Bioinformatic Sequence Markup Language DTD
From:  http://visualgenomics.com/sbir/bsml.dtd
Date:  1999-01-28

---------

<!-- ************************************************************* -->
<!--         BSML (tm) Bioinformatic Sequence Markup Language      -->
<!--   Document Type Definition DTD - Nov. 15,1998 - Version 2.0   -->
<!--                           Copyright 1998                      -->
<!--                       Joseph H. Spitzner, Ph.D.               -->
<!--                         Visual Genomics, 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 Broswer to any person, except if the
original package and its whole original content is 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.                 -->
<!--
     Notes: 1. Content labeled XML was adapted from the
               XML specification.
            2. Content labeled as HTML 4.0 was adapted from the
               HTML 4.0 specification.
            3. Content labeled NCBI was adapted from the
               NCBI ASN.1 specification.
-->
<!-- ************************************************************* -->
<!--                         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 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 CDATA "&#38;"                                          >
<!ENTITY lt CDATA "&#60;"                                           >
<!ENTITY gt CDATA "&#62;"                                           >
<!ENTITY quot CDATA "&#34;"                                          >
<!ENTITY slash CDATA "&#47;"                                         >
<!ENTITY % yesorno "CDATA"           -- boolean as 1=true|0=false -->
<!ENTITY % yes "1"                   -- 1 = true                  -->
<!ENTITY % no "0"                    -- 0 = false                 -->
<!ENTITY % integer "CDATA"           -- positive or negative int  -->
<!ENTITY % real "CDATA"              -- positive or negative real -->
<!ENTITY % length "CDATA"            -- 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 Resource 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)"                       >
<!ENTITY % coords "CDATA"            -- comma sep list of numbers -->
<!ENTITY % frametarget "CDATA"       -- render in this frame      -->
<!--
  ******************** 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" sets the value to 320 pixels. This method is
  most commonly used in resolving coordinates on the 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 the line-width-inc to
    the 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  -- document-wide unique id      --
  class       CDATA      #IMPLIED  -- space separated class list   --
  style       CDATA      #IMPLIED  -- associated style info        --
  title       CDATA      #IMPLIED  -- displayable title            --
  comment     CDATA      #IMPLIED  -- rest added for BSML          --
  value-type  CDATA      #IMPLIED  -- optional value description   --
  value       CDATA      #IMPLIED  -- optional data value(s)       --
  selectable  %yesorno;  #IMPLIED  -- if no, no selection rectangle--
  selected    %yesorno;  #IMPLIED  -- element is selected          --
  display     %yesorno;  #IMPLIED  -- show element                 --
  readonly    %yesorno;  #IMPLIED  -- allow editing if false       --"
>
<!--
  Value-type and value are used, as appropriate, to supply
  data or other numeric values associated with an element.
  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 -- pointer was clicked           --
  ondblclick  %script;   #IMPLIED -- pointer was double clicked    --
  onmousedown %script;   #IMPLIED -- pointer was pressed down      --
  onmouseup   %script;   #IMPLIED -- pointer was released          --
  onmouseover %script;   #IMPLIED -- pointer was moved onto        --
  onmousemove %script;   #IMPLIED -- pointer was moved within      --
  onmouseout  %script;   #IMPLIED -- pointer was moved away        --
  onkeypress  %script;   #IMPLIED -- key was pressed and released  --
  onkeydown   %script;   #IMPLIED -- key was pressed down          --
  onkeyup     %script;   #IMPLIED -- key was released              --"
>
<!ENTITY % attrs "%mainattrs; %events;" --language and dir excluded-->
<!--
  Note: %attrs is added as an attribute group for all major elements.
-->
<!-- ************************************************************* -->
<!--                3.0 Major BSML Document Divisions              -->
<!-- ************************************************************* -->
<!ELEMENT Bsml - - (Attribute*,Info*,Definitions?,Display?)          >
<!--
  for Bsml element, the following Attribute elements are common:
           document-title=title of document
           project=name of project (used with project manager)
           project-id=unique project identifer for this document
           author=defines originator of document
           storage=defines primary storage location
           owner=determines who has complete access
           password=used with security manager 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  -- for adding unspecified info      -->
<!ATTLIST Attribute   -- if > 1 with same name, accumulate comma
                                  separated list of content values --
          name     CDATA  #REQUIRED
          content  CDATA  #IMPLIED  -- if none, merely asserts name-->
<!-- ************************************************************* -->
<!--                 4.0  Definitions Sub-divisions                -->
<!-- ************************************************************* -->
<!ELEMENT Definitions - - (Attribute*,Sequences?,Sets?,Tables?)      >
<!-- ************************************************************* -->
<!--      5.0 Sequences, Features, Annotation, and Citations       -->
<!-- ************************************************************* -->
<!ELEMENT Sequences - - (Sequence|Sequence-import|Attribute)*        >
<!ATTLIST Sequences
            %attrs;                              -- attributes     -->
<!ENTITY % dbsource "CDATA"                                          >
<!--
   Common source database names = %dbsource, represented as CDATA:
        bbone              NCBI backbone
        ddbj               DNA Data Bank of Japan
        carbbank           Carbohydrate Structure Database
        embl               EMBL Data Library
        ecd
        ecoseq
        enzyme
        epd
        flybase
        hdb                Hybridoma Data Bank
        genbank            GenBank
        geninfo
        hgml               Human Gene Map Library
        hiv
        medline
        mim                Mendelian Inheritance in Man
        msd                Microbial Strains Database
        ncbi               National Center for Biotechnology Info.
        ncgr               National Center for Genome Research
        pdb                Protein Data Bank (Brookhaven)
        pir                Protein Identification Resource
        prfseqdb           Protein Research Foundation (Japan)
        prosite            Prosite database
        psd                Protein Sequence Database (Japan)
        swissprot          SwissProt (or sp)
        tfd                Transcription factor database
-->
<!-- ************************************************************* -->
<!--                    5.3  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, etc. --
            identifier CDATA  #IMPLIED
                  -- identifier selects one sequence from a set;
                     if bsml import, identifier = id
                     if other, identifier = primary accession key  -->

<!-- ************************************************************* -->
<!--             5.4 Sequence Element (adapted from NCBI)          -->
<!-- ************************************************************* -->
<!ENTITY % repr-opts "(not-set,virtual,raw,segmented,constructed,
                       reference,consensus,map,derived,other)"       >

<!ELEMENT Sequence - - (Attribute*,Feature-tables?,
                        (Seq-data|Seq-data-import)?,Numbering?)      >
<!ATTLIST Sequence
    %attrs;
    locus                CDATA      #IMPLIED
    ic-acckey            CDATA      #IMPLIED -- internat. collab.   --
    local-acckey         CDATA      #IMPLIED -- local accession key --
    db-source            %dbsource; #IMPLIED
    length               CDATA      #IMPLIED
    end5hang5            %integer;  #IMPLIED
    end3hang5            %integer;  #IMPLIED
    end5phos             %yesorno;  #IMPLIED
    end3phos             %yesorno;  #IMPLIED
    -- 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    -- cross-refs --
            -- including references, features, seqs, 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   -->

<!-- ************************************************************* -->
<!--                         5.5 Sequence Data                     -->
<!-- ************************************************************* -->
<!ELEMENT Seq-data - - (#PCDATA)              -- the sequence data -->
<!--                dna/rna=IUPACna, protein=IUPACaa               -->
<!-- ************************************************************* -->
<!--                       5.8 Location Types                      -->
<!-- ************************************************************* -->
<!ELEMENT Site-loc             - - EMPTY         -- one position   -->
<!ATTLIST Site-loc                     -- NCBI (a) single position --
            %attrs;
            sitepos      CDATA     #REQUIRED
            complement   %yesorno; %no;                              >
<!ELEMENT Interval-loc         - - EMPTY         -- interval       -->
<!ATTLIST Interval-loc               -- NCBI (c) 121.130,onepos=1
                                             (d) 121..130,onepos=0 --
            %attrs;
            startpos     CDATA      #REQUIRED
            endpos       CDATA      #REQUIRED
            startopen    %yesorno;  %no;
            endopen      %yesorno;  %no;
            onepos       %yesorno;  %no;
            complement   %yesorno; %no;                              >
<!ENTITY % location "(Site-loc|Interval-loc)"                        >

