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revision 1.2, Thu Jun 9 19:06:55 2005 UTC revision 1.4, Wed Feb 1 03:18:07 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">
102                        <Notes>Index (1-based) of the region's rightmost nucleotide
103                        in the contig.</Notes>
104                    </Field>
105                                  <Field name="peg" type="name-string">                                  <Field name="peg" type="name-string">
106                                          <Notes>PEG identifier for this block if it is a gene block,                                          <Notes>PEG identifier for this block if it is a gene block,
107                                          or aa string generated from the nearby PEGs if it is an                      or a string generated from the nearby PEGs if it is an
108                                          inter-genic block</Notes>                                          inter-genic block</Notes>
109                                  </Field>                                  </Field>
110              </Fields>              </Fields>
111                <Indexes>
112                    <Index>
113                        <Notes>This index enables the application to find regions
114                        that overlap a specific section of the contig.  The index
115                        can be used to find the first region whose end point is at
116                        or follows the start of the section in question. Because
117                        every nucleotide is in at most one region, this guarantees
118                        that if any region overlaps the section, the region found
119                        by the index will.</Notes>
120                        <IndexFields>
121                            <IndexField name="end" order="ascending" />
122                        </IndexFields>
123                    </Index>
124                </Indexes>
125                  </Entity>                  </Entity>
126      </Entities>      </Entities>
127      <Relationships>      <Relationships>

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