<!-- ************************************************************* -->
<!--         BSML (tm) Bioinformatic Sequence Markup Language      -->
<!--   Document Type Definition DTD - Jan. 1, 2001  - Version 2.2  -->
<!--                         Copyright 1998-2001                   -->
<!--                       Joseph H. Spitzner, Ph.D.               -->
<!--                           Annotated Version                   -->
<!--                           LabBook, Inc.                       -->
<!--                                                               -->
<!--
The authors reserve the right to change, without notice, the
specifications and information contained in the Bioinformatic Sequence
Markup Language (BSML) Document Definition Type (DTD) and in all 
associated annotation, help and documentation. The authors also 
reserve the right to change, without notice, the implementation 
of the BSML Browser. While every effort has been made to ensure that
the information is correct and that the Browser performs as described,
the authors do not assume responsibility for any errors which may
appear. The BSML Browser is provided without warranty of any kind,
whether express, statutory or implied, including all implied warranties
of merchantability and fitness for a particular purpose. The BSML
Browser is provided on an "as is" basis. The limited license grant
means that you may not do any of the following with the BSML Browser or
the BSML DTD: decompile, disassemble, reverse engineer, modify, lease,
loan, sell, distribute or create derivative works based upon the BSML
Browser software in whole or in part without permission of the authors;
transmit the BSML DTD or BSML Browser to any person, except if the
original package and its whole original content are transmitted, and
that this person accepts to be bound by the terms and conditions of
this software license agreement and warranty.

The authors not shall in any event be liable for any direct, 
consequential, incidental, indirect or special damages even if 
advised of the possibility of such damages. In particular, the authors
shall have no liability for any damage, loss or corruption of data or
programs stored in or used in conjunction with BSML Browser, nor shall
the authors be liable for the cost of retrieving or replacing damaged,
lost or corrupted data.

This license shall be governed by and construed in accordance with the
laws of your country. If for any reason a court of competent
jurisdiction finds any provision of this license to be unenforceable,
the other provisions of this limited warranty and software license 
agreement shall remain in effect without limitation.
-->
<!-- ************************************************************* -->
<!-- This document defines an XML-compliant DTD for the            -->
<!-- representation and display of genetic sequence information.   -->
<!-- This public domain standard was developed under a grant from  -->
<!-- the National Human Genome Research Institute.                 -->
<!-- ************************************************************* -->
<!--                         Table of Contents                     -->
<!--  0.0 Note: CDATA attribute values defined by entities.        -->
<!--  1.0 General parameter entities.                              -->
<!--  2.0 General attributes applied to most elements.             -->
<!--  3.0 Major BSML document divisions                            -->
<!--  4.0 Definitions sub-divisions                                -->
<!--  5.0 Sequences, features, annotation, and citations           -->
<!--  6.0 Sets                                                     -->
<!--  7.0 Tables                                                   -->
<!--  8.0 Display sub-divisions                                    -->
<!--  9.0 XML linking elements                                     -->
<!-- 10.0 Fonts                                                    -->
<!-- 11.0 Styles                                                   -->
<!-- 12.0 Pages, views and display widgets                         -->
<!-- ************************************************************* -->
<!--    0.0 Note: CDATA attribute values defined by entities.      -->
<!-- ************************************************************* -->
<!--
  Attribute values are often defined by a parameter entity that is,
  itself, simply defined as CDATA. The purpose of this usage is to
  indicate how the UA (User Agent) should interpret the value.
  Explanations of these CDATA values are usually given near the
  definitions of the relevant parameter entities.
-->
<!-- ************************************************************* -->
<!--            1.0 General Parameter Entity Definitions           -->
<!-- ************************************************************* -->
<!ENTITY amp "&#38;"                                                 >
<!ENTITY lt "&#60;"                                                  >
<!ENTITY gt "&#62;"                                                  >
<!ENTITY quot "&#34;"                                                >
<!ENTITY slash "&#47;"                                               >
<!ENTITY % yesorno "CDATA"         ><!-- boolean as 1=true|0=false -->
<!ENTITY % integer "CDATA"         ><!-- positive or negative int  -->
<!ENTITY % real "CDATA"            ><!-- positive or negative real -->
<!ENTITY % length "CDATA"          ><!-- length units (see 1.1)    -->
<!ENTITY % linewidth "CDATA"       ><!-- line width (see 1.2)      -->
<!ENTITY % linestyle "(solid|dash|dot|none)" ><!-- style of line   -->
<!ENTITY % displayshape "(ellipse|rectangle|roundrectangle)"         >
<!--                                                               -->
<!--     The following entities were adapted from html 4.0:        -->
<!--                                                               -->
<!ENTITY % color "CDATA"          ><!-- name, RGB value (see 1.3)  -->
<!ENTITY % contenttype "CDATA"    ><!-- media type,RFC2045         -->
<!ENTITY % character "CDATA"      ><!-- one character,ISO10646     -->
<!ENTITY % mediadesc "CDATA"      ><!-- single or comma-separated
                                     list of media descriptors     -->
<!ENTITY % url "CDATA" > <!-- Uniform Res. Locator,RFC1808,RFC1738 -->
<!ENTITY % datetime "CDATA"       ><!-- date,time ISO date format  -->
<!ENTITY % date "CDATA"           ><!-- date ISO date format       -->
<!ENTITY % script "CDATA"         ><!-- script expression          -->
<!ENTITY % text "CDATA"           ><!-- render as CDATA            -->
<!ENTITY % shape "(rect|circle|poly|default)"    ><!-- image maps  -->
<!ENTITY % coords "CDATA"         ><!-- comma sep list of numbers  -->
<!ENTITY % frametarget "CDATA"    ><!-- render in this frame       -->
<!--
  Notes: 1. A network url MUST include the prefix http://
         2. A local file url MAY include the prefix file://
-->
<!--
  ******************** 1.1 Length: Units of Distance ***************
  Locations on the page and distance values 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 (length)
   o cm = centimeters
   o in = inches
   o pt = points (1 pt = 1/72 in)
   
  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
  of a point in different dimension units, e.g.,
  hloc="10.2cm" vloc="20%".

  If a length is followed by "@idV:" and an object's ID, the value
  is taken from a location or size of the corresponding widget. "V"
  is one of the following:
    x : horizontal center
    y : vertical center
    w : width
    h : height
    l : left
    r : right
    t : top
    b : bottom
  For example, if a sequence view-line with id="VLN1" has a
  horizontal center of 300 pixels, a horizontal length of
  "20px@idx:VLN1" returns a value of 320 pixels. This method is
  most commonly used in resolving coordinates on the display page.
-->
<!--
  ********************** 1.2 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 types:

  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.,
    line-width-base="0.01in"). The increment applied from one step to
    another is specified as an attribute of the Display element (e.g.,
    line-width-inc="0.005in"). Thus the absolute value of a relative
    value is calculated by adding a multiple of line-width-inc to
    line-width-base, e.g., 3=line-width-base+2*line-width-inc.
  o Enumerated values selected from "thin","medium","thick", which
    correspond to relative values of 1, 2, and 4, respectively.
-->
<!--
  ****************** 1.3  Colors (from HTML 4.0) *********************
  An attribute value type "color" (%color) may be either a hexadecimal
  number (prefixed by a hash mark) or one of the following 16 color
  names:
             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.
-->
<!-- ************************************************************* -->
<!--  2.0 General attributes applied to most elements.             -->
<!-- ************************************************************* -->
<!ENTITY % mainattrs
 "id          ID         #IMPLIED
  class       CDATA      #IMPLIED
  style       CDATA      #IMPLIED
  title       CDATA      #IMPLIED
  comment     CDATA      #IMPLIED
  value-type  CDATA      #IMPLIED
  value       CDATA      #IMPLIED
  selectable  %yesorno;  #IMPLIED
  selected    %yesorno;  #IMPLIED
  display     %yesorno;  #IMPLIED
  readonly    %yesorno;  #IMPLIED"
>
<!--
  Notes:
  1. style is not supported by the current version of the browser
  2. readonly is not supported by the current version of the browser
  3. Value-type and value are used, as appropriate, to supply
     data or other numeric values associated with an element.
  4. Value may be a single entry or a comma separated list.
-->
<!--   Events used to define actions when element are selected:    -->
<!ENTITY % events
 "onclick     %script;   #IMPLIED
  ondblclick  %script;   #IMPLIED
  onmousedown %script;   #IMPLIED
  onmouseup   %script;   #IMPLIED
  onmouseover %script;   #IMPLIED
  onmousemove %script;   #IMPLIED
  onmouseout  %script;   #IMPLIED
  onkeypress  %script;   #IMPLIED
  onkeydown   %script;   #IMPLIED
  onkeyup     %script;   #IMPLIED"
>
<!--
  Notes: 1. Mouse events ondblclick, onmouseover, onmousemove,
            and onmouseout are not supported by the current
            version of the browser.
         2. Keyboard events are not supported by the current
            version of the browser.
-->
<!ENTITY % attrs "%mainattrs; %events;" >
<!--
  Note: %attrs is added as an attribute group for all major elements.
-->
<!-- ************************************************************* -->
<!--                3.0 Major BSML Document Divisions              -->
<!-- ************************************************************* -->
<!ELEMENT Bsml (Attribute*,Info*,Definitions?,Display?)              >
<!--
  Note: For the top level Bsml element, the following Attribute
        elements (name/content pairs) are commonly defined:
           document-title="title of document"
           project="name of project" (used with project manager)
           project-id="unique project identifer for this document"
           author="originator of document"
           storage="primary storage location"
           owner="user who has complete access"
           password="security manager term to validate owner"
           owner-access="(none|read-only|read-write)"
           user-access="(none|read-only|read-write)"
           create-date="date of origination (yyyy-mm-dd)"
           update-date="date of last modification (yyyy-mm-dd)"
                                                                   -->
<!ELEMENT Attribute EMPTY >
<!ATTLIST Attribute
  name     CDATA  #REQUIRED
  content  CDATA  #IMPLIED >
<!-- ************************************************************* -->
<!--                 4.0  Definitions Sub-divisions                -->
<!-- ************************************************************* -->
<!--
     Notes:

        1. The Definitions section may be used without a Display
           section if the goal is simply to encode sequence data;
           for convenience, a few elements in the Definitions
           section have display-related attributes, but these
           attributes are never required. Thus a BSML document may
           be used to convey data independently of a BSML browser,
           and the document may be read and processed by any
           suitable XML parsing software.

        2. The Display section provides information that is mainly
           relevant for the graphical display of bioinformatic data
           and for accessing links in other network resources. Much
           of the content of the Display section only has meaning
           for a browser that works specifically with BSML and has
           been customized to display the widgets defined in the
           BSML standard.
-->
<!-- ************************************************************* -->
<!ELEMENT Definitions (Attribute*,Sequences?,Sets?,Tables?)          >
<!-- ************************************************************* -->
<!--      5.0 Sequences, Features, Annotation, and Citations       -->
<!-- ************************************************************* -->
<!ELEMENT Sequences (Sequence|Sequence-import|Attribute)*            >
<!ATTLIST Sequences
  %attrs; >
<!ENTITY % dbsource "CDATA" ><!-- database source such as swissprot-->
<!-- ************************************************************* -->
<!--                    5.1  Sequence-import                       -->
<!-- ************************************************************* -->
<!ELEMENT Sequence-import (Attribute*)   -- imported from file/url -->
<!ATTLIST Sequence-import
  type   (bsml|asn1|genbank|embl|gsdb) "bsml"   -- format           --
  source    %url;   #REQUIRED                   -- file name or URL --
  id      ID  #IMPLIED
                  -- id identifier selects one sequence from a set;
                     if bsml import, identifier = id
                     if other, identifier = primary accession key  -->
<!--
  Note: Only sequence imports from other BSML documents (bsml
        format) are permitted by the current version of the browser.
-->
<!-- ************************************************************* -->
<!--             5.2 Sequence Element (adapted from NCBI)          -->
<!-- ************************************************************* -->
<!ENTITY % repr-opts "(not-set|virtual|raw|segmented|constructed|
                       reference|consensus|map|derived|other)"       >
<!--                 Sequence representation options               -->
<!ELEMENT Sequence (Attribute*,Feature-tables?,
                        (Seq-data|Seq-data-import)?,Numbering?)      >
<!ATTLIST Sequence
  %attrs;
  locus         CDATA      #IMPLIED -- sequence name               --
  ic-acckey     CDATA      #IMPLIED -- internatl. collaboration    --
  local-acckey  CDATA      #IMPLIED -- local/private accession key --
  db-source     %dbsource; #IMPLIED -- database source of sequence --
  length        CDATA      #IMPLIED -- integer value total length  --
  end5hang5     %integer;  #IMPLIED -- 5' overhang on 5' end       --
  end3hang5     %integer;  #IMPLIED -- 5' overhang on 3' end       --
  end5phos      %yesorno;  #IMPLIED -- yes= 5' end phosphorylated  --
  end3phos      %yesorno;  #IMPLIED -- yes= 3' end phosphorylated  --
  -- NCBI seq-inst attributes --
  representation  %repr-opts;                             "raw"
  molecule (mol-not-set|dna|rna|aa|na|other-mol)          "dna"
  topology (top-not-set|linear|circular|tandem|top-other) "linear"
           -- strand=ds for dna and ss otherwise, if not specified --
  strand   (std-not-set|ss|ds|mixed|std-other)            #IMPLIED
  refs IDREFS #IMPLIED                 -- element cross-references --
          -- including references, features, other sequences, etc. --
    -- if sequence is segmented, constructed, etc., refs includes
       ids of sequences comprising the complete sequence; the
       sequences referred to indicate their status by using
       the alignment-sequences and alignment-positions attributes  --
  alignment-sequence  IDREFS #IMPLIED     -- aligned to sequences  --
  alignment-position  CDATA  #IMPLIED     -- positions on aligned  --
  alignment-inverted  CDATA  #IMPLIED     -- 0=ascend, 1=descend   -->

<!-- ************************************************************* -->
<!--                       5.3 Sequence Data                       -->
<!-- ************************************************************* -->
<!ELEMENT Seq-data (#PCDATA)                  -- the sequence data -->
<!--                dna/rna=IUPACna, protein=IUPACaa               -->
<!-- ************************************************************* -->
<!--                       5.4 Location Types                      -->
<!-- ************************************************************* -->
<!ELEMENT Site-loc EMPTY                         -- one position   -->
<!ATTLIST Site-loc                     -- NCBI (a) single position --
  %attrs;
  sitepos     CDATA     #REQUIRED  -- integer position on sequence --
  complement  %yesorno; "0"       -- on complement if yes         -->
<!ELEMENT Interval-loc EMPTY                           -- interval -->
<!ATTLIST Interval-loc               -- NCBI (c) 121.130,onepos=1
                                             (d) 121..130,onepos=0 --
  %attrs;
  startpos     CDATA      #REQUIRED      -- integer start of range --
  endpos       CDATA      #REQUIRED      --   integer end of range --
  startopen    %yesorno;  "0"           --            open if yes --
  endopen      %yesorno;  "0"           --            open if yes --
  onepos       %yesorno;  "0"           --    one position if yes --
  complement   %yesorno; "0"            --   on complement if yes -->
<!ENTITY % location "(Site-loc|Interval-loc)"                        >
<!-- location entity provides reference to either type of location -->
<!-- ************************************************************* -->
<!--                      5.5 Qualifier Types                      -->
<!-- ************************************************************* -->
<!ELEMENT Qualifier EMPTY                                            >
<!--        Qualifier uses value-type and value attributes         -->
<!ATTLIST Qualifier
   %attrs;                                                           >
<!-- ************************************************************* -->
<!--                       5.6 Feature Types                       -->
<!-- ************************************************************* -->
<!ELEMENT Feature (Attribute|%location;|Qualifier)*                  >
<!ATTLIST Feature
  %attrs;
  -- if display-auto=yes, create and show default display widget   --
  display-auto %yesorno; #IMPLIED
  -- auto-view is view to which to attach display widget           --
  -- if not defined, feature added to first view for this seq      --
  auto-view    IDREF     #IMPLIED
  -- feature type description encoded as value-type core attribute --
  refs         IDREFS    #IMPLIED     -- element cross-references --
            -- including references, other features, seqs, etc.    -->

<!-- ************************************************************* -->
<!--                         5.7 Reference                         -->
<!-- ************************************************************* -->
<!ELEMENT Reference (Attribute*,RefAuthors?,RefTitle?,RefJournal?)   >
<!ATTLIST Reference
  %attrs;
  dbxref CDATA #IMPLIED --reference to external source,e.g.,medline--
  refs IDREFS #IMPLIED                 -- element cross-references --
            -- including references, other features, seqs, etc.
            References may be linked to external resources such as
            medline references by using the ID of a link in refs   -->
<!ELEMENT RefAuthors (#PCDATA)                                       >
<!ELEMENT RefTitle   (#PCDATA)                                       >
<!ELEMENT RefJournal (#PCDATA)                                       >
<!-- ************************************************************* -->
<!--                        5.8 Digest Set                         -->
<!-- ************************************************************* -->
<!ELEMENT Restriction-enzyme EMPTY          -- record for 1 enzyme -->
<!ATTLIST Restriction-enzyme         --  note: title = enzyme name --
  %attrs;
  source           CDATA     #IMPLIED -- sequence or organism      --
  recognition-seq  CDATA     #IMPLIED -- base pattern              --
       -- offset = cut position relative to the 5' end of pattern  --
  offset           %integer; "0"               -- cut position     --
  overhang         %integer; "0"               -- 5' overhang      --
  sites            CDATA     #IMPLIED    -- comma separated list   --
      -- site positions are indicated by the base 3' of the cut;
         negative numbers indicate recognition on minus strand
         for non-palindromic enzymes                               -->

<!ELEMENT Digest-set (Restriction-enzyme)* -- set of enzymes       -->
<!ATTLIST Digest-set
  %attrs;
      -- fragments may be used in place of restriction-enzymes to
         indicate directly the sizes of the fragments,
         which are otherwise computed from the restriction sites   --
  fragments CDATA      #IMPLIED         -- comma separated list    --
  units     CDATA      #IMPLIED         -- if fragments            --
  -- start and end position used if only part of sequence searched --
  start-pos %integer;  #IMPLIED         -- else seq start          --
  end-pos   %integer;  #IMPLIED         -- else seq end            --
      -- for documentation, if generated under search conditions:  --
  min-cuts  %integer;  #IMPLIED         -- allowed in set          --
  max-cuts  %integer;  #IMPLIED         -- allowed in set          -->
<!-- ************************************************************* -->
<!--                      5.9 Feature Table                        -->
<!-- ************************************************************* -->
<!ELEMENT Feature-table (Attribute|Reference|Feature|Digest-set)*    >
<!ATTLIST Feature-table
  %attrs;                                                            >
<!-- ************************************************************* -->
<!--                        5.10 Feature Tables                    -->
<!-- ************************************************************* -->
<!ELEMENT Feature-tables (Attribute|Feature-table)*                  >
<!ATTLIST Feature-tables
  %attrs;                                                            >
<!-- ************************************************************* -->
<!--                       5.11 Seq-data-import                    -->
<!-- ************************************************************* -->
<!--
  IUPACna ::= StringStore    IUPAC 1 letter codes, no spaces
  IUPACaa ::= StringStore    IUPAC 1 letter codes, no spaces
  NCBI2na ::= OCTET STRING   00=A, 01=C, 10=G, 11=T
  NCBI4na ::= OCTET STRING   1 bit each for agct
                             0001=A, 0010=C, 0100=G, 1000=T/U
                             0101=Purine, 1010=Pyrimidine, etc
-->
<!ELEMENT Seq-data-import (Attribute*)         -- import data only -->
<!ATTLIST Seq-data-import
  %attrs;
  format     CDATA  #IMPLIED -- ascii,genbank,embl,fasta,
                            bsml or one of the above for pure data --
  source     %url;  #IMPLIED          -- if none, librarian needed --
  identifier CDATA  #IMPLIED
                  -- identifier selects one sequence from a set;
                     if bsml import, identifier = id
                     if other, identifier = primary accession key  --
  encrypted  %yesorno; #IMPLIED    -- if yes,decryption key needed -->
<!-- ************************************************************* -->
<!--                 5.12 Sequence Numbering - NCBI                -->
<!-- ************************************************************* -->
<!-- ************************* Sequence Units ******************** -->
<!--
 Internally, the length of every sequence is expressed as a positive
 integer. Sequences may specify their unit of measurement (bp, cM,
 etc.) through the use of a Numbering element, which also may define
 a relative numbering basis or a linear transformation rule for
 converting internal sequence positions to display values.
-->
<!ELEMENT Numbering EMPTY         -- combines all numbering types -->
<!ATTLIST Numbering
  %attrs;
  use-numbering  %yesorno; #IMPLIED            -- if no,absolute # --
  type (continuous|real|enumerated|reference) #IMPLIED
  units      CDATA      #IMPLIED            --for display purposes --
                                            -- real = a N + b      --
  a          %real;     #IMPLIED
  b          %real;     #IMPLIED
  dec-places %integer;  #IMPLIED
                                            -- continuous type     --
  refnum     %integer;  #IMPLIED            -- base 1              --
  has-zero   %yesorno;  #IMPLIED            -- else 0 reported -1  --
  ascending  %yesorno;  #IMPLIED            -- numbering order     --
  names      CDATA      #IMPLIED            -- comma sep enum list --
                                            -- reference type      --
  from-aligns %yesorno; #IMPLIED            -- else from sources   --
  aligns     IDREF      #IMPLIED                                     >
<!-- Note: from-aligns and enumerated types are not supported
           by the current version of the browser.                  -->

<!-- ************************************************************* -->
<!--                              6.0 Sets                         -->
<!-- ************************************************************* -->
<!ELEMENT Sets (Attribute|Set)*                       --  any set  -->
<!ATTLIST Sets
  %attrs;                                        -- attributes     -->
<!-- Set = basic hierarchical structure composed of any            -->
<!--    grouping of elements by id using idrefs.                   -->
<!ELEMENT Set (Attribute*)                                           >
<!ATTLIST Set
  %attrs;
  idrefs IDREFS #REQUIRED   -- space-separated list of set members --
  refs   IDREFS #IMPLIED    -- element cross-references            -->

<!-- ************************************************************* -->
<!--                             7.0 Tables                        -->
<!-- ************************************************************* -->
<!ELEMENT Tables (Attribute|Table|Motif-table|
             Seq-pair-alignment|Alignment-point-set|Table-import)*   >
<!ATTLIST Tables
  %attrs;                                        -- attributes     -->
<!-- ************************************************************* -->
<!--                    7.1 Table-import Definition                -->
<!-- ************************************************************* -->
<!ELEMENT Table-data EMPTY -- locally supplied data for import -->
<!ATTLIST Table-data
   %attrs;   --        use title to name table row, if appropriate --
             -- uses value for comma separated data table row list -->

<!ELEMENT Table-import (Attribute*,Table-data*)
     -- internal, if table-data, or external file or internet href -->
<!ATTLIST Table-import
  %attrs;
  format CDATA #IMPLIED -- acceptable formats=bsml|html|txt|sdf|db --
       --     if data in Table-data elements, no format needed     --
  read-field-desc  %yesorno; #IMPLIED           -- use for txt,sdf --
       -- if read-field-desc=yes, read field descriptions at start --
       -- of file = Num (number of fields on first line)           --
       --           FieldName,Type(=T,N,L),Width,Decimals          --
       --           with one line per field                        --
       -- list of columns to include; use all if not defined       --
  column-numbers   CDATA     #IMPLIED
                        -- comma separated list of column headings --
  column-headers   CDATA     #IMPLIED          --  use for txt,sdf --
       -- comma separated lists of start positions and field widths--
  column-starts    CDATA     #IMPLIED          -- used for txt     --
  column-widths    CDATA     #IMPLIED          -- used for txt     --
  header-count     %integer; #IMPLIED          -- text skip lines  --
  display-widths   CDATA     #IMPLIED      -- comma separated
                  list of column widths for display in grid viewer --
  alignments       CDATA     #IMPLIED      -- comma separated
        list of L (left=text) or R (right=numeric) for each column --
  font             IDREF     #IMPLIED           -- font for grid   --
  add-row-numbers  %yesorno; #IMPLIED           -- number grid rows--
  locked-columns   %integer; #IMPLIED           --# to lock at left--
  source           %url;     #REQUIRED          -- file/remote     --
  refs             IDREFS    #IMPLIED  -- element cross-references -->

<!-- ************************************************************* -->
<!--                          7.2 Table                            -->
<!-- ************************************************************* -->
<!-- IETF HTML table standard, see RFC1942                         -->
<!ENTITY % tframe
                "(void|above|below|hsides|lhs|rhs|vsides|box|border)">
<!ENTITY % trules "(none | groups | rows | cols | all)">
<!-- horizontal placement of table relative to document            -->
<!ENTITY % talign "(left|center|right)"                              >
<!-- horizontal alignment attributes for cell contents             -->
<!ENTITY % cellhalign
  "align (left|center|right|justify|char) #IMPLIED
   char    %character;  #IMPLIED  -- alignment char, e.g. char=':' --
   charoff %length;     #IMPLIED  -- offset for alignment char --"
>

<!-- vertical alignment attributes for cell contents               -->
<!ENTITY % cellvalign "valign (top|middle|bottom|baseline) #IMPLIED" >

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

<!ATTLIST Table                   -- table element --
  %attrs;                         -- %coreattrs, %events --
  summary     %text;     #IMPLIED -- purpose/structure for speech  --
  width       %length;   #IMPLIED -- table width relative to window--
  border      CDATA      #IMPLIED -- frame width around table      --
  frame       %tframe;   #IMPLIED -- include which parts of framee --
  rules       %trules;   #IMPLIED -- rulings between rows and cols --
  cellspacing %length;   #IMPLIED -- spacing between cells         --
  cellpadding %length;   #IMPLIED -- spacing within cells          -->

<!ENTITY % calign "(top|bottom|left|right)"                          >

<!ATTLIST Caption
  %attrs;                                   -- %coreattrs, %events -->
<!--
  COLGROUP groups a set of COL elements. It allows you to group
  several semantically related columns together.
-->
<!ATTLIST Colgroup
  %attrs;                       -- attributes                      --
  span        %integer;  "1"    -- default # of columns in group   --
  width       %length; #IMPLIED -- default width for enclosed COLs --
  %cellhalign;                  -- horizontal alignment in cells   --
  %cellvalign;                  -- vertical alignment in cells     -->
<!--
  COL elements define the alignment properties for cells in
  one or more columns. The WIDTH attribute specifies the width of
  the columns, e.g.
     width=64        width in screen pixels
     width=0.5*      relative width of 0.5
  The REPEAT attribute allows you to repeat the effects of
  a COL element as if the same element was repeated n times.
  There are no grouping semantics for repeated columns.
-->
<!ATTLIST Col                     -- column groups and properties  --
  %attrs;                         -- attributes                    --
  repeat      %integer;  "1"      -- repeat count for COL          --
  width       %length; #IMPLIED   -- column width specification    --
  %cellhalign;                    -- horizontal alignment in cells --
  %cellvalign;                     -- vertical alignment in cells  -->
<!--
  Use THEAD to duplicate headers when breaking table across page
  boundaries, or for static headers when TBODY sections are rendered
  in scrolling panel.

  Use TFOOT to duplicate footers when breaking table across page
  boundaries, or for static footers when TBODY sections are rendered
  in scrolling panel.

  Use multiple TBODY sections when rules are needed between groups
  of table rows.
-->
<!ATTLIST Thead                  -- table section                  --
  %attrs;                        -- attributes                     --
  %cellhalign;                   -- horizontal alignment in cells  --
  %cellvalign;                   -- vertical alignment in cells    --
  >
<!ATTLIST Tbody                  -- table section                  --
  %attrs;                        -- attributes                     --
  %cellhalign;                   -- horizontal alignment in cells  --
  %cellvalign;                   -- vertical alignment in cells    --
  >
<!ATTLIST Tfoot                  -- table section                  --
  %attrs;                        -- attributes                     --
  %cellhalign;                   -- horizontal alignment in cells  --
  %cellvalign;                   -- vertical alignment in cells    --
  >

<!ATTLIST Tr                     -- table row                      --
  %attrs;                        -- attributes                     --
  %cellhalign;                   -- horizontal alignment in cells  --
  %cellvalign;                   -- vertical alignment in cells    -->

<!-- Scope is simpler than axes attribute for common tables        -->
<!ENTITY % scope "(row|col|rowgroup|colgroup)"                       >

<!-- TH is for headers, TD for data, but for cells as both use TD  -->
<!ATTLIST Th                     -- header or data cell            --
  %attrs;                        -- attributes                     --
  abbr        %text;    #IMPLIED -- abbreviation for header cell   --
  axis        CDATA     #IMPLIED -- names groups of related headers--
  headers     IDREFS    #IMPLIED -- list of id's for header cells  --
  scope       %scope;   #IMPLIED -- scope covered by header cells  --
  width       %length;  #IMPLIED -- width relative to table        --
  rowspan     %integer; "1"      -- number of rows spanned by cell --
  colspan     %integer; "1"      -- number of cols spanned by cell --
  %cellhalign;                    -- horizontal alignment in cells --
  %cellvalign;                    -- vertical alignment in cells   -->
  
<!ATTLIST Td                     -- header or data cell            --
  %attrs;                        -- attributes                     --
  abbr        %text;    #IMPLIED -- abbreviation for header cell   --
  axis        CDATA     #IMPLIED -- names groups of related headers--
  headers     IDREFS    #IMPLIED -- list of id's for header cells  --
  scope       %scope;   #IMPLIED -- scope covered by header cells  --
  width       %length;  #IMPLIED -- width relative to table        --
  rowspan     %integer; "1"      -- number of rows spanned by cell --
  colspan     %integer; "1"      -- number of cols spanned by cell --
  %cellhalign;                    -- horizontal alignment in cells --
  %cellvalign;                    -- vertical alignment in cells   -->

<!-- ************************************************************* -->
<!--                          7.3 Motif-table                      -->
<!-- ************************************************************* -->
<!ELEMENT Motif-data (Motif-data*)                                   >
<!ATTLIST Motif-data
  %attrs;
  -- if hierachical, top level owns next level, etc.               --
  -- if flat, use comma-separated lists                            --
  -- if flat and site series for 1-element motif, one-element=true --
  one-element %yesorno; "0"   -- by default, multi-element is true --
  positions   CDATA #REQUIRED -- ,-separated list of positions     --
  widths      CDATA #IMPLIED  -- ,-separated list of motif widths  --
  strands     CDATA #IMPLIED  -- ,-separated list of plus=1,minus=0--
  titles      CDATA #IMPLIED  -- ,-separated list of titles        --
  values      CDATA #IMPLIED  -- ,-separated list of values        --
  markers     CDATA #IMPLIED  -- ,-separated 5 prime offsets       --
  overhangs   CDATA #IMPLIED  -- ,-separated overhang on minus std --
  refs        CDATA #IMPLIED  -- space-separated list of IDs       -->

<!ELEMENT Sequence-motif (Interval-loc*,Motif-data*)                 >
<!ATTLIST Sequence-motif
  %attrs;
       -- if display-auto, create default display widget and show  --
  display-auto %yesorno; #IMPLIED
       -- auto-view is view to which to attach display widget      --
       -- if not defined, feature added to first view for this seq --
  auto-view   IDREF      #IMPLIED
  seqref      IDREF      #REQUIRED -- reference sequence           --
  alignment   %integer;  #IMPLIED  -- alignment pos on global seq  --
  startpos    %integer;  #IMPLIED  -- optional start of seq range  --
  endpos      %integer;  #IMPLIED  -- optional end of seq range    --
  refs        CDATA      #IMPLIED  -- space-separated list of IDs  -->

<!ELEMENT Motif-element EMPTY    -- describes one element of motif -->
<!ATTLIST Motif-element
  %attrs;
       -- if display-auto, create default display widget and show  --
  display-auto      %yesorno; #IMPLIED
  -- fill applies to intervals --
  border-color      %color;   #IMPLIED  -- edge of rectangle       --
  fill-fg-color     %color;   #IMPLIED  -- foreground of fill area --
  fill-bg-color     %color;   #IMPLIED  -- background of fill area --
  fill-pattern      (clear|horiz|vert|fdiag|bdiag|
                      cross|diagcross|solid) #IMPLIED
  column-width      %length;  #IMPLIED -- if non-positional display--
  show-values       %yesorno; #IMPLIED -- if 1, show data values   --
  show-titles       %yesorno; #IMPLIED -- if 1, show titles        --
  show-no-position  %yesorno; #IMPLIED -- if 1, show at side       --
  state-names       CDATA     #IMPLIED 
  -- state names are ,separated list for position values= -1,-2,   --
  value-scale       %integer; #IMPLIED  -- divide by power of 10   --
  value-min         %integer; #IMPLIED    -- to show as saturation --
  value-max         %integer; #IMPLIED    -- to show as saturation -->

<!ELEMENT Motif-table (Attribute*,Numbering?,
                       Interval-loc*,Motif-element*,Sequence-motif*) >
<!ATTLIST Motif-table
  %attrs;
  display-height     %length;  #IMPLIED  -- each line of display   --
  display-gap        %length;  #IMPLIED  -- distance between lines --
  point-width        %length;  #IMPLIED  -- line width for points  --
  title-width        %length;  #IMPLIED  -- if defined, show titles--
  value-width        %length;  #IMPLIED  -- if defined, show values--
  values-as-color    %yesorno; #IMPLIED  -- values as saturation   --
  value-scale        %integer; #IMPLIED  -- divide by power of 10  --
  global-length      %integer; #IMPLIED  -- =longest seq otherwise --
  refs               IDREFS    #IMPLIED  --element cross-references-->
<!-- Note: For further information on the use of the display
           parameters, see the browser motif viewer description;
           the display attributes are all optional if the goal
           is simply to convey information content.                -->
           
<!-- ************************************************************* -->
<!--                    7.4 Alignment-point-set                    -->
<!-- ************************************************************* -->

<!ELEMENT Alignment-point-set  (Attribute*,Numbering?)               >
<!ATTLIST Alignment-point-set
  %attrs;
  seqids     IDREFS    #REQUIRED       -- ids of sequencess        --
  featids    CDATA     #REQUIRED       
  -- ids of corresponding features, points or intervals, or actual
                  position values; value="NONE" means not included --
  captions   CDATA     #IMPLIED   -- n - 1 comma separated
                   captions to be shown on lines connecting points --
  consensus %yesorno;  #IMPLIED        --true if 1st=consensus seq --
       -- next 4 borrowed attributes from Dense-seg in ncbi asn.1  --
  numseg     %integer; #IMPLIED           -- number of segments    --
  starts     CDATA     #IMPLIED           -- offsets               --
  strands    CDATA     #IMPLIED           -- "P" or "M" - strand   --
  seglens    CDATA     #IMPLIED           -- lengths of segments   --
  refs       IDREFS    #IMPLIED        -- element cross-references -->

<!-- ************************************************************* -->
<!--                      7.5 Seq-pair-alignment                   -->
<!-- ************************************************************* -->

<!ELEMENT Seq-pair-run (Attribute*)          -- run of similarity  -->
<!ATTLIST Seq-pair-run
  id             IDREF     #IMPLIED         -- unique identifier   --
  translated     %yesorno; #IMPLIED         -- compared translated --
  runlength      %integer; #REQUIRED        -- length on ref seq   --
  comprunlength  %integer; #IMPLIED         -- if <> runlength     --
  refpos         %integer; #REQUIRED        -- position on ref     --
  refcomplement  %yesorno; #IMPLIED         -- true if comp strand --
  comppos        %integer; #REQUIRED        -- position on comp    --
  compcomplement %integer; #IMPLIED         -- true if comp strand --
  runscore       CDATA     #IMPLIED         -- displayable value   --
  runprob        CDATA     #IMPLIED         -- probability         --
  alignment      CDATA     #IMPLIED         -- transform compseq   --
  -- The alignment transforms the reference sequence into
     the comparison sequence; it uses following terminology:
       =N      next N bases/residues are identical
       -N:Mcc...replace next N bases/residues with following M
       for example =5-3:2ac-0:4acgt=20-4:0                    --
  refs          IDREFS     #IMPLIED    -- element cross-references -->

<!ELEMENT Seq-pair-alignment (Attribute*,Seq-pair-run*)              >
<!ATTLIST Seq-pair-alignment
  %attrs;
  refseq        IDREF     #REQUIRED    -- reference sequence       --
  refxref       CDATA     #IMPLIED     -- database reference       --
  refcaption    CDATA     #IMPLIED     -- display caption          --
  refstart      %integer; #IMPLIED     -- overall region searched  --
  refend        %integer; #IMPLIED     -- end of search region     --
  reflength     %integer; #IMPLIED     -- complete seq length      --
  compseq       IDREF     #IMPLIED     -- comparison sequence      --
  compxref      CDATA     #IMPLIED     -- database reference       --
  compcaption   CDATA     #IMPLIED     -- display caption          --
  compstart     %integer; #IMPLIED     -- overall region searched  --
  compend       %integer; #IMPLIED     -- end of search region     --
  complength    %integer; #IMPLIED     -- complete seq length      --
  method        CDATA     #IMPLIED     -- comparison notes         --
  runminscore   CDATA     #IMPLIED     -- minimum run score        --
  runmaxscore   CDATA     #IMPLIED     -- maximum run score        --
  totalscore    CDATA     #IMPLIED     -- total alignment score    --
  refs          IDREFS    #IMPLIED     -- element cross-references -->

<!-- ************************************************************* -->
<!--                   8.0 Display Sub-divisions                   -->
<!-- ************************************************************* -->
<!ELEMENT Display (Links?,Fonts?,Styles?,Screen?,Paper?,Page+)       >
<!-- screen and paper set defaults for all pages, if defined       -->
<!ATTLIST Display
  master-doc      %yesorno;      #IMPLIED           -- project head--
  first-page      %integer;      #IMPLIED           -- display 1st --
  default-unit    (pct|cm|in|px) "in"               -- see 1.2     --
  line-width-base %length;       "0.01in"           -- see 1.2     --
  line-width-inc  %length;       "0.01in"           -- see 1.2     -->
<!-- ************************************************************* -->
<!--                     9.0 XML Linking Elements                  -->
<!-- ************************************************************* -->
<!ELEMENT Attribute-list (Attribute)*              --list of values-->
<!ATTLIST Attribute-list
  %attrs;
  idref  IDREF    #IMPLIED                    -- reference element -->
<!ELEMENT Info (Attribute)*                        --list of values-->
<!ATTLIST Info
  %attrs;
  idref  IDREF    #IMPLIED                    -- reference element -->
<!-- refer to XML documentation for discussion of linking elements -->
<!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
  href            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
  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 Group-link (Document-link)*                                >
<!ATTLIST Group-link
  id              ID       #IMPLIED
  xml-link        CDATA    #FIXED "GROUP"
  steps           CDATA    #IMPLIED
  role            CDATA    #IMPLIED
  href            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 "(Attribute-list|Link|Extended-link|Group-link)*"   >

<!-- ************************************************************* -->
<!--                           Links Element                       -->
<!-- ************************************************************* -->
<!ELEMENT Links  %links;                     -- any number of link -->
<!-- ************************************************************* -->
<!--                           10.0 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,underline). 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.
-->
<!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 numbering default font   --
  fixed-font IDREF #IMPLIED  -- points to fixed width default font --
  font-sizes CDATA #IMPLIED  -- comma separated list of
                                 sizes in points for font size 1-7 -->

<!-- ************************************************************* -->
<!--               HTML 4.0 Fonts -   modified                     -->
<!-- ************************************************************* -->
<!ELEMENT Font EMPTY  -- Note: not used to enclose text as in html -->
<!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 inheritance    --
         -- if no reference font is given, the default font is used --
  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 (BSML)       --
  italic    %yesorno; #IMPLIED -- 1 = italic, 0 = normal (BSML)     --
  underline %yesorno; #IMPLIED -- 1 = underline, 0 = normal (BSML)  --
  fixed   %yesorno; "0"       -- set as fixed pitch font (BSML)   -->
<!--
  Attribute definitions
  size = cdata
  This attribute sets the size of the font. Possible values:
   o An integer between 1 and 7. This sets the font to a fixed size;
     rendering depends on the user agent. Not all user agents may
     render all seven sizes.
   o A relative increase in font size. The value "+1" means one size
     larger. The value "-3" means three sizes smaller. All sizes
     belong to the scale of 1 to 7.
   o An absolute size in pts, e.g., size="14pt".
color = color
     This attribute sets the text color.
face = cdata-list
     This attribute defines a comma-separated list of font names
     the user agent should search for in order of preference.
-->
<!-- ************************************************************* -->
<!--                             11.0 Styles                       -->
<!-- ************************************************************* -->
<!ELEMENT Styles (Style-import*,Style?)        -- CSS Style Sheets -->

<!ELEMENT Style-import EMPTY             -- imported Style section -->
<!ATTLIST Style-import
            %attrs;                               -- attributes    --
            source             %url;  #REQUIRED   -- CSS document  -->

<!ELEMENT Style   (#PCDATA)                     -- CSS style info  -->
<!ATTLIST Style
  type     %contenttype; #REQUIRED --content type of style lang.   --
                                   -- = "css/text" for now         --
  media    %mediadesc;   #IMPLIED  --for use with these media      --
  title    %text;        #IMPLIED  --advisory title                -->
<!-- ************************************************************* -->
<!--           12.0 Pages, Views and Display Objects               -->
<!-- ************************************************************* -->
<!-- ************************************************************* -->
<!--       12.1 HTML 4.0 Object and Param, slightly modified       -->
<!-- ************************************************************* -->
<!ELEMENT Object (Param)*           -- generic embedded object -->
<!ATTLIST Object
  %attrs;                          -- attributes                   --
  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 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         -->

<!-- ************************************************************* -->
<!--    12.2 HTML 4.0 Client-side image maps slightly modified     -->
<!-- ************************************************************* -->
<!ELEMENT Image-map (Area)+               -- client-side image map -->
<!ATTLIST Image-map
  %attrs;                           -- attributes                  --
  name        CDATA      #REQUIRED  -- name of image map for refs  -->

<!ELEMENT Area EMPTY      -- client-side image map area            -->
<!ATTLIST Area
  %attrs;                          -- attributes                   --
  shape       %shape;    "rect"    -- interpretation of coords     --
  coords      %coords;   #IMPLIED  -- comma separated length list  --
  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   -->
<!-- Note: Most of these attributes are not supported by the
           current version of the browser.                         -->

<!-- ************************************************************* -->
<!--                  12.3 Page Utility Elements                   -->
<!-- ************************************************************* -->
<!ELEMENT Coord  EMPTY                   -- coordinates of a point -->
<!ATTLIST Coord
  %attrs;
  hloc %length; #IMPLIED                 -- horizontal coordinate  --
  vloc %length; #IMPLIED                 -- vertical coordinate    -->

<!ELEMENT Quantifier EMPTY            -- display aspect quantifier -->
<!ATTLIST Quantifier
  %attrs;
  type (color|saturation|length) #REQUIRED
  min-val     %real;  "0.0"             -- (value - min)/(max-min) --
  max-val     %real;  "1.0"
                              -- base and slope used if not color  --
  val-name    CDATA   #IMPLIED            -- if color or length    --
  base        %real;  #IMPLIED --y = slope * val + base --
  slope       %real;  #IMPLIED
  minimum     %real;  #IMPLIED                    -- do not exceed --
  maximum     %real;  #IMPLIED                    -- do not exceed --
  red-base    %real;  #IMPLIED                    -- if type=color --
  red-slope   %real;  #IMPLIED
  blue-base   %real;  #IMPLIED                    -- if type=color --
  blue-slope  %real;  #IMPLIED
  green-base  %real;  #IMPLIED                    -- if type=color --
  green-slope %real;  #IMPLIED
  to-white    %yesorno; #IMPLIED            -- saturation to white -->

<!ELEMENT Margin EMPTY                      -- page and other uses -->
<!ATTLIST Margin
  %attrs;
  margin     %length; #IMPLIED
  horizontal %length; #IMPLIED
  vertical   %length; #IMPLIED
  left       %length; #IMPLIED
  right      %length; #IMPLIED
  top        %length; #IMPLIED
  bottom     %length; #IMPLIED                                        >

<!ELEMENT Screen (Margin?)     --default attribs of screen display -->
<!ATTLIST Screen
  %attrs;
  width      %length;  #IMPLIED       -- width of drawing canvas   --
  height     %length;  #IMPLIED       -- height of drawing canvas  --
  color      %color;   #IMPLIED       -- color for screen,or white --
  monochrome %yesorno; "0"           -- print black/white only    -->

<!ELEMENT Paper  (Margin?)    -- default attribs of printed output -->
<!ATTLIST Paper
  %attrs;
  monochrome %yesorno; "0"           -- print black/white only    --
  landscape  %yesorno; "0"           -- if not, print portrait    -->

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

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

<!ELEMENT X-axis (Numbering?)           -- sequence scale -->
<!ATTLIST X-axis
  use-interval   %yesorno;   #IMPLIED           -- else default    --
  interval-value %integer;   #IMPLIED           -- if user-int     --
  tick-length    %length;    #IMPLIED           -- scale tick      --
  tick-width     %linewidth; #IMPLIED           -- tick width      --
  tick-color     %color;     #IMPLIED           -- tick mark color --
  axis-font      IDREF       #IMPLIED           -- font reference  -->

<!ELEMENT Y-axis (Numbering?)           -- sequence scale -->
<!ATTLIST Y-axis
  use-interval   %yesorno;   #IMPLIED           -- else default    --
  interval-value %integer;   #IMPLIED           -- if user-int     --
  tick-length    %length;    #IMPLIED           -- scale tick      --
  tick-width     %linewidth; #IMPLIED           -- tick width      --
  tick-color     %color;     #IMPLIED           -- tick mark color --
  axis-font      IDREF       #IMPLIED           -- font reference  -->

<!ELEMENT Chart (Border?)    -- chart display to locate chart data -->
<!ATTLIST Chart
  %attrs;
  source        %url;     #IMPLIED               -- source=file    --
  tableid       IDREF     #IMPLIED               -- source=table   --
  bycolumn      %yesorno; "1"          -- if false, data by rows --
  colrownum     %integer; #IMPLIED         -- number of row or col -->

<!ELEMENT Member EMPTY   -- used to define sequence point in group -->
<!ATTLIST Member
  caption        CDATA     #IMPLIED           -- optional title    --
  position       %integer; #REQUIRED          -- sequence position --
  plus           %yesorno; #IMPLIED           -- on plus strand    --
  display        %yesorno; #IMPLIED           -- select to show    --
  value          CDATA     #IMPLIED           -- optional          -->

<!-- ************************************************************* -->
<!--                      12.4 Display Set Types                   -->
<!-- ************************************************************* -->
<!-- ************************************************************* -->
<!--                      12.4.1 Simple-set                        -->
<!-- ************************************************************* -->
<!ELEMENT Simple-set-widget (Coord,Border?,Set*,Object?,%links;)
                           -- is Set elements, these refer to links-->
<!ATTLIST Simple-set-widget
  %attrs;
  own-window %yesorno;   #IMPLIED        -- embed on page if false --
  setids     IDREFS      #IMPLIED        -- ids of set             --
  caption    CDATA       #IMPLIED        -- display title          --
  capt-font  IDREF       #IMPLIED        -- caption font           --
  list-font  IDREF       #IMPLIED        -- item list font         --
  align     (left|center|right) #IMPLIED -- align list             --
  line-link  %yesorno;   #IMPLIED        -- link set members       --
  line-width %linewidth; #IMPLIED        -- linking line           --
  line-color %color;     #IMPLIED        -- line color             --
  depth      %integer;   #IMPLIED        -- recursion depth        --
  indent     %length;    #IMPLIED        -- distance for child     -->

<!-- ************************************************************* -->
<!--                         12.4.2 Tree-set                       -->
<!-- ************************************************************* -->
<!--
  Tree-set = 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-node EMPTY                                            >
<!ATTLIST Tree-node
  %attrs;
  hloc       %length;  #REQUIRED      -- relative position on page --
  vloc       %length;    #REQUIRED    -- relative position on page --
  setid      IDREF       #IMPLIED     -- if none = node only       --
  parentid   IDREF       #IMPLIED     -- if none is root           --
  node-font  IDREF       #IMPLIED     -- item list font            --
  line-width %linewidth; #IMPLIED     -- linking line              --
  line-color %color;     #IMPLIED     -- line color                --
  branchlen  %length;    #IMPLIED     -- branch length             --
  text-gap   %length;    #IMPLIED     -- gap line to text          --
  text-space %length;    #IMPLIED     -- vertical space            --
  node-caption CDATA     #IMPLIED     -- print at node             --
                             -- vertical alignment of node caption --
  node-cap-valign (top|middle|bottom|baseline) #IMPLIED
                           -- horizontal aligmment of node caption --
  node-cap-halign (left|center|right) #IMPLIED
  branch-caption CDATA                #IMPLIED
  branch-cap-above %yesorno;          #IMPLIED  -- true=above line -->

<!ELEMENT Tree-set-widget (Coord,Border?,Tree-node*,Object?,%links;) >
<!ATTLIST Tree-set-widget
  %attrs;
            -- content attributes, sequence includes intervals     --
  seqtype       (nucleotide|protein|both) #IMPLIED
  elementtype   (sequence|feature|mixed)  #IMPLIED
            --                  display attributes                 --
  caption        CDATA       #IMPLIED        -- display title      --
  capt-font      IDREF       #IMPLIED        -- caption font       --
  node-cap-font   IDREF      #IMPLIED        -- node captions      --
  branch-cap-font IDREF      #IMPLIED        -- branch captions    --
  leaf-value-font IDREF      #IMPLIED        -- leaf captions      --
  show-leaf-values %yesorno; #IMPLIED
  show-sequence %yesorno;    #IMPLIED        -- only names if no   --
  orientation (vertical|horizontal) #IMPLIED -- sequences          --
           -- if link-straight is false, rectangular links drawn   --
  link-straight  %yesorno;   #IMPLIED       -- straight lines      --
            --      attributes used by default for all links       --
  node-font  IDREF    #IMPLIED              -- item list font      --
  line-width %linewidth; #IMPLIED           -- linking line        --
  line-color %color;     #IMPLIED           -- line color          --
  branchlen %length;     #IMPLIED           -- branch length       --
  text-gap  %length;     #IMPLIED           -- gap line to text    --
  text-space %length;    #IMPLIED           -- vertical spacing    -->

<!-- ************************************************************* -->
<!--                   12.4.3 Alignment-point-sets                 -->
<!-- ************************************************************* -->
<!ELEMENT Alignment-point-sets-widget (Symbol?,Object?,%links;)  >
<!ATTLIST Alignment-point-sets-widget
          %attrs;
          pointsets  IDREFS    #REQUIRED -- ids of point sets      --
          alignto    IDREF     #IMPLIED  -- reference view         --
          viewids    IDREFS    #REQUIRED  -- ids of views          --
          capt-font  IDREF     #IMPLIED   -- caption font          --
          capt-above %yesorno; #IMPLIED  -- captions above line    --
          line-width %length;  #IMPLIED
          line-color %color;   #IMPLIED                              >

<!-- ************************************************************* -->
<!--          12.4.4 Dot-plot using Seq-pair-alignment             -->
<!-- ************************************************************* -->
<!ELEMENT Dot-plot-widget (Coord,
                        X-axis?,Y-axis?,Quantifier?,Object?,%links;) >
<!-- display a dot matrix plot for a pair of sequences showing runs-->
<!ATTLIST Dot-plot-widget
  %attrs;
  seqpair        IDREF       #REQUIRED     -- reference pair align --
  width          %length;    #IMPLIED
  height         %length;    #IMPLIED
  use-x-axis     %yesorno;   #IMPLIED
  use-y-axis     %yesorno;   #IMPLIED
  y-proportional %yesorno;   #IMPLIED      -- ignore height        --
  y-on-top       %yesorno;   #IMPLIED      -- number from top down --
  line-width     %linewidth; #IMPLIED
  line-color     %color;     #IMPLIED
  border-width   %linewidth; #IMPLIED
  border-color   %color;     #IMPLIED
  min-runlength  %integer;   #IMPLIED      -- display threshold    --
  min-runscore   %real;      #IMPLIED      -- display threshold    --
  max-runscore   %real;      #IMPLIED      -- display threshold    -->

<!ENTITY % setwidgets "(Simple-set-widget|Tree-set-widget|
  Alignment-point-sets-widget|Dot-plot-widget)" >

<!-- ************************************************************* -->
<!--        12.5 View (Sequence)-relative Display Widgets          -->
<!-- ************************************************************* -->
<!ELEMENT View-line-widget  EMPTY                 -- sequence line -->
<!ATTLIST View-line-widget
  %attrs;
  strands        (one|two)    #IMPLIED
  shape          (circular|horizontal|vertical) #IMPLIED
  hcenter        %length;     #IMPLIED        -- center - horiz    --
  vcenter        %length;     #IMPLIED        -- center - vert     --
  haligned       %yesorno;    #IMPLIED        -- aligned to view   --
  halignview     IDREF        #IMPLIED        -- view ref          --
  valigned       %yesorno;    #IMPLIED        -- aligned to view   --
  valignview     IDREF        #IMPLIED        -- view ref          --
  width          %linewidth;  #IMPLIED        -- strand line width --
  gap            %length;     #IMPLIED        -- between strands   --
  linear-length  %length;     #IMPLIED        -- line length       --
  circular-diam  %length;     #IMPLIED        -- circle diam       --
  plus-color     %color;      #IMPLIED        -- strand color      --
  minus-color    %color;      #IMPLIED        -- strand color      --
  interval-gap-width %length; #IMPLIED        -- gap for intervals --
  site-criterion  CDATA #IMPLIED  -- absolute units or %
       of complete sequence in current view below which to display --
  group-criterion  CDATA #IMPLIED  -- absolute units or %
       of complete sequence in current view below which to display --
  interval-criterion CDATA #IMPLIED  -- absolute units or %
       of complete sequence in current view below which to display --
  interval-as-point CDATA #IMPLIED  -- absolute units or % of
     complete sequence in current view below which to show as point-->

<!ELEMENT View-axis-widget EMPTY                 -- sequence scale -->
<!ATTLIST View-axis-widget
  %attrs;
  linear-at-side  %yesorno; #IMPLIED             -- if linear      --
  linear-offset   %length;  #IMPLIED             -- from seq line  --
  circular-rotate %yesorno; #IMPLIED             -- base at top    --
  base-at-top     %integer; #IMPLIED             -- if circular    --
  use-interval    %yesorno; #IMPLIED             -- else default   --
  interval-value  %integer; #IMPLIED             -- if user-int    --
  axis-strand     (both|minus|plus) #IMPLIED     -- strand         --
  tick-length     %length;  #IMPLIED             -- scale tick     --
  tick-width      %linewidth; #IMPLIED           -- tick width     --
  tick-color      %color;   #IMPLIED             -- tick mark color--
  axis-font       IDREF     #IMPLIED             -- font reference -->

<!ELEMENT Point-widget (Symbol?,Object?,%links;)     --1 pt on seq -->
<!ATTLIST Point-widget
  %attrs;  featureref    IDREF     #IMPLIED -- id of feature      --
  position      %integer; #IMPLIED -- from source feature,
                                                if not specified   --
  on-strand     (both|plus|minus|source) #IMPLIED
  caption       CDATA     #IMPLIED           -- no text needed     --
  caption-font  IDREF     #IMPLIED           -- select by idref    --
  position-font IDREF     #IMPLIED           -- font by idref      --
  align-text    (auto-align|top|center|bottom) #IMPLIED
  text-length   %length;  #IMPLIED          -- maximum line length --
  wrap-text     %yesorno; #IMPLIED          -- wrap at max line    --
  show-text     %yesorno; #IMPLIED          -- display caption     --
  show-position %yesorno; #IMPLIED          -- display pos number  --
  line-gap      %length;  #IMPLIED          -- gap to seq line     --
  text-gap      %length;  #IMPLIED          -- gap to caption      --
  line-width    %length;  #IMPLIED          -- pointer width       --
  line-color    %color;   #IMPLIED          -- pointer color       --
  line-length   %length;  #IMPLIED          -- pointer length      -->

