# HG changeset patch
# User davidmurphy
# Date 1327976270 18000
# Node ID 20716450be87602ab4899aab33812d2146d2c230
# Parent  f3462128e87ca313d63f1e7ffcccb4dbd24c817a
Uploaded

diff -r f3462128e87c -r 20716450be87 Codonlogo.xml
--- a/Codonlogo.xml	Mon Jan 30 08:17:57 2012 -0500
+++ b/Codonlogo.xml	Mon Jan 30 21:17:50 2012 -0500
@@ -407,8 +407,8 @@
         <option value="none" >No small sample correction</option>       
         <option value="equiprobable" >Equiprobable</option>
         <option value="Homosapiens" >Human</option>
-        <option value="Yeast" >Saccharomycescerevisiae</option>
-        <option value="E.Coli" >Escherichiacoli</option>
+        <option value="Saccharomycescerevisiae" >Yeast</option>
+        <option value="Escherichiacoli" >E.Coli</option>
         <option value="From File">from file</option>
         
       </param>
diff -r f3462128e87c -r 20716450be87 codonlogo
diff -r f3462128e87c -r 20716450be87 test.eps
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.eps	Mon Jan 30 21:17:50 2012 -0500
@@ -0,0 +1,1247 @@
+%!PS-Adobe-3.0 EPSF-3.0
+%%Title:        Sequence Logo: 
+%%Creator:      ('CodonLogo 1.1 (2011-09-17)',)
+%%CreationDate: 2012-01-30 20:49:03.377996
+%%BoundingBox:  0  0  270  126 
+%%Pages: 0
+%%DocumentFonts: 
+%%EndComments
+
+
+% ---- VARIABLES ----
+
+/True   true def
+/False  false def
+
+/debug              False        def
+
+/logo_height        126  def
+/logo_width         270  def
+/logo_title         () def
+/show_title         False def
+
+/logo_margin        2 def
+/xaxis_label_height 6.0 def
+/title_height       0 def
+/stroke_width       0.5 def
+/tic_length         5 def
+
+/lines_per_logo     1 def
+/line_width         266.8 def
+/line_height        116.0 def
+/line_margin_left   30.0 def
+/line_margin_right  10 def
+/line_margin_bottom 12.0 def
+/line_margin_top    4 def
+
+/stack_width         32.4 def
+/stack_height        100 def
+/stacks_per_line     7 def
+/stack_margin        0.5 def
+
+/show_yaxis             True def      
+/show_yaxis_label       True def
+/yaxis_label            (bits) def
+/yaxis_scale          6.0 def              % height in units 
+/yaxis_tic_interval     1.0 def           % in units
+/yaxis_minor_tic_interval 0.2 def   % in units
+
+/show_xaxis_label       False def             % True or False
+/show_xaxis             True def                   % True or False
+/xaxis_label            () def
+/xaxis_tic_interval     1 def
+/rotate_numbers         False def               % True or False
+/number_interval        5 def
+/show_ends              False def          
+/end_type               (-) def          % d: DNA, p: PROTEIN, -: none
+
+/show_fineprint         True def
+/fineprint              (CodonLogo 1.1) def
+/logo_label             () def
+
+/show_boxes             False def    % True or False
+/shrink                 false def    % True or False
+/shrink_fraction        0.5 def               
+
+/show_errorbars         True def      % True or False
+/errorbar_fraction      0.9 def
+/errorbar_width_fraction  0.25 def
+/errorbar_gray          0.5 def
+
+/fontsize               10 def
+/small_fontsize         6 def
+/title_fontsize         12 def
+/number_fontsize        8 def
+
+
+/UseCIEColor true def       % Fix for issue 4
+/default_color [ 0.0 0.0 0.0 ] def 
+/color_dict << 
+  (CAT) [ 0.0 1.0 1.0 ]
+  (CAU) [ 0.0 1.0 1.0 ]
+  (CAC) [ 0.0 1.0 1.0 ]
+  (AAA) [ 0.0 1.0 1.0 ]
+  (AAG) [ 0.0 1.0 1.0 ]
+  (CGT) [ 0.0 1.0 1.0 ]
+  (CGU) [ 0.0 1.0 1.0 ]
+  (CGC) [ 0.0 1.0 1.0 ]
+  (CGA) [ 0.0 1.0 1.0 ]
+  (CGG) [ 0.0 1.0 1.0 ]
+  (AGA) [ 0.0 1.0 1.0 ]
+  (AGG) [ 0.0 1.0 1.0 ]
+  (GAT) [ 1.0 0.0 0.0 ]
+  (GAU) [ 1.0 0.0 0.0 ]
+  (GAC) [ 1.0 0.0 0.0 ]
+  (GAA) [ 1.0 0.0 0.0 ]
+  (GAG) [ 1.0 0.0 0.0 ]
+  (TCT) [ 0.0 1.0 0.0 ]
+  (UCU) [ 0.0 1.0 0.0 ]
+  (TCC) [ 0.0 1.0 0.0 ]
+  (UCC) [ 0.0 1.0 0.0 ]
+  (TCA) [ 0.0 1.0 0.0 ]
