|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--AFLPcore.Operation | +--AFLPcore.ImportFilter | +--AFLPcore.ABI3x00Filter
This class reads data from a ABI 3100 and a 3700 capillary machine. As far as the program is concerned, a capilary is identical to a lane in a gel. The file format for the file is nearly identical to the format for the ABI 377 (the ABILaneFilter class), and the description will not be duplicated here. The major difference is that the LANS data does not always seem to be present. This means that the color of the size standard must be selected by the user.
ABILaneFilter
Field Summary | |
static int |
ALL
|
static int |
BLUE
color channel |
static int |
GREEN
color channel |
static int |
RED
color channel |
static int |
YELLOW
color channel |
Fields inherited from class AFLPcore.ImportFilter |
filetype, GEL, LANE |
Fields inherited from class AFLPcore.Operation |
descript, helpFile, name, options |
Constructor Summary | |
ABI3x00Filter()
Creates a new filter to read in ABI files. |
Method Summary | |
java.lang.String |
getDescription()
Retrieves a short, approximately one sentence, description of the filter. |
int |
getFileType()
Returns the type of input file supported by this filter In this case ImportFilter.LANE , since the filter reads in lane data. |
java.lang.String |
getHelpFile()
The help file describes which files the filter reads and the options that this filter accepts. |
java.lang.String |
getName()
Access the name of the filter. |
Option[] |
getOptions()
Returns the options for this filter, which includes the color of the data, the size function to use, and the size standard. |
Gel |
readGel(java.io.File inputFile)
This filter does not read gels. |
Lane[] |
readLane(java.io.File inputFile)
This is the method that is called to preform the actual reading of the file. |
Peak |
readPeak(java.io.RandomAccessFile in)
Read in a peak from the file. |
void |
setOptions(Option[] opts)
Sets the parameters for the filter to the specified values, including color. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
public static final int YELLOW
public static final int RED
public static final int BLUE
public static final int GREEN
public static final int ALL
Constructor Detail |
public ABI3x00Filter()
Method Detail |
public java.lang.String getName()
getName
in class Operation
public int getFileType()
ImportFilter.LANE
, since the filter reads in lane data.getFileType
in class ImportFilter
public java.lang.String getDescription()
getDescription
in class Operation
public java.lang.String getHelpFile()
getHelpFile
in class Operation
public Option[] getOptions()
Option
of type CHOICE
. The second option
allows the color of the size standard to be selected. The third
option is also of type CHOICE
. It tells which size
method should be used to compute the size of the fragements. Please
see the help files and the code for the size functions for a
description of how the work. The third option describes the size
standard to use. This simply gives the program a list of values.
These are stored in a file called "standards.cfg" Possible values
for all of these options are read in from the
FeatureList
class.getOptions
in class Operation
Option
,
FeatureList
,
SizeFunction
,
SizeStandard
public void setOptions(Option[] opts)
SizeFunction
. Note that
the name is not the class name of the SizeFunction
, but
the name each SizeFunction
stores internally. The
third option must also be set.setOptions
in class Operation
opts
- an array of length 4 which contains the options
mentioned above and described in getOptions()
The order must be: color, size function, size standard.MissingParameterError
- occurs when the filter fails to
extract a string from the first option in opts
.java.lang.IllegalArgumentException
- occurs when a string is found but
cannot be matched to one of the colors: Red, Blue, Green, or Yellow.
Or if an array with length not equal to 3 is given as
opts
, or if the specified size function, the second
option, could not be matched to a defined size function.public Lane[] readLane(java.io.File inputFile) throws java.io.IOException
setOptions
, and if they are not, an exception will be
thrown.readLane
in class ImportFilter
inputFile
- The file that contains the lane data.MissingParameterError
- occurs if the options are not
set. Since this includes the required color, the filter cannot
read in the lane.java.io.IOException
- If an error is encountered in the file,
then this exception will be thrownpublic Gel readGel(java.io.File inputFile) throws java.io.IOException
readGel
in class ImportFilter
null
public Peak readPeak(java.io.RandomAccessFile in) throws java.io.IOException
Value Start Length(bytes) Type scan 0 4 integer (1000 + this value) height 4 2 integer area 18 4 integer size 26 4 IEEE 754 single-percision float
in
- the input sourcejava.io.IOException
- occurs if the file cannot be read.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |