source: plugins/base2/net.sf.basedb.illumina/trunk/META-INF/base-configurations.xml @ 678

Last change on this file since 678 was 624, checked in by Nicklas Nordborg, 15 years ago

References #102: Intensity calculator for Illumina SNP data

The main parts are working. Need more testing and probably better error handling and/or configuration options.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 25.3 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
3  <configuration pluginClassName="net.sf.basedb.illumina.plugins.BgxReporterImporter">
4    <configname>Illumina default reporter import</configname>
5    <description>A standard configuration that assumes that the default configuration for extended properties are used + the extra extended properties that are shipped with this plug-in package</description>
6    <parameter>
7      <name>extendedColumnMapping.accession</name>
8      <label>Accession</label>
9      <description />
10      <class>java.lang.String</class>
11      <value>\Accession\</value>
12    </parameter>
13    <parameter>
14      <name>minDataColumns</name>
15      <label>Min data columns</label>
16      <description>The minimum number of columns for a line to be counted as a data line.</description>
17      <class />
18      <value />
19    </parameter>
20    <parameter>
21      <name>extendedColumnMapping.cytoband</name>
22      <label>Cytoband</label>
23      <description>The cytoband from which the reporter is derived</description>
24      <class />
25      <value />
26    </parameter>
27    <parameter>
28      <name>dataFooterRegexp</name>
29      <label>Data footer</label>
30      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
31      <class />
32      <value />
33    </parameter>
34    <parameter>
35      <name>extendedColumnMapping.source</name>
36      <label>Source</label>
37      <description />
38      <class>java.lang.String</class>
39      <value>\Source\</value>
40    </parameter>
41    <parameter>
42      <name>extendedColumnMapping.markers</name>
43      <label>Markers</label>
44      <description />
45      <class />
46      <value />
47    </parameter>
48    <parameter>
49      <name>extendedColumnMapping.omim</name>
50      <label>OMIM</label>
51      <description />
52      <class />
53      <value />
54    </parameter>
55    <parameter>
56      <name>extendedColumnMapping.searchKey</name>
57      <label>Search key</label>
58      <description />
59      <class>java.lang.String</class>
60      <value>\Search_Key\</value>
61    </parameter>
62    <parameter>
63      <name>extendedColumnMapping.tissue</name>
64      <label>Tissue</label>
65      <description>The tissue from which the reporter is derived</description>
66      <class />
67      <value />
68    </parameter>
69    <parameter>
70      <name>descriptionColumnMapping</name>
71      <label>Description</label>
72      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
73      <class>java.lang.String</class>
74      <value>\Definition\</value>
75    </parameter>
76    <parameter>
77      <name>ignoreRegexp</name>
78      <label>Ignore</label>
79      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
80      <class />
81      <value />
82    </parameter>
83    <parameter>
84      <name>extendedColumnMapping.clusterId</name>
85      <label>Cluster ID</label>
86      <description>A unique identifier for a Unigene entry</description>
87      <class>java.lang.String</class>
88      <value>\Unigene_ID\</value>
89    </parameter>
90    <parameter>
91      <name>decimalSeparator</name>
92      <label>Decimal separator</label>
93      <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>
94      <class>java.lang.String</class>
95      <value>dot</value>
96    </parameter>
97    <parameter>
98      <name>trimQuotes</name>
99      <label>Remove quotes</label>
100      <description>If true quotes (" or ') around data value will be removed.</description>
101      <class>java.lang.Boolean</class>
102      <value>true</value>
103    </parameter>
104    <parameter>
105      <name>extendedColumnMapping.locusLink</name>
106      <label>LocusLink</label>
107      <description />
108      <class>java.lang.String</class>
109      <value>\Entrez_Gene_ID\</value>
110    </parameter>
111    <parameter>
112      <name>extendedColumnMapping.synonyms</name>
113      <label>Synonyms</label>
114      <description />
115      <class>java.lang.String</class>
116      <value>\Synonyms\</value>
