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revision 1.6, Mon Dec 27 15:52:08 2010 UTC revision 1.7, Tue Feb 1 03:57:00 2011 UTC
# Line 42  Line 42 
42         -d   desc_file     - add description to each tip       # table: [id description]         -d   desc_file     - add description to each tip       # table: [id description]
43         -f   focus_list    - highlight a list of tips          # table: [id]         -f   focus_list    - highlight a list of tips          # table: [id]
44         -l   link_file     - add URL to each tip               # table: [id URL]         -l   link_file     - add URL to each tip               # table: [id URL]
45           -lt  link_w_text   - add additional linked text        # table: [id text URL]
46         -m   popup_file    - add simple mouseover to each tip  # table: [id popup]         -m   popup_file    - add simple mouseover to each tip  # table: [id popup]
47         -nc  n_colors      - number of colors to use (D = 10)         -nc  n_colors      - number of colors to use (D = 10)
48         -p   g|s|file      - collapse trees by genus, species,         -p   g|s|file      - collapse trees by genus, species,
49                              or groups specified in a file     # table: [id group]                              or groups specified in a file     # table: [id group]
50           -s   show_list     - preferred tips to show when collapsing subtrees
51                                (D = Woese' list of 69 common organisms)
52         -t   title         - title for html page         -t   title         - title for html page
53         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)
54         -y   dy            - vertical separation of consecutive tips (D = 1)         -y   dy            - vertical separation of consecutive tips (D = 1)
# Line 105  Line 108 
108    
109  A two-column table [ id, url ] for inserting URL for tree tips.  A two-column table [ id, url ] for inserting URL for tree tips.
110    
111    =item -lt linked_text_file
112    
113    A three-column table [ id, text, url ] for inserting linked text for tree tips.
114    
115  =item -m mouseover_file  =item -m mouseover_file
116    
117  A two-column table [ id, mouseover_description ]. The mouseover  A two-column table [ id, mouseover_description ]. The mouseover
# Line 124  Line 131 
131  The default behavior is to collapse subtrees whose nodes all belong to  The default behavior is to collapse subtrees whose nodes all belong to
132  the same genus.  the same genus.
133    
134    =item -s show_list (D = Woese' list of 69 common organisms)
135    
136    Show a list of preferred tips when collapsing subtrees.
137    
138  =item -t html_title  =item -t html_title
139    
140  This title of the HTML page.  This title of the HTML page.
# Line 187  Line 198 
198         -d   desc_file     - add description to each tip       # file: [id description]         -d   desc_file     - add description to each tip       # file: [id description]
199         -f   focus_list    - highlight a list of tips          # file: [id]         -f   focus_list    - highlight a list of tips          # file: [id]
200         -l   link_file     - add URL to each tip               # file: [id URL]         -l   link_file     - add URL to each tip               # file: [id URL]
201           -lt  link_w_text   - add additional linked text        # file: [id text URL]
202         -m   popup_file    - add simple mouseover to each tip  # file: [id popup]         -m   popup_file    - add simple mouseover to each tip  # file: [id popup]
203         -nc  n_colors      - number of colors to use (D = 10)         -nc  n_colors      - number of colors to use (D = 10)
204         -p   g|s|file      - collapse trees by genus, species,         -p   g|s|file      - collapse trees by genus, species,
205                              or groups specified in a file     # file: [id group]                              or groups specified in a file     # file: [id group]
206           -s   show_list     - preferred tips to show when collapsing subtrees
207                                (D = Woese' list of 69 common organisms)
208         -t   title         - title for html page         -t   title         - title for html page
209         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)
210         -y   dy            - vertical separation of consecutive tips (D = 1)         -y   dy            - vertical separation of consecutive tips (D = 1)
# Line 202  Line 216 
216    
217  End_of_Usage  End_of_Usage
218    
219  my ($help, $url, $alias_file, $focus_file, $branch, $collapse_by,  my ($help, $url, $alias_file, $focus_file, $branch, $collapse_by, $show_file,
220      $desc_file, $link_file, $popup_file, $id_file, $title, $min_dx, $dy,      $desc_file, $link_file, $text_link, $popup_file, $id_file, $title,
221      $ncolor, $color_by, $anno, $gray, $pseed, $raw);      $min_dx, $dy, $ncolor, $color_by, $anno, $gray, $pseed, $raw);
222    
223  GetOptions("h|help"         => \$help,  GetOptions("h|help"         => \$help,
224             "a|alias=s"      => \$alias_file,             "a|alias=s"      => \$alias_file,
# Line 214  Line 228 
228             "f|focus=s"      => \$focus_file,             "f|focus=s"      => \$focus_file,
229             "i|id=s"         => \$id_file,             "i|id=s"         => \$id_file,
230             "l|link=s"       => \$link_file,             "l|link=s"       => \$link_file,
231               "lt=s"           => \$text_link,
232             "m|popup=s"      => \$popup_file,             "m|popup=s"      => \$popup_file,
233             "nc=i"           => \$ncolor,             "nc=i"           => \$ncolor,
234             "p|collapse=s"   => \$collapse_by,             "p|collapse=s"   => \$collapse_by,
235               "s|show=s"       => \$show_file,
236             "t|title=s"      => \$title,             "t|title=s"      => \$title,
237             "x|dx=i"         => \$min_dx,             "x|dx=i"         => \$min_dx,
238             "y|dy=i"         => \$dy,             "y|dy=i"         => \$dy,
# Line 236  Line 252 
252  $opts->{alias}       = ffxtree::read_hash($alias_file)  if $alias_file  && -s $alias_file;  $opts->{alias}       = ffxtree::read_hash($alias_file)  if $alias_file  && -s $alias_file;
253  $opts->{color_by}    = ffxtree::read_hash($color_by)    if $color_by    && -s $color_by;  $opts->{color_by}    = ffxtree::read_hash($color_by)    if $color_by    && -s $color_by;
254  $opts->{collapse_by} = ffxtree::read_hash($collapse_by) if $collapse_by && -s $collapse_by;  $opts->{collapse_by} = ffxtree::read_hash($collapse_by) if $collapse_by && -s $collapse_by;
255    $opts->{collapse_show} = ffxtree::read_set($show_file)     if $show_file     && -s $show_file;
256  $opts->{desc}        = ffxtree::read_hash($desc_file)   if $desc_file   && -s $desc_file;  $opts->{desc}        = ffxtree::read_hash($desc_file)   if $desc_file   && -s $desc_file;
257  $opts->{popup}       = ffxtree::read_hash($popup_file)  if $popup_file  && -s $popup_file;  $opts->{popup}       = ffxtree::read_hash($popup_file)  if $popup_file  && -s $popup_file;
258  $opts->{link}        = ffxtree::read_hash($link_file)   if $link_file   && -s $link_file;  $opts->{link}        = ffxtree::read_hash($link_file)   if $link_file   && -s $link_file;
259    $opts->{text_link}     = ffxtree::read_hash($text_link)    if $text_link     && -s $text_link;
260  $opts->{tree}        = ffxtree::read_tree();  $opts->{tree}        = ffxtree::read_tree();
261  $opts->{ncolor}      = $ncolor || 10;  $opts->{ncolor}      = $ncolor || 10;
262  $opts->{gray}        = $gray   || 2;  $opts->{gray}        = $gray   || 2;
# Line 250  Line 268 
268    
269  $opts->{color_by}    ||= $raw ? 'none' : 'taxonomy';  $opts->{color_by}    ||= $raw ? 'none' : 'taxonomy';
270  $opts->{collapse_by} ||= $raw ? 'none' : 'genus';  $opts->{collapse_by} ||= $raw ? 'none' : 'genus';
271  $opts->{color_by}      = undef if $opts->{color_by}    =~ /none/i;  $opts->{collapse_show} ||= $raw ? 'none' : 'woese';
272  $opts->{collapse_by}   = undef if $opts->{collapse_by} =~ /none/i;  
273    $opts->{color_by}      = 0 if $opts->{color_by}    =~ /none/i;
274    $opts->{collapse_by}   = 0 if $opts->{collapse_by} =~ /none/i;
275    $opts->{collapse_show} = 0 if $show_file           =~ /(none|0)/i;
276    
277  my $envParm = $ENV{SAS_SERVER};  my $envParm = $ENV{SAS_SERVER};
278    

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