<!-- ************************************************************** -->
<!--                        Qualifier Types                         -->
<!-- ************************************************************** -->

<!-- qualifier value-types
    anticodon,bound-moiety,cell-line,cell-type,chromosome,chloroplast,
    chromoplast,citation,clone,clone-lib,codon,codon-start,cons-splice,
    cultivar,cyanelle,db-xref,dev-stage,direction,EC-number,evidence,
    frequency,function,gene,gdb-xref,germline,haplotype,insertion-seq,
    kinetoplast,label,lab-host,map,macronuclear,mitochondrion,mod-base,
    note,number,organism,partial,PCR-conditions,pop-variant,phenotype,
    plasmid,product,pseudo,rearranged,rpt-family,rpt-type,rpt-unit,
    sequenced-mol,serotype,sex,specific-host,standard-name,strain,
    sub-clone,sub-species,sub-strain,tissue-lib,tissue-type,
    translation,transl-exception,transl-table,transposon,usedin
-->

<!ELEMENT Qualifier          - - EMPTY                               >
<!-- Qualifier uses value-type and value attributes                -->
<!ATTLIST Qualifier
            %attrs;                                                  >

<!-- ************************************************************* -->
<!--                          Feature Types                        -->
<!-- ************************************************************* -->
<!-- feature value-type list
      allele,attenuator,binding-site,C-region,CAAT-signal,CDS,
      cap-site,coding-region,conflict,D-loop,D-segment,enhancer,exon,
      GC-signal,iDNA,insertion-sequence,intron,J-segment,LTR,
      mature-peptide,misc-binding,miscellaneous-difference,
      miscellaneous-feature,miscellaneous-recombination,
      miscellaneous-RNA,misc-signal,miscellaneous-structure,
      modified-base,mRNA,mutation,N-region,origin-of-replication,
      polyA-site,precursor-RNA,primary-transcript,primer-bind,
      promoter,protein-bind,RBS,repeat,repeat-unit,rRNA,
      S-region,satellite,scRNA,sig-peptide,snRNA,source,stem-loop,
      STS,TATA-signal,terminator,transit-peptide,transposon,tRNA,
      unsure,V-region,V-segment,variation,virion,splice-site3,
      splice-site5,UTR3,UTR5,signal-10,signal-35,user-defined
-->

<!ELEMENT Feature - - (%location;|Qualifier|Attribute)*              >
<!ATTLIST Feature
            %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
            -- type encoded from last as value-type core attribute --
            refs            IDREFS       #IMPLIED    -- cross-refs --
            -- including references, other features, seqs, etc.    -->

<!-- ************************************************************* -->
<!--                          Reference                            -->
<!-- ************************************************************* -->
<!ELEMENT Reference - - (Attribute*,RefAuthors?,RefTitle?,RefJournal?) >
<!ATTLIST Reference
            %attrs;
            refs            IDREFS       #IMPLIED    -- cross-refs --
            -- including references, other features, seqs, etc.    -->
<!ELEMENT RefAuthors - - (#PCDATA)                                   >
<!ELEMENT RefTitle   - - (#PCDATA)                                   >
<!ELEMENT RefJournal - - (#PCDATA)                                   >
<!-- ************************************************************* -->
<!--                          Feature Table                        -->
<!-- ************************************************************* -->
<!ELEMENT Feature-table - -
    (Attribute|Reference|Feature|Digest-set)*                        >
<!ATTLIST Feature-table
            %attrs;                                                  >
<!-- ************************************************************* -->
<!--                          Feature Tables                       -->
<!-- ************************************************************* -->
<!ELEMENT Feature-tables       - - (Attribute|Feature-table)*        >
<!ATTLIST Feature-tables
            %attrs;                                                  >
<!-- ************************************************************* -->
<!--                        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
  NCBI8na ::= OCTET STRING   for modified nucleic acids
  NCBIpna ::= OCTET STRING   5 octets/base, prob for a,c,g,t,n
                             probabilities are coded 0-255 = 0.0-1.0
  NCBI8aa ::= OCTET STRING   for modified amino acids
  NCBIeaa ::= StringStore    ASCII extended 1 letter aa codes
                             IUPAC codes + U=selenocysteine
  NCBIpaa ::= OCTET STRING   25 octets/aa, prob for IUPAC aas in order:
                             A-Y,B,Z,X,(ter),anything
                             probabilities are coded 0-255 = 0.0-1.0
NCBIstdaa ::= OCTET STRING   codes 0-25, 1 per byte
-->
<!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,key needed -->
<!-- ************************************************************* -->
<!--                    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                           >

