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## org.biojava.bio.structure.io
Interface StructureIOFile

All Superinterfaces:
  StructureIO

All Known Implementing Classes:
  MMCIFFileReader, PDBFileReader

    public interface StructureIOFile

extends StructureIO

interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.

Author:
  Andreas Prlic

Method Summary
`void` | `addExtension(String ext)` add a known File extension.
`void` | `clearExtensions()` clear all file extensions
`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.
`boolean` | `isAutoFetch()` Fetch files automatically from FTP server.
`void` | `setAutoFetch(boolean autoFetch)` Tell the parser to fetch missing PDB files from the FTP server automatically.
`void` | `setPath(String path)` Set path to file / connection string to db.

Methods inherited from interface org.biojava.bio.structure.io.StructureIO
`getStructureById`

Method Detail

### setPath

    void setPath(String path)

  Set path to file / connection string to db. This is for installations of PDB/mmCif where all files are located in one directory.

  Parameters:
    `path` - a String specifying the path value

### getPath

    String getPath()

  get the directory path to the files

  Returns:
    path

### addExtension

    void addExtension(String ext)

  add a known File extension.

  Parameters:
    `ext` - a String ...

### clearExtensions

    void clearExtensions()

  clear all file extensions

### getStructure

    Structure getStructure(String filename)
                           throws IOException

  open filename and returns a Structure object.

  Parameters:
    `filename` - a String
  Returns:
    a Structure object
  Throws:
    `IOException` - ...

### getStructure

    Structure getStructure(File file)
                           throws IOException

  read file from File and returns a Structure object.

  Parameters:
    `file` - file containing a PDB or mmcif file
  Returns:
    a Structure object
  Throws:
    `IOException` - ...

### isAutoFetch

    boolean isAutoFetch()

  Fetch files automatically from FTP server. Default: false

  Returns:
    flag is true or false.

### setAutoFetch

    void setAutoFetch(boolean autoFetch)

  Tell the parser to fetch missing PDB files from the FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.

  Parameters:
    `autoFetch` - flag.

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