public class ClusterQuantiserOptions extends AbstractClusterQuantiserOptions
ClusterQuantiser tool.| Modifier and Type | Field and Description |
|---|---|
protected Class<? extends SpatialClusters<?>> |
clusterClass |
protected ClusterType.ClusterTypeOp |
clusterTypeOp |
protected File |
input_file |
protected Class<? extends SpatialClusters<?>> |
otherClusterClass |
protected File |
samplesFile |
protected boolean |
samplesFileMode |
exactQuant, extension, EXTRA_USAGE_INFO, fileType, info_mode, infoFile, inputFiles, otherInfoFile, quant_mode, quantLocation| Constructor and Description |
|---|
ClusterQuantiserOptions()
Construct with defaults
|
ClusterQuantiserOptions(String[] args)
Construct with arguments
|
| Modifier and Type | Method and Description |
|---|---|
Class<? extends SpatialClusters<?>> |
getClusterClass() |
ClusterType.ClusterTypeOp |
getClusterType() |
String |
getInputFileCommonRoot() |
List<File> |
getInputFiles() |
String |
getInputFileString() |
Class<? extends SpatialClusters<?>> |
getOtherInfoClass() |
String |
getOtherInfoFile() |
ClusterType.ClusterTypeOp |
getOtherInfoType() |
File |
getOutputFile() |
String |
getOutputFileString() |
byte[][] |
getSampleKeypoints() |
int |
getSamples() |
File |
getSamplesFile() |
String |
getTreeFile() |
boolean |
isBatchedSampleMode() |
boolean |
isCreateMode() |
boolean |
isSamplesFileMode() |
void |
loadSamplesFile()
load the samples file
|
boolean |
printTiming() |
void |
setClusterType(ClusterType clusterType)
Set the cluster type
|
void |
setClusterTypeOp(ClusterType.ClusterTypeOp clusterTypeOp)
Set the clusterTypeOp
|
void |
setInputFiles(List<File> files)
Set the input files
|
void |
setSamples(int nsamples)
Set the number of samples
|
void |
validate()
Validate the options
|
getConcurrency, getCountMode, getExtension, getFileType, getRandomSeed, getVerbosity, isInfoMode, isQuantMode, prepare, setFileTypeprotected ClusterType.ClusterTypeOp clusterTypeOp
protected Class<? extends SpatialClusters<?>> clusterClass
protected Class<? extends SpatialClusters<?>> otherClusterClass
protected File samplesFile
protected boolean samplesFileMode
protected File input_file
public ClusterQuantiserOptions(String[] args)
args - public ClusterQuantiserOptions()
public boolean isSamplesFileMode()
public byte[][] getSampleKeypoints()
public int getSamples()
public File getSamplesFile()
public ClusterType.ClusterTypeOp getClusterType()
getClusterType in class AbstractClusterQuantiserOptionspublic void loadSamplesFile()
public void validate() throws org.kohsuke.args4j.CmdLineException
AbstractClusterQuantiserOptionsvalidate in class AbstractClusterQuantiserOptionsorg.kohsuke.args4j.CmdLineExceptionpublic String getTreeFile() throws IOException
getTreeFile in class AbstractClusterQuantiserOptionsIOExceptionpublic boolean isCreateMode()
public boolean isBatchedSampleMode()
public List<File> getInputFiles() throws IOException
IOExceptionpublic File getOutputFile() throws IOException
IOExceptionpublic String getInputFileString()
getInputFileString in class AbstractClusterQuantiserOptionspublic String getOutputFileString()
getOutputFileString in class AbstractClusterQuantiserOptionspublic String getOtherInfoFile()
getOtherInfoFile in class AbstractClusterQuantiserOptionspublic ClusterType.ClusterTypeOp getOtherInfoType()
getOtherInfoType in class AbstractClusterQuantiserOptionspublic Class<? extends SpatialClusters<?>> getClusterClass()
getClusterClass in class AbstractClusterQuantiserOptionspublic Class<? extends SpatialClusters<?>> getOtherInfoClass()
getOtherInfoClass in class AbstractClusterQuantiserOptionspublic void setInputFiles(List<File> files)
files - public void setClusterType(ClusterType clusterType)
clusterType - public void setClusterTypeOp(ClusterType.ClusterTypeOp clusterTypeOp)
clusterTypeOp - public String getInputFileCommonRoot() throws IOException
IOExceptionpublic boolean printTiming()
public void setSamples(int nsamples)
nsamples - the number of samples