<!-- ************************************************************* -->
<!--                              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 set members --
            refs   IDREFS #IMPLIED  -- xrefs                       -->


<!-- ************************************************************* -->
<!--                             7.0 Tables                        -->
<!-- ************************************************************* -->
<!ELEMENT Tables - - (Attribute|Table|Motif-table|Table-import)*
                                                   -- tabular data -->
<!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 row if appropriate --
                  -- uses value for comma separated data table row -->

<!ELEMENT Table-import - - (Attribute*,Table-data*)
       -- internal of table-data or external file or internet href -->
<!ATTLIST Table-import
       %attrs;
       format (bsml,html,txt,sdf,db) #IMPLIED   -- to be extended  --
       --     if data in Table-data elements, no format needed     --
       -- list of columns to include; use all if not defined       --
       column-numbers   CDATA     #IMPLIED
       column-headers   CDATA     #IMPLIED      -- use for txt,sdf --
                        -- comma separated list of column headings --
       column-starts    CDATA     #IMPLIED      -- used for txt    --
       column-widths    CDATA     #IMPLIED      -- used for txt    --
       -- comma separated lists of start positions and field widths--
       header-count     %integer; #IMPLIED      -- txt 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) or R (right) 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      -- xrefs           -->

<!-- ************************************************************* -->
<!--                          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    - O (Tr)+      -- table header                  -->
<!ELEMENT Tfoot    - O (Tr)+      -- table footer                  -->
<!ELEMENT Tbody    O O (Tr)+      -- table body                    -->
<!ELEMENT Colgroup - O (Col)*     -- table column group            -->
<!ELEMENT Col      - O EMPTY      -- table column                  -->
<!ELEMENT Tr       - O (Th|Td)+   -- table row                     -->
<!ELEMENT (Th|Td)  - O (#PCDATA)  -- table header 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|Tbody|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|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
  -- 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 top=1,bottom=0 --
  titles      CDATA #IMPLIED  -- ,-separated list of titles         --
  values      CDATA #IMPLIED  -- ,-separated list of values         -->

<!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
  alignment    %integer; #IMPLIED -- align pos on global seq  --
  startpos     %integer; #IMPLIED -- start of seq range       --
  endpos       %integer; #IMPLIED -- end of seq range         -->

<!ELEMENT Motif-element - - EMPTY >
<!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
  fill-fg-color   %color;   #IMPLIED
  fill-bg-color   %color;   #IMPLIED
  fill-pattern    (clear,horiz,vert,fdiag,bdiag,
                   cross,diagcross,solid)   #IMPLIED
  -- shape applies to points --
  shape  (opencircle,closedcircle,
          opensquare,closedsquare,triangle) #IMPLIED >

<!ELEMENT Motif-table - - (Attribute*,Numbering?,
                       Interval-loc*,Motif-element*,Sequence-motif*) >
<!ATTLIST Motif-table
  %attrs;
  display-height     %length;  #IMPLIED
  display-gap        %length;  #IMPLIED
  point-offset       %length;  #IMPLIED
  point-width        %length;  #IMPLIED
  global-length      %integer; #IMPLIED -- =longest seq otherwise --
  refs               IDREFS    #IMPLIED      --    xrefs           -->

