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<LI><A HREF="#name">NAME</A></LI>
<LI><A HREF="#synopsis">SYNOPSIS</A></LI>
<LI><A HREF="#description">DESCRIPTION</A></LI>
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<LI><A HREF="#output">OUTPUT</A></LI>
<LI><A HREF="#algorithm">ALGORITHM</A></LI>
<LI><A HREF="#author">AUTHOR</A></LI>
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<LI><A HREF="#see also">SEE ALSO</A></LI>
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<H1><A NAME="name">NAME</A></H1>
<P>stag-diff.pl - finds the difference between two stag files</P>
<P>
<HR>
<H1><A NAME="synopsis">SYNOPSIS</A></H1>
<PRE>
stag-diff.pl -ignore foo-id -ignore bar-id file1.xml file2.xml</PRE>
<P>
<HR>
<H1><A NAME="description">DESCRIPTION</A></H1>
<P>Compares two data trees and reports whether they match. If they do not
match, the mismatch is reported.</P>
<DL>
<DT><STRONG><A NAME="item_%2Dhelp%7Ch">-help|h</A></STRONG><BR>
<DD>
shows this document
<P></P>
<DT><STRONG><A NAME="item_%2Dignore%7Ci_ELEMENT">-ignore|i ELEMENT</A></STRONG><BR>
<DD>
these nodes are ignored for the purposes of comparison. Note that
attributes are treated as elements, prefixed by the containing element
id. For example, if you have
<PRE>
<foo ID="wibble"></PRE>
<P>And you wish to ignore the ID attribute, then you would use the switch</P>
<PRE>
-ignore foo-ID</PRE>
<P>You can specify multiple elements to ignore like this</P>
<PRE>
-i foo -i bar -i baz</PRE>
<P>You can also specify paths</P>
<PRE>
-i foo/bar/bar-id</PRE>
<P></P>
<DT><STRONG><A NAME="item_%2Dparser%7Cp_FORMAT">-parser|p FORMAT</A></STRONG><BR>
<DD>
which parser to use. The default is XML. This can also be autodetected
by the file suffix. Other alternatives are <STRONG>sxpr</STRONG> and <STRONG>itext</STRONG>. See
<A HREF="./Data/Stag.html">the Data::Stag manpage</A> for details.
<P></P>
<DT><STRONG><A NAME="item_%2Dreport%7Cr_ELEMENT">-report|r ELEMENT</A></STRONG><BR>
<DD>
report mismatches as they occur on each element of type ELEMENT
<P>multiple elements can be specified</P>
<P></P>
<DT><STRONG><A NAME="item_%2Dverbose%7Cv">-verbose|v</A></STRONG><BR>
<DD>
used in conjunction with the <STRONG>-report</STRONG> switch
<P>shows the tree of the mismatching element</P>
<P></P></DL>
<P>
<H2><A NAME="output">OUTPUT</A></H2>
<P>If a mismatch is reported, a report is generated displaying the
subpart of the tree that could not be matched. This will look like
this:</P>
<P>REASON:
no_matching_node: annotation
no_matching_node: feature_set
no_matching_node: feature_span
no_matching_node: evidence
no_matching_node: evidence-id
data_mismatch(:15077290 ne :15077291): evidence-id AND evidence-id</P>
<P>Due to the nature of tree matching, it can be difficult to specify
exactly how trees do not match. To investigate this, you may need to
use the <STRONG>-r</STRONG> and <STRONG>-v</STRONG> options. For the above output, I would
recommend using</P>
<PRE>
stag-diff.pl -r feature_span -v</PRE>
<P>
<H2><A NAME="algorithm">ALGORITHM</A></H2>
<P>Both trees are recursively traversed... see the actual code for how this works</P>
<P>The order of elements is not important; eg
</P>
<PRE>
<foo>
<bar>
<baz>1</baz>
</bar>
<bar>
<baz>2</baz>
</bar>
</foo></PRE>
<P>matches</P>
<PRE>
<foo>
<bar>
<baz>2</baz>
</bar>
<bar>
<baz>1</baz>
</bar>
</foo></PRE>
<P>The recursive nature of this algorithm means that certain tree
comparisons will explode wrt time and memory. I think this will only
happen with very deep trees where nodes high up in the tree can only
be differentiated by nodes low down in the tree.</P>
<P>Both trees are loaded into memory to begin with, so it may thrash with
very large documents</P>
<P>
<H2><A NAME="author">AUTHOR</A></H2>
<P>Chris Mungall
cjm at fruitfly dot org</P>
<P>
<HR>
<H1><A NAME="see also">SEE ALSO</A></H1>
<P><A HREF="./Data/Stag.html">the Data::Stag manpage</A></P>
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