| 1352 : | |||
| 1353 : | this.attached = object; | ||
| 1354 : | object.tooltip = this; | ||
| 1355 : | } | ||
| 1356 : | |||
| 1357 : | function getDiv() { | ||
| 1358 : | if (ie5 || ie4) { return document.all[tooltip_name]; } | ||
| 1359 : | else if (document.layers) { return document.layers[tooltip_name]; } | ||
| 1360 : | else if (document.all) { return document.all[tooltip_name]; } | ||
| 1361 : | return document.getElementById(tooltip_name); | ||
| 1362 : | } | ||
| 1363 : | |||
| 1364 : | function hideTip() { | ||
| 1365 : | if (this.div.tooltip_visible) { | ||
| 1366 : | this.div.innerHTML=""; | ||
| 1367 : | this.div.style.visibility=ns4?"hide":"hidden"; | ||
| 1368 : | this.div.tooltip_visible=0; | ||
| 1369 : | } | ||
| 1370 : | } | ||
| 1371 : | |||
| 1372 : | function hideMenu() { | ||
| 1373 : | if (this.div && this.div.menu_visible) { | ||
| 1374 : | this.div.innerHTML=""; | ||
| 1375 : | this.div.style.visibility=ns4?"hide":"hidden"; | ||
| 1376 : | this.div.menu_visible=0; | ||
| 1377 : | } | ||
| 1378 : | } | ||
| 1379 : | |||
| 1380 : | function fillTip() { | ||
| 1381 : | this.hideTip(); | ||
| 1382 : | this.hideMenu(); | ||
| 1383 : | if (this.tooltip_title && this.tooltip_text) { | ||
| 1384 : | this.div.innerHTML='<table width='+DIV_WIDTH+' border=0 cellpadding=2 cellspacing=0 bgcolor="'+this.head_color+'"><tr><td class="tiptd"><table width="100%" border=0 cellpadding=0 cellspacing=0><tr><th><span class="ptt"><b><font color="#FFFFFF">'+this.tooltip_title+'</font></b></span></th></tr></table><table width="100%" border=0 cellpadding=2 cellspacing=0 bgcolor="'+this.body_color+'"><tr><td><span class="pst"><font color="#000000">'+this.tooltip_text+'</font></span></td></tr></table></td></tr></table>'; | ||
| 1385 : | this.div.tooltip_visible=1; | ||
| 1386 : | } | ||
| 1387 : | } | ||
| 1388 : | |||
| 1389 : | function fillMenu() { | ||
| 1390 : | this.hideTip(); | ||
| 1391 : | this.hideMenu(); | ||
| 1392 : | if (this.popup_menu) { | ||
| 1393 : | this.div.innerHTML='<table cellspacing="2" cellpadding="1" bgcolor="#000000"><tr bgcolor="#eeeeee"><td><div style="max-height:300px;min-width:100px;overflow:auto;">'+this.popup_menu+'</div></td></tr></table>'; | ||
| 1394 : | this.div.menu_visible=1; | ||
| 1395 : | } | ||
| 1396 : | } | ||
| 1397 : | |||
| 1398 : | function showDiv(x,y) { | ||
| 1399 : | winW=(window.innerWidth)? window.innerWidth+window.pageXOffset-16 : | ||
| 1400 : | document.body.offsetWidth-20; | ||
| 1401 : | winH=(window.innerHeight)?window.innerHeight+window.pageYOffset : | ||
| 1402 : | document.body.offsetHeight; | ||
| 1403 : | if (window.getComputedStyle) { | ||
| 1404 : | current_style = window.getComputedStyle(this.div,null); | ||
| 1405 : | div_width = parseInt(current_style.width); | ||
| 1406 : | div_height = parseInt(current_style.height); | ||
| 1407 : | } | ||
| 1408 : | else { | ||
| 1409 : | div_width = this.div.offsetWidth; | ||
| 1410 : | div_height = this.div.offsetHeight; | ||
| 1411 : | } | ||
| 1412 : | this.div.style.left=(((x + div_width) > winW) ? winW - div_width : x) + px; | ||
| 1413 : | this.div.style.top=(((y + div_height) > winH) ? winH - div_height: y) + px; | ||
| 1414 : | // this.div.style.color = "#eeeeee"; | ||
| 1415 : | this.div.style.visibility=ns4?"show":"visible"; | ||
| 1416 : | } | ||
| 1417 : | |||
| 1418 : | function showTip(e,y) { | ||
| 1419 : | if (!this.div.menu_visible) { | ||
| 1420 : | if (!this.div.tooltip_visible) { | ||
| 1421 : | this.fillTip(); | ||
| 1422 : | } | ||
| 1423 : | var x; | ||
| 1424 : | if (typeof(e) == 'number') { | ||
| 1425 : | x = e; | ||
| 1426 : | } | ||
| 1427 : | else { | ||
| 1428 : | x=e.pageX?e.pageX:e.clientX?e.clientX:0; | ||
| 1429 : | y=e.pageY?e.pageY:e.clientY?e.clientY:0; | ||
| 1430 : | } | ||
| 1431 : | x+=2; y+=2; | ||
| 1432 : | this.showDiv(x,y); | ||
| 1433 : | this.div.tooltip_visible=1; | ||
| 1434 : | } | ||
| 1435 : | } | ||
| 1436 : | |||
| 1437 : | function showMenu(e) { | ||
| 1438 : | if (this.div) { | ||
| 1439 : | if (!this.div.menu_visible) { | ||
| 1440 : | this.fillMenu(); | ||
| 1441 : | } | ||
| 1442 : | var x; | ||
| 1443 : | var y; | ||
| 1444 : | |||
| 1445 : | // if the menu position was given as parameter | ||
| 1446 : | // to the constructor, then use that position | ||
| 1447 : | // or fall back to mouse position | ||
| 1448 : | |||
| 1449 : | if (this.popup_menu_x != -1) { | ||
| 1450 : | x = this.popup_menu_x; | ||
| 1451 : | y = this.popup_menu_y; | ||
| 1452 : | } | ||
| 1453 : | else { | ||
| 1454 : | x = e.pageX ? e.pageX : e.clientX ? e.clientX : 0; | ||
| 1455 : | y = e.pageY ? e.pageY : e.clientY ? e.clientY : 0; | ||
| 1456 : | } | ||
| 1457 : | this.showDiv(x,y); | ||
| 1458 : | this.div.menu_visible=1; | ||
| 1459 : | } | ||
| 1460 : | } | ||
| 1461 : | |||
| 1462 : | // Add the event handler to the parent object. | ||
| 1463 : | // The tooltip is managed by the mouseover and mouseout | ||
| 1464 : | // events. mousemove is captured, too | ||
| 1465 : | |||
| 1466 : | function addHandler() { | ||
| 1467 : | if (iemac) { return; } // ignore Ie on mac | ||
| 1468 : | |||
| 1469 : | if(this.tooltip_text) { | ||
| 1470 : | this.fillTip(); | ||
| 1471 : | this.attached.onmouseover = function (e) { | ||
| 1472 : | this.tooltip.showTip(e); | ||
| 1473 : | return false; | ||
| 1474 : | }; | ||
| 1475 : | this.attached.onmousemove = function (e) { | ||
| 1476 : | this.tooltip.mousemove(e); | ||
| 1477 : | return false; | ||
| 1478 : | }; | ||
| 1479 : | } | ||
| 1480 : | |||
| 1481 : | if (this.popup_menu) { | ||
| 1482 : | this.attached.onclick = function (e) { | ||
| 1483 : | this.tooltip.showMenu(e); | ||
| 1484 : | |||
| 1485 : | // reset event handlers | ||
| 1486 : | if (this.tooltip_text) { | ||
| 1487 : | this.onmousemove=null; | ||
| 1488 : | this.onmouseover=null; | ||
| 1489 : | this.onclick=null; | ||
| 1490 : | } | ||
| 1491 : | |||
| 1492 : | // there are two mouseout events, | ||
| 1493 : | // one when the mouse enters the inner region | ||
| 1494 : | // of our div, and one when the mouse leaves the | ||
| 1495 : | // div. we need to handle both of them | ||
| 1496 : | // since the div itself got no physical region on | ||
| 1497 : | // the screen, we need to catch event for its | ||
| 1498 : | // child elements | ||
| 1499 : | this.tooltip.div.moved_in=0; | ||
| 1500 : | this.tooltip.div.onmouseout=function (e) { | ||
| 1501 : | var div = getDiv(tooltip_name); | ||
| 1502 : | if (e.target.parentNode == div) { | ||
| 1503 : | if (div.moved_in) { | ||
| 1504 : | div.menu_visible = 0; | ||
| 1505 : | div.innerHTML=""; | ||
| 1506 : | div.style.visibility=ns4?"hide":"hidden"; | ||
| 1507 : | } | ||
| 1508 : | else { | ||
| 1509 : | div.moved_in=1; | ||
| 1510 : | } | ||
| 1511 : | return true; | ||
| 1512 : | }; | ||
| 1513 : | return true; | ||
| 1514 : | }; | ||
| 1515 : | this.tooltip.div.onclick=function() { | ||
| 1516 : | this.menu_visible = 0; | ||
| 1517 : | this.innerHTML=""; | ||
| 1518 : | this.style.visibility=ns4?"hide":"hidden"; | ||
| 1519 : | return true; | ||
| 1520 : | } | ||
| 1521 : | return false; // do not follow existing links if a menu was defined! | ||
| 1522 : | |||
| 1523 : | }; | ||
| 1524 : | } | ||
| 1525 : | this.attached.onmouseout = function () { | ||
| 1526 : | this.tooltip.delHandler(); | ||
| 1527 : | return false; | ||
| 1528 : | }; | ||
| 1529 : | } | ||
| 1530 : | |||
| 1531 : | function delHandler() { | ||
| 1532 : | if (this.div.menu_visible) { return true; } | ||
| 1533 : | |||
| 1534 : | // clean up | ||
| 1535 : | |||
| 1536 : | if (this.popup_menu) { this.attached.onmousedown = null; } | ||
| 1537 : | this.hideMenu(); | ||
| 1538 : | this.hideTip(); | ||
| 1539 : | this.attached.onmousemove = null; | ||
| 1540 : | this.attached.onmouseout = null; | ||
| 1541 : | |||
| 1542 : | // re-register the handler for mouse over | ||
| 1543 : | |||
| 1544 : | this.attached.onmouseover = function (e) { | ||
| 1545 : | this.tooltip.addHandler(e); | ||
| 1546 : | return true; | ||
| 1547 : | }; | ||
| 1548 : | return false; | ||
| 1549 : | } | ||
| 1550 : | |||
| 1551 : | function mousemove(e) { | ||
| 1552 : | if (this.div.tooltip_visible) { | ||
| 1553 : | if (e) { | ||
| 1554 : | x=e.pageX?e.pageX:e.clientX?e.clientX:0; | ||
| 1555 : | y=e.pageY?e.pageY:e.clientY?e.clientY:0; | ||
| 1556 : | } | ||
| 1557 : | else if (event) { | ||
| 1558 : | x=event.clientX; | ||
| 1559 : | y=event.clientY; | ||
| 1560 : | } | ||
| 1561 : | else { | ||
| 1562 : | x=0; y=0; | ||
| 1563 : | } | ||
| 1564 : | |||
| 1565 : | if(document.documentElement) // Workaround for scroll offset of IE | ||
| 1566 : | { | ||
| 1567 : | x+=document.documentElement.scrollLeft; | ||
| 1568 : | y+=document.documentElement.scrollTop; | ||
| 1569 : | } | ||
| 1570 : | this.showTip(x,y); | ||
| 1571 : | } | ||
| 1572 : | } | ||
| 1573 : | |||
| 1574 : | function setValue(id , val) { | ||
| 1575 : | var element = document.getElementById(id); | ||
| 1576 : | element.value = val; | ||
| 1577 : | } | ||
| 1578 : | |||
| 1579 : | </SCRIPT> | ||
| 1580 : | End_of_JavaScript | ||
| 1581 : | } | ||
| 1582 : | |||
| 1583 : | |||
| 1584 : | 1; |
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