<!-- ************************************************************* -->
<!--                   8.0 Display Sub-divisions                   -->
<!-- ************************************************************* -->
<!ELEMENT Display - - (Links?,Fonts?,Styles?,Screen?,Paper?,Page+)   >
<!-- screen and paper set defaults for all pages if used           -->
<!ATTLIST Display
            master-doc      %yesorno;      #IMPLIED -- project head--
            first-page      %integer;      #IMPLIED -- display 1st --
            default-unit    (pct,cm,in,px) "in"
            line-width-base %length        "0.01in"
            line-width-inc  %length        "0.01in"                  >
<!-- ************************************************************* -->
<!--                     9.0 XML Linking Elements                  -->
<!-- ************************************************************* -->
<!ELEMENT (Attribute-list | Info) - - (Attribute)* --list of values-->
<!ATTLIST (Attribute-list | 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
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                        >
<!ELEMENT Document-link - - EMPTY                                    >
<!ATTLIST Document-link
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "DOCUMENT"
            role            CDATA    #IMPLIED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                        >
<!ELEMENT Group-link - - (Document-link)*                            >
<!ATTLIST Group-link
            id              ID       #IMPLIED
            xml-link        CDATA    #FIXED "GROUP"
            steps           CDATA    #IMPLIED
            role            CDATA    #IMPLIED
            title           CDATA    #IMPLIED
            rel             CDATA    #IMPLIED
            rev             CDATA    #IMPLIED
            show            (embed|replace|new) "embed"
            actuate         (auto|user) "user"
            behavior        CDATA    #IMPLIED                        >

<!ENTITY % links "(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 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    -- 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; %no;       -- 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 - -  CDATA                      -- 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 - O EMPTY                  -- named property value -->
<!ATTLIST Param
  id          ID         #IMPLIED    -- document-wide unique id    --
  name        CDATA      #REQUIRED   -- property name              --
  value       CDATA      #IMPLIED    -- property value             --
  valuetype (data|ref|object) "data" -- How to interpret value     --
  type     %contenttype; #IMPLIED    -- content type for value
                                        when valuetype=ref         -->

<!-- ************************************************************* -->
<!--    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 - O 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   -->

<!-- ************************************************************* -->
<!--                  12.3 Pages 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 color --
             red-slope   %real;  #IMPLIED
             blue-base   %real;  #IMPLIED -- if color --
             blue-slope  %real;  #IMPLIED
             green-base  %real;  #IMPLIED -- if color --
             green-slope %real;  #IMPLIED                            >

<!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; %no;  -- print black/white only   -->

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

<!-- ************************************************************* -->
<!--                      12.4 Display Set Types                   -->
<!-- ************************************************************* -->
<!-- ************************************************************* -->
<!--                          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 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  -->

<!-- ************************************************************* -->
<!--                            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 --position on page    --
            vloc       %length;    #REQUIRED --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, retangular 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    -->

<!-- ************************************************************* -->
<!--                       Alignment-point-sets                    -->
<!-- ************************************************************* -->
<!-- Alignment-point-set defines set of related sites on > 1 seq   -->
<!ELEMENT Alignment-point-set  - - (Numbering?)                      >
<!-- Numbering element is used for multiple alignment display      -->
<!ATTLIST Alignment-point-set
       %attrs;
       seqids     IDREFS    #REQUIRED  -- ids of views or seqs     --
       featids    CDATA     #REQUIRED  -- ids of corresponding
                     features, points or intervals, or actual
                     position values; value="NONE" means not shown --
       captions   CDATA     #IMPLIED   -- n - 1 comma separated
                   captions to be shown on lines connecting points --
       capt-font  IDREF     #IMPLIED   -- caption font             --
       capt-above %yesorno; #IMPLIED   -- captions above line      --
       consensus %yesorno;  #IMPLIED   --true if 1st=consensus seq --
       -- next 4 borrowed attributes from Dense-seg in ncbi asn.1  --
       numseg     %integer; #IMPLIED   -- #segments, see example   --
       starts     CDATA     #IMPLIED   -- offsets, see example     --
       strands    CDATA     #IMPLIED   -- "P" or "M",see example   --
       seglens    CDATA     #IMPLIED   -- lengths of segments      -->
 <!-- start of -1 indicates a gap for that sequence of length len. -->

<!ELEMENT Alignment-point-sets-widget
                  - - (Symbol?,Alignment-point-set*,Object?,%links;) >
<!ATTLIST Alignment-point-sets-widget
            %attrs;
            alignto       IDREF      #IMPLIED  -- reference view   --
            line-width    %length;   #IMPLIED
            line-color    %color;    #IMPLIED                        >

<!-- ************************************************************* -->
<!--                         Multi-seq-set                         -->
<!-- ************************************************************* -->
<!--Multi-seq-set=flat set of sequences or interval features       -->

<!ELEMENT Multi-seq-set-widget  - -
                     (Alignment-point-sets-widget?,Object?,%links;)  >
<!ATTLIST Multi-seq-set-widget
            %attrs;
            setids     IDREFS  #REQUIRED  -- ids of seqs or views  --
            -- content elements are sequences or intervals         --
            -- multiple sets are concatenated to one flat set      --
            seqtype       (nucleotide,protein)         "nucleotide"
            -- construct type collapses sequences to one seq line  --
            treetype      (homology,contig,construct)  "homology"
            userefseq     %yesorno;                    %no;
            refseqid      IDREF                        #IMPLIED
            -- uses sequence order in sets if sortmode=none        --
            sortmode      (none,start,midpoint,end)    "none"
            --display properties                                   --
            -- set styles for all using style sheet for seq        --
            -- automatic spacing uses interval specified below     --
            spacing       (automatic,manual)           "automatic"
            -- automatic uses first or reference seq as reference  --
            hloc          %length;                     #IMPLIED
            vloc          %length;                     #IMPLIED
            seqlength     %length;                     #IMPLIED
            interval      %length;                     #IMPLIED
            -- lengthmode applies to length of other sequences     --
            lengthmode    (constant,proportional)     "proportional" >

<!-- ************************************************************* -->
<!--                       Seq-pair-alignment                      -->
<!-- ************************************************************* -->
<!ELEMENT Seq-pair-run - - EMPTY     -- run of similarity for pair -->
<!ATTLIST Seq-pair-run
            runlength     %integer; #REQUIRED
            refpos        %integer; #REQUIRED
            comppos       %integer; #REQUIRED
            runscore      CDATA     #IMPLIED   -- displayable value-->

<!ELEMENT Seq-pair-alignment - - (Seq-pair-run*,Object?,%links;)    >
<!ATTLIST Seq-pair-alignment
            %attrs;
            refseq        IDREF     #REQUIRED
            refcaption    CDATA     #IMPLIED
            refstart      %integer; #IMPLIED  -- overall region    --
            refend        %integer; #IMPLIED
            reflength     %integer; #IMPLIED  -- or get from seq   --
            compseq       IDREF     #REQUIRED
            compcaption   CDATA     #IMPLIED
            compstart     %integer; #IMPLIED  -- overall region    --
            compend       %integer; #IMPLIED
            complength    %integer; #IMPLIED  -- or get from seq   --
            method        CDATA     #IMPLIED  -- comparison notes  --
            runminscore   CDATA     #IMPLIED  -- minimum run score --
            runmaxscore   CDATA     #IMPLIED  -- maximum run score --
            totalscore    CDATA     #IMPLIED                         >

<!ELEMENT (X-axis|Y-axis) - - (Numbering?)       -- sequence scale -->
<!ATTLIST (X-axis|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 Dot-plot-widget - - (Coord,Seq-pair-alignment,
                        X-axis?,Y-axis?,Quantifier?,Object?,%links;) >
<!-- display a dot matrix plot for a pair of sequences showing runs-->
<!ATTLIST Dot-plot-widget
       %attrs;
       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|Multi-seq-set-widget|Dot-plot-widget)" >

<!-- ************************************************************* -->
<!--                       12.5 Display Widgets                    -->
<!-- ************************************************************* -->

<!ELEMENT Chart - - (Border?)                -- chart display atts -->
<!ATTLIST Chart
          %attrs;
          source        %url;     #IMPLIED     -- source=file    --
          tableid       IDREF     #IMPLIED     -- source=table   --
          bycolumn      %yesorno; %yes;
          colrownum     %integer; #IMPLIED -- number of row or col -->

<!ELEMENT Member - - EMPTY                                           >
<!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          -->

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

<!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 wid--
     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     (plus,minus,source,auto-strand) #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 defined Members,Features,Point-widgets-->

<!ELEMENT Point-group-widget - - (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
      show-positions  (no,plus,minus) #IMPLIED
      start-pos-only  %yesorno;       #IMPLIED
      position-font   IDREF           #IMPLIED
      line-width      %linewidth;     #IMPLIED
      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
      auto-offset     %yesorno; #IMPLIED
      offset-from-seq %length;  #IMPLIED
      arrow-start-len %length;  #IMPLIED
      arrow-end-len   %length;  #IMPLIED
      arrow-width     %length;  #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
      plus-text        CDATA    #IMPLIED
      plus-font        IDREF    #IMPLIED
      plus-bracket     CDATA    #IMPLIED --none,angled,tee (linear)--
      minus-text       CDATA    #IMPLIED
      minus-font       IDREF    #IMPLIED
      minus-bracket    CDATA    #IMPLIED --none,angled,tee (linear)--
      center-text      CDATA    #IMPLIED
      center-font      IDREF    #IMPLIED
      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
      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
      plus-font        IDREF    #IMPLIED
      minus-text       CDATA    #IMPLIED
      minus-color      %color;  #IMPLIED
      inside-text      CDATA    #IMPLIED
      inside-font      IDREF    #IMPLIED
      outside-text     CDATA    #IMPLIED
      outside-font     IDREF    #IMPLIED                             >

<!ELEMENT Aligned-chart-widget - -
                                  (Chart,Quantifier?,Object?,%links;)>
<!ATTLIST Aligned-chart-widget
      %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
      endpos          %integer;   #REQUIRED
      min-offset      %length;    #REQUIRED
      max-offset      %length;    #REQUIRED
      on-plus         %yesorno;   #IMPLIED
      min-data        %real;      #REQUIRED
      max-data        %real;      #REQUIRED
      dec-places      %integer;   #IMPLIED
      show-y-axis     %yesorno;   #IMPLIED
      histogram       %yesorno;   #IMPLIED
      line-width      %linewidth; #IMPLIED
      line-color      %color;     #IMPLIED
      caption         CDATA       #IMPLIED
      caption-font    IDREF       #IMPLIED
      data-font       IDREF       #IMPLIED                           >

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

<!-- ************************************************************* -->
<!--                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
            font          IDREF                       #IMPLIED
            orientation   (horizontal,down,angled)    #IMPLIED
            angle         %integer;                   #IMPLIED
            border        %yesorno;                   #IMPLIED
            border-gutter %length;                    #IMPLIED
            border-width  %length;                    #IMPLIED
            border-color  %color;                     #IMPLIED
            wordwrap      %yesorno;                   #IMPLIED
            wrap-length   %length;                    #IMPLIED
            -- if horizontal, apply alignment --
            align         (left,center,right)         #IMPLIED       >

<!ELEMENT Line-pointer-widget - - (Coord+,%links;)                   >
<!ATTLIST Line-pointer-widget
            %attrs;
            line-style %linestyle;       #IMPLIED
            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                    >

<!ELEMENT Shape-widget - - (Coord,%links;)                           >
<!ATTLIST Shape-widget
            %attrs;
            height        %length;       #IMPLIED
            width         %length;       #IMPLIED
            filled        %yesorno;      #IMPLIED
            line-width    %linewidth;    #IMPLIED
            shape         %displayshape; #IMPLIED
            color         %color;        #IMPLIED                    >

<!ELEMENT File-widget - - (Coord,Border?,Image-map?,Object?,%links;) >
<!ATTLIST File-widget
           %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                                     >
<!ATTLIST Table-column
            colnum %integer;           #REQUIRED
            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 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
          explanation CDATA #REQUIRED                                >

