edu.sdsc.sirius.util
Class IOHandler

java.lang.Object
  edu.sdsc.sirius.util.IOHandler

public class IOHandler

extends java.lang.Object

Field Summary

static boolean

selection

Constructor Summary

IOHandler()

Method Summary

static java.lang.String	convertMol2ToString(Structure structure, boolean fragment, StructureViewer viewer, java.util.HashMap atomMap) Flag fragment denotes whether this string will be used to write out a custom fragment.
static java.lang.String	convertStructureToPdb(Structure structure, Manager parent)
static java.lang.String	convertStructureToSDF(Structure structure, java.lang.String name, java.util.HashMap initial)
static Structure	getStructure(java.util.Hashtable components, java.lang.String n)
static Entry	loadAln(java.lang.String content)
static Entry	loadFasta(java.lang.String content)
static Entry	loadGenbank(java.lang.String content)
static Entry	loadMol2FromString(java.lang.String content)
static Entry	loadMsf(java.lang.String content)
static Entry	loadPDBFromString(java.lang.String content, int number)
static Entry	loadUniprot(java.lang.String content)
static Structure	readPDB(java.io.File file)
static java.util.Vector	readPDBHeaders(java.lang.String content)
static void	saveAlignment(java.util.Vector sequences, Manager parent) sequences is a Vector of Sequence objects that need to be saved
static void	saveFile(Manager parent, java.lang.String content, java.lang.String extension, java.lang.String descriptor)
static void	savePdb(Structure structure, java.lang.String fname, Manager parent, java.util.HashMap initial)
static void	saveStructureFile(Structure structure, Manager parent)
static void	saveTextFile(java.lang.String content, Manager parent, java.lang.String extension)
static void	saveTextFile(java.lang.String content, java.lang.String name) This method saves the provided content to a text file with the given path

Methods inherited from class java.lang.Object

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

Field Detail

selection

public static boolean selection

Constructor Detail

IOHandler

public IOHandler()

Method Detail

saveAlignment

public static void saveAlignment(java.util.Vector sequences,
                                 Manager parent)

sequences is a Vector of Sequence objects that need to be saved

Parameters:

sequences -

parent -

saveTextFile

public static void saveTextFile(java.lang.String content,
                                Manager parent,
                                java.lang.String extension)

saveTextFile

public static void saveTextFile(java.lang.String content,
                                java.lang.String name)
                         throws java.io.IOException

This method saves the provided content to a text file with the given path

Parameters:

content - - content of the file

name - - full path to the file

Throws:

java.io.IOException

saveFile

public static void saveFile(Manager parent,
                            java.lang.String content,
                            java.lang.String extension,
                            java.lang.String descriptor)
                     throws java.io.IOException

Throws:

java.io.IOException

saveStructureFile

public static void saveStructureFile(Structure structure,
                                     Manager parent)

convertStructureToSDF

public static java.lang.String convertStructureToSDF(Structure structure,
                                                     java.lang.String name,
                                                     java.util.HashMap initial)

convertStructureToPdb

public static java.lang.String convertStructureToPdb(Structure structure,
                                                     Manager parent)

savePdb

public static void savePdb(Structure structure,
                           java.lang.String fname,
                           Manager parent,
                           java.util.HashMap initial)
                    throws java.io.IOException

Throws:

java.io.IOException

convertMol2ToString

public static java.lang.String convertMol2ToString(Structure structure,
                                                   boolean fragment,
                                                   StructureViewer viewer,
                                                   java.util.HashMap atomMap)

Flag fragment denotes whether this string will be used to write out a custom fragment. In that case, some lines are omitted, and no substructure information is saved. StructureViewer, when non-null, is used to check whether atoms are part of an independently moved group. In that case, their transformed coordinates are saved, instead of the recorded ones

Parameters:

structure -

fragment -

Returns:

readPDB

public static Structure readPDB(java.io.File file)

loadPDBFromString

public static Entry loadPDBFromString(java.lang.String content,
                                      int number)

loadMol2FromString

public static Entry loadMol2FromString(java.lang.String content)

readPDBHeaders

public static java.util.Vector readPDBHeaders(java.lang.String content)

getStructure

public static Structure getStructure(java.util.Hashtable components,
                                     java.lang.String n)

loadAln

public static Entry loadAln(java.lang.String content)

loadMsf

public static Entry loadMsf(java.lang.String content)

loadGenbank

public static Entry loadGenbank(java.lang.String content)

loadUniprot

public static Entry loadUniprot(java.lang.String content)

loadFasta

public static Entry loadFasta(java.lang.String content)