Tag List Report
The following document contains the listing of user tags found in the code. Below is the summary of the occurrences per tag.
| Tag Class | Total number of occurrences | Tag strings used by tag class |
|---|---|---|
| @todo | 7 | @todo |
| FIXME | 17 | FIXME |
| TODO | 9 | TODO |
Each tag is detailed below:
@todo
Number of occurrences found in the code: 7
| ubic.basecode.dataStructure.graph.DirectedGraph | Line |
|---|---|
| do something about cyclicity; make this a dag or a subclass... | 46 |
| ubic.basecode.datafilter.RowAbsentFilter | Line |
| this should check more carefully - actually test that the rows are all the same. | 196 |
| ubic.basecode.math.DescriptiveWithMissing | Line |
| this will still break in some situations where there are missing values | 196 |
| possibly implement so a copy is not made. | 446 |
| possibly implement so a copy is not made. | 498 |
| ubic.basecode.math.MatrixRowStats | Line |
| Have min() and max() throw an EmptyMatrixException -- this exception class does not yet exist and needs to be defined somewhere. | 31 |
| ubic.basecode.math.Stats | Line |
| offer a regularized version of this function. | 103 |
FIXME
Number of occurrences found in the code: 17
| ubic.basecode.dataStructure.graph.UndirectedGraphNode | Line |
|---|---|
| why not? | 35 |
| ubic.basecode.dataStructure.matrix.CompressedBitMatrix | Line |
| set up the row/column names. | 338 |
| ubic.basecode.dataStructure.matrix.ObjectMatrixImpl | Line |
| set up the row/column names. | 185 |
| ubic.basecode.graphics.MatrixDisplay | Line |
| this is all a bit of a hack | 624 |
| ubic.basecode.math.MatrixNormalizer | Line |
| this should be factored out | 125 |
| ubic.basecode.math.MultipleTestCorrection | Line |
| make this API more consistent. | 31 |
| ubic.basecode.math.linalg.QRDecomposition | Line |
| we use this again later, but we recompute it. Try to cache it. | 392 |
| ubic.basecode.math.linearmodels.LeastSquaresFitTest | Line |
| this is always non-null, we need assertions about the actual values assertNotNull( interactionEffectP ); | 306 |
| this is always non-null, we need assertions about the actual values assertNotNull( interactionEffectP ); | 332 |
| why is precision of these tests so low? It was 0.1! I changed it to 0.001 | 465 |
| ubic.basecode.ontology.OntologyTermTest | Line |
| this uses NIF, which we are no longer using actively - not a big deal since this just tests mechanics | 86 |
| ubic.basecode.ontology.model.OntologyClassRestriction | Line |
| make separate subclass use this. public Object getRestrictedToValue(); | 29 |
| ubic.basecode.ontology.ncbo.AnnotatorClient | Line |
| only knows about HP and DOID | 132 |
| ubic.basecode.ontology.providers.MedicOntologyService | Line |
| this shouldn't be hard-coded like this, we should load it like any other ontology service. | 37 |
| ubic.basecode.ontology.providers.UberonOntologyServiceTest | Line |
| indexing Uberon is very slow, so we disable it so if the tests are breaking, try force-indexing | 30 |
| ubic.basecode.util.r.AbstractRClient | Line |
| only partly implemented, possibly not going to stay. | 523 |
| !!!! | 557 |
TODO
Number of occurrences found in the code: 9
| ubic.basecode.dataStructure.matrix.AbstractDoubleMatrixTest | Line |
|---|---|
| Document Me | 31 |
| ubic.basecode.dataStructure.matrix.AbstractMatrix3D | Line |
| Document Me | 27 |
| ubic.basecode.dataStructure.matrix.DoubleMatrix3D | Line |
| Document Me | 24 |
| ubic.basecode.io.ByteArrayConverter | Line |
| these could be static methods. | 39 |
| ubic.basecode.io.excel.CreateSpreadSheet | Line |
| Document Me | 28 |
| ubic.basecode.math.linearmodels.LeastSquaresFitTest | Line |
| R code please | 462 |
| add more tests here. | 1140 |
| ubic.basecode.math.linearmodels.ModeratedTstatTest | Line |
| Document Me | 39 |
| ubic.basecode.ontology.ncbo.OmimAnnotatorClient | Line |
| Document Me | 23 |