+  (UCA) [ 0.0 1.0 0.0 ]
+  (TCG) [ 0.0 1.0 0.0 ]
+  (UCG) [ 0.0 1.0 0.0 ]
+  (AGT) [ 0.0 1.0 0.0 ]
+  (AGU) [ 0.0 1.0 0.0 ]
+  (AGC) [ 0.0 1.0 0.0 ]
+  (ACT) [ 0.0 1.0 0.0 ]
+  (ACU) [ 0.0 1.0 0.0 ]
+  (ACC) [ 0.0 1.0 0.0 ]
+  (ACA) [ 0.0 1.0 0.0 ]
+  (ACG) [ 0.0 1.0 0.0 ]
+  (CAA) [ 0.0 1.0 0.0 ]
+  (CAG) [ 0.0 1.0 0.0 ]
+  (AAT) [ 0.0 1.0 0.0 ]
+  (AAU) [ 0.0 1.0 0.0 ]
+  (AAC) [ 0.0 1.0 0.0 ]
+  (GCT) [ 0.333333333333 0.333333333333 1.0 ]
+  (GCU) [ 0.333333333333 0.333333333333 1.0 ]
+  (GCC) [ 0.333333333333 0.333333333333 1.0 ]
+  (GCA) [ 0.333333333333 0.333333333333 1.0 ]
+  (GCG) [ 0.333333333333 0.333333333333 1.0 ]
+  (GTT) [ 0.333333333333 0.333333333333 1.0 ]
+  (GUU) [ 0.333333333333 0.333333333333 1.0 ]
+  (GTC) [ 0.333333333333 0.333333333333 1.0 ]
+  (GUC) [ 0.333333333333 0.333333333333 1.0 ]
+  (GTA) [ 0.333333333333 0.333333333333 1.0 ]
+  (GUA) [ 0.333333333333 0.333333333333 1.0 ]
+  (GTG) [ 0.333333333333 0.333333333333 1.0 ]
+  (GUG) [ 0.333333333333 0.333333333333 1.0 ]
+  (CTT) [ 0.333333333333 0.333333333333 1.0 ]
+  (CUU) [ 0.333333333333 0.333333333333 1.0 ]
+  (CTC) [ 0.333333333333 0.333333333333 1.0 ]
+  (CUC) [ 0.333333333333 0.333333333333 1.0 ]
+  (CTA) [ 0.333333333333 0.333333333333 1.0 ]
+  (CUA) [ 0.333333333333 0.333333333333 1.0 ]
+  (CTG) [ 0.333333333333 0.333333333333 1.0 ]
+  (CUG) [ 0.333333333333 0.333333333333 1.0 ]
+  (TTA) [ 0.333333333333 0.333333333333 1.0 ]
+  (UUA) [ 0.333333333333 0.333333333333 1.0 ]
+  (TTG) [ 0.333333333333 0.333333333333 1.0 ]
+  (UUG) [ 0.333333333333 0.333333333333 1.0 ]
+  (ATT) [ 0.333333333333 0.333333333333 1.0 ]
+  (AUU) [ 0.333333333333 0.333333333333 1.0 ]
+  (ATC) [ 0.333333333333 0.333333333333 1.0 ]
+  (AUC) [ 0.333333333333 0.333333333333 1.0 ]
+  (ATA) [ 0.333333333333 0.333333333333 1.0 ]
+  (AUA) [ 0.333333333333 0.333333333333 1.0 ]
+  (ATG) [ 0.333333333333 0.333333333333 1.0 ]
+  (AUG) [ 0.333333333333 0.333333333333 1.0 ]
+  (TTT) [ 1.0 0.0 1.0 ]
+  (UUU) [ 1.0 0.0 1.0 ]
+  (TTC) [ 1.0 0.0 1.0 ]
+  (UUC) [ 1.0 0.0 1.0 ]
+  (TAT) [ 1.0 0.0 1.0 ]
+  (UAU) [ 1.0 0.0 1.0 ]
+  (TAC) [ 1.0 0.0 1.0 ]
+  (UAC) [ 1.0 0.0 1.0 ]
+  (TGG) [ 1.0 0.0 1.0 ]
+  (UGG) [ 1.0 0.0 1.0 ]
+  (GGT) [ 0.6 0.4 0.0 ]
+  (GGU) [ 0.6 0.4 0.0 ]
+  (GGC) [ 0.6 0.4 0.0 ]
+  (GGA) [ 0.6 0.4 0.0 ]
+  (GGG) [ 0.6 0.4 0.0 ]
+  (CCT) [ 0.6 0.4 0.0 ]
+  (CCU) [ 0.6 0.4 0.0 ]
+  (CCC) [ 0.6 0.4 0.0 ]
+  (CCA) [ 0.6 0.4 0.0 ]
+  (CCG) [ 0.6 0.4 0.0 ]
+  (TGT) [ 1.0 1.0 0.0 ]
+  (UGU) [ 1.0 1.0 0.0 ]
+  (TGC) [ 1.0 1.0 0.0 ]
+  (UGC) [ 1.0 1.0 0.0 ]
+  (TAA) [ 0.0 0.0 0.0 ]
+  (UAA) [ 0.0 0.0 0.0 ]
+  (TAG) [ 0.0 0.0 0.0 ]
+  (UAG) [ 0.0 0.0 0.0 ]
+  (TGA) [ 0.0 0.0 0.0 ]
+  (UGA) [ 0.0 0.0 0.0 ]
+>> def
+
+
+
+% ---- DERIVED PARAMETERS ----
+
+/char_width stack_width 2 stack_margin mul sub def
+/char_width2 char_width 2 div def
+/char_width4 char_width 4 div def
+
+% movements to place 5'/N and 3'/C symbols
+/leftEndDeltaX  fontsize neg         def
+/leftEndDeltaY  fontsize 1.25 mul neg def
+/rightEndDeltaX fontsize 0.25 mul     def
+/rightEndDeltaY leftEndDeltaY        def
+
+
+% ---- PROCEDURES ----
+
+
+/SetTitleFont {/ArialMT findfont title_fontsize scalefont setfont} bind def
+/SetLogoFont  {/Arial-BoldMT findfont char_width  scalefont setfont} bind def
+/SetStringFont{/ArialMT findfont fontsize scalefont setfont} bind def
+/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
+/SetSmallFont {/ArialMT findfont small_fontsize scalefont setfont} bind def
+/SetNumberFont {/ArialMT findfont number_fontsize scalefont setfont} bind def
+
+/DrawBox { % width height 
+    /hh exch def
+    /ww exch def
+    gsave
+        0.2 setlinewidth
+        %0.5 setgray
+        
+        %0 0 moveto 
+        hh 0 rlineto
+        0 ww rlineto
+        hh neg 0 rlineto
+        0 ww neg rlineto
+        stroke
+    grestore
+} bind def
+
+
+/StartLogo { 
+  %save 
+  gsave 
+
+  
+  debug { 
+    logo_margin logo_margin moveto
+    logo_height logo_margin 2 mul sub
+    logo_width logo_margin 2 mul sub
+    DrawBox } if
+    
+  show_title { DrawTitle } if
+  show_xaxis_label { DrawXaxisLable } if
+  show_fineprint { DrawFineprint } if
+  DrawLogoLabel
+  
+  
+  MoveToFirstLine
+} bind def
+
+
+/DrawLogoLabel {
+  gsave 
+    SetTitleFont
+    
+    logo_margin
+    logo_height title_fontsize sub logo_margin sub
+    moveto
+    
+    debug { title_fontsize logo_label stringwidth pop DrawBox } if
+    0 title_fontsize 4 div rmoveto % Move up to baseline (approximatly)
+    logo_label show
+    
+  grestore
+} bind def
+
+/DrawTitle {
+  gsave 
+    SetTitleFont
+    
+    logo_width 2 div logo_title stringwidth pop 2 div sub 
+    logo_height title_fontsize sub logo_margin sub
+    moveto
+    
+    debug { title_fontsize logo_title stringwidth pop DrawBox } if
+    
+    0 title_fontsize 4 div rmoveto % Move up to baseline (approximatly)
+    logo_title show
+    
+  grestore
+} bind def
+
+/DrawXaxisLable {
+  % Print X-axis label, bottom center
+  gsave
+    SetStringFont
+
+    logo_width 2 div xaxis_label stringwidth pop 2 div sub
+    xaxis_label_height logo_margin add fontsize sub
+    moveto
+    %fontsize 3 div
+    
+    debug { fontsize xaxis_label stringwidth pop DrawBox } if
+
+    xaxis_label show
+
+  grestore
+} bind def
+
+
+/DrawFineprint {
+    gsave
+    
+    SetSmallFont
+
+    logo_width fineprint stringwidth pop sub 
+        logo_margin sub line_margin_right sub
+    logo_margin 
+    moveto
+    
+    debug { small_fontsize fineprint stringwidth pop DrawBox } if
+        
+    fineprint show
+    grestore
+} bind def
+
+/MoveToFirstLine {
+    logo_margin 
+    logo_height logo_margin sub title_height sub line_height sub
+    moveto
+} bind def
+
+/EndLogo { 
+  grestore 
+  %showpage 
+  %restore 
+} bind def
+
+
+/StartLine{ 
+    gsave 
+  
+    % Draw outer box
+    debug { line_height line_width DrawBox } if  
+
+    % Move to lower left corner of content area
+    line_margin_left line_margin_bottom rmoveto
+
+    % Draw inner content box
+    debug { 
+        line_height line_margin_bottom sub line_margin_top sub
+        line_width line_margin_left sub line_margin_right sub
+        DrawBox
+    } if  
+  
+    show_yaxis { DrawYaxis } if
+    show_xaxis { DrawLeftEnd } if
+    
+} bind def
+
+/EndLine{ 
+    show_xaxis { DrawRightEnd } if
+    grestore 
+    0 line_height neg rmoveto 
+} bind def
+
+
+/DrawYaxis {
+  gsave    
+    stack_margin neg 0 translate
+    DrawYaxisBar
+    DrawYaxisLabel
+  grestore
+} bind def
+
+
+/DrawYaxisBar { 
+  gsave  
+    stack_margin neg 0 rmoveto
+    
+    SetNumberFont
+    stroke_width setlinewidth
+    
+    /str 10 string def % string to hold number  
+    /smallgap stack_margin  def
+
+    % Draw first tic and bar
+    gsave    
+      tic_length neg 0 rmoveto 
+      tic_length 0 rlineto 
+      0 stack_height rlineto
+      stroke
+    grestore
+
+    % Draw the tics
+    % initial increment limit proc for
+    0 yaxis_tic_interval yaxis_scale abs 
+    {/loopnumber exch def
+
+      % convert the number coming from the loop to a string
+      % and find its width
+      loopnumber 10 str cvrs
+      /stringnumber exch def % string representing the number
+
+      stringnumber stringwidth pop
+      /numberwidth exch def % width of number to show
+
+      /halfnumberheight
+         stringnumber CharBoxHeight 2 div
+      def
+
+      gsave
+        numberwidth % move back width of number
+        neg loopnumber stack_height yaxis_scale div mul % shift on y axis
+        halfnumberheight sub % down half the digit
+        rmoveto % move back the width of the string
+
+        tic_length neg smallgap sub % Move back a bit more  
+        0 rmoveto % move back the width of the tic  
+