<!--Point-group may refer to Members, Features, or Point-widgets   -->

<!ELEMENT Point-group-widget (Quantifier?,Member*,Object?,%links;)   >
<!ATTLIST Point-group-widget
  %attrs;
  featureref    IDREF     #IMPLIED -- id of feature                --
  show-as-one   %yesorno; #IMPLIED -- show as one site using
                         defcaption and caption-font and group-pos --
  check-members %yesorno; #IMPLIED -- check display on for each    --
  group-pos     %integer; #IMPLIED     -- if show-as-one=1         --
  featurerefs   IDREFS    #IMPLIED -- get sites from features
                                          or digest sets           --
  sites         CDATA     #IMPLIED    -- comma separated site list --
  on-strand     (plus|minus|source|auto-strand) #IMPLIED
  auto-plot     %yesorno; #IMPLIED -- plot automatically           --
  one-vert-col  %yesorno; #IMPLIED -- applies to vertical only     --
  defcaption    CDATA     #IMPLIED -- default caption              --
  caption-font  IDREF     #IMPLIED -- select by idref              --
  position-font IDREF     #IMPLIED -- font by idref                --
  align-text    (auto-align|top|center|bottom) #IMPLIED
  text-length   %length;  #IMPLIED -- maximum line length          --
  wrap-text     %yesorno; #IMPLIED -- wrap at max line             --
  show-text     %yesorno; #IMPLIED -- display caption              --
  show-position %yesorno; #IMPLIED -- display position number      --
  line-gap      %length;  #IMPLIED -- default if not specified     --
  text-gap      %length;  #IMPLIED -- default if not specified     --
  line-width    %length;  #IMPLIED -- default if not specified     --
  line-color    %color;   #IMPLIED -- default if not specified     --
  line-length   %length;  #IMPLIED -- default if not specified     -->

<!ELEMENT Interval-widget (Object?,%links;)    -- display interval -->
<!ATTLIST Interval-widget
  %attrs;
  featureref      IDREF     #IMPLIED  -- id of feature             --
  startpos        %integer; #REQUIRED -- start of interval         --
  endpos          %integer; #REQUIRED -- end of interval           --
  show-start-err  %yesorno; #IMPLIED  -- error bar at start        --
  start-err-len   %integer; #IMPLIED  -- length of bar             --
  show-end-err    %yesorno; #IMPLIED  -- error bar at end          --
  end-err-len     %integer; #IMPLIED  -- length of bar             --
  on-sequence     CDATA     #IMPLIED
                      -- position on sequence = (center,plus,minus)--
  gap-in-seq-line %yesorno;       #IMPLIED -- yes=gap around intvl --
  show-positions  (no|plus|minus) #IMPLIED -- show numbers         --
  start-pos-only  %yesorno;       #IMPLIED -- show only start pos  --
  position-font   IDREF           #IMPLIED -- font for numbers     --
  line-width      %linewidth;     #IMPLIED -- border of rectangle  --
  interior-gap    %length;        #IMPLIED -- interior of rect     --
  fill-pattern    (clear|horiz|vert|fdiag|bdiag|
                   cross|diagcross|solid) #IMPLIED -- fill of rect --
  border-color    %color;   #IMPLIED       -- color or rect border --
  fill-fg-color   %color;   #IMPLIED       -- interior foreground  --
  fill-bg-color   %color;   #IMPLIED       -- interior background  --
  auto-offset     %yesorno; #IMPLIED       -- find open area auto  --
  offset-from-seq %length;  #IMPLIED       -- distance from seq    --
  arrow-start-len %length;  #IMPLIED       -- arrow length if used --
  arrow-end-len   %length;  #IMPLIED       -- arrow length if used --
  arrow-width     %length;  #IMPLIED       -- width of either      --
  bracket-text-gap %length; #IMPLIED       -- text to bracket      --
  bracket-line-gap %length; #IMPLIED       -- bracket to rect      --
  bracket-line-len %length; #IMPLIED       -- length of bracket    --
  bracket-line-wid %length; #IMPLIED       -- width of bracket line--
  bracket-color    %color;  #IMPLIED       -- color of bracket line--
  plus-text        CDATA    #IMPLIED       -- plus strand caption  --
  plus-font        IDREF    #IMPLIED       -- for for caption      --
  plus-bracket     CDATA    #IMPLIED -- none,angled,tee (linear)   --
  minus-text       CDATA    #IMPLIED       -- minus strand caption --
  minus-font       IDREF    #IMPLIED       -- font for caption     --
  minus-bracket    CDATA    #IMPLIED -- none,angled,tee (linear)   --
  center-text      CDATA    #IMPLIED       -- caption in rectangle --
  center-font      IDREF    #IMPLIED       -- font for caption     --
  start-type       CDATA    #IMPLIED -- none,blunt,round,arrow     --
  end-type         CDATA    #IMPLIED -- none,blunt,round,arrow     -->

<!ELEMENT Blowup-widget (Object?,%links;)       -- display blowup  -->
<!ATTLIST Blowup-widget
  %attrs;
  featureref       IDREF     #IMPLIED      -- id of feature        --
  startpos         %integer; #REQUIRED     -- start of interval    --
  endpos           %integer; #REQUIRED     -- end of interval      --
  on-plus          %yesorno; #IMPLIED      -- position on sequence --
  line-width       %linewidth; #IMPLIED    -- see interval widget  --
  interior-gap     %length;    #IMPLIED
  fill-pattern     (clear|horiz|vert|fdiag|bdiag|
                         cross|diagcross|solid) #IMPLIED
  border-color     %color;  #IMPLIED
  fill-fg-color    %color;  #IMPLIED
  fill-bg-color    %color;  #IMPLIED
  bracket-text-gap %length; #IMPLIED
  bracket-line-gap %length; #IMPLIED
  bracket-line-len %length; #IMPLIED
  bracket-line-wid %length; #IMPLIED
  bracket-color    %color;  #IMPLIED
  cut-thickness    %length; #IMPLIED
  plus-text        CDATA    #IMPLIED      -- text inside blowup    --
  plus-font        IDREF    #IMPLIED      -- caption for text      --
  minus-text       CDATA    #IMPLIED      -- second line of text   --
  minus-color      %color;  #IMPLIED      -- caption for text      --
  inside-text      CDATA    #IMPLIED      -- text opposite blowup  --
  inside-font      IDREF    #IMPLIED      -- font for text         --
  outside-text     CDATA    #IMPLIED      -- text outside blowup   --
  outside-font     IDREF    #IMPLIED      -- font for text         -->

<!ELEMENT Aligned-chart-widget (Chart,Quantifier?,Object?,%links;)   >
<!ATTLIST Aligned-chart-widget -- gets its data from Chart element --
  %attrs;
  featureref      IDREF       #IMPLIED      -- id of feature       --
  full-only       %yesorno;   #IMPLIED      -- show only all data  --
  min-points      %integer;   #IMPLIED      -- min points to show  --
  field-number    %integer;   #IMPLIED      -- if fields are space
      or comma separated, indicate which field to read, else first --
  startpos        %integer;   #REQUIRED -- 1st alignment pos on seq--
  endpos          %integer;   #REQUIRED --last alignment pos on seq--
  min-offset      %length;    #REQUIRED -- plot region start offset--
  max-offset      %length;    #REQUIRED -- plot region end offset  --
  on-plus         %yesorno;   #IMPLIED  --if yes, plot on plus side--
  min-data        %real;      #REQUIRED --lowest plotted data value--
  max-data        %real;      #REQUIRED --highest                  --
  dec-places      %integer;   #IMPLIED  -- dec places in display   --
  show-y-axis     %yesorno;   #IMPLIED  -- yes=show y axis range   --
  histogram       %yesorno;   #IMPLIED  -- yes=plot points as histo--
  line-width      %linewidth; #IMPLIED  -- width of plotting line  --
  line-color      %color;     #IMPLIED  -- color of plotting line  --
  caption         CDATA       #IMPLIED  -- chart caption           --
  caption-font    IDREF       #IMPLIED  -- font for caption        --
  data-font       IDREF       #IMPLIED  -- font for axis labels    --
  standard-height %yesorno;   #IMPLIED   -- histogram + quantifier -->

<!ENTITY % seqdisplaywidgets "(Point-widget|Point-group-widget|
                              Interval-widget|Blowup-widget|
                              View-axis-widget|View-line-widget|
                              Aligned-chart-widget)*">

<!-- ************************************************************* -->
<!--               12.6 View and View-related Elements             -->
<!-- ************************************************************* -->
<!-- ************************************************************* -->
<!--                           12.6.1 View                         -->
<!-- ************************************************************* -->
<!ELEMENT View (Numbering?,Margin?,%seqdisplaywidgets;,
                             Object?,%links;)  -- view of sequence -->
<!ATTLIST View
  %attrs;
  seqref       IDREF     #REQUIRED           -- sequence id        --
  histref      IDREF     #IMPLIED            -- histogram widget   --
  title1       CDATA     #IMPLIED            -- first title line   --
  title1-font  IDREF     #IMPLIED            -- font for first     --
  title2       CDATA     #IMPLIED            -- second title line  --
  title2-font  IDREF     #IMPLIED            -- font for second    --
  startpos     %integer; #IMPLIED            -- first if not given --
  endpos       %integer; #IMPLIED            -- full if not given  -->
<!-- ************************************************************* -->
<!--                  12.6.2 Feature-histogram-widget              -->
<!-- ************************************************************* -->
<!ELEMENT Feature-histogram-widget (Coord,Object?,%links;)           >
<!ATTLIST Feature-histogram-widget
  %attrs;
  viewref             IDREF       #REQUIRED -- reference view      --
  caption             CDATA       #IMPLIED  -- caption for histo   --
  capt-font           IDREF       #IMPLIED  -- caption font        --
  numb-font           IDREF       #IMPLIED  -- number font         --
  features-histogram  %integer;   #IMPLIED
                     -- 0 = none, 1 = all, 2 = hidden, 3 = showing --
  feature-position    %integer;   #IMPLIED
           -- 0 = left end, 1 = right end, 2 = midpoint, 3 = range --
  nbins               %integer;   #IMPLIED -- number of bins       --
  height-per-bin      %length;    #IMPLIED -- height units         --
  line-width          %linewidth; #IMPLIED -- width of plotting    --
  bin-width           %length;    #IMPLIED -- per bin              --
  line-color          %color;     #IMPLIED -- plotting color       --
  fill-bins           %yesorno;   #IMPLIED -- if true, solid       --
  maximum-height      %length;    #IMPLIED -- total allowed height --
  auto-fit            %yesorno;   #IMPLIED
   -- if true, set height of highest frequency to maximum-height   -->
<!-- ************************************************************* -->
<!--                    12.6.3 View-master                         -->
<!-- ************************************************************* -->
<!ELEMENT View-master-widget (Coord,Object?,%links;)                 >
<!ATTLIST View-master-widget
  views          IDREFS       #IMPLIED     -- if none, all on page --
  width          %length;     #IMPLIED     -- overall width        --
  height         %length;     #IMPLIED     -- overall height       --
  outerwidth     %linewidth;  #IMPLIED     -- dimensions and colors--
  outerborder    %color;      #IMPLIED
  outerfill      %color;      #IMPLIED
  innerwidth     %linewidth;  #IMPLIED
  innerborder    %color;      #IMPLIED
  innerfill      %color;      #IMPLIED
  shapeborder    %color;      #IMPLIED
  shapefill      %color;      #IMPLIED
  disabledborder %color;      #IMPLIED
  disabledfill   %color;      #IMPLIED
  shape       (circular|horizontal|vertical) #IMPLIED
  hcenter        %length;     #IMPLIED           -- center - horiz --
  vcenter        %length;     #IMPLIED           -- center - vert  --
  hoffset        %length;     #IMPLIED           -- to next view   --
  voffset        %length;     #IMPLIED           -- to next view   --
  numviews       %integer;    #IMPLIED           -- # to show      --
  linear-length  %length;     #IMPLIED           -- line length    --
  circular-diam  %length;     #IMPLIED           -- circle diam    -->
<!-- ************************************************************* -->
<!--                     12.6.4 Sequence-viewer                    -->
<!-- ************************************************************* -->
<!--      Sequence-viewer controls display in a separate viewer    -->
<!ELEMENT Class-key EMPTY                                            >
<!ATTLIST Class-key
  key-title     CDATA       #REQUIRED
  key-class     CDATA       #REQUIRED
  border-color  %color;     #IMPLIED
  fill-color    %color;     #IMPLIED
  row           %integer;   #IMPLIED
  enabled       %yesorno;   #IMPLIED
  set-number    %integer;   #IMPLIED                                 >

<!ELEMENT Sequence-viewer (Class-key*,Object?,%links;)               >
<!ATTLIST Sequence-viewer
  %attrs;
  refseq               IDREF       #IMPLIED -- else get from user  --
  maximize-window      %yesorno;   #IMPLIED -- max display window  --
  complete-seq         %yesorno;   #IMPLIED -- show full seq       --
  view-start           %integer;   #IMPLIED -- n/a if complete     --
  view-end             %integer;   #IMPLIED -- n/a if complete     --
  fit-to-window        %yesorno;   #IMPLIED -- whole view shown    --
  spacing              %integer;   #IMPLIED -- 0 to 10 pixels      --
  bases-per-line       %integer;   #IMPLIED -- <=0 = use default   --
  bases-per-window     %integer;   #IMPLIED -- <=0 = use default   --
  int-pos              %integer;   #IMPLIED -- 0 to 10 of min/max  --
  interval-height-min  %integer;   #IMPLIED -- height in pixels    --
  interval-height-max  %integer;   #IMPLIED -- height in pixels    --
  font-pos             %integer;   #IMPLIED -- 0 to 10 of min/max  --
  font-size-min        %integer;   #IMPLIED -- size in points      --
  font-size-max        %integer;   #IMPLIED -- size in points      --
  show-sites           %yesorno;   #IMPLIED -- yes=show sites      --
  sites-as-ints        %yesorno;   #IMPLIED -- sites as intervals  --
  sites-not-full       %yesorno;   #IMPLIED -- if true, no sites
                                               when full view      --
  sites-by-pct         %yesorno;   #IMPLIED -- plot sites only if
                                               view < % of full    --
  sites-percent        %integer;   #IMPLIED
  interval-pos         %integer;   #IMPLIED -- 0=none,1=online,
                                               2=top,3=strand      --
  interval-overlap     %yesorno;   #IMPLIED -- allow overlap       --
  interval-separate    %yesorno;   #IMPLIED -- separate classes    --
  interval-by-width    %yesorno;   #IMPLIED -- if yes, plot as
                                               interval if width   --
 int-pixels            %integer;   #IMPLIED -- criterion or plot   --
 int-as-point          %yesorno;   #IMPLIED -- if test fails, plot
                                              as point if true
                                               or not at all       --
 plus-strand           %yesorno;   #IMPLIED -- plot features on    --
 minus-strand          %yesorno;   #IMPLIED -- plot features on    --
 frame                 %yesorno;   #IMPLIED -- 0=all, or 1,2,3     --
 show-point-titles     %yesorno;   #IMPLIED -- only of int titles  --
 show-interval-titles  %yesorno;   #IMPLIED -- plot text           --
 interval-titles-above %yesorno;   #IMPLIED -- if false plot in box--
 interval-title-once   %yesorno;   #IMPLIED -- if true, show once  --
 title-length          %integer;   #IMPLIED -- text length for plot--
 show-key              %yesorno;   #IMPLIED -- display class key   --
 feature-histogram     %integer;   #IMPLIED -- none,all,hide,show  --
 feature-position      %integer;   #IMPLIED -- start,end,mid,range --
 density-per-window    %yesorno;   #IMPLIED -- false=per 1000 pix  --
 density-method        %integer;   #IMPLIED -- hide,plot,as points --
 density-threshold     %integer;   #IMPLIED -- cutoff              --
 nbins                 %integer;   #IMPLIED -- plotting bins       --
 pixels-per-countX1000 %integer;   #IMPLIED --pixels per countX1000--
 max-histo-height      %integer;   #IMPLIED --maximum height,pixels--
 auto-fit-histogram    %yesorno;   #IMPLIED -- set highest bin max -->

<!-- ************************************************************* -->
<!--           12.7 Other Sequence-related Display Objects         -->
<!-- ************************************************************* -->
<!-- ************************************************************* -->
<!--                        12.7.1 Gel-widget                      -->
<!-- ************************************************************* -->
<!ELEMENT Gel-widget (Coord,Border?,Object?,%links;)                 >
<!--        gel-widget simulates gel electrophoresis display       -->
<!--        using data from Digest-set elements                    -->
<!ATT LIST Gel-widget
  %attrs;
  digests          IDREFS        #REQUIRED  -- digests in sets     --
  title-font       IDREF         #IMPLIED   -- font for title      --
  min-length       %integer;     #IMPLIED   -- minimum frag length --
  max-length       %integer;     #IMPLIED   -- maximum frag length --
  min-label        %integer;     #IMPLIED   -- low axis position   --
  scale-factor     %real;        #IMPLIED   -- scale label         --
  label-decimals   %integer;     #IMPLIED   -- for display         --
  label-ratio      %real;        #IMPLIED   -- labelling ratio     --
  label-font       IDREF         #IMPLIED   -- font for axis       --
  gel-length       %length;      #IMPLIED   -- length of gel       --
  lane-width       %length;      #IMPLIED   -- width per lane      --
  lane-gap         %length;      #IMPLIED   -- between lanes       --
  lane-thick       %linewidth;   #IMPLIED   -- lane border line    --
      -- band thickness inversely proportional to mobility if true --
  lane-color       %color;       #IMPLIED   -- lane edge color     --
  band-prop        %yesorno;     #IMPLIED   -- proportional        --
      -- thickness is used if not proportional or sets the maximum
      if band width is inversely proportional to fragment mobility --
  band-thick       %linewidth;   #IMPLIED   -- band thickness      --
      -- band-low is width of the thinnest band if proportional    --
  band-low         %linewidth;   #IMPLIED   -- thinnest band       --
      -- confusion = distance between bands used to label bands
         as confusable; if 0, bands must touch or overlap          --
  band-color       %color;       #IMPLIED   -- color of bands      --
  confusion        %linewidth;   #IMPLIED   -- overlap test        --
  confusion-color  %color;       #IMPLIED   -- color of confusable --
  plot-big         %yesorno;     #IMPLIED   -- plot if off end     --
  use-key          %yesorno;     #IMPLIED   -- label bands in key  --
  show-band-on-seq %yesorno;     #IMPLIED   -- if true,
            show temporary interval on sequence when band selected -->

<!-- ************************************************************* -->
<!--                     12.7.2 Seq-Data-widget                    -->
<!-- ************************************************************* -->
<!ELEMENT Seq-data-widget (Coord,Border?,Seq-data?,Object?,%links;)  >
<!ATTLIST Seq-data-widget
   -- if has Seq-data element, get data there; if seqref defined,
      get data from sequence; otherwise use source file            --
  %attrs;
  featureref       IDREF         #IMPLIED    -- id of feature      --
  seqref           IDREF         #IMPLIED    -- id of sequence     --
  startpos         %integer;     #REQUIRED   -- offset on sequence --
  length           %integer;     #REQUIRED   -- length of region   --
  caption          CDATA         #IMPLIED    -- caption for display--
  seq-font         IDREF         #IMPLIED    -- font for data      --
  caption-font     IDREF         #IMPLIED    -- font for caption   --
  bases-per-line   %integer;     #IMPLIED    -- wrap after # bases --
  number-bases     %yesorno;     #IMPLIED    -- yes=show numbers   --
  space-blocks     %yesorno;     #IMPLIED    -- yes=space every 10 --
  double-stranded  %yesorno;     #IMPLIED    -- yes=show 2 strands --
  translate-dna    (yes|no|only) #IMPLIED    -- yes/only=translate --
  translate-start  %integer;     #IMPLIED    -- start of translate --
  translate-length %integer;     #IMPLIED    -- length of translate--
  source           %url;         #IMPLIED    -- source of seq data --
  seq-len          %integer;     #IMPLIED    -- if url or Seq-data --
  is-protein       %yesorno;     #IMPLIED    -- if url or Seq-data -->

<!-- ************************************************************* -->
<!--            12.8 Sequence-Independent Display widgets          -->
<!-- ************************************************************* -->
<!ELEMENT Popup-text-widget (#PCDATA)                                >
<!ATTLIST Popup-text-widget
  %attrs;                                                            >
<!ELEMENT Caption-widget (Coord,%links;)                             >
<!ATTLIST Caption-widget
  %attrs;
  text          CDATA                    #IMPLIED  -- caption      --
  font          IDREF                    #IMPLIED  -- capton font  --
  orientation   (horizontal|down|angled) #IMPLIED  -- default=horz --
  angle         %integer;                #IMPLIED  -- if angled    --
  border        %yesorno;                #IMPLIED  -- yes=border   --
  border-gutter %length;                 #IMPLIED  -- border indent--
  border-width  %length;                 #IMPLIED  -- line width   --
  border-color  %color;                  #IMPLIED  -- line color   --
  wordwrap      %yesorno;                #IMPLIED  -- yes=wrap     --
  wrap-length   %length;                 #IMPLIED  -- line length  --
                              -- if horizontal, apply alignment --
  align         (left|center|right)      #IMPLIED                    >

<!ELEMENT Line-pointer-widget (Coord+,%links;)                       >
<!ATTLIST Line-pointer-widget  -- multi-segmented line with arrows --
  -- if specified, the caption is displayed on first segment       --
  -- segments are defined by lust of at least two Coord elements   --
  %attrs;
  line-style %linestyle;       #IMPLIED        -- solid, dash, dot --
  line-width %linewidth;       #IMPLIED
  line-color %color;           #IMPLIED
  use-start-arrow    %yesorno; #IMPLIED
  start-arrow-length %length;  #IMPLIED
  start-arrow-width  %length;  #IMPLIED
  use-end-arrow      %yesorno; #IMPLIED
  end-arrow-length   %length;  #IMPLIED
  end-arrow-width    %length;  #IMPLIED
  caption            CDATA     #IMPLIED
  font               IDREF     #IMPLIED
  above-line         %yesorno; #IMPLIED   -- if caption displayed  -->

<!ELEMENT Shape-widget (Coord,%links;)                               >
<!ATTLIST Shape-widget
  %attrs;
  height        %length;       #IMPLIED   --overall height of shape--
  width         %length;       #IMPLIED   --overall width of shape --
  filled        %yesorno;      #IMPLIED   -- if yes, solid shape   --
  line-width    %linewidth;    #IMPLIED   -- if no, use line width --
  shape         %displayshape; #IMPLIED   -- see shape definition  --
  color         %color;        #IMPLIED   -- color of shape        -->

<!ELEMENT File-widget (Coord?,Border?,Image-map?,Object?,%links;)    >
<!ATTLIST File-widget        -- file may contained graphic or text --
  %attrs;
  own-window    %yesorno; #IMPLIED          -- embed if false      --
  caption       CDATA     #IMPLIED          -- if own window       --
  height        %length;  #IMPLIED          -- 0=use graphic size  --
  width         %length;  #IMPLIED          -- 0=use graphic size  --
  text-font     IDREF     #IMPLIED          -- if text file        --
  type          CDATA     #IMPLIED          --text,gif,jpeg,png,tif--
  source        %url;     #REQUIRED         -- file name or url    -->

<!ELEMENT Table-column EMPTY -- used by table widget to define data-->
<!ATTLIST Table-column
  colnum %integer;           #REQUIRED             -- data column  --
  colwid %length;            #IMPLIED              -- column width --
  align  (left|center|right) "right"                                 >
<!ELEMENT Table-widget (Coord?,Border?,Table-column+,Object?,%links;)>
<!ATTLIST Table-widget
  %attrs;
  own-window  %yesorno;  #IMPLIED  -- display in its own window    --
  own-in-grid %yesorno;  #IMPLIED  -- if own window, grid or html  --
  tableid     IDREF      #REQUIRED -- id of source HTML table      --
  rownums     CDATA      #IMPLIED  -- optional comma separated
                                       row numbers, else all rows  --
  title-font  IDREF      #IMPLIED  -- font for title               --
  header-font IDREF      #IMPLIED  -- font for headers             --
  cell-font   IDREF      #IMPLIED  -- font for cells               --
  row-height  %length;   #IMPLIED  -- else text height             --
  rules       %trules;   #IMPLIED -- rulings between rows and cols --
  rule-color  %color;    #IMPLIED -- color of rule lines           --
  rule-width  %linewidth; #IMPLIED -- width of rule lines          --
  cellspacing %length;   #IMPLIED -- spacing between cells         --
  cellpadding %length;   #IMPLIED -- spacing within cells          -->

<!ELEMENT Text-key-item EMPTY                                        >
<!ATTLIST Text-key-item
  key         CDATA #REQUIRED               -- term defined in key --
  explanation CDATA #REQUIRED               -- definition of term  -->

<!ELEMENT Text-key-widget (Coord,Border?,Text-key-item+,%links;)     >
<!ATTLIST Text-key-widget
  %attrs;
  key-font         IDREF    #IMPLIED      -- key text font         --
  explanation-font IDREF    #IMPLIED      -- explanation text font --
  key-width        %length; #IMPLIED      -- width of key text     --
  item-gap         %length; #IMPLIED      -- vertical gap          -->

<!ELEMENT Fill-key-widget (Coord,Border?,%links;)                    >
<!ATTLIST Fill-key-widget
  %attrs;
  font             IDREF    #IMPLIED -- text font                  --
  pattern-width    %length; #IMPLIED -- box width                  --
  pattern-height   %length; #IMPLIED -- box height                 --
  line-width       %linewidth; #IMPLIED -- shading line width      --
  pattern-gap      %length; #IMPLIED -- gap between boxes          --
        --    clear,horiz,vert,fdiag,bdiag,cross,diagcross,solid   --
  patterns         CDATA    #IMPLIED -- comma-sep list of fills    --
  fore-colors      CDATA    #IMPLIED -- comma-sep list of colors   --
  back-colors      CDATA    #IMPLIED -- comma-sep list of colors   --
  explanations     CDATA    #IMPLIED -- comma-sep separated list   -->

<!ELEMENT Symbol-key-widget (Coord,Border?,%links;)                  >
<!ATTLIST Symbol-key-widget
  %attrs;
  do-substitute %yesorno;   #IMPLIED  -- no substitutions if false --
  font          IDREF       #IMPLIED       -- font for symbol text --
  size          %length;    #IMPLIED       -- diameter of symbol   --
  line-width    %linewidth; #IMPLIED       -- width if open        --
  color         %color;     #IMPLIED       -- symbol color         --
  open-circle   CDATA       #IMPLIED       -- text to replace      --
  closed-circle CDATA       #IMPLIED
  open-square   CDATA       #IMPLIED
  closed-square CDATA       #IMPLIED
  triangle      CDATA       #IMPLIED
  suppress      CDATA       #IMPLIED       -- supppress if on list -->

<!ELEMENT Axis-widget (Coord,(X-axis|Y-axis)) -- free standing axis-->
<!-- display the axis-widget beginning at Coord.X and Coord.Y      -->
<!ATTLIST Axis-widget
  %attrs;
        -- if labels is defined, it is treated as a comma-separated
           list of labels to be shown at successive intervals,
           including the first; use ,, to indicate an unlabled pos --
  caption          CDATA       #IMPLIED        -- caption for axis --
  capt-font        IDREF       #IMPLIED        -- font for caption --
  ascending        %yesorno;   #IMPLIED        -- numbering direc. --
  topright         %yesorno;   #IMPLIED        -- above or right   --
  axis-length      %length;    #REQUIRED       -- length of line   --
  start            %integer;   #REQUIRED       -- integer range    --
  end              %integer;   #REQUIRED       -- low to high      --
  num-divisions    %integer;   #IMPLIED        -- if not use-int   --
  show-first       %yesorno;   #IMPLIED        -- display number
                                                  at start of line --
  zero-as-1        %yesorno;   #IMPLIED        -- show position 0
                                                    as position 1  --
  labels           CDATA       #IMPLIED        -- label points     -->

<!-- ************************************************************* -->
<!--               12.9 Chart Widget and Related Elements          -->
<!-- ************************************************************* -->
<!ELEMENT X-chart-axis EMPTY                          >
<!ATTLIST X-chart-axis
  scale-automatic %yesorno;      #IMPLIED
  lower-limit     %real;         #IMPLIED
  upper-limit     %real;         #IMPLIED
  display-mode (decimal-places|best-fit|log|suppressed) #IMPLIED
  dec-places      %integer;      #IMPLIED
  grid   (none|at-zero|at-ticks) #IMPLIED                            >

<!ELEMENT Y-chart-axis EMPTY                          >
<!ATTLIST Y-chart-axis
  scale-automatic %yesorno;      #IMPLIED
  lower-limit     %real;         #IMPLIED
  upper-limit     %real;         #IMPLIED
  display-mode (decimal-places|best-fit|log|suppressed) #IMPLIED
  dec-places      %integer;      #IMPLIED
  grid   (none|at-zero|at-ticks) #IMPLIED                            >

<!ELEMENT Chart-page EMPTY                                           >
<!ATTLIST Chart-page
  left     %length;  #IMPLIED
  top      %length;  #IMPLIED
  width    %length;  #IMPLIED
  length   %length;  #IMPLIED
  portrait %yesorno; #IMPLIED                                        >

<!ELEMENT Chart-screen-display EMPTY           >
<!ATTLIST Chart-screen-display
  monochrome             %yesorno;   #IMPLIED
  text-font-size         %integer;   #IMPLIED
  text-font-bold         %yesorno;   #IMPLIED
  numb-font-size         %integer;   #IMPLIED
  numb-font-bold         %yesorno;   #IMPLIED
  plot-thickness         %linewidth; #IMPLIED
  frame-thickness        %linewidth; #IMPLIED
  text-color             %color;     #IMPLIED
  numb-color             %color;     #IMPLIED
  plot-color             %color;     #IMPLIED
  frame-color            %color;     #IMPLIED
  plot-background-color  %color;     #IMPLIED
  frame-background-color %color;     #IMPLIED
  symbol-size            %length;    #IMPLIED                        >

<!ELEMENT Chart-print-display EMPTY           >
<!ATTLIST Chart-print-display
  monochrome             %yesorno;   #IMPLIED
  text-font-size         %integer;   #IMPLIED
  text-font-bold         %yesorno;   #IMPLIED
  numb-font-size         %integer;   #IMPLIED
  numb-font-bold         %yesorno;   #IMPLIED
  plot-thickness         %linewidth; #IMPLIED
  frame-thickness        %linewidth; #IMPLIED
  text-color             %color;     #IMPLIED
  numb-color             %color;     #IMPLIED
  plot-color             %color;     #IMPLIED
  frame-color            %color;     #IMPLIED
  plot-background-color  %color;     #IMPLIED
  frame-background-color %color;     #IMPLIED
  symbol-size            %length;    #IMPLIED                        >

<!ELEMENT Chart-data EMPTY                                           >
<!ATTLIST Chart-data
  setnum %integer; #REQUIRED  -- set 0 to 6 allowed --
  symbol (nosymbol|plus|ex|opencircle|
              filledcircle|opensquare|filledsquare) #IMPLIED
  line-format (none|line-only|symbol-only|both|err-bar) #IMPLIED
  line-color    %color;   #IMPLIED
  fill-color    %color;   #IMPLIED
  do-fill       %yesorno; #IMPLIED
  fill-pattern  (clear|horiz|vert|fdiag|bdiag|
                     cross|diagcross|solid) #IMPLIED
  legend        CDATA     #IMPLIED
  drop-left     CDATA     #IMPLIED
  drop-right    CDATA     #IMPLIED
  colrownum     %integer; #IMPLIED      -- number of row or col    --
  values   CDATA #IMPLIED     -- if no table, comma separated data -->

<!ELEMENT Chart-widget (Coord?,X-chart-axis?,Y-chart-axis?,
    Chart-page?,Chart-screen-display?,Chart-print-display?,
                                        Chart-data*,Object?,%links;) >
<!ATTLIST Chart-widget
  %attrs;
  own-window %yesorno; #IMPLIED
  width      %length;  #IMPLIED
  length     %length;  #IMPLIED
  chart-type (xy|multi-xy|box-plot|bar|histogram|line) #IMPLIED
  text-font  IDREF     #IMPLIED
  numb-font  IDREF     #IMPLIED
  title-1    CDATA     #IMPLIED
  title-2    CDATA     #IMPLIED
  x-title    CDATA     #IMPLIED
  y-title    CDATA     #IMPLIED
  legend-pos (below|upper-left|upper-right|
              lower-left|lower-right) #IMPLIED
  presort    %yesorno; #IMPLIED
  x-no-zero  %yesorno; #IMPLIED -- no zero position on x axis --
  -- if format not specified, data are supplied in chart-data --
  format     CDATA #IMPLIED -- acceptable = bsml|html|txt|sdf|db   --
  source        %url;        #IMPLIED         -- none if in values --
  tableid       IDREF        #IMPLIED         -- none if in values --
  bycolumn      %yesorno;    #IMPLIED         -- none if in values --
      -- comma separated lists of start positions and field widths --
  column-starts    CDATA     #IMPLIED         -- used for txt      --
  column-widths    CDATA     #IMPLIED         -- used for txt      --
  header-count     %integer; #IMPLIED         -- txt skip lines    -->

<!ENTITY % pagedisplaywidgets "(Popup-text-widget|Sequence-viewer|
    Feature-histogram-widget|Caption-widget|Line-pointer-widget|
    Shape-widget|Table-widget|File-widget|Gel-widget|Axis-widget|
    Text-key-widget|Fill-key-widget|Symbol-key-widget|
    Seq-data-widget|Chart-widget|View-master-widget)" >

<!-- ************************************************************* -->
<!--                          12.10 Page                           -->
<!-- ************************************************************* -->
<!ELEMENT Page (Screen?,Paper?,Border?,
          (%pagedisplaywidgets;|%setwidgets;|View|%links;)*,Object?) >
<!ATTLIST Page
   %attrs;                                                           >