/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.ebi;\r
-\r
-import java.io.BufferedInputStream;\r
-import java.io.BufferedReader;\r
-import java.io.File;\r
-import java.io.FileOutputStream;\r
-import java.io.InputStreamReader;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.StringTokenizer;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class EBIFetchClient\r
-{\r
- String format = "default";\r
-\r
- String style = "raw";\r
-\r
- /**\r
- * Creates a new EBIFetchClient object.\r
- */\r
- public EBIFetchClient()\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedDBs()\r
- {\r
- // TODO - implement rest call for dbfetch getSupportedDBs\r
- throw new Error("Not yet implemented");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedFormats()\r
- {\r
- // TODO - implement rest call for dbfetch getSupportedFormats\r
- throw new Error("Not yet implemented");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedStyles()\r
- {\r
- // TODO - implement rest call for dbfetch getSupportedStyles\r
- throw new Error("Not yet implemented");\r
- }\r
-\r
- public File fetchDataAsFile(String ids, String f, String s)\r
- throws OutOfMemoryError\r
- {\r
- File outFile = null;\r
- try\r
- {\r
- outFile = File.createTempFile("jalview", ".xml");\r
- outFile.deleteOnExit();\r
- fetchData(ids, f, s, outFile);\r
- if (outFile.length() == 0)\r
- {\r
- outFile.delete();\r
- return null;\r
- }\r
- } catch (Exception ex)\r
- {\r
- }\r
- return outFile;\r
- }\r
-\r
- /**\r
- * Single DB multiple record retrieval\r
- * \r
- * @param ids\r
- * db:query1;query2;query3\r
- * @param f\r
- * raw/xml\r
- * @param s\r
- * ?\r
- * \r
- * @return Raw string array result of query set\r
- */\r
- public String[] fetchData(String ids, String f, String s)\r
- throws OutOfMemoryError\r
- {\r
- return fetchData(ids, f, s, null);\r
- }\r
-\r
- public String[] fetchData(String ids, String f, String s, File outFile)\r
- throws OutOfMemoryError\r
- {\r
- // Need to split\r
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
- String[] rslts = new String[0];\r
- StringTokenizer queries = new StringTokenizer(ids, ";");\r
- String db = null;\r
- StringBuffer querystring = null;\r
- int nq = 0;\r
- while (queries.hasMoreTokens())\r
- {\r
- String query = queries.nextToken();\r
- int p;\r
- if ((p = query.indexOf(':')) > -1)\r
- {\r
- db = query.substring(0, p);\r
- query = query.substring(p + 1);\r
- }\r
- if (querystring == null)\r
- {\r
- querystring = new StringBuffer(query);\r
- nq++;\r
- }\r
- else\r
- {\r
- querystring.append("," + query);\r
- nq++;\r
- }\r
- }\r
- if (db == null)\r
- {\r
- System.err.println("Invalid Query string : '" + ids\r
- + "'\nShould be of form 'dbname:q1;q2;q3;q4'");\r
- return null;\r
- }\r
- String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);\r
- if (rslt != null)\r
- {\r
- String[] nrslts = new String[rslt.length + rslts.length];\r
- System.arraycopy(rslts, 0, nrslts, 0, rslts.length);\r
- System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);\r
- rslts = nrslts;\r
- }\r
-\r
- return (rslts.length == 0 ? null : rslts);\r
- }\r
-\r
- public String[] fetchBatch(String ids, String db, String f, String s,\r
- File outFile) throws OutOfMemoryError\r
- {\r
- long time = System.currentTimeMillis();\r
- // max 200 ids can be added at one time\r
- try\r
- {\r
- URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"\r
- + db.toLowerCase() + "/" + ids.toLowerCase()\r
- + (f != null ? "/" + f : ""));\r
-\r
- BufferedInputStream is = new BufferedInputStream(rcall.openStream());\r
- if (outFile != null)\r
- {\r
- FileOutputStream fio = new FileOutputStream(outFile);\r
- byte[] bb = new byte[32 * 1024];\r
- int l;\r
- while ((l = is.read(bb)) > 0)\r
- {\r
- fio.write(bb, 0, l);\r
- }\r
- fio.close();\r
- is.close();\r
- }\r
- else\r
- {\r
- BufferedReader br = new BufferedReader(new InputStreamReader(is));\r
- String rtn;\r
- ArrayList<String> arl = new ArrayList<String>();\r
- while ((rtn = br.readLine()) != null)\r
- {\r
- arl.add(rtn);\r
- }\r
- return arl.toArray(new String[arl.size()]);\r
- }\r
- } catch (OutOfMemoryError er)\r
- {\r
-\r
- System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db\r
- + ":\n" + ids);\r
- throw er;\r
- } catch (Exception ex)\r
- {\r
- if (ex.getMessage().startsWith(\r
- "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))\r
- {\r
- return null;\r
- }\r
- System.err.println("Unexpected exception when retrieving from " + db\r
- + "\nQuery was : '" + ids + "'");\r
- ex.printStackTrace(System.err);\r
- return null;\r
- } finally\r
- {\r
- //System.err.println("Took " + (System.currentTimeMillis() - time)\r
- // / 1000 + " secs for one call.");\r
- }\r
- return null;\r
- }\r
-}\r
+package jalview.ws.ebi;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.StringTokenizer;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+ String format = "default";
+
+ String style = "raw";
+
+ /**
+ * Creates a new EBIFetchClient object.
+ */
+ public EBIFetchClient()
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedDBs()
+ {
+ // TODO - implement rest call for dbfetch getSupportedDBs
+ throw new Error("Not yet implemented");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedFormats()
+ {
+ // TODO - implement rest call for dbfetch getSupportedFormats
+ throw new Error("Not yet implemented");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedStyles()
+ {
+ // TODO - implement rest call for dbfetch getSupportedStyles
+ throw new Error("Not yet implemented");
+ }
+
+ public File fetchDataAsFile(String ids, String f, String s)
+ throws OutOfMemoryError
+ {
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("jalview", ".xml");
+ outFile.deleteOnExit();
+ fetchData(ids, f, s, outFile);
+ if (outFile.length() == 0)
+ {
+ outFile.delete();
+ return null;
+ }
+ } catch (Exception ex)
+ {
+ }
+ return outFile;
+ }
+
+ /**
+ * Single DB multiple record retrieval
+ *
+ * @param ids
+ * db:query1;query2;query3
+ * @param f
+ * raw/xml
+ * @param s
+ * ?
+ *
+ * @return Raw string array result of query set
+ */
+ public String[] fetchData(String ids, String f, String s)
+ throws OutOfMemoryError
+ {
+ return fetchData(ids, f, s, null);
+ }
+
+ public String[] fetchData(String ids, String f, String s, File outFile)
+ throws OutOfMemoryError
+ {
+ // Need to split
+ // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+ String[] rslts = new String[0];
+ StringTokenizer queries = new StringTokenizer(ids, ";");
+ String db = null;
+ StringBuffer querystring = null;
+ int nq = 0;
+ while (queries.hasMoreTokens())
+ {
+ String query = queries.nextToken();
+ int p;
+ if ((p = query.indexOf(':')) > -1)
+ {
+ db = query.substring(0, p);
+ query = query.substring(p + 1);
+ }
+ if (querystring == null)
+ {
+ querystring = new StringBuffer(query);
+ nq++;
+ }
+ else
+ {
+ querystring.append("," + query);
+ nq++;
+ }
+ }
+ if (db == null)
+ {
+ System.err.println("Invalid Query string : '" + ids
+ + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
+ return null;
+ }
+ String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);
+ if (rslt != null)
+ {
+ String[] nrslts = new String[rslt.length + rslts.length];
+ System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
+ System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
+ rslts = nrslts;
+ }
+
+ return (rslts.length == 0 ? null : rslts);
+ }
+
+ public String[] fetchBatch(String ids, String db, String f, String s,
+ File outFile) throws OutOfMemoryError
+ {
+ long time = System.currentTimeMillis();
+ // max 200 ids can be added at one time
+ try
+ {
+ URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+ + db.toLowerCase() + "/" + ids.toLowerCase()
+ + (f != null ? "/" + f : ""));
+
+ BufferedInputStream is = new BufferedInputStream(rcall.openStream());
+ if (outFile != null)
+ {
+ FileOutputStream fio = new FileOutputStream(outFile);
+ byte[] bb = new byte[32 * 1024];
+ int l;
+ while ((l = is.read(bb)) > 0)
+ {
+ fio.write(bb, 0, l);
+ }
+ fio.close();
+ is.close();
+ }
+ else
+ {
+ BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ String rtn;
+ ArrayList<String> arl = new ArrayList<String>();
+ while ((rtn = br.readLine()) != null)
+ {
+ arl.add(rtn);
+ }
+ return arl.toArray(new String[arl.size()]);
+ }
+ } catch (OutOfMemoryError er)
+ {
+
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
+ + ":\n" + ids);
+ throw er;
+ } catch (Exception ex)
+ {
+ if (ex.getMessage().startsWith(
+ "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+ {
+ return null;
+ }
+ System.err.println("Unexpected exception when retrieving from " + db
+ + "\nQuery was : '" + ids + "'");
+ ex.printStackTrace(System.err);
+ return null;
+ } finally
+ {
+ //System.err.println("Took " + (System.currentTimeMillis() - time)
+ // / 1000 + " secs for one call.");
+ }
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff