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revision 1.3, Fri Jan 6 20:35:01 2006 UTC revision 1.5, Tue Feb 7 16:06:55 2006 UTC
# Line 9  Line 9 
9                  <Field name="description" type="string">                  <Field name="description" type="string">
10                      <Notes>Brief description of this genome.</Notes>                      <Notes>Brief description of this genome.</Notes>
11                  </Field>                  </Field>
12                    <Field name="group-name" type="name-string">
13                        <Notes>Name of this genome's close-strain group.</Notes>
14                    </Field>
15    
16              </Fields>              </Fields>
17                <Indexes>
18                    <Index>
19                        <Notes>This index sorts the genomes by group so that
20                        close strains are placed next to each other.</Notes>
21                        <IndexFields>
22                            <IndexField name="group-name" order="ascending" />
23                            <IndexField name="id" order="ascending" />
24                        </IndexFields>
25                    </Index>
26                </Indexes>
27          </Entity>          </Entity>
28          <Entity name="Contig" keyType="key-string">          <Entity name="Contig" keyType="key-string">
29              <Notes>A [i]contig[/i] is a contiguous run of nucleotides. The contig's              <Notes>A [i]contig[/i] is a contiguous run of nucleotides. The contig's
# Line 17  Line 31 
31              which contig this is for the parent genome. The individual components              which contig this is for the parent genome. The individual components
32              are separated by a colon.</Notes>              are separated by a colon.</Notes>
33          </Entity>          </Entity>
34          <Entity name="GroupBlock" keyType="int">          <Entity name="GroupBlock" keyType="name-string">
35              <Notes>A [i]group block[/i] is a set of similar genome regions.              <Notes>A [i]group block[/i] is a set of similar genome regions.
36              A group block can represent a gene or an inter-genic region.              A group block can represent a gene or an inter-genic region.
37              The result is that every position in a contig belongs to exactly              The result is that every position in a contig belongs to exactly
# Line 84  Line 98 
98                      <Notes>Length of this region. This may be slightly smaller                      <Notes>Length of this region. This may be slightly smaller
99                      than the block length.</Notes>                      than the block length.</Notes>
100                  </Field>                  </Field>
101                  <Field name="end" type="int">                  <Field name="endpoint" type="int">
102                      <Notes>Index (1-based) of the region's rightmost nucleotide                      <Notes>Index (1-based) of the region's rightmost nucleotide
103                      in the contig.</Notes>                      in the contig.</Notes>
104                  </Field>                  </Field>
# Line 104  Line 118 
118                      that if any region overlaps the section, the region found                      that if any region overlaps the section, the region found
119                      by the index will.</Notes>                      by the index will.</Notes>
120                      <IndexFields>                      <IndexFields>
121                          <IndexField name="end" order="ascending" />                          <IndexField name="endpoint" order="ascending" />
122                      </IndexFields>                      </IndexFields>
123                  </Index>                  </Index>
124              </Indexes>              </Indexes>

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