PIP.IO.StampPackage
Class RunStamp

java.lang.Object
  PIP.IO.StampPackage.RunStamp

public class RunStamp
extends java.lang.Object

Constructor Summary

RunStamp()

Method Summary

static void	cleanDomainDefsFile(java.lang.String descriptionFileName, java.lang.String dir, java.util.List<Domain> domsToKeep)
static void	cleanStampScanFile(java.lang.String scanFileName, java.lang.String dir, java.util.List<Domain> domsToKeep)
static void	generateAlignments(java.lang.String nameScanFile, java.lang.String outputDirectory, java.lang.String alignmentFileName)
static void	moveScanFile(java.lang.String nameOfFile, java.lang.String originalDir, java.lang.String destinationDir)
static void	removeFilesInDirectory(java.lang.String directory)
static void	removeFilesInDirectoryExceptOnesEndingIn(java.lang.String directory, java.lang.String end)
static void	removeFileThatEndsWith(java.lang.String directory, java.lang.String endsWith)
static void	removeFileThatStartsWith(java.lang.String directory, java.lang.String startsWith)
static void	removePreviousStampFiles(java.lang.String directory)
static void	roughFitCmd(java.lang.String referenceFileName, java.lang.String alternativeFileName, java.lang.String outputDirectory, java.lang.String scanFileName)
static void	run(java.lang.String cmd)
static java.util.List<Stamper>	stampDomainInteractions(java.util.List<DomainInteraction> domainInteractions, java.lang.String directory, boolean isHomodimer, FamilyType ft)
static Stamper	stampDomains(java.util.List<Domain> domains)
static void	stampScanStructures(java.lang.String referenceFileName, java.lang.String alternativeFileName, java.lang.String outputDirectory, java.lang.String scanFileName)
static void	writeOutStampInput(StampComparison stamp, java.lang.String referenceFileName, java.lang.String alternativeFileName, java.lang.String outputDirectory)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RunStamp

public RunStamp()

Method Detail

stampDomains

public static Stamper stampDomains(java.util.List<Domain> domains)
                            throws java.io.IOException,
                                   java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

stampDomainInteractions

public static java.util.List<Stamper> stampDomainInteractions(java.util.List<DomainInteraction> domainInteractions,
                                                              java.lang.String directory,
                                                              boolean isHomodimer,
                                                              FamilyType ft)
                                                       throws java.io.IOException,
                                                              java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

writeOutStampInput

public static void writeOutStampInput(StampComparison stamp,
                                      java.lang.String referenceFileName,
                                      java.lang.String alternativeFileName,
                                      java.lang.String outputDirectory)
                               throws java.io.IOException

Throws:

java.io.IOException

run

public static void run(java.lang.String cmd)
                throws java.io.IOException,
                       java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

stampScanStructures

public static void stampScanStructures(java.lang.String referenceFileName,
                                       java.lang.String alternativeFileName,
                                       java.lang.String outputDirectory,
                                       java.lang.String scanFileName)
                                throws java.io.IOException,
                                       java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

generateAlignments

public static void generateAlignments(java.lang.String nameScanFile,
                                      java.lang.String outputDirectory,
                                      java.lang.String alignmentFileName)
                               throws java.io.IOException,
                                      java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

roughFitCmd

public static void roughFitCmd(java.lang.String referenceFileName,
                               java.lang.String alternativeFileName,
                               java.lang.String outputDirectory,
                               java.lang.String scanFileName)
                        throws java.io.IOException,
                               java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

removeFilesInDirectory

public static void removeFilesInDirectory(java.lang.String directory)

removeFilesInDirectoryExceptOnesEndingIn

public static void removeFilesInDirectoryExceptOnesEndingIn(java.lang.String directory,
                                                            java.lang.String end)

removePreviousStampFiles

public static void removePreviousStampFiles(java.lang.String directory)

removeFileThatStartsWith

public static void removeFileThatStartsWith(java.lang.String directory,
                                            java.lang.String startsWith)

removeFileThatEndsWith

public static void removeFileThatEndsWith(java.lang.String directory,
                                          java.lang.String endsWith)

cleanDomainDefsFile

public static void cleanDomainDefsFile(java.lang.String descriptionFileName,
                                       java.lang.String dir,
                                       java.util.List<Domain> domsToKeep)
                                throws java.io.IOException

Throws:

java.io.IOException

cleanStampScanFile

public static void cleanStampScanFile(java.lang.String scanFileName,
                                      java.lang.String dir,
                                      java.util.List<Domain> domsToKeep)
                               throws java.io.IOException

Throws:

java.io.IOException

moveScanFile

public static void moveScanFile(java.lang.String nameOfFile,
                                java.lang.String originalDir,
                                java.lang.String destinationDir)
                         throws java.io.IOException

Throws:

java.io.IOException