<!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 list of fills  --
        fore-colors      CDATA    #IMPLIED -- comma list of colors --
        back-colors      CDATA    #IMPLIED -- comma list of colors --
        explanations     CDATA    #IMPLIED -- comma separated list -->

<!ELEMENT Symbol-key-widget  - - (Coord,Border?,%links;)             >
<!ATTLIST Symbol-key-widget
          %attrs;
         do-substitute %yesorno;   #IMPLIED
         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 Restriction-enzyme - - EMPTY -- record for 1 enzyme      -->
<!ATTLIST Restriction-enzyme  --        title = enzyme name        --
      %attrs;
      source           CDATA          #IMPLIED -- sequence         --
      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 sep 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 are 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 sep list    --
      units            CDATA         #IMPLIED -- if fragments      --
      seqref           IDREF         #IMPLIED -- if none, use below--
      seqname          CDATA         #IMPLIED -- display name      --
      is-circular      %yesorno;     #IMPLIED -- true if circle    --
      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    -->

<!ELEMENT Gel-widget - - (Coord,Border?,Digest-set*,Object?,%links;) >
<!-- gel-widget simulates gel electrophoresis display              -->
<!ATTLIST Gel-widget
      %attrs;
      digests          IDREFS        #IMPLIED -- 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 -- porportional      --
      -- 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 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 -->

<!ELEMENT Axis-widget - - (Coord,(X-axis|Y-axis))  --free standing -->
<!-- display the axis-widget beginning at Coord.X and .Y           -->
<!ATTLIST Axis-widget
         %attrs;
         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  -->

<!ELEMENT Seq-data-widget - -
                            (Coord,Border?,Seq-data?,Object?,%links;)>
<!ATTLIST Seq-data-widget --if has Seq-data element, get data there--
      %attrs;
      featureref       IDREF         #IMPLIED  -- id of feature    --
      seqref           IDREF         #IMPLIED  -- id of sequence   --
      startpos         %integer;     #REQUIRED
      length           %integer;     #REQUIRED
      caption          CDATA         #IMPLIED
      seq-font         IDREF         #IMPLIED
      caption-font     IDREF         #IMPLIED
      bases-per-line   %integer;     #IMPLIED
      number-bases     %yesorno;     #IMPLIED
      space-blocks     %yesorno;     #IMPLIED
      double-stranded  %yesorno;     #IMPLIED
      translate-dna    (yes|no|only) #IMPLIED
      translate-start  %integer;     #IMPLIED
      translate-length %integer;     #IMPLIED
      source           %url;         #IMPLIED
      seq-len          %integer;     #IMPLIED -- if url or Seq-data--
      is-protein       %yesorno;     #IMPLIED -- if url or Seq-data-->

<!ELEMENT (X-chart-axis|Y-chart-axis) - - EMPTY                      >
<!ATTLIST (X-chart-axis|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|Chart-print-display) - - EMPTY       >
<!ATTLIST (Chart-screen-display|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         %integer; #IMPLIED
    frame-thickness        %integer; #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 (bsml,html,txt,sdf,db) #IMPLIED   -- to be extended  --
   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)" >

<!-- ************************************************************* -->
<!--                                Page                           -->
<!-- ************************************************************* -->
<!ELEMENT Page - - (Screen?,Paper?,Border?,
          (%pagedisplaywidgets;|%setwidgets;|View)*,Object?,%links;) >
<!ATTLIST Page
            %attrs;                                                  >
<!-- ************************************************************* -->
<!--                                View                           -->
<!-- ************************************************************* -->
<!ELEMENT View      - -  (Numbering?,Margin?,%seqdisplaywidgets;,
                                  Object?,%links;)  -- view of seq -->
<!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  -->

<!ELEMENT View-master-widget - - (Coord,Object?,%links;)             >
<!ATTLIST View-master-widget
   views          IDREFS       #IMPLIED  -- if none, all on page --
   width          %length;     #IMPLIED
   height         %length;     #IMPLIED
   outerwidth     %linewidth;  #IMPLIED
   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    --      >

<!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                                 >

<!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
  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          %integer;   #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 -->

<!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   -->