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revision 1.29, Fri Jun 30 18:31:34 2006 UTC revision 1.30, Sun Jul 9 21:16:47 2006 UTC
# Line 389  Line 389 
389                  </Field>                  </Field>
390              </Fields>              </Fields>
391          </Entity>          </Entity>
392          <Entity name="PCH" keyType="hash-string">          <Entity name="PCH" keyType="counter">
393              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
394              pair of physically close features on a contig) to a second pair of physically              pair of physically close features on a contig) to a second pair of physically
395              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 397  Line 397 
397              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
398              this would be to simply relate clusterings to each other; however, not all              this would be to simply relate clusterings to each other; however, not all
399              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
400              a pair of features. The key is the clustering key followed by the IDs              a pair of features. The key a unique ID number.</Notes>
             of the features in the second pair.</Notes>  
401              <Fields>              <Fields>
402                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
403                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,

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