/
convert2html.pl
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convert2html.pl
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#!/usr/bin/perl
# convert2html.pl - this file is created from convert2html.txt
#
# $Id: convert2html.txt 1339 2006-09-21 19:46:28Z tbailey $
# $Log$
# Revision 1.2 2005/08/23 23:52:41 nadya
# change form module back into pl file. Too much trouble to
# do separation of functions with *2html.pl files.
#
# Revision 1.1 2005/08/11 18:53:09 nadya
# rename from 2html. Perl does not understand modules if their name start as numeric.
#
# Revision 1.3 2005/08/11 17:42:58 nadya
# add exporting functionality
#
# Revision 1.2 2005/08/06 01:22:37 nadya
# add exporting info to the package
#
# Revision 1.1.1.1 2005/07/28 23:51:34 nadya
# Importing from meme-3.0.14, and adding configure/make
#
#
# subroutines and globals used by meme2html, mast2html and mhmm2html
#
$DIVIDER = "^\\*\\*\\*\\*\\*"; # section divider in output
$SUBDIV = "^--------------------------------------------------------------------------------"; # subsection divider in output
$ELIPSIS = "<B> · <BR> · <BR> · </B>";
$BODY = "#D5F0FF"; # the background color of the page (light blue by default)
$WEAK_FONT = "50% sans-serif"; # font size for weak motifs
$SCALE = 0.5; # (sequence position)/(number of pixels)
$MAX_DIAGRAM = 2000; # maximum number of pixels per diagram
$THIN_LINE = 4; # thickness of thin spacer lines
$FAT_LINE = 8; # thickness of fat spacer lines (for too long seqs)
$MIN_WIDTH = 30; # minimum width (in pixels) for motifs
$MAX_NAME_LEN = 34; # maximum length of truncated sequence name
# Colors for the motifs and their labels (motif numbers).
@MOTIF_COLORS=( aqua, blue, red, fuchsia,
yellow, lime, teal, '#444444',
green, silver, purple, olive,
navy, maroon, black, white );
@MOTIF_LABEL_COLORS=( black, white, white, black,
black, black, white, white,
white, black, white, black,
white, white, white, black );
@IC_COLORS=( red, blue, orange, green, black,
magenta, pink, yellow, turquoise );
#-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
#-* SUBROUTINES
#-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
#------------------------------------------------------------------------------
# print the HTML header (including style sheet) and set the body color
# $title title of HTML page
# $body_color background color; light blue if omitted
#------------------------------------------------------------------------------
sub print_header {
local (
$title, # title of HTML page
$body_color # background color; light blue if omitted
) = @_;
local ($i);
if (defined($body_color)) { $BODY = $body_color; }
print <<END;
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<HTML>
<HEAD>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<TITLE>$title</TITLE>
END
# print the style sheet
print '<STYLE type="text/css">', "\n";
# these save space compared with <FONT></FONT>
# color for invisible lines
print " TD.invisible { color: '$BODY'; }\n";
# TD classes for motifs
for ($i=0; $i<@MOTIF_COLORS; $i++) {
# normal motifs
print " TD.c$i { background: $MOTIF_COLORS[$i]; color: $MOTIF_LABEL_COLORS[$i]; }\n";
# weak motifs
print " TD.cw$i { background: $MOTIF_COLORS[$i]; color: $MOTIF_LABEL_COLORS[$i]; font: $WEAK_FONT; }\n";
}
# B, TD and TH classes for IC diagrams and scale
foreach $color (@IC_COLORS) {
print " B.$color { color: $color; }\n";
print " TD.$color { color: $color; }\n";
print " TH.$color { color: $color; }\n";
}
print "</STYLE>\n";
#
# end the header and start the body
#
print "</HEAD>\n";
print "<BODY BGCOLOR='$BODY'>\n";
} # print_header
#------------------------------------------------------------------------------
# find a section marker with the specified keyword (case sensitive)
#------------------------------------------------------------------------------
sub find_section {
local( $key ) = @_;
local( $line );
LINE:
while ( <STDIN> ) {
unless ( /\*\*\*\*\*/ ) { next LINE; }
$line = <STDIN>;
unless ( $line =~ /$key/ ) {
<STDIN>;
next LINE;
}
last;
}
return( $line );
} # find_section
#------------------------------------------------------------------------------
# next_section:
# Find a section marker and return the title line. The following line of
# stars is removed.
#
# USAGE: $text = &next_section();
#------------------------------------------------------------------------------
sub next_section {
local( $div ) = @_;
local( $line );
unless ( defined($div) ) {
$div = $DIVIDER;
}
while ( <STDIN> ) {
unless ( /^$div/ ) { next; }
$line = <STDIN>;
<STDIN>;
last;
}
chop $line;
return( $line );
} # next_section
#------------------------------------------------------------------------------
# read_block:
# Read a block of text until terminated by a blank line.
#------------------------------------------------------------------------------
sub read_block {
local( $line );
LINE:
while ( <STDIN> ) {
if ( /^\s*$/ ) { last LINE; }
$line .= $_;
}
return( $line );
} # read_block
#------------------------------------------------------------------------------
# next_block:
# Read the next block of text until terminated by a divider line. The divider
# by default, is specificed in $DIVIDER (normally a line of *). If a
# parameter is passed in, it is used as the divider.
# Removes \r from input.
#
# USAGE: $text = &next_block();
# $text = &next_block( divider );
#------------------------------------------------------------------------------
sub next_block {
local( $div ) = @_;
local( $line );
unless ( defined($div) ) {
$div = $DIVIDER;
}
while ( <STDIN> ) {
s/\r//g;
if ( /$div/ ) { last; }
$line .= $_;
}
return( $line );
} # next_block
#------------------------------------------------------------------------------
# format_section:
# Add HTML formatting for a section or subsection head.
# The specified heading appears as
# the section title with the specified name as an internal link.
#
# USAGE: $text = &format_section( pre, link, rest, name, ext)
#------------------------------------------------------------------------------
sub format_section {
my(
$pre, # just print this part
$link, # add link to this part
$rest, # just print this part
$name, # tag is "$name$ext"
$ext # ref is to "$name_doc"
) = @_;
my( $out, $ref, $tag );
if ( $name =~ /^\s*$/ ) { # all blank name
$out = "<HR><CENTER> $pre <BIG><B>\n $link $rest\n</B></BIG></CENTER><HR>";
} else { # name given
$ref = $name . "_doc";
$tag = $name . $ext;
$link = "<A HREF=\"#$ref\">$link</A>";
$out = "<HR><CENTER><A NAME=$tag></A>\n $pre <BIG><B> $link $rest\n</B></BIG></CENTER><HR>";
}
return($out);
} # format_section
#------------------------------------------------------------------------------
# format_para:
# Add HTML formatting for a paragraph. New lines are ignored, blank lines are
# converted to paragraphs.
#
# USAGE: $new_text = &format_para( text );
#------------------------------------------------------------------------------
sub format_para {
local ( $line ) = @_;
local( $out );
$out = "<P>\n$line";
$out =~ s/\n\s*\n/\n<P>\n/g;
return( $out );
} # format_para
#------------------------------------------------------------------------------
# format_pre:
# Add HTML formatting for a preformatted block.
#
# USAGE: $new_text = &format_pre( text );
#------------------------------------------------------------------------------
sub format_pre {
local ( $line ) = @_;
local( $out );
$out = ($line=~ /\w/) ? "<PRE>\n$line</PRE>\n" : "";
return( $out );
} # format_pre
#------------------------------------------------------------------------------
# format_diagrams:
# Convert the text diagrams to colored diagrams in HTML. The scale is 1/$scale
# pixels per sequence position for sequences of up to $max_diagram*$scale pixel.
# Diagrams for longer sequences are scaled to fit in $max_diagram pixels
# and the spacer lines are made thicker (and motif boxes may shrink).
# Weak motifs are labeled with font size $WEAK_FONT.
# When the motifs are protein and the database DNA, the motif widths are
# multiplied by 3 since they are in codon units to start with.
# Uses global variables @MOTIF_COLORS, $WEAK_FONT, $FAT_LINE, $THIN_LINE
# and @width (motif widths).
#
# Sets global $META to contain information from SUMMARY of MOTIFS for
# Meta-MEME.
#
# USAGE: $text = &format_diagrams( scale, max_diagram, text, db, stype, xlate,
# make_buttons, col2hdr, no_gi_names, field_delim);
#------------------------------------------------------------------------------
sub format_diagrams {
my( $scale, $max_diagram, $text, $db, $stype, $xlate, $make_buttons,
$col2hdr, $no_gi_names, $field_delim) = @_;
my( $i, $out, @line, $l, $w, $wid_sum, $nmotifs, $nspacers);
my( $max_spacers, $max_motifs, $name, $evalue, $diagram);
my( @field, $f, $motif, $link, $seqno );
my( @scale1, $col, $color, $font, $fsize, $wide, $fill, $mscale );
my( $ncol, $dist, $w2, $loc, @nocc, @seqlen, $lno, $ncolors );
$re_en = "\\([+-]?\\d*\\.?\\d*e[+-]?\\d+\\)"; # an e-format in parens
# start a table and header row
$out = "<TABLE SUMMARY='motif diagrams' BORDER=1>\n<TR>";
$ncol = 0; # number of columns in table
$ncolors = scalar(@MOTIF_LABEL_COLORS); # number of distinct motif colors
# put buttons linking to score and annotation?
if ($make_buttons) { $out .= "<TH>Links"; $ncol += 1; }
if ($stype eq "s") { # scoring DNA strands separately
$out .= "<TH>Name<TH>Strand<TH>$col2hdr<TH ALIGN=LEFT> Motifs\n";
$ncol += 4;
} else { # PROTEIN
$out .="<TH>Name<TH>$col2hdr<TH ALIGN=LEFT> Motifs\n";
$ncol += 3;
}
# split the text into lines
$text =~ s/\n\s+//g; # concat continued lines
@line = split /\n/, $text;
# find the width of each diagram
if ($xlate) { # translating DNA
$mscale = 3;
} else {
$mscale = 1;
}
$max_width = 0;
# remove header lines
for ($i=0; $i<=$#line; $i++) {
$l = $line[$i];
last if ($l =~ /-------------/);
}
while ($i>=0) { shift @line; $i--; }
#
# calculate the approximate width of diagram
#
$lno = 0; # line number
foreach $l (@line) {
if ($stype eq "s") {
($name,$strand,$evalue,$diagram) = ($field_delim eq " ") ?
split( " ", $l ) :
split( $field_delim, $l );
} else {
($name,$evalue,$diagram) = ($field_delim eq " ") ?
split( " ", $l ) :
split( $field_delim, $l );
}
# get sequence number
if ($stype eq "s" && $strand eq "-") {
$seqno = $SEQNO{"-".$name}; # negative DNA strand
} else {
$seqno = $SEQNO{$name};
}
if (defined($SKIP[$seqno])) { next; } # skip this sequence
# split the diagram into fields
@field = split( '[ _]', $diagram );
# calculate the approximate width
$wid_sum = $nocc[$lno] = 0;
foreach $f (@field) {
if ( $f =~ /[<>\[\]]/ ) { # motif occurrence
($motif) = $f =~ /[<\[][+-]?(\d+)[abc]?($re_en)?[>\]]/;
$wid_sum += $width{$motif} * $mscale;
$seqlen[$lno] += $width{$motif}; # length of sequence
$nocc[$lno]++; # number of motif occurrences
} else { # spacer
$seqlen[$lno] += $f; # length of sequence
$wid_sum += $f;
}
}
# calculate a scale so that diagram fits in $max_diagram pixels
$scale1[$seqno] = $scale;
if ($wid_sum/$scale > $max_diagram) {
$scale1[$seqno] = $wid_sum/$max_diagram;
}
# calculate the exact scaled diagram width
$wid_sum = 0;
$nmotifs = 0;
$nspacers = 0;
foreach $f (@field) {
if ( $f =~ /[<>\[\]]/ ) {
($motif) = $f =~ /[<\[][+-]?(\d+)[abc]?($re_en)?[>\]]/;
$wide = int($mscale*$width{$motif}/$scale1[$seqno]+0.5);
if ($wide < $MIN_WIDTH) { $wide = $MIN_WIDTH; }
$nmotifs++;
} else {
$wide = $f/$scale1[$seqno];
$wide = int($wide + 0.5); # round to integer
$nspacers++;
}
$wid_sum += $wide;
}
# save the length of the longest diagram
if ($wid_sum > $max_width) {
$max_width = $wid_sum;
$max_motifs = $nmotifs;
$max_spacers = $nspacers;
}
$lno++; # line number
} # line
# kludge for Netscape 4.0; make width larger
$max_width += 14 + (2*$max_motifs) + (3*$max_spacers);
# set max_width to at least
$min_width = int(50.0/$scale + 0.5);
if ($max_width < $min_width) { $max_width = $min_width; }
# make the diagrams
$META = "";
$lno = 0; # line number
foreach $l (@line) {
# length of space holder at end of diagram
if ($stype eq "s") {
($name,$strand,$evalue,$diagram) = ($field_delim eq " ") ?
split( " ", $l ) :
split( $field_delim, $l );
} else {
($name,$evalue,$diagram) = ($field_delim eq " ") ?
split( " ", $l ) :
split( $field_delim, $l );
}
if ($stype eq 's' && $strand eq "-") {
$seqno = $SEQNO{"-".$name}; # negative DNA strand
} else {
$seqno = $SEQNO{$name};
}
if (defined($SKIP[$seqno])) {
if (!defined($SKIP[$seqno-1])) { $out .= "<TR><TD COLSPAN=5>$ELIPSIS\n"; }
next; # skip this sequence
}
# start row of table
$out .= "<TR>\n ";
if ($make_buttons) {
$evalue = "$evalue";
if ( $name =~ /\|/ ) {
$button = make_button_panel("!", \%buttons,
$db."entrez!$name", "score!$seqno", "align!$seqno", "help" );
} else {
$button = make_button_panel("!", \%buttons,
"score!$seqno", "align!$seqno", "help" );
}
$out .= "<TD>$button\n";
} # make_buttons
# write name of sequence
if ($no_gi_names) {
$name =~ s/^gi\|\d+\|//; # leading gi|123 removed
}
$link = "<A NAME=d$seqno></A>$name";
$out .= " <TD>$link\n";
$META .= "$name";
if ($stype eq "s") {
$out .= " <TD ALIGN=CENTER>$strand\n";
}
$out .= " <TD ALIGN=RIGHT NOWRAP>$evalue\n";
$META .= " $evalue $nocc[$lno] $seqlen[$lno]";
$out .= " <TD><TABLE SUMMARY='diagram $seqno' WIDTH=$max_width BORDER=0 ALIGN=LEFT CELLSPACING=0 CELLPADDING=0><TR ALIGN=CENTER>\n";
@field = split( '[ _]', $diagram );
$fsize = $THIN_LINE; # font size for spacer line
if ($scale1[$seqno] != $scale) { $fsize = $FAT_LINE; }
$tail = $max_width;
$position = 0; # position in sequence
foreach $f (@field) {
if ( $f =~ /[<>\[\]]/ ) { # motif occurence
($st, $motif, $frame, $pv) = $f =~
/[<\[]([+-]?)(\d+)([abc]?)($re_en)?[>\]]/;
($pv) = $pv =~ /\(([^)]+)\)/;
$wide = int($mscale*$width{$motif}/$scale1[$seqno]+0.5);
if ($wide < $MIN_WIDTH) { $wide = $MIN_WIDTH; }
if ($motif eq ""){
$color = "gray";
$motif = " ";
} else {
$col = ( $motif - 1 ) % $ncolors;
$color = $MOTIF_COLORS[$col];
}
# set color and size of motif label;
# weak motifs have font size $WEAK_FONT
$font = "";
$endfont = "";
$class = ($f =~ /</) ? "cw$col" : "c$col";
$out .= " <TD CLASS='$class' WIDTH=$wide>$st$motif$frame\n";
$META .= " $st$motif $position $pv"; # for meta-meme
$position += $width{$motif}; # letter position in sequence
} else { # spacer
$wide = $f/$scale1[$seqno];
$wide = int($wide + 0.5); # round to integer
$out .=
" <TD WIDTH=$wide><HR SIZE=$fsize NOSHADE>\n";
$position += $f; # letter position in sequence
}
$tail -= $wide;
}
if ($tail > 0) { $out .= " <TD WIDTH=$tail>\n"; }
$out .= " </TABLE>\n";
$META .= "\n"; # metameme data
$lno++; # line number
} # line
#
# print a scale
#
$dist = 50; # pixel distance between rules
$w2 = $dist - 1.0/$scale; # distance to second rule
$ncol--; # number of columns scale spans
$out .= "<TR><TH CLASS='blue' COLSPAN=$ncol ROWSPAN=2 ALIGN=LEFT>SCALE\n";
$out .= " <TD><TABLE SUMMARY='scale' WIDTH=$max_width BORDER=0 ALIGN=LEFT CELLSPACING=0 CELLPADDING=0><TR ALIGN=CENTER>\n";
$out .= " <TD CLASS='blue' WIDTH=$w2 ALIGN=LEFT>|</TD>\n";
for ($i=$dist; $i<$max_width; $i+=$dist) {
$loc = $i * $scale;
last if ($i > $max_width-50); # make sure number will fit
$out .= " <TD CLASS='blue' WIDTH=$dist ALIGN=LEFT>|</TD>\n";
}
$out .= " <TR><TD CLASS='blue' WIDTH=$w2 ALIGN=LEFT>1</TD>\n";
for ($i=$dist; $i<$max_width; $i+=$dist) {
$loc = $i * $scale;
last if ($i > $max_width-50); # make sure number will fit
$out .= " <TD CLASS='blue' WIDTH=$dist ALIGN=LEFT>$loc</TD>\n";
}
$out .= " </TABLE>\n";
# end the table
$out .= "</TABLE>\n";
return( $out );
} # format_diagrams
#------------------------------------------------------------------------------
# find_line
#------------------------------------------------------------------------------
sub find_line {
local( $key ) = @_;
local( $line );
LINE:
while ( $line = <STDIN> ) {
unless ( $line =~ /$key/ ) {
next LINE;
}
last;
}
return( $line );
} # find_line
#------------------------------------------------------------------------------
# make_button_panel:
#
# Use the input associative array, and the specified keys to create a HTML
# table with labeled buttons.
#
# The buttons are defined in the associative array passed in the second
# parameter. This array is indexed by the key, and contains three fields
# separated by the divider specified in the 1st parameter. The fields
# are the tag template, the background color, and the font color. Note that
# a tag template that is a link will override the font color.
#
# The tag template is a string that, optionally, can have the key substituted
# into it at all positions marked by $MBPSUB (this is a symbol to avoid
# collisions with arbitrary strings).
#
# Note that each line containing a button panel should be followed with a
# <BR CLEAR=LEFT> to prevent the next line from being indented to the position
# following the panel. This is because, even though the panel uses a -1 font,
# it is still taller than the text and therefore creates an apparent indent in
# the same way a drop capital would.
#
# USAGE:
# <string> = &make_button_panel( <div>, <button def>, [<key1>,<key2>...] );
#
# button def:
# button defs have three elements separated by the divider (div) :
# Element 1: template for text that will appear on the button. This
# can be static text, or contain a place hold where key information will
# be inserted ($MBPSUB).
# Element 2: background color for the button.
# Element 3: foreground color for the button. Note if button is a link,
# this color will be overridden by the link color.
#
# key:
# keys have one or two elements separated by the divider:
# Element 1: mandatory. this is the button type and is used to look up
# the button definition.
# Element 2: optional. If present, this is the key information that will
# be substituted for $MBPSUB. If absent, the button type is used.
#
# default behavior:
# if a button type is undefined, a black and white button will be displayed
# using the key information as the label on the button.
#
# EXAMPLE
# $MBPSUB = "XXXXXXX";
#
# %p1 = (
# 'aaa',
# '<A HREF=http://www.sdsc.edu/~gribskov>$MBPSUB</A>&#FFAAAA&white',
# 'b', 'B&#DDDDFF&white',
# 'c', 'C&white&black'
# );
#
# %p2 = ( 'fff', 'F green white',
# 'ggg', 'G blue white' );
#
# $bpanel = &make_button_panel( "&", \%def, "a&?", "c" );
# print "$bpanel text following the buttons goes here<BR CLEAR=LEFT>\n";
# $bpanel = &make_button_panel( " ", \%p2, "fff", "ggg", "hhh" );
# print "$bpanel A second panel with text<BR CLEAR=LEFT>\n";
#
# 19 November 1997 Michael Gribskov
#------------------------------------------------------------------------------
sub make_button_panel {
local ($div, *def, @parm) = @_;
local ($p, $n, $type, $text, $tag, $bkg, $bcolor, $font, $fcolor, $out);
$out = "<TABLE SUMMARY='buttons' ALIGN=LEFT CELLSPACING=0><TR>";
foreach $p ( @parm ) {
# split the key into the tag (type) and text
$n = ($type, $text) = split /$div/, $p;
if ( $n > 1 ) {
$key = $text;
} else { $type=$p; $key = $p; }
#look up the button definition using the type as key
($tag, $bcolor, $fcolor) = split /$div/, $def{$type};
unless ( defined($tag) ) { $tag = $key; }
unless ( defined($bcolor) ) { $bcolor = "white"; }
unless ( defined($fcolor) ) { $fcolor = "black"; }
# replace all occurrences of $MBPSUB with the key
while ( $tag =~ s/$MBPSUB/$key/ ){};
$out .= "\n <TD BGCOLOR='$bcolor'>$tag";
$c++;
}
$out .= "</TABLE>";
return( $out );
} # make_button_panel
################################################################################
# get_color
#
# Get the name of the color for the given DNA or Protein letter.
# Colors are similar to those used by CLUSTAL.
#
################################################################################
sub get_color {
local ($type, $letter) = @_;
$_ = $letter;
if ($type =~ /DNA|dna/) {
if (/[Aa]/) {
$color = "red";
} elsif (/[Cc]/) {
$color = "blue";
} elsif (/[Gg]/) {
$color = "orange";
} elsif (/[Tt]/) {
$color = "green";
} else {
$color = "black";
}
} elsif ($type =~ /PROTEIN|protein/) {
if (/[ACFILMVWacfilmvw]/) {
$color = "blue";
} elsif (/[NQSTnqst]/) {
$color = "green";
} elsif (/[DEde]/) {
$color = "magenta";
} elsif (/[KRkr]/) {
$color = "red";
} elsif (/[Hh]/) {
$color = "pink";
} elsif (/[Gg]/) {
$color = "orange";
} elsif (/[Pp]/) {
$color = "yellow";
} elsif (/[Yy]/) {
$color = "turquoise";
} else {
$color = "black";
}
}
$color;
} # get_color
#------------------------------------------------------------------------------
# Cleanup any temporary files
#------------------------------------------------------------------------------
sub cleanup {
#system "rm $pgm.$$.*.tmp";