+        stringnumber show
+        smallgap 0 rmoveto % Make a small gap  
+
+        % now show the tic mark
+        0 halfnumberheight rmoveto % shift up again
+        tic_length 0 rlineto
+        stroke
+     grestore
+    } for
+    
+    % Draw the minor tics
+    % initial increment limit proc for
+    0 yaxis_minor_tic_interval yaxis_scale abs 
+    {/loopnumber2 exch def
+      gsave
+        0
+        loopnumber2 stack_height yaxis_scale div mul 
+        rmoveto 
+
+        tic_length 2 div neg 0 rlineto
+        stroke
+     grestore
+    } for    
+    
+  grestore
+} bind def
+
+/DrawYaxisLabel {
+  gsave
+    SetStringFont
+
+    % How far we move left depends on the size of
+    % the tic labels.
+    /str 10 string def % string to hold number  
+    yaxis_scale yaxis_tic_interval div cvi yaxis_tic_interval mul 
+    str cvs stringwidth pop
+    tic_length 1.25 mul  add neg  
+
+    stack_height
+    yaxis_label stringwidth pop
+    sub 2 div
+
+    rmoveto
+    90 rotate
+    
+    yaxis_label show
+  grestore
+} bind def
+
+
+%Take a single character and return the bounding box
+/CharBox { % <char> CharBox <lx> <ly> <ux> <uy>
+  gsave
+    newpath
+    0 0 moveto
+    % take the character off the stack and use it here:
+    true charpath 
+    flattenpath 
+    pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
+    % the path is here, but toss it away ...
+  grestore
+} bind def
+
+
+% The height of a characters bounding box
+/CharBoxHeight { % <char> CharBoxHeight <num>
+  CharBox
+  exch pop sub neg exch pop
+} bind def
+
+
+% The width of a characters bounding box
+/CharBoxWidth { % <char> CharBoxHeight <num>
+  CharBox
+  pop exch pop sub neg 
+} bind def
+
+
+/DrawLeftEnd {
+  gsave
+    SetStringFont
+    leftEndDeltaX leftEndDeltaY rmoveto
+    
+    show_ends {
+        debug { leftEndDeltaY neg leftEndDeltaX neg DrawBox } if
+        end_type (d) eq {(5) show DrawPrime} if
+        end_type (p) eq {(N) show} if
+    } if
+  grestore
+} bind def
+
+/DrawRightEnd { 
+  gsave
+    SetStringFont
+    rightEndDeltaX rightEndDeltaY rmoveto
+    
+    show_ends {
+        debug { rightEndDeltaY neg leftEndDeltaX neg  DrawBox } if
+        end_type (d) eq {(3) show DrawPrime} if
+        end_type (p) eq {(C) show} if
+    } if
+  grestore
+} bind def
+
+/DrawPrime {
+  gsave
+    SetPrimeFont
+    (\242) show 
+  grestore
+} bind def
+
+
+/StartStack {  % <stackNumber> startstack
+  show_xaxis {DrawNumber}{pop} ifelse
+  gsave
+  debug { stack_height stack_width DrawBox } if
+    
+} bind def
+
+/EndStack {
+  grestore
+  stack_width 0 rmoveto
+} bind def
+
+
+/DrawNumber { % number MakeNumber
+    /n exch def
+    
+    
+  gsave
+    %0 stack_margin neg rmoveto
+    stroke_width setlinewidth
+    stack_width  0 rlineto
+    stack_width 2 div neg 0 rmoveto
+    
+    n () eq 
+    {  0 tic_length 4 div neg rlineto  } 
+    { 0 tic_length 2 div neg rlineto } 
+    ifelse
+
+    stroke
+  grestore   
+
+
+
+  gsave
+    n
+    SetNumberFont
+    stack_width 2 div tic_length 2 div neg rmoveto 
+
+    rotate_numbers {
+        90 rotate     
+        dup stringwidth pop neg % find the length of the number
+        stack_margin sub        % Move down a bit
+        (0) CharBoxHeight 2 div neg % left half height of numbers
+        rmoveto 
+        show
+    } {
+        dup stringwidth pop neg 2 div number_fontsize neg  rmoveto
+        show
+    } ifelse
+    
+    
+
+  grestore
+} bind def
+
+
+
+% Draw a character whose height is proportional to symbol bits
+/ShowSymbol{ % interval character ShowSymbol
+    /char exch def
+    /interval exch def
+    /fraction_width exch def
+    
+    /char_height 
+       interval yaxis_scale div stack_height mul
+       stack_margin sub
+       dup 
+       % if char_height is negative or very small replace with zero 
+       % BUG FIX: This used to be '0.0 gt' but it seems that DrawHeight
