[DAS] 1.0 spec questions

[Andrew Dalke]

Hi,

Let me start by saying that I haven't looked at DAS in a while
nor have I followed the list.  I searched the list for my
questions but didn't find anything appropriate.

So I'm starting to get a feel for DAS at the data interchange
level.  I'm using a DTD to Python class generator called 'PAXB'
(it's based on JAXB but is 0.1 code and it shows).  It looks
like there are differences between

http://www.biodas.org/dtd/dasstyle.dtd
  and
http://www.biodas.org/documents/sample_stylesheet.xml
  and the 1.0 spec at
http://biodas.org/documents/spec.html

These are still present in the CVS files.

Here's the differences I found so far.

That XML file is not well-formed -

* End tag 'BOXS' does not match the start tag 'BOX'. Line 166, Position 13

Here's the relevant XML
          <BOX>
            <HEIGHT>3</HEIGHT>
            <FGCOLOR>black</FGCOLOR>
            <LABEL>yes</LABEL>
            <BGCOLOR>red</BGCOLOR>
            <BUMP>yes</BUMP>
          </BOXS>
          ^^^^^^^ should be 'BOX'

The DTD needs to have "WIDTH" changed to "HEIGHT" (according to
Version 0.99 changelog info)

The DTD doesn't include the "FGCOLOR" nor "BGCOLOR" definitions.

In the DTD, LINE needs to include a "STYLE" and a "LINEWIDTH",
which are used in the XML file.

The DTD is missing ANCHORED_ARROW, which is in the XML file
and in the spec.  (I see that Brian's XMLSPY output at

http://www-genome.wi.mit.edu/personal/gilmanb/i3c/xmlspy_docs/das/style.html
also doesn't have ANCHORED_ARROW nor does any of the code in the
CVS release.)

The spec has a "HIDDEN" glyph which is not in the DTD nor is
in the XML.  (Added in Version 1.0)

The XML file has LINEWIDTH for ANCHORED_ARROW, which probably
implies ARROW needs it as well in the DTD.

The XML file has "POINT"s for TRIANGLE and BOX, but there is
no POINT in the XML.  Nor is there a "POINT" in the spec.

The DTD defines a "CONNECTOR" which is not listed in the spec.

What's the interpretation of "PRIMERS"?

        <GLYPH>
          <PRIMERS>
            <HEIGHT>50</HEIGHT>
            <FGCOLOR>#33ff33</FGCOLOR>
            <LABEL>yes</LABEL>
          </PRIMERS>
        </GLYPH>

What's the interpretation of "SEGMENTS"?
        <GLYPH>
          <SEGMENTS>
            <HEIGHT>50</HEIGHT>
            <FGCOLOR>#666666</FGCOLOR>
            <LABEL>yes</LABEL>
            <LINEWIDTH>1</LINEWIDTH>
          </SEGMENTS>
        </GLYPH>

And 'TRANSCRIPT'?  Shouldn't all three of these be stored
as a TYPE id?

There's still a 'FILLCOLOR' in sample_stylesheets.xml .
I believe this should be 'BGCOLOR'

Line 571 of that file needs a /CATEGORY as otherwise the
document is not well formed.  Eg, see the comment in the
following grep

cvs:documents {410} grep CATEGORY sample_stylesheet.xml
  <CATEGORY id="group">
  </CATEGORY>
  <CATEGORY id="structural">
    </CATEGORY>
    <CATEGORY id="similarity">
    </CATEGORY>
    <CATEGORY id="variation">
    </CATEGORY>
    <CATEGORY id="experimental">
    </CATEGORY>
    <CATEGORY id="translation">  *--- Where's the close?
    <CATEGORY id="transcription">
    </CATEGORY>
    <CATEGORY id="repeat">
    </CATEGORY>
    <CATEGORY id="default">
    </CATEGORY>
cvs:documents {411}

Am I working off of outdated documents?  Or is the DTD really
incomplete?


I also did a quick scan of the geodesic code to see what it
handles.  I see that:
 - "CONNECTOR" is not on the spec page
 - it doesn't support "ANCHORED_ARROW"
 - it doesn't support "HIDDEN"
 - it has "OUTLINECOLOR" instead of "BGCOLOR"
I did not to a full search so may have missed things.

Also, where are the regression tests?  I wanted to see how
easy it is to use them from Python.

                    Andrew Dalke
                    dalke@dalkescientific.com