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revision 1.8, Wed Jun 22 21:31:47 2005 UTC revision 1.12, Tue Sep 13 03:50:59 2005 UTC
# Line 25  Line 25 
25                      the user's access codes must match this value.</Notes>                      the user's access codes must match this value.</Notes>
26                      <DataGen>RandParam('low','medium','high')</DataGen>                      <DataGen>RandParam('low','medium','high')</DataGen>
27                  </Field>                  </Field>
28                    <Field name="complete" type="boolean">
29                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
30                    </Field>
31                  <Field name="taxonomy" type="text">                  <Field name="taxonomy" type="text">
32                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
33                      separated by semi-colons (and optional white space), starting with the domain and ending with                      separated by semi-colons (and optional white space), starting with the domain and ending with
# Line 38  Line 41 
41                      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
42                      such groups or none at all.</Notes>                      such groups or none at all.</Notes>
43                  </Field>                  </Field>
                 <!-- <Field name="complete" type="boolean">  
                     <Notes>This field is TRUE if the genome is believed to be complete, else  
                     FALSE.</Notes>  
                 </Field> -->  
44              </Fields>              </Fields>
45              <Indexes>              <Indexes>
46                  <Index>                  <Index>
# Line 102  Line 101 
101                      <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>                      <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
102                  </Field>                  </Field>
103                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
104                      <Notes>String describing the quality data for each . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
105                      be separated by periods. The value represents negative exponent of the probability                      be separated by periods. The value represents negative exponent of the probability
106                      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
107                      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
108                      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
109                      vector will contain the [b]unknown[/b].</Notes>                      vector will contain the [b]unknown[/b].</Notes>
110                      <DataGen>unknown</DataGen>                      <DataGen>unknown</DataGen>
111                  </Field>                  </Field>
# Line 123  Line 122 
122                      <DataGen>RandParam('peg','rna')</DataGen>                      <DataGen>RandParam('peg','rna')</DataGen>
123                  </Field>                  </Field>
124                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="name-string" relation="FeatureAlias">
125                      <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>
126                      <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                      <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
127                  </Field>                  </Field>
128                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
# Line 139  Line 138 
138                      <DataGen testCount="0"></DataGen>                      <DataGen testCount="0"></DataGen>
139                  </Field>                  </Field>
140                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
141                      <Notes>TRUE if this feature is still considered valid, if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
142                      <DataGen>1</DataGen>                      <DataGen>1</DataGen>
143                  </Field>                  </Field>
144                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">

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