<!-- BioSap DTD - provides a structured output for the BIOSAP project 
  -----------------------------------------------------------------------
  Copyright (c) 2001 David Shteynberg, dshteyn@systemsbiology.org

  This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

  The Institute for Systems Biology, hereby disclaims all copyright
  interest in this program written by David Shteynberg.

  ----------------------------------------------------------------------
-->


<!ELEMENT BioSapRun (FeaturamaParameters, FeaturamaStatistics, FilteredBlastResults?, FilteredBlastStatistics?)>
<!ATTLIST BioSapRun 
        comments             CDATA #REQUIRED >

<!ELEMENT FeaturamaParameters EMPTY>
<!ATTLIST FeaturamaParameters 
        gene_library             CDATA #REQUIRED
        melting_temp             CDATA #REQUIRED
        melting_temp_range       CDATA #REQUIRED
        minimum_length           CDATA #REQUIRED
        maximum_length           CDATA #REQUIRED
        maximum_selfcomp         CDATA #REQUIRED
        step_size                CDATA #REQUIRED
        maximum_3prime_distance  CDATA #REQUIRED
        initial_3prime_offset    CDATA #REQUIRED
        maximum_features         CDATA #REQUIRED
        maximum_polyAT_length    CDATA #REQUIRED
        maximum_polyGC_length    CDATA #REQUIRED
        content_window_size      CDATA #REQUIRED
        maximum_windowAT_content CDATA #REQUIRED
        maximum_windowGC_content CDATA #REQUIRED
        oligo_concentration_mMol CDATA #REQUIRED
        salt_concentration_mMol  CDATA #REQUIRED >

<!ELEMENT FeaturamaStatistics EMPTY>
<!ATTLIST FeaturamaStatistics
        n_features_found       CDATA #REQUIRED
        n_featureless_genes    CDATA #REQUIRED
        gene_rep_fraction      CDATA #REQUIRED
        success_fraction       CDATA #REQUIRED
        self_comp_features_rej CDATA #REQUIRED
        high_Tm_features_rej   CDATA #REQUIRED
        low_Tm_features_rej    CDATA #REQUIRED
        content_features_rej   CDATA #REQUIRED
        duplicate_features     CDATA #REQUIRED
        n_features_considered  CDATA #REQUIRED
        featurama_version      CDATA #REQUIRED >

<!ELEMENT FilteredBlastResults (Feature)*>

<!ELEMENT Feature (Hit)*>
<!ATTLIST Feature
        gene_name           CDATA #REQUIRED
        gene_description    CDATA #REQUIRED
        melting_temp        CDATA #REQUIRED
        threeprime_distance CDATA #REQUIRED
        sequence_length     CDATA #REQUIRED
        sequence            CDATA #REQUIRED >

<!ELEMENT Hit EMPTY>
<!ATTLIST Hit 
        gene_name            CDATA #REQUIRED
        expect_value         CDATA #REQUIRED
        score                CDATA #REQUIRED
        hit_sequence         CDATA #REQUIRED       
        number_of_identities CDATA #REQUIRED >

<!ELEMENT FilteredBlastStatistics EMPTY>
<!ATTLIST FilteredBlastStatistics
        filter_blast_version CDATA #REQUIRED
        n_unique_features    CDATA #REQUIRED
        n_multiple_features  CDATA #REQUIRED >