org.metaqtl.main
Class MetaMain
java.lang.Object
org.metaqtl.main.MetaMain
- Direct Known Subclasses:
- A2Xml, ConsMap, InfoMap, MapView, MetaDB, MMapView, MQTLView, QTLClust, QTLClustInfo, QTLModel, QTLProj, QTLTree, Xml2A
public abstract class MetaMain
- extends java.lang.Object
Method Summary |
static void |
generalHelp()
|
static java.lang.String |
generalUsage()
|
static Chromosome[] |
getChromByNames(Chromosome[] chroms,
java.lang.String[] chromNames)
|
static ChromGraph[] |
getChromGraph(Chromosome[] chroms,
boolean withQtl,
int modeQtl,
IBioOntology ontology,
MetaQtlAnalysis treeAnalysis)
|
protected static MetaQtlModel |
getCluster(java.lang.String cluFile)
|
static ChromCluster[] |
getClusterByNames(ChromCluster[] clusters,
java.lang.String[] chromNames)
|
protected static MetaDico |
getDico(java.lang.String dicoFile)
|
protected static IBioLocus[] |
getDubious(java.lang.String dubFile)
|
static IBioGenome |
getMap(IBioGenome[] maps,
java.lang.String mapName)
|
protected static IBioGenome |
getMap(java.lang.String mapFile)
|
protected static IBioGenome[] |
getMaps(java.lang.String qtlDir)
|
static java.util.Hashtable |
getMrkToRm(java.io.File file)
|
protected static IBioOntology |
getOntology(java.lang.String ontoF,
char format)
|
static QtlPartition |
getQtlPartition(Chromosome chromosome,
IBioOntology ontology)
|
static QtlPartition |
getQtlPartition(Chromosome chrom,
MetaQtlAnalysis analysis,
java.lang.String trait,
int k,
char tclust)
|
protected static MetaQtlAnalysis |
getResult(java.lang.String resFile)
|
void |
initCmdLineParser()
|
static java.lang.String[] |
parseChromList(java.lang.String list)
|
void |
parseCmdLine(java.lang.String[] args)
|
abstract void |
printHelp()
|
static void |
printImgFormat(int indent)
|
static void |
printLicense(java.lang.String program,
java.lang.String version)
|
abstract void |
printUsage()
|
static void |
removeLocus(IBioGenome[] maps,
java.lang.String mrkRmFile)
|
static void |
setParameter(java.lang.String parFile)
|
static void |
synchChromGraphs(ChromGraph[] chromGraphs,
java.util.Set partNames)
|
static void |
writeImg(ChromGraph[] chroms,
java.io.File file,
java.lang.String imgFormat)
|
protected static void |
writeMap(IBioGenome map,
java.lang.String outFile)
|
protected static void |
writeMap(IBioGenome genome,
java.lang.String format,
java.lang.String outFile)
|
static void |
writePar(java.io.File file)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
parser
protected CmdLineParser parser
verbose
protected java.lang.Boolean verbose
help
protected java.lang.Boolean help
MetaMain
public MetaMain()
printUsage
public abstract void printUsage()
printHelp
public abstract void printHelp()
initCmdLineParser
public void initCmdLineParser()
parseCmdLine
public void parseCmdLine(java.lang.String[] args)
generalHelp
public static void generalHelp()
generalUsage
public static java.lang.String generalUsage()
- Returns:
writeMap
protected static void writeMap(IBioGenome genome,
java.lang.String format,
java.lang.String outFile)
throws java.io.IOException
- Parameters:
genome
- format
- outFile
-
- Throws:
java.io.IOException
writeMap
protected static void writeMap(IBioGenome map,
java.lang.String outFile)
throws java.io.IOException
- Parameters:
ap
- outFile
-
- Throws:
java.io.IOException
getCluster
protected static MetaQtlModel getCluster(java.lang.String cluFile)
throws java.io.IOException
- Parameters:
cluFile
-
- Returns:
-
- Throws:
java.io.IOException
getResult
protected static MetaQtlAnalysis getResult(java.lang.String resFile)
throws java.io.IOException
- Parameters:
resFile
-
- Returns:
-
- Throws:
I
java.io.IOException
getMap
protected static IBioGenome getMap(java.lang.String mapFile)
throws java.io.IOException
- Parameters:
mapFile
-
- Returns:
-
- Throws:
java.io.IOException
getDubious
protected static IBioLocus[] getDubious(java.lang.String dubFile)
throws java.io.IOException
- Parameters:
dubFile
-
- Returns:
-
- Throws:
java.io.IOException
getDico
protected static MetaDico getDico(java.lang.String dicoFile)
throws java.io.IOException
- Parameters:
dicoFile
-
- Returns:
-
- Throws:
java.io.IOException
getMaps
protected static IBioGenome[] getMaps(java.lang.String qtlDir)
throws java.io.IOException
- Parameters:
qtlDir
-
- Returns:
-
- Throws:
java.io.IOException
getOntology
protected static IBioOntology getOntology(java.lang.String ontoF,
char format)
throws java.io.IOException
- Parameters:
qtlF
-
- Returns:
-
- Throws:
java.io.IOException
printLicense
public static void printLicense(java.lang.String program,
java.lang.String version)
- Parameters:
string
- version
-
getQtlPartition
public static QtlPartition getQtlPartition(Chromosome chromosome,
IBioOntology ontology)
getQtlPartition
public static QtlPartition getQtlPartition(Chromosome chrom,
MetaQtlAnalysis analysis,
java.lang.String trait,
int k,
char tclust)
printImgFormat
public static void printImgFormat(int indent)
setParameter
public static void setParameter(java.lang.String parFile)
throws java.io.IOException
- Parameters:
parFile
-
- Throws:
java.io.IOException
parseChromList
public static java.lang.String[] parseChromList(java.lang.String list)
- Parameters:
list
-
- Returns:
getChromByNames
public static Chromosome[] getChromByNames(Chromosome[] chroms,
java.lang.String[] chromNames)
getClusterByNames
public static ChromCluster[] getClusterByNames(ChromCluster[] clusters,
java.lang.String[] chromNames)
getChromGraph
public static ChromGraph[] getChromGraph(Chromosome[] chroms,
boolean withQtl,
int modeQtl,
IBioOntology ontology,
MetaQtlAnalysis treeAnalysis)
- Parameters:
chroms
- withQtl
-
- Returns:
synchChromGraphs
public static void synchChromGraphs(ChromGraph[] chromGraphs,
java.util.Set partNames)
- Parameters:
chromGraphs
- partNames
-
writeImg
public static void writeImg(ChromGraph[] chroms,
java.io.File file,
java.lang.String imgFormat)
throws java.io.IOException
- Throws:
java.io.IOException
writePar
public static void writePar(java.io.File file)
throws java.io.IOException
- Parameters:
file
-
- Throws:
java.io.IOException
getMrkToRm
public static java.util.Hashtable getMrkToRm(java.io.File file)
throws java.io.IOException
- Parameters:
file
-
- Returns:
-
- Throws:
java.io.IOException
removeLocus
public static void removeLocus(IBioGenome[] maps,
java.lang.String mrkRmFile)
throws java.io.IOException
- Parameters:
maps
- mrkRmFile
-
- Throws:
java.io.IOException
getMap
public static IBioGenome getMap(IBioGenome[] maps,
java.lang.String mapName)
- Parameters:
maps
- mapName
-
- Returns: