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Add links to SearchIO documentation pages

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1 parent bdc11a7 commit ced734637e4efb3e2f9bac7839e2ec983c963a55 @bow bow committed with peterjc Feb 4, 2013
Showing with 9 additions and 5 deletions.
  1. +9 −5 Doc/Tutorial.tex
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14 Doc/Tutorial.tex
@@ -5786,7 +5786,10 @@ \subsection{QueryResult}
\end{verbatim}
For a complete list of accessible attributes, you can check each format-specific
-documentation.
+documentation. Here are the ones
+\href{http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html}{for BLAST}
+and for
+\href{http://biopython.org/DIST/docs/api/Bio.SearchIO.BlatIO-module.html}{BLAT}.
Having looked at using \verb|print| on \verb|QueryResult| objects, let's drill
down deeper. What exactly is a \verb|QueryResult|? In terms of Python objects,
@@ -6247,8 +6250,9 @@ \subsection{HSP}
61
\end{verbatim}
-Check out the \verb|HSP| documentation for a full list of these predefined
-properties.
+Check out the \verb|HSP|
+\href{http://biopython.org/DIST/docs/api/Bio.SearchIO._model.hsp-module.html}{documentation}
+for a full list of these predefined properties.
Furthermore, each sequence search tool usually computes its own statistics /
details for its \verb|HSP| objects. For example, an XML BLAST search also
@@ -6434,8 +6438,8 @@ \subsection{HSP}
\verb|hit_all|, and \verb|aln_all|. These properties will return a list containing
\verb|SeqRecord| or \verb|MultipleSeqAlignment| objects from each of the HSP
fragment. There are other attributes that behave similarly, i.e. they only work
-for HSPs with one fragment. Check out the \verb|HSP| documentation for a full
-list.
+for HSPs with one fragment. Check out the \verb|HSP| \href{http://biopython.org/DIST/docs/api/Bio.SearchIO._model.hsp-module.html}{documentation}
+for a full list.
Finally, to check whether you have multiple fragments or not, you can use the
\verb|is_fragmented| property like so:

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