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| AnnotationTable.get.vector | Get a named vector from an AnnotationTable column |
| AnnotationTable.read | Read an AnnotationTable object |
| Array.add | Add an element to the array |
| Array.getFile | Get the file associated to the given key or index |
| Array.getFiles | Get the files contained in the array |
| Array.getKey | Get the key associated to the given index |
| Array.new | Initialize a new Array instance |
| Array.read | Read the array index file |
| Array.remove | Remove the given key |
| Array.size | Get the size of the array |
| Array.write | Write the array index file |
| copy.dir | Copy Directory |
| create.lookup | Create a hashed lookup from strings to indices |
| CSV.read | Read a CSV file |
| CSV.read.large | Read a CSV file |
| CSV.write | Write data frame or matrix to CSV file |
| delegate.defined | Tell whether delegate is defined |
| extract.directory | Extract Directory From a Filename |
| get.delegate.input | Get input filename of delegate |
| get.delegate.output | Get output filename of delegate |
| get.input | Get input filename |
| get.input.array.index | Get the array index file |
| get.metadata | Get metadata value |
| get.output | Get output filename |
| get.output.array.index | Get the array index file |
| get.parameter | Get parameter value |
| get.temp.dir | Get temporary directory for a component instance |
| input.defined | Tell whether input file is available |
| latex.figure | LaTeX code for inserting a figure |
| latex.quote | Quote a LaTeX string |
| latex.table | LaTeX code for a floating table |
| latex.tabular | LaTeX code for inserting a tabular environment |
| latex.write.main | Write a LaTeX document to an output port |
| launch.delegate | Launch delegate. |
| LogMatrix.read | Read an LogMatrix matrix from a CSV file |
| main | Component main function |
| Matrix.read | Read a matrix from CSV file |
| png.close | Close a PNG file |
| png.open | Open a PNG device |
| SampleGroupTable.add.group | Add a group to a SampleGroupTable object |
| SampleGroupTable.find.group | Find a sample group that is composed of given group IDs |
| SampleGroupTable.get.description | Get description of a group |
| SampleGroupTable.get.groups | Get group IDs of a SampleGroupTable object |
| SampleGroupTable.get.source.groups | Get vector of source group IDs |
| SampleGroupTable.get.type | Get type of given group |
| SampleGroupTable.new | Create a new emtpy SampleGroupTable object |
| SampleGroupTable.read | Read a SampleGroupTable object |
| SampleGroupTable.write | Write a SampleGroupTable object |
| SetList.assign | Create or update a set |
| SetList.get.ids | Return the set identifiers of a SetList |
| SetList.get.members | Return the contents of given set |
| SetList.new | Initialize a new SetList instance |
| SetList.read | Read a SetList instance from file |
| split.trim | Split and Trim a String |
| touch.output | Create an empty file for output port |
| trim | Remove heading and trailing whitespace from string |
| write.delegate.parameter | Write an entry into delegate parameter file |
| write.error | Write error message |
| write.log | Write log message |