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revision 1.7, Thu Jun 16 19:10:04 2005 UTC revision 1.10, Mon Aug 15 18:43:49 2005 UTC
# Line 98  Line 98 
98                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
99                                  </Field>                                  </Field>
100                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
101                                          <Notes>String describing the quality data for each . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
102                                          be separated by periods. The value represents negative exponent of the probability                                          be separated by periods. The value represents negative exponent of the probability
103                                          of error. Thus, for example, a quality of 30 indicates the probability of error is                                          of error. Thus, for example, a quality of 30 indicates the probability of error is
104                                          10^-30. A higher quality number a better chance of a correct match. It is possible                                          10^-30. A higher quality number a better chance of a correct match. It is possible
105                                          that the quality data is known for a sequence. If that is the case, the quality                      that the quality data is not known for a sequence. If that is the case, the quality
106                                          vector will contain the [b]unknown[/b].</Notes>                                          vector will contain the [b]unknown[/b].</Notes>
107                                          <DataGen>unknown</DataGen>                                          <DataGen>unknown</DataGen>
108                                  </Field>                                  </Field>
# Line 119  Line 119 
119                                          <DataGen>RandParam('peg','rna')</DataGen>                                          <DataGen>RandParam('peg','rna')</DataGen>
120                                  </Field>                                  </Field>
121                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="name-string" relation="FeatureAlias">
122                                          <Notes>Alternative name for this feature. feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
123                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
124                                  </Field>                                  </Field>
125                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
126                                          <Notes>[i](optional)[/i] A of this feature's residues into character codes, formed by concatenating                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
127                          the pieces of the feature together.</Notes>                      codes, formed by concatenating the pieces of the feature together. For a
128                        protein encoding group, this is the protein characters. For other types
129                        it is the DNA characters.</Notes>
130                                          <DataGen testCount="0"></DataGen>                                          <DataGen testCount="0"></DataGen>
131                                  </Field>                                  </Field>
132                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
# Line 144  Line 146 
146                                          "&amp;Number=" . IntGen(1,99)</DataGen>                                          "&amp;Number=" . IntGen(1,99)</DataGen>
147                                  </Field>                                  </Field>
148              </Fields>              </Fields>
149                <Indexes>
150                    <Index>
151                        <Notes>This index allows the user to find the feature corresponding to
152                        the specified alias name.</Notes>
153                        <IndexFields>
154                            <IndexField name="alias" order="ascending" />
155                        </IndexFields>
156                    </Index>
157                </Indexes>
158          </Entity>          </Entity>
159          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
160              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.

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