org.metaqtl.main
Class MetaMain

java.lang.Object
  extended by 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


Field Summary
protected  java.lang.Boolean help
           
protected  CmdLineParser parser
           
protected  java.lang.Boolean verbose
           
 
Constructor Summary
MetaMain()
           
 
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
 

Field Detail

parser

protected CmdLineParser parser

verbose

protected java.lang.Boolean verbose

help

protected java.lang.Boolean help
Constructor Detail

MetaMain

public MetaMain()
Method Detail

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: