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revision 1.6, Thu Jun 9 19:06:55 2005 UTC revision 1.9, Sun Aug 14 23:59:03 2005 UTC
# Line 38  Line 38 
38                                          page or of particular interest to a research group or web site. A single genome can belong to multiple                                          page or of particular interest to a research group or web site. A single genome can belong to multiple
39                                          such groups or none at all.</Notes>                                          such groups or none at all.</Notes>
40                                  </Field>                                  </Field>
41                    <Field name="complete" type="boolean">
42                        <Notes>This field is TRUE if the genome is believed to be complete, else
43                        FALSE.</Notes>
44                    </Field>
45              </Fields>              </Fields>
46              <Indexes>              <Indexes>
47                  <Index>                  <Index>
# Line 98  Line 102 
102                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
103                                  </Field>                                  </Field>
104                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
105                                          <Notes>String describing the quality data for each . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
106                                          be separated by periods. The value represents negative exponent of the probability                                          be separated by periods. The value represents negative exponent of the probability
107                                          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
108                                          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
109                                          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
110                                          vector will contain the [b]unknown[/b].</Notes>                                          vector will contain the [b]unknown[/b].</Notes>
111                                          <DataGen>unknown</DataGen>                                          <DataGen>unknown</DataGen>
112                                  </Field>                                  </Field>
# Line 119  Line 123 
123                                          <DataGen>RandParam('peg','rna')</DataGen>                                          <DataGen>RandParam('peg','rna')</DataGen>
124                                  </Field>                                  </Field>
125                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="name-string" relation="FeatureAlias">
126                                          <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>
127                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
128                                  </Field>                                  </Field>
129                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
130                                          <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
131                          the pieces of the feature together.</Notes>                      codes, formed by concatenating the pieces of the feature together. For a
132                        protein encoding group, this is the protein characters. For other types
133                        it is the DNA characters.</Notes>
134                                          <DataGen testCount="0"></DataGen>                                          <DataGen testCount="0"></DataGen>
135                                  </Field>                                  </Field>
136                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
# Line 144  Line 150 
150                                          "&amp;Number=" . IntGen(1,99)</DataGen>                                          "&amp;Number=" . IntGen(1,99)</DataGen>
151                                  </Field>                                  </Field>
152              </Fields>              </Fields>
153                <Indexes>
154                    <Index>
155                        <Notes>This index allows the user to find the feature corresponding to
156                        the specified alias name.</Notes>
157                        <IndexFields>
158                            <IndexField name="alias" order="ascending" />
159                        </IndexFields>
160                    </Index>
161                </Indexes>
162          </Entity>          </Entity>
163          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
164              <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.
# Line 334  Line 349 
349                      to decode that relationship. Currently, this field is either "1" or                      to decode that relationship. Currently, this field is either "1" or
350                      "2".</Notes>                      "2".</Notes>
351                  </Field>                  </Field>
                 <Field name="percentMatch" type="float">  
                     <Notes>Percent similarity between our target feature and the  
                     corresponding feature of the coupling.</Notes>  
                 </Field>  
                 <Field name="paralogs" type="int">  
                     <Notes>Number of features on the same genome that are analogous  
                     to our target feature. A higher paralog count indicates less  
                     valuable evidence.</Notes>  
                 </Field>  
352              </Fields>              </Fields>
353              <FromIndex>              <FromIndex>
354                  <Notes>This index enables the application to view the features of                  <Notes>This index enables the application to view the features of

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