org.biojava.bio.structure.server
Class PrepareIndexFile

java.lang.Object
  extended by org.biojava.bio.structure.server.PrepareIndexFile
Direct Known Subclasses:
PrepareMMcifIndexFile

public class PrepareIndexFile
extends java.lang.Object


Constructor Summary
PrepareIndexFile()
           
 
Method Summary
 void createPDBInfoList(java.io.File[] pdbfiles, java.io.File outputFile, java.io.File chainInfoFile)
          parses a set of PDB files and writes info into a file the file is tab separated and has the following columns: name length resolution depositionDate modificationDate technique title classification filename binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup This method needs to be run, before a DBSearch can be performed, since the files created by this method are required for the DBSearch
 java.io.File[] getAllPDB(java.io.File dir)
          get all PDBfiles from a directory
protected  void logPDBInfoFile(java.io.PrintWriter pdbWriter, java.io.PrintWriter chainWriter, StructureIOFile pdbreader, java.io.File[] pdbfiles)
           
static void main(java.lang.String[] args)
           
 void prepareIndexFileForInstallation(FlatFileInstallation installation)
          prepare the index file for this installation
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PrepareIndexFile

public PrepareIndexFile()
Method Detail

main

public static void main(java.lang.String[] args)

prepareIndexFileForInstallation

public void prepareIndexFileForInstallation(FlatFileInstallation installation)
                                     throws java.io.FileNotFoundException,
                                            java.io.IOException
prepare the index file for this installation

Parameters:
installation -
Throws:
java.io.FileNotFoundException
java.io.IOException

createPDBInfoList

public void createPDBInfoList(java.io.File[] pdbfiles,
                              java.io.File outputFile,
                              java.io.File chainInfoFile)
                       throws java.io.FileNotFoundException,
                              java.io.IOException
parses a set of PDB files and writes info into a file the file is tab separated and has the following columns: name length resolution depositionDate modificationDate technique title classification filename binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup This method needs to be run, before a DBSearch can be performed, since the files created by this method are required for the DBSearch

Parameters:
pdbfiles -
outputFile -
Throws:
java.io.FileNotFoundException
java.io.IOException

logPDBInfoFile

protected void logPDBInfoFile(java.io.PrintWriter pdbWriter,
                              java.io.PrintWriter chainWriter,
                              StructureIOFile pdbreader,
                              java.io.File[] pdbfiles)
                       throws java.io.IOException
Throws:
java.io.IOException

getAllPDB

public java.io.File[] getAllPDB(java.io.File dir)
get all PDBfiles from a directory

Parameters:
dir - the directory that contains all PDB files
Returns:
an array of PDB Files