117    </parameter>
118    <parameter>
119      <name>extendedColumnMapping.isoformType</name>
120      <label>Isoform type</label>
121      <description />
122      <class>java.lang.String</class>
123      <value>\Probe_Type\</value>
124    </parameter>
125    <parameter>
126      <name>extendedColumnMapping.sourceReferenceId</name>
127      <label>Source reference id</label>
128      <description />
129      <class>java.lang.String</class>
130      <value>\Source_Reference_ID\</value>
131    </parameter>
132    <parameter>
133      <name>extendedColumnMapping.ilmnGene</name>
134      <label>ILMN Gene</label>
135      <description />
136      <class>java.lang.String</class>
137      <value>\ILMN_Gene\</value>
138    </parameter>
139    <parameter>
140      <name>extendedColumnMapping.library</name>
141      <label>Library</label>
142      <description>The library from which the reporter is derived</description>
143      <class />
144      <value />
145    </parameter>
146    <parameter>
147      <name>maxDataColumns</name>
148      <label>Max data columns</label>
149      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
150      <class />
151      <value />
152    </parameter>
153    <parameter>
154      <name>extendedColumnMapping.probeCoordinates</name>
155      <label>Probe coordinates</label>
156      <description />
157      <class>java.lang.String</class>
158      <value>\Probe_Coordinates\</value>
159    </parameter>
160    <parameter>
161      <name>extendedColumnMapping.chromosome</name>
162      <label>Chromosome</label>
163      <description>The chromosome from which the reporter is derived</description>
164      <class>java.lang.String</class>
165      <value>\Chromosome\</value>
166    </parameter>
167    <parameter>
168      <name>symbolColumnMapping</name>
169      <label>Gene symbol</label>
170      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
171      <class>java.lang.String</class>
172      <value>\Symbol\</value>
173    </parameter>
174    <parameter>
175      <name>headerRegexp</name>
176      <label>Header</label>
177      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
178      <class />
179      <value />
180    </parameter>
181    <parameter>
182      <name>scoreColumnMapping</name>
183      <label>Score</label>
184      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
185      <class />
186      <value />
187    </parameter>
188    <parameter>
189      <name>dataHeaderRegexp</name>
190      <label>Data header</label>
191      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
192      <class>java.lang.String</class>
193      <value>.*Probe_Id.+Array_Address_Id.*</value>
194    </parameter>
195    <parameter>
196      <name>extendedColumnMapping.controlCompositeMap</name>
197      <label>Control composite map</label>
198      <description />
199      <class />
200      <value />
201    </parameter>
202    <parameter>
203      <name>reporterType</name>
204      <label>Reporter type</label>
205      <description>The reporter type assigned to the imported reporters</description>
206      <class />
207      <value />
208    </parameter>
209    <parameter>
210      <name>extendedColumnMapping.length</name>
211      <label>Length</label>
212      <description>The length of the sequence</description>
213      <class />
214      <value />
215    </parameter>
216    <parameter>
217      <name>extendedColumnMapping.probeChrOrientation</name>
218      <label>Probe chr orientation</label>
219      <description />
220      <class>java.lang.String</class>
221      <value>\Probe_Chr_Orientation\</value>
222    </parameter>
223    <parameter>
224      <name>complexExpressions</name>
225      <label>Complex column mappings</label>
226      <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\'
227allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description>
228      <class>java.lang.String</class>
229      <value>disallow</value>
230    </parameter>
231    <parameter>
232      <name>reporterTypeColumnMapping</name>
233      <label>Reporter type</label>
234      <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
235      <class />
236      <value />
237    </parameter>
238    <parameter>
239      <name>charset</name>
240      <label>Character set</label>
241      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
242      <class>java.lang.String</class>
243      <value>ISO-8859-1</value>
244    </parameter>
245    <parameter>
246      <name>extendedColumnMapping.controlGroupName</name>
247      <label>Control group name</label>
248      <description />
249      <class />
250      <value />
251    </parameter>
252    <parameter>
253      <name>extendedColumnMapping.controlGroupId</name>
254      <label>Control group id</label>
255      <description />
256      <class />
257      <value />
258    </parameter>
259    <parameter>
260      <name>dataSplitterRegexp</name>
261      <label>Data splitter</label>
262      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
263      <class>java.lang.String</class>
264      <value>\t</value>
265    </parameter>
266    <parameter>
267      <name>extendedColumnMapping.antibiotics</name>
268      <label>Antibiotics</label>
269      <description />
270      <class />
271      <value />
272    </parameter>
273    <parameter>
274      <name>reporterIdColumnMapping</name>
275      <label>Reporter ID</label>
276      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
277      <class>java.lang.String</class>
278      <value>\Probe_Id\</value>
279    </parameter>
280    <parameter>
281      <name>extendedColumnMapping.species</name>
282      <label>Species</label>
283      <description>The organism from which the reporter is derived</description>
284      <class>java.lang.String</class>
285      <value>\Species\</value>
286    </parameter>
287    <parameter>
288      <name>extendedColumnMapping.sequence</name>
289      <label>Sequence</label>
290      <description>The nucleotide sequence of the reporter</description>
291      <class>java.lang.String</class>
292      <value>\Probe_Sequence\</value>
293    </parameter>
294    <parameter>
295      <name>nameColumnMapping</name>
296      <label>Name</label>
297      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
298      <class>java.lang.String</class>
299      <value>\Probe_Id\</value>
300    </parameter>
301    <parameter>
302      <name>extendedColumnMapping.vector</name>
303      <label>Vector</label>
304      <description>The vector from which the reporter is derived</description>
305      <class />
306      <value />
307    </parameter>
308    <parameter>
309      <name>extendedColumnMapping.nid</name>
310      <label>NID</label>
311      <description />
312      <class />
313      <value />
314    </parameter>
315  </configuration>
316  <configuration pluginClassName="net.sf.basedb.illumina.plugins.BgxFeatureImporter">
317    <configname>Features from BGX file</configname>
318    <description>This is a standard configuration to import features from a BGX file.</description>
319    <parameter>
320      <name>trimQuotes</name>
321      <label>Remove quotes</label>
322      <description>If true quotes (" or ') around data value will be removed.</description>
323      <class>java.lang.Boolean</class>
324      <value>true</value>
325    </parameter>
326    <parameter>
327      <name>dataHeaderRegexp</name>
328      <label>Data header</label>
329      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
330      <class>java.lang.String</class>
331      <value>.*Probe_Id.+Array_Address_Id.*</value>
332    </parameter>
333    <parameter>
334      <name>reporterIdColumnMapping</name>
335      <label>Reporter ID</label>
336      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
337      <class>java.lang.String</class>
338      <value>\Probe_Id\</value>
339    </parameter>
340    <parameter>
341      <name>featureIdentification</name>
342      <label>Identify features by</label>
343      <description>Choose which method to use for identifying features:
344COORDINATES: Use block, meta-grid, row and column coordinates
345POSITION: Use a position number only
346FEATURE_ID: Use the feature ID value (string)
347In all cases, the identifier value must be unique.</description>
348      <class>java.lang.String</class>
349      <value>FEATURE_ID</value>
350    </parameter>
351    <parameter>
352      <name>complexExpressions</name>
353      <label>Complex column mappings</label>
354      <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\'
355allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description>
356      <class>java.lang.String</class>
357      <value>disallow</value>
358    </parameter>
359    <parameter>
360      <name>charset</name>
361      <label>Character set</label>
362      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
363      <class>java.lang.String</class>
364      <value>ISO-8859-1</value>
365    </parameter>
366    <parameter>
367      <name>featureIdColumnMapping</name>
368      <label>Feature ID</label>
369      <description>Mapping that picks the feature's ID from the data columns. This column is only used when the array design uses the FEATURE_ID method for identifying features. In the other cases, the value is just stored as it is.For example: \Feature ID\</description>
370      <class>java.lang.String</class>
371      <value>\Array_Address_Id\</value>
372    </parameter>
373    <parameter>
374      <name>dataSplitterRegexp</name>
375      <label>Data splitter</label>
376      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
377      <class>java.lang.String</class>
378      <value>\t</value>
379    </parameter>
380    <parameter>
381      <name>headerRegexp</name>
382      <label>Header</label>
383      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
384      <class>java.lang.String</class>
385      <value>(.+)=(.*)</value>
386    </parameter>
387  </configuration>
388  <configuration pluginClassName="net.sf.basedb.illumina.plugins.SnpReporterImporter">
389    <configname>Reporters from Illumina SNP manifest file</configname>
390    <description>Import reporter annotations from an Illumina SNP manifest file.</description>
391    <parameter>
392      <name>extendedColumnMapping.accession</name>
393      <label>Accession</label>
394      <description />
395      <class />
396      <value />
397    </parameter>
398    <parameter>
399      <name>minDataColumns</name>
400      <label>Min data columns</label>
401      <description>The minimum number of columns for a line to be counted as a data line.</description>
402      <class />
403      <value />
404    </parameter>
405    <parameter>
406      <name>dataFooterRegexp</name>
407      <label>Data footer</label>
408      <description>A regular expression that matches the first line of non-data after the data lines. For example: __END_OF_DATA__</description>
409      <class />
410      <value />
411    </parameter>
412    <parameter>
413      <name>extendedColumnMapping.cytoband</name>
414      <label>Cytoband</label>
415      <description>The cytoband from which the reporter is derived</description>
416      <class />
417      <value />
418    </parameter>
419    <parameter>
420      <name>extendedColumnMapping.markers</name>
421      <label>Markers</label>
422      <description />
423      <class />
424      <value />
425    </parameter>
426    <parameter>
427      <name>extendedColumnMapping.source</name>
428      <label>Source</label>
429      <description />
430      <class />
431      <value />
432    </parameter>
433    <parameter>
434      <name>extendedColumnMapping.omim</name>
435      <label>OMIM</label>
436      <description />
437      <class />
438      <value />
439    </parameter>
440    <parameter>
441      <name>extendedColumnMapping.searchKey</name>
442      <label>Search key</label>
443      <description />
444      <class />
445      <value />
446    </parameter>
447    <parameter>
448      <name>extendedColumnMapping.tissue</name>
449      <label>Tissue</label>
450      <description>The tissue from which the reporter is derived</description>
451      <class />
452      <value />
453    </parameter>
454    <parameter>
455      <name>descriptionColumnMapping</name>
456      <label>Description</label>
457      <description>Mapping that picks the reporter's description from the data columns. For example: \Description\</description>
458      <class />
459      <value />
460    </parameter>
461    <parameter>
462      <name>ignoreRegexp</name>
463      <label>Ignore</label>
464      <description>A regular expression that matches any line that should be ignored. For example, ignore lines starting with #: ^#.*</description>
465      <class />
466      <value />
467    </parameter>
468    <parameter>
469      <name>extendedColumnMapping.clusterId</name>
470      <label>Cluster ID</label>
471      <description>A unique identifier for a Unigene entry</description>
472      <class />
473      <value />
474    </parameter>
475    <parameter>
476      <name>decimalSeparator</name>
477      <label>Decimal separator</label>
478      <description>The decimal separator used in numeric values, if not specified dot is assumed.</description>
479      <class>java.lang.String</class>
480      <value>dot</value>
481    </parameter>
