<!DOCTYPE gs540_hw [ 
  <!ELEMENT gs540_hw (results, program)>
  <!ATTLIST gs540_hw assignment CDATA #REQUIRED>
  <!ATTLIST gs540_hw name CDATA #REQUIRED>
  <!ATTLIST gs540_hw email CDATA #REQUIRED>
  <!ELEMENT results (result|model)*>
  <!ELEMENT result ANY>
  <!ATTLIST result type (first_line|EM_result|iterations|log_likelihood) #REQUIRED>
  <!ATTLIST result file CDATA #IMPLIED>
  <!ATTLIST result iterations CDATA #IMPLIED>
  <!ELEMENT model ANY>
  <!ATTLIST model type (hmm) #REQUIRED>
  <!ELEMENT states ANY>
  <!ELEMENT initial_state_probabilities ANY>  
  <!ELEMENT transition_probabilities ANY>
  <!ATTLIST transition_probabilities state CDATA #REQUIRED>
  <!ELEMENT emission_probabilities ANY>
  <!ATTLIST emission_probabilities state CDATA #REQUIRED>
  <!ELEMENT program (comments, file+)>
  <!ELEMENT comments ANY>
  <!ELEMENT file ANY>
  <!ATTLIST file filename CDATA #IMPLIED>
]>
<gs540_hw assignment='6' name='student name' email='student email'>  
  <results> 
   <result type='first_line' file='filename'>  
      first line of the .fna file that you use for
      viterbi training.  NOTE: please do not change the filename or the first line, in 
      any way. Please include all characters 
      of the first line (including the '>' character).

   </result>
   <result type='EM_result'>
      <result type='iterations'>
         put the number of iterations it took for the algorithm
         to converge here.
      </result>
      <result type = 'log_likelihood'>
         put the final log likelihood here.
      </result>
      <model type='hmm'>
        <states>
          1,2
        </states>
        <initial_state_probabilities>
          1=0.900,2=0.100
        </initial_state_probabilities>
        <transition_probabilities state='1'>
           1=0.990,2=0.010
        </transition_probabilities>
        <transition_probabilities state='2'>
           1=0.200,2=0.800
        </transition_probabilities>
        <emission_probabilities state='1'>
          A=.250,C=.250,G=.250,T=.250
        </emission_probabilities>
        <emission_probabilities state='2'>
          A=.300,C=.250,G=.250,T=.200
        </emission_probabilities>
     </model>
  </result>
  </results>
  <program>
    <comments> 
       put comments about your code here 
    </comments>
    <file filename='main.c'>
       <![CDATA[
         file contents here
       ]]>
       
    </file>
  </program>
</gs540_hw>
