BSML Bioinformatic Sequence Markup Language
From: http://www.topogen.com/sbir/bsml.dtd, 980113
<!-- ******************************************************************** -->
<!--                BSML Bioinformatic Sequence Markup Language           -->
<!--                DTD Outline - Dec. 1, 1997 - Version 0.1              -->
<!--                                                                      -->
<!-- Note: This is an abbreviated, non-working, annotated version of      -->
<!-- the DTD that omits attribute lists for many elements                 -->
<!--                                                                      -->
<!-- To understand this document you should be somewhat familiar with     -->
     XML/SGML specifications, at least as described in rfc.html           -->
<!--                                                                      -->
<!-- ******************************************************************** -->
<!--                                                                      -->
<!-- ***************************** Units of Distance ********************

     Locations on the page and distances such as line lengths are specified in
     terms of horizontal and vertical coordinates, expressed as a %length
     attribute value. Distance and location may use a variety of measures:

     o px = pixels
     o %  = percentage of the page width or length
     o cm = centimeters
     o in = inches

     The default measurement unit is set in an attribute of the Display element,
     (e.g., default-unit="cm"). This unit is supplied if no unit is specified
     (e.g.,hloc="10").

     It is permissible to specify horizontal and vertical coordinates
     in different dimension units, e.g., hloc="10.2cm" vloc="20%".

     If a length is followed by "+id:", the value is taken from the location
     (horizontal or vertical) of the corresponding object. For example,
     if a sequence line with id="SEQ1" has a horizontal offset of 300 pixels,
     a horizontal length of "20px+id:SEQ1" sets the value to 320 pixels.
-->
<!-- *************************** Units of Line Width ********************

     Line width is specified in an attribute with the value %linewidth,
     which may be expressed as a relative or absolute value, or using
     one of a set of enumerated values:

     o Absolute value units include pixels (px), inches (in) and
       centimeters (cm), e.g.,line-width="0.01in".
     o Relative values are stated without units as values between +1 (thinnest)
       and +7 (thickest). The value of the thinnest line is specified as an
       attribute of the Display element (e.g.,base-line-width="0.01in"). The
       increment applied from one step to another is specified as an attribute
       of the Display element (e.g.,base-line-inc="0.005in"). Thus the absolute
       width of a relative value is calculated by adding a multiple of the
       base-line-inc to the base-line-width, e.g.,
       +3=base-line-width+2*base-line-inc.
     o Enumerated values selected from "thin","medium","thick", which
       correspond to relative values of 1, 2, and 4, respectively.
-->
<!-- ************************* Colors (from HTML 4.0) *******************

    The attribute value type "color" (%color) refers to color definitions as
    specified for HTML. A color value may either be a hexadecimal number
    (prefixed by a # hash mark) or one of the following sixteen color names:

                         Color names and sRGB values

             Black = "#000000"              Green = "#008000"
             Silver = "#C0C0C0"             Lime = "#00FF00"
             Gray = "#808080"               Olive = "#808000"
             White = "#FFFFFF"              Yellow = "#FFFF00"
             Maroon = "#800000"             Navy = "#000080"
             Red = "#FF0000"                Blue = "#0000FF"
             Purple = "#800080"             Teal = "#008080"
             Fuchsia = "#FF00FF"            Aqua = "#00FFFF"

    Thus, the color values "#800080" and "Purple" both refer to the color
    purple.
-->
<!-- ****************************** Fonts *********************** -->
<!--
    BSML uses a modified version of the HTML 4.0 font element. Fonts
    are described by their face, color, size (pts), and style (bold,italics).
    Fonts may refer to base fonts and specify only attributes that they
    wish to change. Display objects refer to a specific font
    or use default fonts assigned for particular types of text.
-->
<!-- ************************* Sequence Units ******************* -->
<!--
   Each sequence specifies its unit of measurement as one of the following:

   o bp = base pairs for a nucleotide (DNA or RNA) sequence.
   o aa = amino acids = number of resides for a protein sequence.
   o cM = centiMorgans = mu (map units) for genetic maps.
   o %  = percentage for a sequence with its complete length expressed as 100%

   Internally, the length of every sequence is expressed as a positive integer.
   For display purposes, a position on the sequence may be expressed in one
   of two ways:

   o A relative base/residue number computed by using an offset for the first
     base/residue and a direction of counting (e.g., if rel-base="100" and
     ascending="true", the second base is reported as "101"). There is no base
     0 when a relative basis is used.
     
   o A linear transformation rule specifying the reported value as a slope and
     intercept along with the number of decimal places to be reported. For
     example, if intercept="10.0", slope="2.0", and decimals="2", the 11th base
     is reported as "30.00" = 10.0 + 2.0 * (11-1).
-->
<!-- **************************************************** -->
<!--        General Parameter Entity Definitions          -->
<!--
     Note: parameter entities are used as simple macros:
           their values (quoted) simply replace their
           names when they are used as elements or
           attribute values. The use of parameter entities
           clarifies and simplifies expression of the DTD.
-->
<!-- **************************************************** -->
<!ENTITY % yesorno "CDATA"   -- boolean as 1=true|0=false -->
<!ENTITY % yes "1"           -- 1 = true                  -->
<!ENTITY % no "0"            -- 0 = false                 -->
<!ENTITY % integer "CDATA"   -- positive or negative int  -->
<!ENTITY % real "CDATA"      -- positive or negative real -->
<!ENTITY % length "CDATA" -- various line length units    -->
<!ENTITY % linewidth "CDATA" -- line width alternates     -->
<!ENTITY % linestyle "(solid,dash,dot,none)"                >
<!ENTITY % displayshape
                  "(ellipse,rectangle,roundrectangle)"      >
<!--                                                      -->
<!--               adapted from html 4.0                  -->
<!--                                                      -->
<!ENTITY % color "CDATA"          -- as name or RGB value -->
<!ENTITY % contenttype "CDATA"               --media type -->
<!ENTITY % character "CDATA"            -- one character  -->
<!ENTITY % mediadesc "CDATA" -- single or comma-separated
                             list of media descriptors    -->
<!ENTITY % url "CDATA"      -- a Uniform Resource Locator -->
<!ENTITY % datetime "CDATA" -- date,time  ISO date format -->
<!ENTITY % date     "CDATA" -- date,time  ISO date format -->
<!ENTITY % script "CDATA"            -- script expression -->
<!ENTITY % text "CDATA"                -- render as CDATA -->
<!ENTITY % shape "(rect|circle|poly|default)"               >
<!ENTITY % coords "CDATA"    -- comma sep list of numbers -->
<!ENTITY % frametarget "CDATA"    -- render in this frame -->

<!--       apply mainattrs to all major elements          -->

<!ENTITY % mainattrs
 "id          ID         #IMPLIED  -- document-wide unique id --
  class       CDATA      #IMPLIED  -- space separated list of classes --
  style       CDATA      #IMPLIED  -- associated style info --
  title       CDATA      #IMPLIED  -- displayable title --
  comment     CDATA      #IMPLIED  -- rest added for BSML --
  value-type  CDATA      #IMPLIED  -- optional value description --
  value       CDATA      #IMPLIED  -- optional data value(s) --
  selected    %yesorno;  %yes;     -- element is selected --
  display     %yesorno;  %yes;     -- show element --
  readonly    %yesorno;  %no;      -- allow editing if false --"
>

<!--   uses events to define actions when element selected        -->

<!ENTITY % events
 "onclick     %script;   #IMPLIED -- pointer was clicked          --
  ondblclick  %script;   #IMPLIED -- pointer was double clicked   --
  onmousedown %script;   #IMPLIED -- pointer was pressed down     --
  onmouseup   %script;   #IMPLIED -- pointer was released         --
  onmouseover %script;   #IMPLIED -- pointer was moved onto       --
  onmousemove %script;   #IMPLIED -- pointer was moved within     --
  onmouseout  %script;   #IMPLIED -- pointer was moved away       --
  onkeypress  %script;   #IMPLIED -- key was pressed and released --
  onkeydown   %script;   #IMPLIED -- key was pressed down         --
  onkeyup     %script;   #IMPLIED -- key was released             --"
>

<!ENTITY % attrs "%mainattrs; %events;"   -- full attribute set   -->

<!-- ************************************************************ -->
<!--                       Major BSML Divisions                   -->
<!-- ************************************************************ -->
<!--
     BSML documents are divided into two sections:

       1. Definitions: Sequences and their features,
                       Sets of sequences or features,
                       and Tables of data associated with
                       sequences.