482    <parameter>
483      <name>extendedColumnMapping.ilmnStrand</name>
484      <label>Ilmn strand</label>
485      <description>Strand definition of the SNP</description>
486      <class>java.lang.String</class>
487      <value>\IlmnStrand\</value>
488    </parameter>
489    <parameter>
490      <name>extendedColumnMapping.snp</name>
491      <label>SNP</label>
492      <description>Type of SNP</description>
493      <class>java.lang.String</class>
494      <value>\SNP\</value>
495    </parameter>
496    <parameter>
497      <name>extendedColumnMapping.startPosition</name>
498      <label>Start position</label>
499      <description>Start position</description>
500      <class>java.lang.String</class>
501      <value>\MapInfo\</value>
502    </parameter>
503    <parameter>
504      <name>trimQuotes</name>
505      <label>Remove quotes</label>
506      <description>If true quotes (" or ') around data value will be removed.</description>
507      <class>java.lang.Boolean</class>
508      <value>true</value>
509    </parameter>
510    <parameter>
511      <name>extendedColumnMapping.locusLink</name>
512      <label>LocusLink</label>
513      <description />
514      <class />
515      <value />
516    </parameter>
517    <parameter>
518      <name>extendedColumnMapping.synonyms</name>
519      <label>Synonyms</label>
520      <description />
521      <class />
522      <value />
523    </parameter>
524    <parameter>
525      <name>extendedColumnMapping.isoformType</name>
526      <label>Isoform type</label>
527      <description />
528      <class />
529      <value />
530    </parameter>
531    <parameter>
532      <name>extendedColumnMapping.sourceReferenceId</name>
533      <label>Source reference id</label>
534      <description />
535      <class />
536      <value />
537    </parameter>
538    <parameter>
539      <name>extendedColumnMapping.ilmnGene</name>
540      <label>ILMN Gene</label>
541      <description />
542      <class />
543      <value />
544    </parameter>
545    <parameter>
546      <name>extendedColumnMapping.library</name>
547      <label>Library</label>
548      <description>The library from which the reporter is derived</description>
549      <class />
550      <value />
551    </parameter>
552    <parameter>
553      <name>maxDataColumns</name>
554      <label>Max data columns</label>
555      <description>The maximum number of columns for a line to be counted as a data line, or 0 to allow any number of columns.</description>
556      <class />
557      <value />
558    </parameter>
559    <parameter>
560      <name>extendedColumnMapping.chromosome</name>
561      <label>Chromosome</label>
562      <description>The chromosome from which the reporter is derived</description>
563      <class>java.lang.String</class>
564      <value>\Chr\</value>
565    </parameter>
566    <parameter>
567      <name>symbolColumnMapping</name>
568      <label>Gene symbol</label>
569      <description>Mapping that picks the reporter's gene symbol from the data columns. For example: \Gene symbol\</description>
570      <class />
571      <value />
572    </parameter>
573    <parameter>
574      <name>headerRegexp</name>
575      <label>Header</label>
576      <description>A regular expression that matches a header line and extracts the name and a value parts. For example, split on equal symbol: (.+)=(.*)</description>
577      <class />
578      <value />
579    </parameter>
580    <parameter>
581      <name>scoreColumnMapping</name>
582      <label>Score</label>
583      <description>Mapping that picks the reporter's score in some context. This mapping is only used when importing to a reporter list.</description>
584      <class />
585      <value />
586    </parameter>
587    <parameter>
588      <name>dataHeaderRegexp</name>
589      <label>Data header</label>
590      <description>A regular expression that matches the header line just before the data begins. For example: Block\tRow\tColumn.*</description>
591      <class>java.lang.String</class>
592      <value>IlmnID,.*AddressA_ID.*</value>
593    </parameter>
594    <parameter>
595      <name>extendedColumnMapping.controlCompositeMap</name>
596      <label>Control composite map</label>
597      <description />
598      <class />
599      <value />
600    </parameter>
601    <parameter>
602      <name>reporterType</name>
603      <label>Reporter type</label>
604      <description>The reporter type assigned to the imported reporters</description>
605      <class />
606      <value />
607    </parameter>
608    <parameter>
609      <name>extendedColumnMapping.length</name>
610      <label>Length</label>
611      <description>The length of the sequence</description>
612      <class />
613      <value />
614    </parameter>
615    <parameter>
616      <name>extendedColumnMapping.probeChrOrientation</name>
617      <label>Probe chr orientation</label>
618      <description />
619      <class />
620      <value />
621    </parameter>
622    <parameter>
623      <name>reporterTypeColumnMapping</name>
624      <label>Reporter type</label>
625      <description>Mapping that pick the reporter's type from the data columns. This will overide the reporter type parameter. For example: \Reporter type\</description>
626      <class />
627      <value />
628    </parameter>
629    <parameter>
630      <name>complexExpressions</name>
631      <label>Complex column mappings</label>
632      <description>disallow = Only allow simple mappings that are constant value or pick the value from one column only, for example, '1.6' or '\Row\'
633allow = Allow expression and complex mappings, for example, '\Row\, \Column\' or '=2*col('radius')'</description>
634      <class>java.lang.String</class>
635      <value>disallow</value>
636    </parameter>
637    <parameter>
638      <name>extendedColumnMapping.controlGroupName</name>
639      <label>Control group name</label>
640      <description />
641      <class />
642      <value />
643    </parameter>
644    <parameter>
645      <name>charset</name>
646      <label>Character set</label>
647      <description>The character set used in the file, if not specified the default character set is used (ISO-8859-1).</description>
648      <class>java.lang.String</class>
649      <value>ISO-8859-1</value>
650    </parameter>
651    <parameter>
652      <name>extendedColumnMapping.probeCoordinates</name>
653      <label>Probe coordinates</label>
654      <description />
655      <class />
656      <value />
657    </parameter>
658    <parameter>
659      <name>extendedColumnMapping.controlGroupId</name>
660      <label>Control group id</label>
661      <description />
662      <class />
663      <value />
664    </parameter>
665    <parameter>
666      <name>dataSplitterRegexp</name>
667      <label>Data splitter</label>
668      <description>A regular expression that splits each data line into individual columns. For example, split on tabs: \t</description>
669      <class>java.lang.String</class>
670      <value>,</value>
671    </parameter>
672    <parameter>
673      <name>extendedColumnMapping.antibiotics</name>
674      <label>Antibiotics</label>
675      <description />
676      <class />
677      <value />
678    </parameter>
679    <parameter>
680      <name>reporterIdColumnMapping</name>
681      <label>Reporter ID</label>
682      <description>Mapping that picks the reporter's ID from the data columns. For example: \ID\</description>
683      <class>java.lang.String</class>
684      <value>\IlmnID\</value>
685    </parameter>
686    <parameter>
687      <name>extendedColumnMapping.species</name>
688      <label>Species</label>
689      <description>The organism from which the reporter is derived</description>
690      <class>java.lang.String</class>
691      <value>\Species\</value>
692    </parameter>
693    <parameter>
694      <name>extendedColumnMapping.sequence</name>
695      <label>Sequence</label>
696      <description>The nucleotide sequence of the reporter</description>
697      <class />
698      <value />
699    </parameter>
700    <parameter>
701      <name>nameColumnMapping</name>
702      <label>Name</label>
703      <description>Mapping that picks the reporter's name from the data columns. For example: \Name\</description>
704      <class>java.lang.String</class>
705      <value>\Name\</value>
706    </parameter>
707    <parameter>
708      <name>extendedColumnMapping.vector</name>
709      <label>Vector</label>
710      <description>The vector from which the reporter is derived</description>
711      <class />
712      <value />
713    </parameter>
714    <parameter>
715      <name>extendedColumnMapping.nid</name>
716      <label>NID</label>
717      <description />
718      <class />
719      <value />
720    </parameter>
721  </configuration>
722</configfile>
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