+       % has a finite, non-zero minimum, which results in a rangecheck error
+       0.01 gt {}{pop 0.0} ifelse 
+    def 
+
+    char_height 0.0 gt {
+        show_boxes {
+            gsave
+                /ww char_height stack_margin add def
+                /hh stack_width def
+                stroke_width setlinewidth
+                hh 0 rlineto
+                0 ww rlineto
+                hh neg 0 rlineto
+                0 ww neg rlineto
+                stroke
+            grestore     
+        } if
+
+        gsave
+            stack_margin stack_margin rmoveto
+            debug { char_height char_width DrawBox } if
+            1 fraction_width sub char_width mul 2 div  0 rmoveto
+            fraction_width char_width mul char_height char DrawChar
+        grestore
+        
+    } if
+    0 interval yaxis_scale div stack_height mul rmoveto
+} bind def
+
+
+/DrawChar { % <width> <height> <char> ShowChar
+    /tc exch def    % The character
+    /ysize exch def % the y size of the character
+    /xsize exch def % the x size of the character
+    /xmulfactor 1 def 
+    /ymulfactor 1 def
+    
+    gsave
+        SetLogoFont    
+        tc SetColor
+
+        % IReplacementHack
+        % Deal with the lack of bars on the letter 'I' in Arial and Helvetica
+        % by replacing with 'I' from Courier.
+        tc (I) eq {
+            /Courier findfont char_width  scalefont setfont    
+        } if
+
+
+        shrink {
+            xsize 1 shrink_fraction sub 2 div mul
+            ysize 1 shrink_fraction sub 2 div mul rmoveto 
+            shrink_fraction shrink_fraction scale
+        } if
+        
+        % Calculate the font scaling factors
+        % Loop twice to catch small correction due to first scaling
+        2 {
+            gsave
+            xmulfactor ymulfactor scale
+      
+            ysize % desired size of character in points
+            tc CharBoxHeight 
+            dup 0.0 ne {
+                div % factor by which to scale up the character
+                /ymulfactor exch def
+            } {pop pop} ifelse
+
+            xsize % desired size of character in points
+            tc CharBoxWidth  
+            dup 0.0 ne {
+                div % factor by which to scale up the character
+                /xmulfactor exch def
+            } {pop pop} ifelse
+            grestore
+        } repeat
+
+
+  
+        % Draw the character
+        xmulfactor ymulfactor scale
+        % Move lower left corner of character to start point
+        tc CharBox pop pop % llx lly : Lower left corner
+        exch neg exch neg
+        rmoveto
+        
+        tc show    
+
+    grestore
+} bind def
+
+/SetColor{ % <char> SetColor
+  dup color_dict exch known {
+    color_dict exch get aload pop setrgbcolor
+  } {
+    pop
+    default_color aload pop setrgbcolor
+  } ifelse 
+} bind def
+
+
+/DrawErrorbar{ % interval_down interval_up DrawErrorbar
+    
+    gsave
+    /points_per_unit stack_height yaxis_scale div def 
+    /height_up   exch points_per_unit mul def 
+    /height_down exch points_per_unit mul def
+    
+    show_errorbars {
+    
+    stroke_width setlinewidth
+    errorbar_gray setgray     
+    stack_width 2 div 0 rmoveto
+    
+    /errorbar_width char_width errorbar_width_fraction mul def
+    /errorbar_width2 errorbar_width 2 div def
+    
+    gsave 
+        0 height_down neg rmoveto
+        errorbar_width2 neg 0 rlineto
+        errorbar_width 0 rlineto
+        errorbar_width2 neg 0 rlineto
+        0 height_down errorbar_fraction mul rlineto 
+        stroke
+    grestore
+
+    gsave 
+        0 height_up  rmoveto
+        errorbar_width2 neg 0 rlineto
+        errorbar_width 0 rlineto
+        errorbar_width2 neg 0 rlineto
+        0 height_up neg errorbar_fraction mul rlineto 
+        stroke
+    grestore
+    } if
+           
+    grestore
+    
+} bind def
+
+/DrawErrorbarFirst{ % interval_down interval_up center DrawErrorbarFirst
+    gsave
+    /points_per_unit stack_height yaxis_scale div def 
+    /center   exch points_per_unit mul def 
+
+    0 center rmoveto
+    DrawErrorbar
+    grestore
+} bind def
+
+%%EndProlog
+
+%%Page: 1 1
+
+% Example Data
+%StartLogo
+%    StartLine
+%        (1) StartStack
+%            1.2 (C) ShowSymbol
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+EndLogo
+
+
+%%EOF
+
diff -r f3462128e87c -r 20716450be87 weblogolib/__init__.py
--- a/weblogolib/__init__.py	Mon Jan 30 08:17:57 2012 -0500
+++ b/weblogolib/__init__.py	Mon Jan 30 21:17:50 2012 -0500
@@ -983,11 +983,20 @@
         prior = weight * equiprobable_distribution(len(alphabet)) 
         
     elif comp.lower() == 'escherichiacoli' :
-	composition="{'CTT': 0.7616, 'ATG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'ATC': 1.1648, 'AAC': 1.5615999999999999, 'ATA': 0.2368, 'AGG': 0.1024, 'CCT': 0.5376000000000001, 'ACT': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAT': 1.0112, 'AAT': 1.4016, 'ATT': 1.952, 'CTG': 3.0016, 'CTA': 0.3392, 'CTC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGT': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'TAT': 1.0752000000000002, 'GGT': 1.3632, 'TGT': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'TCT': 0.3648, 'GAT': 2.4255999999999998, 'CGG': 0.26239999999999997, 'TTT': 1.2608, 'TGC': 0.512, 'GGG': 0.5504, 'TAG': 1e-06, 'GGA': 0.5888, 'TAA': 0.1152, 'GGC': 2.1376, 'TAC': 0.9344, 'TTC': 0.96, 'TCG': 0.512, 'TTA': 0.9728, 'TTG': 0.7616, 'TCC': 0.352, 'ACC': 1.4592, 'TCA': 0.4992, 'GCA': 1.3504, 'GTA': 0.736, 'GCC': 2.0224, 'GTC': 0.7487999999999999, 'GCG': 2.464, 'GTG': 1.6896, 'GAG': 1.1776, 'GTT': 1.0752000000000002, 'GCT': 0.6848, 'TGA': 0.064, 'GAC': 1.312, 'CGT': 1.3504, 'TGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}"
+      if(altype=="codonsT"):
+        composition="{'CTT': 0.7616, 'ATG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'ATC': 1.1648, 'AAC': 1.5615999999999999, 'ATA': 0.2368, 'AGG': 0.1024, 'CCT': 0.5376000000000001, 'ACT': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAT': 1.0112, 'AAT': 1.4016, 'ATT': 1.952, 'CTG': 3.0016, 'CTA': 0.3392, 'CTC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGT': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'TAT': 1.0752000000000002, 'GGT': 1.3632, 'TGT': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'TCT': 0.3648, 'GAT': 2.4255999999999998, 'CGG': 0.26239999999999997, 'TTT': 1.2608, 'TGC': 0.512, 'GGG': 0.5504, 'TAG': 1e-06, 'GGA': 0.5888, 'TAA': 0.1152, 'GGC': 2.1376, 'TAC': 0.9344, 'TTC': 0.96, 'TCG': 0.512, 'TTA': 0.9728, 'TTG': 0.7616, 'TCC': 0.352, 'ACC': 1.4592, 'TCA': 0.4992, 'GCA': 1.3504, 'GTA': 0.736, 'GCC': 2.0224, 'GTC': 0.7487999999999999, 'GCG': 2.464, 'GTG': 1.6896, 'GAG': 1.1776, 'GTT': 1.0752000000000002, 'GCT': 0.6848, 'TGA': 0.064, 'GAC': 1.312, 'CGT': 1.3504, 'TGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}"
+      else:
+        composition="{'CUU': 0.7616, 'AUG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'AUC': 1.1648, 'AAC': 1.5615999999999999, 'AUA': 0.2368, 'AGG': 0.1024, 'CCU': 0.5376000000000001, 'ACU': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAU': 1.0112, 'AAU': 1.4016, 'AUU': 1.952, 'CUG': 3.0016, 'CUA': 0.3392, 'CUC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGU': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'UAU': 1.0752000000000002, 'GGU': 1.3632, 'UGU': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'UCU': 0.3648, 'GAU': 2.4255999999999998, 'CGG': 0.26239999999999997, 'UUU': 1.2608, 'UGC': 0.512, 'GGG': 0.5504, 'UAG': 1e-06, 'GGA': 0.5888, 'UAA': 0.1152, 'GGC': 2.1376, 'UAC': 0.9344, 'UUC': 0.96, 'UCG': 0.512, 'UUA': 0.9728, 'UUG': 0.7616, 'UCC': 0.352, 'ACC': 1.4592, 'UCA': 0.4992, 'GCA': 1.3504, 'GUA': 0.736, 'GCC': 2.0224, 'GUC': 0.7487999999999999, 'GCG': 2.464, 'GUG': 1.6896, 'GAG': 1.1776, 'GUU': 1.0752000000000002, 'GCU': 0.6848, 'UGA': 0.064, 'GAC': 1.312, 'CGU': 1.3504, 'UGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}"
     elif comp.lower() == 'homosapiens' :
-	composition="{'CTT': 0.8448, 'ATG': 1.408, 'ACA': 0.9663999999999999, 'ACG': 0.39039999999999997, 'ATC': 1.3312, 'AAC': 1.2224000000000002, 'ATA': 0.48, 'AGG': 0.768, 'CCT': 1.12, 'ACT': 0.8383999999999999, 'AGC': 1.248, 'AAG': 2.0416, 'AGA': 0.7807999999999999, 'CAT': 0.6976, 'AAT': 1.088, 'ATT': 1.024, 'CTG': 2.5344, 'CTA': 0.4608, 'CTC': 1.2544000000000002, 'CAC': 0.9663999999999999, 'AAA': 1.5615999999999999, 'CCG': 0.44160000000000005, 'AGT': 0.7744, 'CCA': 1.0816, 'CAA': 0.7872, 'CCC': 1.2672, 'TAT': 0.7807999999999999, 'GGT': 0.6912, 'TGT': 0.6784, 'CGA': 0.3968, 'CAG': 2.1888, 'TCT': 0.9728, 'GAT': 1.3952, 'CGG': 0.7296, 'TTT': 1.1264, 'TGC': 0.8064, 'GGG': 1.056, 'TAG': 0.0512, 'GGA': 1.056, 'TAA': 0.064, 'GGC': 1.4208, 'TAC': 0.9792000000000001, 'TTC': 1.2992000000000001, 'TCG': 0.2816, 'TTA': 0.4928, 'TTG': 0.8256, 'TCC': 1.1328, 'ACC': 1.2096, 'TCA': 0.7807999999999999, 'GCA': 1.0112, 'GTA': 0.45439999999999997, 'GCC': 1.7728, 'GTC': 0.928, 'GCG': 0.4736, 'GTG': 1.7984, 'GAG': 2.5344, 'GTT': 0.704, 'GCT': 1.1776, 'TGA': 0.1024, 'GAC': 1.6064, 'CGT': 0.288, 'TGG': 0.8448, 'GAA': 1.856, 'CGC': 0.6656}"
-    elif comp.lower() == 'saccharomycescerevisiae' :
-	composition="{'CTT': 0.7872, 'ATG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'ATC': 1.1008, 'AAC': 1.5872, 'ATA': 1.1392, 'AGG': 0.5888, 'CCT': 0.864, 'ACT': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAT': 0.8704, 'AAT': 2.2848, 'ATT': 1.9264000000000001, 'CTG': 0.672, 'CTA': 0.8576, 'CTC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGT': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'TAT': 1.2032, 'GGT': 1.5295999999999998, 'TGT': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'TCT': 1.504, 'GAT': 2.4064, 'CGG': 0.1088, 'TTT': 1.6704, 'TGC': 0.3072, 'GGG': 0.384, 'TAG': 0.032, 'GGA': 0.6976, 'TAA': 0.0704, 'GGC': 0.6272000000000001, 'TAC': 0.9472, 'TTC': 1.1776, 'TCG': 0.5504, 'TTA': 1.6767999999999998, 'TTG': 1.7408, 'TCC': 0.9087999999999999, 'ACC': 0.8128, 'TCA': 1.1967999999999999, 'GCA': 1.0368, 'GTA': 0.7552000000000001, 'GCC': 0.8064, 'GTC': 0.7552000000000001, 'GCG': 0.3968, 'GTG': 0.6912, 'GAG': 1.2288, 'GTT': 1.4144, 'GCT': 1.3568, 'TGA': 0.0448, 'GAC': 1.2928, 'CGT': 0.4096, 'TGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}"
+      if(altype=="codonsT"):
+        composition="{'CTT': 0.8448, 'ATG': 1.408, 'ACA': 0.9663999999999999, 'ACG': 0.39039999999999997, 'ATC': 1.3312, 'AAC': 1.2224000000000002, 'ATA': 0.48, 'AGG': 0.768, 'CCT': 1.12, 'ACT': 0.8383999999999999, 'AGC': 1.248, 'AAG': 2.0416, 'AGA': 0.7807999999999999, 'CAT': 0.6976, 'AAT': 1.088, 'ATT': 1.024, 'CTG': 2.5344, 'CTA': 0.4608, 'CTC': 1.2544000000000002, 'CAC': 0.9663999999999999, 'AAA': 1.5615999999999999, 'CCG': 0.44160000000000005, 'AGT': 0.7744, 'CCA': 1.0816, 'CAA': 0.7872, 'CCC': 1.2672, 'TAT': 0.7807999999999999, 'GGT': 0.6912, 'TGT': 0.6784, 'CGA': 0.3968, 'CAG': 2.1888, 'TCT': 0.9728, 'GAT': 1.3952, 'CGG': 0.7296, 'TTT': 1.1264, 'TGC': 0.8064, 'GGG': 1.056, 'TAG': 0.0512, 'GGA': 1.056, 'TAA': 0.064, 'GGC': 1.4208, 'TAC': 0.9792000000000001, 'TTC': 1.2992000000000001, 'TCG': 0.2816, 'TTA': 0.4928, 'TTG': 0.8256, 'TCC': 1.1328, 'ACC': 1.2096, 'TCA': 0.7807999999999999, 'GCA': 1.0112, 'GTA': 0.45439999999999997, 'GCC': 1.7728, 'GTC': 0.928, 'GCG': 0.4736, 'GTG': 1.7984, 'GAG': 2.5344, 'GTT': 0.704, 'GCT': 1.1776, 'TGA': 0.1024, 'GAC': 1.6064, 'CGT': 0.288, 'TGG': 0.8448, 'GAA': 1.856, 'CGC': 0.6656}"
+      else:
+        composition="{'CUU': 0.8448, 'AUG': 1.408, 'ACA': 0.9663999999999999, 'ACG': 0.39039999999999997, 'AUC': 1.3312, 'AAC': 1.2224000000000002, 'AUA': 0.48, 'AGG': 0.768, 'CCU': 1.12, 'ACU': 0.8383999999999999, 'AGC': 1.248, 'AAG': 2.0416, 'AGA': 0.7807999999999999, 'CAU': 0.6976, 'AAU': 1.088, 'AUU': 1.024, 'CUG': 2.5344, 'CUA': 0.4608, 'CUC': 1.2544000000000002, 'CAC': 0.9663999999999999, 'AAA': 1.5615999999999999, 'CCG': 0.44160000000000005, 'AGU': 0.7744, 'CCA': 1.0816, 'CAA': 0.7872, 'CCC': 1.2672, 'UAU': 0.7807999999999999, 'GGU': 0.6912, 'UGU': 0.6784, 'CGA': 0.3968, 'CAG': 2.1888, 'UCU': 0.9728, 'GAU': 1.3952, 'CGG': 0.7296, 'UUU': 1.1264, 'UGC': 0.8064, 'GGG': 1.056, 'UAG': 0.0512, 'GGA': 1.056, 'UAA': 0.064, 'GGC': 1.4208, 'UAC': 0.9792000000000001, 'UUC': 1.2992000000000001, 'UCG': 0.2816, 'UUA': 0.4928, 'UUG': 0.8256, 'UCC': 1.1328, 'ACC': 1.2096, 'UCA': 0.7807999999999999, 'GCA': 1.0112, 'GUA': 0.45439999999999997, 'GCC': 1.7728, 'GUC': 0.928, 'GCG': 0.4736, 'GUG': 1.7984, 'GAG': 2.5344, 'GUU': 0.704, 'GCU': 1.1776, 'UGA': 0.1024, 'GAC': 1.6064, 'CGU': 0.288, 'UGG': 0.8448, 'GAA': 1.856, 'CGC': 0.6656}"
+    elif comp.lower() == 'saccharomycescerevisiae' :      
+      if(altype=="codonsT"):
+        composition="{'CTT': 0.7872, 'ATG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'ATC': 1.1008, 'AAC': 1.5872, 'ATA': 1.1392, 'AGG': 0.5888, 'CCT': 0.864, 'ACT': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAT': 0.8704, 'AAT': 2.2848, 'ATT': 1.9264000000000001, 'CTG': 0.672, 'CTA': 0.8576, 'CTC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGT': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'TAT': 1.2032, 'GGT': 1.5295999999999998, 'TGT': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'TCT': 1.504, 'GAT': 2.4064, 'CGG': 0.1088, 'TTT': 1.6704, 'TGC': 0.3072, 'GGG': 0.384, 'TAG': 0.032, 'GGA': 0.6976, 'TAA': 0.0704, 'GGC': 0.6272000000000001, 'TAC': 0.9472, 'TTC': 1.1776, 'TCG': 0.5504, 'TTA': 1.6767999999999998, 'TTG': 1.7408, 'TCC': 0.9087999999999999, 'ACC': 0.8128, 'TCA': 1.1967999999999999, 'GCA': 1.0368, 'GTA': 0.7552000000000001, 'GCC': 0.8064, 'GTC': 0.7552000000000001, 'GCG': 0.3968, 'GTG': 0.6912, 'GAG': 1.2288, 'GTT': 1.4144, 'GCT': 1.3568, 'TGA': 0.0448, 'GAC': 1.2928, 'CGT': 0.4096, 'TGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}"
+      else:
+        composition="{'CUU': 0.7872, 'AUG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'AUC': 1.1008, 'AAC': 1.5872, 'AUA': 1.1392, 'AGG': 0.5888, 'CCU': 0.864, 'ACU': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAU': 0.8704, 'AAU': 2.2848, 'AUU': 1.9264000000000001, 'CUG': 0.672, 'CUA': 0.8576, 'CUC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGU': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'UAU': 1.2032, 'GGU': 1.5295999999999998, 'UGU': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'UCU': 1.504, 'GAU': 2.4064, 'CGG': 0.1088, 'UUU': 1.6704, 'UGC': 0.3072, 'GGG': 0.384, 'UAG': 0.032, 'GGA': 0.6976, 'UAA': 0.0704, 'GGC': 0.6272000000000001, 'UAC': 0.9472, 'UUC': 1.1776, 'UCG': 0.5504, 'UUA': 1.6767999999999998, 'UUG': 1.7408, 'UCC': 0.9087999999999999, 'ACC': 0.8128, 'UCA': 1.1967999999999999, 'GCA': 1.0368, 'GUA': 0.7552000000000001, 'GCC': 0.8064, 'GUC': 0.7552000000000001, 'GCG': 0.3968, 'GUG': 0.6912, 'GAG': 1.2288, 'GUU': 1.4144, 'GCU': 1.3568, 'UGA': 0.0448, 'GAC': 1.2928, 'CGU': 0.4096, 'UGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}"
     elif comp.lower() == 'auto' or comp.lower() == 'automatic':
         if alphabet == unambiguous_protein_alphabet :
             prior =  weight * asarray(aa_composition, float64)
@@ -1002,7 +1011,7 @@
     elif isfloat(comp) :
         prior = weight * base_distribution( float(comp)*100. )
 
-    elif composition[0] == '{' and composition[-1] == '}' : 
+    if composition[0] == '{' and composition[-1] == '}' : 
         explicit = composition[1: -1]
         explicit = explicit.replace(',',' ').replace("'", ' ').replace('"',' ').replace(':', ' ').split()