if ($_[0] eq "INT") { exit(1); } else { exit($_[0]); }
} # cleanup
#
# Haoyuan added some functions here in order to convert mhmm result from
# plain text to html (mhmm2html)
#
#-----------------------------------------------------------------------------
# format_subtile
# Add HTML sub_title, <hr><b><center> .... </center></b><hr>.
#
# USAGE: $new_text = &format_subtitle(text)
#-----------------------------------------------------------------------------
sub format_subtitle {
my ($line) = @_;
my ($out);
$out = "<HR>\n<CENTER><B>$line</B></CENTER>\n<HR>\n";
return($out);
} #format_subtitle
#----------------------------------------------------------------------------
# format_hidden
# Add HTML Hidden Field
#
# USAGE: $new_text = &format_hidden(textname,textfield)
#----------------------------------------------------------------------------
sub format_hidden {
my ($name, $field) = @_;
my ($out);
# replace confounding characters (">) that won't work in HIDDEN values
$field =~ s/\"/"/g;
$field =~ s/\>/>/g;
$out = "<INPUT TYPE = \"HIDDEN\" NAME = \"$name\"".
" VALUE = \"\n".
"$field".
" \">\n";
} #format_hidden
#----------------------------------------------------------------------------
# delete_first_letter
# Delete the first letter of a sentence
# In mhmm2html file, it is used to chop "#"
# USAGE: $new_text = &delete_first_letter(text)
#----------------------------------------------------------------------------
sub delete_first_letter{
my ($line) = @_;
my ($out);
if (length($line) == 0){
print (STDERR "Error: The length of your input is 0\n");
exit(0);
}
else{
my($length) = length($line);
$out = substr($line,1,$length-1);
}
return($out);
}
#--------------------------------------------------------------------------
# make_end
# Add some "last" info. to the html output page
#
# USAGE: $end = &make_end()
#--------------------------------------------------------------------------
sub make_end{
my ($out, $button);
# button to take user to top of form
$button = make_button_panel("!", \%buttons, "top");
# finish form, body and documument
$out = "<HR>$button<BR>\n</FORM>\n</BODY>\n</HTML>\n";
return ($out);
}
#-------------------------------------------------------------------------
# format_table
# format html table from input plain text
#
# USAGE: $new_text = &format_table($text,$num_col)
#-------------------------------------------------------------------------
sub format_table{
my ($out,@temp1,$i,@temp2,$end_mark,$j);
my ($line,$num_col) = @_;
print "<table border = \"1\">\n";
@temp1 = split("\n",$line);
for ($i=0;$i<=$#temp1;$i++){
@temp2 = split(" ",$temp1[$i]);
if ($num_col eq "0"){
$end_mark = $#temp2;
}
else{
$end_mark = $num_col-1;
for ($j=$num_col;$j<=$#temp2;$j++){
$temp2[$num_col-1] = $temp2[$num_col-1]." ".$temp2[$j];
}
}
print "<tr>\n";
for ($j=0;$j<=$end_mark;$j++){
print "<td>";
print "$temp2[$j]";
print "</td>";
}
print "\n</tr>\n";
}
print "</table>\n";
}
#######################################################################
# Add Entrez link
#######################################################################
sub add_entrez_link{
my ($line, $alphabet) = @_;
my($return_value);
$return_value =
"<A HREF=\'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=";
if ($alphabet eq "dna"){
$return_value .= "Nucleotide";
} else {
$return_value .= "Protein";
}
$return_value .= "&cmd=Search&term=$line&doptcmdl=GenBank\' TARGET =\'_blank\'>$line</a>";
return($return_value);
} # add_entrez_link