In my case, I had a bunch of pdb files in a jar archive, so here's the codeI
try to use:
public static InputStream get_pdbinputstream(String fileName,Stringpdb_id) {
System.out.println(fileName); InputStream returnstream =
null; JarFile jarFile = null; try { jarFile =
new JarFile(fileName); for (Enumeration e = jarFile.entries();
e.hasMoreElements();) {
JarEntry jarEntry = (JarEntry) e.nextElement();
if (jarEntry.isDirectory()) continue;
String pdbid = jarEntry.getName(); pdbid =
pdbid.substring(0, 4).toUpperCase();
System.out.println(pdbid); if (pdbid.intern() != pdb_id)
continue;
returnstream = jarFile.getInputStream(jarEntry);
} } catch (IOException ioe) { System.out.println("An
IOException occurred: " +ioe.getMessage()); } finally {
if (jarFile != null) { try { jarFile.close(); } catch
(IOException ioe) {} } } return
returnstream; }
public static Object parse_pdb(String pdb_datafile, String pdb_id) {
Structure structure = null; pdb_inputstream =
Utils.get_pdbinputstream(pdb_datafile,pdb_id); if (pdb_inputstream !=
null) structure
=org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(pdb_inputstream);
return structure; }
The 1st function is supposed to get the desired InputStream from thespecified
archive file, while the second supposed to generate the structure.However:
"Utils.java": non-static method parsePDBFile(java.io.InputStream) cannot
bereferenced from a static context at line 1132, column 92as it kindly sais...
Is there a solution of this problem?
On 11/30/05, Andreas Prlic <[EMAIL PROTECTED]> wrote:>> Hi Tamas,>> In case you
are working with a PDB file that is located> somewhere on your hard disk, you
could use the code from below> to parse it in.>> Cheers,> Andreas>>> String
filename = "path/to/pdbfile.ent" ;>> PDBFileReader pdbreader = new
PDBFileReader();>> try{> Structure struc =
pdbreader.getStructure(filename);> System.out.println(struc);> }
catch (Exception e) {> e.printStackTrace();> }>>>> On 29 Nov 2005, at
16:25, Tamas Horvath wrote:>> > I've got an ArrayList<String> object containing
a PDB file's> > information.How may I feed it to the structure parser? As far
as I> > could see, it onlyaccepts BufferdReader or imputStream...>>> >
---------------------------------------------------------------------->>
Andreas Prlic Wellcome Trust Sanger Institute>
Hinxton, Cambridge CB10 1SA, UK> +44 (0) 1223 49
6891>> ___________!
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