AffyChipTypeExtractor (Gemma 1.31.4 API)

java.lang.Object
- ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor

```
public class AffyChipTypeExtractor
extends Object
```
Extract the chip type from Affymetrix CEL files. Handles both version 3 (ASCII) and 4 (binary) files.
See CEL and GENERIC
Note that the Affymetrix documentation does not mention a chip type, explicitly, but it's in the "DatHeader", and in GCOS files as affymetrix-array-type

Author:

paul

Constructor Summary

Constructors
Constructor Description

AffyChipTypeExtractor()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static String`	`extract(InputStream is)`
`static Map<BioAssay,String>`	`getChipTypes(ExpressionExperiment ee, Collection<LocalFile> files)`	Extract a string like "Rat230_2" from CEL files.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AffyChipTypeExtractor
```
public AffyChipTypeExtractor()
```
- Method Detail
  - getChipTypes
```
public static Map<BioAssay,String> getChipTypes(ExpressionExperiment ee,
                                                      Collection<LocalFile> files)
```
    Extract a string like "Rat230_2" from CEL files. This is to help match BioAssays to platforms when reanalyzing from CEL, especially if the original platform information has been lost (e.g., by switching to a merged platform, or from a custom CDF-based version)
    
    Parameters:
    
    ee - experiment
    
    files - CEL files
    
    Returns:
    
    map of bioassays to cel identifiers
  - extract
```
public static String extract(InputStream is)
```
    Parameters:
    
    is - input stream
    
    Returns:
    
    text