       2. Display: Page-oriented displays of sequence Views and sets.
-->
<!ELEMENT Bsml                 - - (Definitions?,Display?)          >
<!-- ************************************************************ -->
<!--                     Definitions Element                      -->
<!-- ************************************************************ -->
<!ELEMENT Definitions          - - (Sequences?,
                                    Sets?,
                                    Tables?)                        >
<!-- ************************************************************ -->
<!--                    Definitions Subelements                   -->
<!-- ************************************************************ -->
<!--
     Sequences include and number of direct representations of Sequence
     elements or indirect references to Sequence-import elements
-->
<!ELEMENT Sequences            - - (Sequence|Sequence-import)*      >
<!ATTLIST Sequences
            %attrs;                             -- attributes     -->

<!--
    Sets include any number of Set elements
-->
<!ELEMENT Sets                 - - (Set*)            --  any set  -->
<!ATTLIST Sets
            %attrs;                             -- attributes     -->
<!--
    Tables include any number of Table or Table-import elements
-->
<!ELEMENT Tables               - - (Table|Table-import)* -- data  -->
<!ATTLIST Tables
            %attrs;                             -- attributes     -->
            
<!-- ************************************************************ -->
<!--                    Sequences Elements                        -->
<!-- ************************************************************ -->
<!--
     The Sequences element contains any number of Sequence
     or Sequence-import elements.
-->
<!-- ************************************************************ -->
<!--                     Sequence-import                          -->
<!-- ************************************************************ -->
<!--
     A Sequence-import element specifies the source of the import as
     well as the type of file format; formats will expand
     as the standard is implemented.
-->
<!ELEMENT Sequence-import - - EMPTY     -- imported from file     -->
<!ATTLIST Sequence-import
            type   (bsml,asn1,genbank,embl,gsdb) "bsml" -- format --
            source    %url;   #REQUIRED        -- file name, etc. --
            identifier CDATA  #IMPLIED
                  -- identifier selects one sequence from a set;
                     if a bsml import, identifier = id
                     if other, identifier = primary accession key -->
<!-- *************************************************************-->
<!--                        Sequence Element                      -->
<!-- ************************************************************ -->
<!--
     A Sequence element may be virtual (no data), may contain
     its own data, or may refer to a number of other sequences.
     A Sequence may contain any number of Feature-tables.
-->
<!ELEMENT Sequence             - - ((Seq-data?|Sequence-piece*),
                                    Source*,Numbering?,
                                    Feature-tables?)                >
<!ATTLIST Sequence
            %attrs;                                                 >
<!-- *************************************************************-->
<!--                     Sequence-piece Element                   -->
<!-- ************************************************************ -->
<!--
     A Sequence-piece element is used by a Sequence element
     that consists of a number of other Sequence elements.
-->
<!ELEMENT Sequence-piece       - - EMPTY  -- for discontig seqs   -->
<!ATTLIST Sequence-piece
            %attrs;
            sp-id              IDREF     #REQUIRED -- sequence    -->
<!-- ************************************************************ -->
<!--                          Source Element                      -->
<!-- ************************************************************ -->
<!--
     A Source element provides descriptive information about
     all or part of the sequence.
-->
<!ELEMENT Source               - - EMPTY                            >
<!ATTLIST Source
          %attrs;                                                   >
<!-- *************************************************************-->
<!--                      Seq-data Element                        -->
<!-- ************************************************************ -->
<!ELEMENT Seq-data              - - (#PCDATA)                       >
<!ATTLIST Seq-data
            a-count     %integer; #IMPLIED
            c-count     %integer; #IMPLIED
            g-count     %integer; #IMPLIED
            t-count     %integer; #IMPLIED
            other-count %integer; #IMPLIED
            total-count %integer; #IMPLIED>
<!-- *************************************************************-->
<!--                        Sequence Numbering                    -->
<!-- ************************************************************ -->
<!--
  Numbering element is used to define a relative numbering basis
-->
<!ELEMENT Numbering       - - EMPTY                                 >
<!-- ************************************************************ -->
<!--                      Feature-tables Element                  -->
<!-- ************************************************************ -->
<!--
     Each Sequence may have any number of Feature-table elements
-->
<!ELEMENT Feature-tables       - - (Feature-table*)                 >
<!ATTLIST Feature-tables
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                       Feature-table Element                  -->
<!-- ************************************************************ -->
<!--
     Each Feature-table may be marked as temporary.
-->
<!ELEMENT Feature-table        - - (Feature*)                       >
<!ATTLIST Feature-table
            %attrs;
            temporary %yesorno;     %no; -- do not save if temp   -->
<!-- ************************************************************ -->
<!--                          Feature Element                     -->
<!-- ************************************************************ -->
<!--
     Each Feature-table contains any number of Feature elements,
     each of which contains any number of Qualifier and Location
     elements.

