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public interface StructureIOFile
interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.
Method Summary | |
---|---|
void |
addExtension(String ext)
add a known File extension. |
void |
clearExtensions()
clear all file extensions |
FileParsingParameters |
getFileParsingParameters()
Get the parameters that should be used for file parsing |
String |
getPath()
get the directory path to the files |
Structure |
getStructure(File file)
read file from File and returns a Structure object. |
Structure |
getStructure(String filename)
open filename and returns a Structure object. |
Structure |
getStructureById(String pdbId)
Get a Structure based on its PDB id. |
boolean |
isAutoFetch()
Fetch files automatically from FTP server. |
boolean |
isPdbDirectorySplit()
The PDB files are organized hierarchically (as on the PDB - FTP server. |
void |
setAutoFetch(boolean autoFetch)
Tell the parser to fetch missing PDB files from the FTP server automatically. |
void |
setFileParsingParameters(FileParsingParameters params)
Set the parameters that should be used for file parsing |
void |
setPath(String path)
Set path to file / connection string to db. |
void |
setPdbDirectorySplit(boolean isSplit)
The PDB files are organized hierarchically (as on the PDB - FTP server. |
Method Detail |
---|
void setPath(String path)
path
- a String specifying the path valueString getPath()
void addExtension(String ext)
ext
- a String ...void clearExtensions()
Structure getStructure(String filename) throws IOException
filename
- a String
IOException
- ...Structure getStructure(File file) throws IOException
file
- file containing a PDB or mmcif file
IOException
- ...boolean isAutoFetch()
void setAutoFetch(boolean autoFetch)
autoFetch
- flag.void setPdbDirectorySplit(boolean isSplit)
isSplit
- boolean isPdbDirectorySplit()
Structure getStructureById(String pdbId) throws IOException
getStructureById
in interface StructureIO
pdbId
- a String specifying the id value (PDB code)
IOException
- ...void setFileParsingParameters(FileParsingParameters params)
params
- FileParsingParametersFileParsingParameters getFileParsingParameters()
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