001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure.rcsb; 022 023import java.io.BufferedReader; 024import java.io.IOException; 025import java.io.InputStreamReader; 026import java.net.URL; 027import java.net.URLConnection; 028import java.util.ArrayList; 029import java.util.HashMap; 030import java.util.List; 031import java.util.Map; 032 033public class RCSBUpdates { 034 035 // The URL for acquiring the data 036 public static final String baseURL = "http://ftp.rcsb.org/pub/pdb/data/status/latest/"; 037 038 /** 039 * 040 * @return A map mapping each field (defined by a separate FTP file) to the PDB ids in the field. The possible fields 041 * are: added.models, added.nmr, added.pdb, added.sf, modified.cs, modified.models, modified.nmr, modified.pdb, modified.sf, 042 * obsolete.cs, obsolete.models, obsolete.nmr, obsolete.pdb, obsolete.sf 043 * @throws IOException 044 */ 045 public Map<String,String[]> getUpdates() throws IOException{ 046 047 Map<String,String[]> outMap = new HashMap<String, String[]>(); 048 // A list of files to get 049 String[] newStringList = {"added.models","added.nmr","added.pdb","added.sf","modified.cs","modified.models", 050 "modified.nmr","modified.pdb","modified.sf","obsolete.cs","obsolete.models","obsolete.nmr","obsolete.pdb","obsolete.sf"}; 051 for(String fileName: newStringList){ 052 String[] thisList = readURL(baseURL+""+fileName); 053 outMap.put(fileName, thisList); 054 } 055 return outMap; 056 057 } 058 059 060 /** 061 * 062 * @param urlIn The url to be read 063 * @return A list of PDB ids as strings 064 * @throws IOException 065 */ 066 private String[] readURL(String urlIn) throws IOException{ 067 List<String> outList = new ArrayList<String>(); 068 // create a url object 069 URL url = new URL(urlIn); 070 071 // create a urlconnection object 072 URLConnection urlConnection = url.openConnection(); 073 074 // wrap the urlconnection in a bufferedreader 075 try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(urlConnection.getInputStream()))) { 076 077 String line; 078 079 // read from the urlconnection via the bufferedreader 080 while ((line = bufferedReader.readLine()) != null) 081 { 082 outList.add(line); 083 } 084 085 } 086 087 return outList.toArray(new String[outList.size()]); 088 } 089}