     The %featuretype entity defines a list of types for Feature
     elements (e.g., coding-region).
-->
<!ENTITY % featuretype "(feature-type-list)">

<!ELEMENT Feature              - - (%location;|Qualifier)*          >
<!ATTLIST Feature
            %attrs;
            type      %featuretype #REQUIRED                        >                                                >
<!-- *************************************************************-->
<!--                        Location Element                      -->
<!-- ************************************************************ -->
<!--
    The %location entity refers to a variety of ways of defining a
    Location of a Feature on a Sequence, as implemented in the NCBI
    and NCGR standards. In the case of nucleotide sequences,
    the Location indicates whether the position is on the
    complementary strand.
-->

<!ENTITY % location "(location-list)">
<!ELEMENT Location-list     -  - EMPTY  -- dummy location element -->

<!-- *************************************************************-->
<!--                        Qualifier Element                     -->
<!-- ************************************************************ -->
<!--
    Qualifiers indicate characteristics of Feature elements
    by a type (e.g., gene) and an optional value (e.g.,tetR).
    The %qualifiertype entity defines a list of possible values.
-->
<!ENTITY % qualifiertype "(qualifier-type-list)">

<!ELEMENT Qualifier          - - EMPTY                              >
<!ATTLIST Qualifier
            %attrs;
            type  %qualifiertype; #REQUIRED
            qual-value CDATA      #IMPLIED>

<!-- ************************************************************ -->
<!--                      Set Element                             -->
<!-- ************************************************************ -->
<!--
     A Set in a basic flat or hierarchical structure composed of
     any grouping of elements by id using idrefs, including other
     Set elements.
-->
<!ELEMENT Set                  - - EMPTY                            >
<!ATTLIST Set
            %attrs;
            idrefs          IDREFS        #REQUIRED -- set members-->

<!-- ************************************************************ -->
<!--                      Table-import Definition                 -->
<!-- ************************************************************ -->
<!--
     A Table-import element reads tabular data from an
     external source that uses an acceptable format.
-->
<!ELEMENT Table-import         - - EMPTY -- external file format  -->
<!ATTLIST Table-import
            %attrs;
            format (bsml,html,dif) "bsml"
            source  %url;          #REQUIRED                        >
<!-- ************************************************************ -->
<!--                           Table                              -->
<!-- ************************************************************ -->
<!--
     IETF HTML table standard. Full definition not included here.
-->

<!ELEMENT Table - -
     (Caption?, (Col*|Colgroup*), Thead?, Tfoot?, Tbody+)>
<!ELEMENT Caption  - - (#PCDATA)   -- table caption -->
<!ELEMENT Thead    - O (Tr)+       -- table header -->
<!ELEMENT Tfoot    - O (Tr)+       -- table footer -->
<!ELEMENT Tbody    O O (Tr)+       -- table body -->
<!ELEMENT Colgroup - O (Col)*      -- table column group -->
<!ELEMENT Col      - O EMPTY       -- table column -->
<!ELEMENT Tr       - O (Th|Td)+    -- table row -->
<!ELEMENT (Th|Td)  - O (#PCDATA)   -- table header cell, table data cell -->

<!-- ************************************************************ -->
<!--                         Display Element                      -->
<!-- ************************************************************ -->
<!--
     The Display element contains all other display and linking
     elements of the document. Also, its attributes set basic
     display properties for the entire document.
-->
<!ELEMENT Display - - (Links?,Fonts?,Styles?,Page+)                 >
<!ATTLIST Display
            default-unit    (pct,cm,in,px) "px"
            base-line-width %length        "1px"
            base-line-inc   %length        "1px"
>
<!-- ************************************************************ -->
<!--                      XML Linking Elements                    -->
<!-- ************************************************************ -->
<!--
     The XML linking elements are used with display objects and
     within the separate Links element.
-->
<!ELEMENT Locator              - - EMPTY       -- link resource   -->
<!ATTLIST Locator
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "LOCATOR"
            role            CDATA    #IMPLIED
            href            CDATA    #REQUIRED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                       >
<!ELEMENT Link                 - - EMPTY       -- simple link     -->
<!ATTLIST Link
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "SIMPLE"
            role            CDATA    #IMPLIED
            href            CDATA    #REQUIRED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                       >
<!ELEMENT Extended-link        - - (Locator)+                       >
<!ATTLIST Extended-link
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "EXTENDED"
            inline          CDATA    #FIXED "TRUE"
            content-title   CDATA    #IMPLIED
            content-role    CDATA    #IMPLIED
            role            CDATA    #IMPLIED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                       >    
<!ELEMENT Document-link        - -   EMPTY                          >
<!ATTLIST Document-link
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "DOCUMENT"
            role            CDATA    #IMPLIED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                       >
<!ELEMENT Group-link           - -   (Document-link)*               >
<!ATTLIST Group-link
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "GROUP"
            steps           CDATA    #IMPLIED
            role            CDATA    #IMPLIED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                       >

<!ENTITY % links "(Link|Extended-link|Locator|Document-link|Group-link)*">

<!-- ************************************************************ -->
<!--                           Links Element                      -->
<!-- ************************************************************ -->
<!ELEMENT Links                - -  %links; --any number of links -->
<!-- ************************************************************ -->
<!--                           Styles Element                     -->
<!-- ************************************************************ -->
<!--
     The Styles element contains imported CSS style sheets
     and directly encoded style information.
-->
<!ELEMENT Styles               - - (Style-import*,Style)            >

<!ELEMENT Style-import         - - EMPTY -- imported Style section-->
<!ATTLIST Style-import
            source-doc         %url;  #REQUIRED -- BSML document  -->

<!ELEMENT Style                - -  CDATA      -- CSS style info  -->
<!ATTLIST Style
  type     %contenttype; #REQUIRED --content type of style lang.  --
  media    %mediadesc;   #IMPLIED  --for use with these media     --
  title    %text;        #IMPLIED  --advisory title               -->

<!-- ************************************************************ -->
<!--                                Fonts                         -->
<!-- ************************************************************ -->
<!--
     The Fonts element contains any number of Font elements.
     Its attribute list provides id references to Font elements
     that serve as base font elements.
-->
<!ELEMENT Fonts  - - (Font*)   -- list of all defined fonts       -->
<!ATTLIST Fonts
            base-font IDREF #IMPLIED --points to main default font--
            text-font IDREF #IMPLIED --points to text default font--
            numb-font IDREF #IMPLIED --points to numb default font-->

<!-- ************************************************************ -->
<!--                            Font Element                      -->
<!-- ************************************************************ -->

<!ELEMENT Font - - EMPTY  >
<!ATTLIST Font
  id          ID         #IMPLIED  -- document-wide unique id --
  class       CDATA      #IMPLIED  -- space separated list of classes --
  title       CDATA      #IMPLIED  -- displayable title --
  comment     CDATA      #IMPLIED  -- added for BSML --
  reffont     IDREF      #IMPLIED  -- reference font for default properties --
  size        CDATA      #IMPLIED  -- [+]nn e.g. size="+1", size=4 --
  color       CDATA      #IMPLIED  -- #RRGGBB in hex, e.g. red: "#FF0000" --
  face        CDATA      #IMPLIED  -- comma separated list of font names --
  bold        %yesorno;  #IMPLIED  -- 1 = bold, 0 = normal --
  italic      %yesorno;  #IMPLIED  -- 1 = italic, 0 = normal --
>
<!-- ************************************************************ -->
<!--           HTML 4.0 Object and Param, slightly modified       -->
<!-- ************************************************************ -->
<!--
     The Object and Param elements are use to allow external
     applications to be used in the display of BSML objects.
-->
<!ELEMENT Object - - (Param)*          -- generic embedded object -->
<!ATTLIST Object
  %attrs;                          -- %coreattrs, %events --
  declare     (declare)  #IMPLIED  -- declare but don't instantiate flag --
  classid     %url;      #IMPLIED  -- identifies an implementation --
  codebase    %url;      #IMPLIED  -- base URL for classid, data, archive --
  data        %url;      #IMPLIED  -- reference to object's data --
  type     %contenttype; #IMPLIED  -- content type for data --
  codetype %contenttype; #IMPLIED  -- content type for code --
  archive     %url;      #IMPLIED  -- space separated archive list --
  standby     %text;     #IMPLIED  -- message to show while loading --
  height      %length;   #IMPLIED  -- override height --
  width       %length;   #IMPLIED  -- override width --
  usemap      %url;      #IMPLIED  -- use client-side image map --
  shapes      (shapes)   #IMPLIED  -- object has shaped hypertext links --
  export      (export)   #IMPLIED  -- export shapes to parent  --
  name        CDATA      #IMPLIED  -- submit as part of form --
  tabindex    %integer;  #IMPLIED  -- position in tabbing order --
>

<!ELEMENT Param - O EMPTY                 -- named property value -->
<!ATTLIST Param
  id          ID         #IMPLIED    -- document-wide unique id --
  name        CDATA      #REQUIRED   -- property name --
  value       CDATA      #IMPLIED    -- property value --
  valuetype (data|ref|object) "data" -- How to interpret value --
  type     %contenttype; #IMPLIED    -- content type for value
                                        when valuetype=ref        -->

<!-- ************************************************************ -->
<!--      HTML 4.0 Client-side image maps slightly modified       -->
<!-- ************************************************************ -->
<!--
  The Image-map element is defined so that graphic display elements
  (e.g., gif files) may be used as links.
-->
<!ELEMENT Image-map - - (Area)+          -- client-side image map -->
<!ATTLIST Image-map
  %attrs;                           -- %coreattrs, %events --
  name        CDATA      #REQUIRED  -- name of image map for refs -->

<!ELEMENT Area - O EMPTY -- client-side image map area            -->
<!ATTLIST Area
  %attrs;                          -- %coreattrs, %events --
  shape       %shape;    rect      -- controls interpretation of coords --
  coords      %coords;   #IMPLIED  -- comma separated list of lengths --
  href        %url;      #IMPLIED  -- URL for linked resource --
  target   %frametarget; #IMPLIED  -- render in this frame --
  nohref      (nohref)   #IMPLIED  -- this region has no action --
  alt         %text;     #REQUIRED -- short description --
  tabindex    %integer;  #IMPLIED  -- position in tabbing order --
  accesskey  %character; #IMPLIED  -- accessibility key character --
  onfocus     %script;   #IMPLIED  -- the element got the focus --
  onblur      %script;   #IMPLIED  -- the element lost the focus  -->
  
<!-- ************************************************************ -->
<!--                          Pages Element                       -->
<!-- ************************************************************ -->
<!--
     The display of a BSML document is page-oriented, and the
     Pages element contains a base definition of the Screen
     and Paper for output and a list of Page elements.
-->
<!ELEMENT Pages                - - (Screen,Paper,Page+)             >

<!--
     Screen and Paper set defaults for all pages
-->

<!ELEMENT Screen - - (Margin?) --default attribs of screen display-->
<!ATTLIST Screen
            width   %length;  #IMPLIED -- width of drawing canvas --
            length  %length;  #IMPLIED -- length of drawing canvas--
            monochrome %yesorno; %no;  -- print black/white only  -->

<!ELEMENT Paper  - - (Margin?) --default attribs of printed output-->
<!ATTLIST Paper
            monochrome %yesorno; %no; -- print black/white only--
            print-mode (portrait,landscape) "portrait"              >

<!ELEMENT Margin - - EMPTY >
<!ATTLIST Margin
            margin     %length #IMPLIED
            horizontal %length #IMPLIED
            vertical   %length #IMPLIED
            left       %length #IMPLIED
            right      %length #IMPLIED
            top        %length #IMPLIED
            bottom     %length #IMPLIED                             >

<!ELEMENT Border - - EMPTY -- any border around a rectangular area-->
<!ATTLIST Border
            line-width %linewidth; #IMPLIED
            line-color %color;     "black"
            gutter     %length;    #IMPLIED   -- indent to border -->

<!-- ************************************************************ -->
<!--                          Display Set Types                   -->
<!-- ************************************************************ -->
<!--
     A variety of set based display objects are defined by BSML.
-->
<!-- ************************************************************ -->
<!--                          Simple-set                          -->
<!-- ************************************************************ -->
<!ELEMENT Simple-set           - - (Border?,Object?,%links;)
                                                  --basic set type-->
<!ATTLIST Simple-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                            Tree-set                          -->
<!-- ************************************************************ -->
<!--      Tree-set=simple hierarchy displayed as tree             -->
<!--  basic display is titles obtained from list by ids;          -->
<!--  length of branch specified in value of set is               -->
<!--  relative to branchunit and branchbase;                      -->
<!--  set points to the root of the tree                          -->

<!ELEMENT Tree-set           - - (Border?,Object?,%links;)          >
<!ATTLIST Tree-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                       Multi-site-set                         -->
<!-- ************************************************************ -->
<!-- Multi-site-set is set of sites on same sequence              -->
<!-- any number of sets of sites may be merged as one set         -->
<!ELEMENT Multi-site-set      - - (Object?,%links;)                 >
<!ATTLIST Multi-site-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                         Multi-seq-set                        -->
<!-- ************************************************************ -->
<!--Multi-seq-set=flat set of sequences or intervals              -->

<!ELEMENT Alignment-site-set  - - (Object?,%links;)                 >
<!ATTLIST Alignment-site-set
            %attrs;                                                 >

<!ELEMENT Alignment-site-sets - - (Alignment-site-set*,
                                                   Object?,%links;) >
<!ATTLIST Alignment-site-sets
            %attrs;                                                 >

<!ELEMENT Multi-seq-set     - - (AlignmentSiteSets,Object?,%links;) >
<!ATTLIST Multi-seq-set
            %attrs;                                                 >

<!-- ************************************************************ -->
<!--                       Alignment-point-set                    -->
<!-- ************************************************************ -->
<!-- Alignment-point-set defines set of related sites             -->
<!ELEMENT Alignment-point-set  - - (Object?,%links;)                >
<!ATTLIST Alignment-point-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                       Seq-pair-alignment-set                 -->
<!-- ************************************************************ -->
<!ELEMENT Seq-pair-alignment  - - (Object?,%links;)                 >
<!ATTLIST Seq-pair-alignment
            %attrs;                                                 >
<!ELEMENT Seq-pair-alignment-set - - (Seq-pair-alignment*,
                                                   Object?,%links;) >
<!ATTLIST Seq-pair-alignment-set
   --a set of aligned regions, displayed in views with added
  zones to indicate regions of homology - note - zones are added
  to views, not sequences, because of their temporary nature--
    %attrs;                                                         >
<!-- ************************************************************ -->
<!--                       Consensus-set                          -->
<!-- ************************************************************ -->
<!ELEMENT Consensus-match    - - EMPTY                              >
<!ATTLIST Consensus-match
            %attrs;                                                 >
<!ELEMENT Consensus-set    - - (Consensus-match*,Object?,%links;)   >
<!ATTLIST Consensus-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                          Motif-set                           -->
<!-- ************************************************************ -->
<!ELEMENT Motif-element      - - (Motif-element*)                   >
<!ATTLIST Motif-element
            %attrs;                                                 >
<!-- motifs for individual sequences                              -->
<!ELEMENT Motif-set          - - (Object?,%links;)                  >
<!ATTLIST Motif-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                          Motif-seq-set                       -->
<!-- ************************************************************ -->
<!-- motifs for sets of sequences                                 -->
<!ELEMENT Motif-seq-set       - - (Motif-set*,Object?,%links;)      >
<!-- ************************************************************ -->
<!--                          Variation-set                       -->
<!-- ************************************************************ -->
<!-- variation/mutation set                                       -->
<!ELEMENT Variant-pos       - - EMPTY                               >
<!ELEMENT Region            - - EMPTY                               >
<!ELEMENT Variant           - - (VariantPos*,Region*)               >
<!ELEMENT Variant-set       - - (Variant*,Object?,%links;)          >
<!ATTLIST Variant-set
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                        Display Objects                       -->
<!-- ************************************************************ -->

<!ELEMENT Symbol            - - EMPTY    -- symbol display object -->
<!ATTLIST Symbol
            shape  (plus,cross,opencircle,closedcircle,
                    opensquare,closedsquare,triangle) #IMPLIED
            color  %color;  #IMPLIED -- use default if unspecified--
            diam   %length; #IMPLIED -- use default if unspecified-->

<!ELEMENT Chart      - - (Border?)           -- chart display atts-->
<!ATTLIST Chart
            %attrs;                                                 >

<!ELEMENT Member            - - EMPTY                               >

<!ENTITY % settypes "(Simple-set|Tree-set|Multi-site-set|
                      Multi-seq-set|Seq-pair-alignment-set|
                      Alignment-point-set|Consensus-set|
                      Motif-set|Motif-seq-set|Variation-set)*">

<!-- ************************************************************ -->
<!--                Sequence-relative Display Objects             -->
<!-- ************************************************************ -->

<!ELEMENT Point-object      - - (Symbol?,Object?,%links;)
                                           -- display 1 pt on seq -->

<!ATTLIST Point-object                                              >
            %attrs;

<!-- Point-group may refer to defined Members, Features, Point-objects   -->

<!ELEMENT Point-group-object - - (Member*,Object?,%links;) -- site group -->
<!ATTLIST Point-group-object
            %attrs;
            featurerefs   IDREFS    #IMPLIED >
            
<!ELEMENT Interval-object   - - (Object?,%links;) -- display interval    -->
<!ATTLIST Interval-object
            %attrs; >

<!ELEMENT Blowup-object     - - (Object?,%links;)    -- display blowup   -->
<!ATTLIST Blowup-object
            %attrs; >

<!ELEMENT Axis-object       - - (Object?,%links;)    -- display scale    -->
<!ATTLIST Axis-object
            %attrs; >

<!ELEMENT Sequence-object   - - (Object?,%links;) --display sequence line-->
<!ATTLIST Sequence-object
            %attrs; >
<!--
     A histogram or frequency polygon derived from a row or
     column of a table is added with an Aligned-chart-object element
-->
<!ELEMENT Aligned-chart-object - - (Object?,Chart?,%links;)                >
<!ATTLIST Aligned-chart
            %attrs; >

<!ELEMENT Seq-data-object     - - (Object?,Border?,%links;)                >
<!ATTLIST Seq-data-object
            %attrs; >

<!ENTITY % seqdisplayobjects "(Point-object|Point-group-object|
                              Interval-object|Blowup-object|
                              Axis-object|Sequence-object|
                              Aligned-chart-object|Seq-data-object)*">

<!-- ************************************************************ -->
<!--                Sequence-Independent Display Objects          -->
<!-- ************************************************************ -->
<!--
     Text is added with a Caption-object element
-->
<!ELEMENT Caption-object     - - (%links;)                                 >
<!ATTLIST Caption-object
            %attrs; >

<!--
     A line (single or segmented with arrow-heads is added with a
     Line-pointer-object element
-->
<!ELEMENT Line-pointer-object - - (%links;)                                >
<!ATTLIST Line-pointer-object
            %attrs; >
<!--
     A shape - ellipse, rectangle or rounded-rectangle is added with
     a Shapen-object element
-->
<!ELEMENT Shape-object       - - (%links;)                                 >
<!ATTLIST Shape-object
            %attrs; >

<!ELEMENT Text-file-object   - - (Object?,Border?,%links;)                 >
<!ATTLIST Text-file-object
            %attrs; >

<!ELEMENT Image-object      - - (Object?,Image-map?,Border?,%links)        >
<!ATTLIST Image-object
            %attrs; >

<!--
     A histogram or frequency polygon derived from a row or
     column of a table is added with an Unaligned-chart-object element
-->
<!ELEMENT Unaligned-chart-object   - - (Object?,Chart?,%links;)            >
<!ATTLIST Unaligned-chart-object
            %attrs;
            tableid          IDREF #REQUIRED >

<!--
     Tabular data associated with a Table element are added
     with a Table-object element
-->
<!ELEMENT Table-object       - - (Border?,%links;)                         >
<!ATTLIST Table-object
            %attrs;>
<!--
     Keys provided explanations for text, fill patterns (hatching)
     and symbols
-->

<!ELEMENT Text-key-object    - - (Border?,%links;)                         >
<!ATTLIST Text-key-object
            %attrs; >

<!ELEMENT Fill-key-object    - - (Border?,%links;)                         >
<!ATTLIST Fill-key-object
            %attrs; >

<!ELEMENT Symbol-key-object  - - (Border?,%links;)                         >
<!ATTLIST Symbol-key-object
            %attrs; >

<!ENTITY % pagedisplayobjects "(Caption-object|Line-pointer-object|
                               Shape-object|Text-file-object|
                               Image-object|Unaligned-chart-object|
                               Table-object|Text-key-object|
                               Fill-key-object|Symbol-key-object)*" >

<!-- ************************************************************ -->
<!--                            Page Element                     -->
<!-- ************************************************************ -->
<!--
     A Page element contains any number of display objects,
     either associated with the Page itself or with Sequence
     elements displayed as View elements on the Page.
-->
<!ELEMENT Page                 - - (Screen?,Paper?,Border?,
                                    View*,%pagedisplayobjects;,
                                    %settypes;,Object?,%links;)     >
<!ATTLIST Page
            %attrs;                                                 >
<!-- ************************************************************ -->
<!--                            View Element                      -->
<!-- ************************************************************ -->
<!--
     Each View refers to a Sequence or another View and
     indicates whether the Sequence should be displayed as
     a linear or circular object or as a set of gel bands.
     A View element may have any number of sequence display
     objects attached to it.
-->
<!ELEMENT View              - -  (%seqdisplayobjects;,
                                  Object?,%links;)  --view of seq -->
<!ATTLIST View
            %attrs;                                                 >