-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
+/*
+ * 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
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * 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/>.
+ */
package jalview.ws;\r
\r
import jalview.datamodel.Alignment;\r
*/\r
public SequenceFetcher()\r
{\r
+ this(true);\r
+ }\r
+ public SequenceFetcher(boolean addDas)\r
+ {\r
addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
// PFAM\r
addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);\r
- registerDasSequenceSources();\r
+ if (addDas) {\r
+ registerDasSequenceSources();\r
+ }\r
}\r
\r
/**\r
- * return an ordered list of database sources suitable for using in a GUI\r
- * element\r
+ * return an ordered list of database sources where non-das database classes\r
+ * appear before das database classes\r
*/\r
public String[] getOrderedSupportedSources()\r
{\r
String[] srcs = this.getSupportedDb();\r
+ ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();\r
+ for (int i = 0; i < srcs.length; i++)\r
+ {\r
+ boolean das = false, skip = false;\r
+ String nm;\r
+ for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
+ {\r
+ // Skip the alignment databases for the moment - they're not useful for\r
+ // verifying a single sequence against its reference source\r
+ if (dbs.isA(DBRefSource.ALIGNMENTDB))\r
+ {\r
+ skip = true;\r
+ }\r
+ else\r
+ {\r
+ nm = dbs.getDbName();\r
+ if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
+ {\r
+ if (nm.startsWith("das:"))\r
+ {\r
+ nm = nm.substring(4);\r
+ das = true;\r
+ }\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (skip)\r
+ {\r
+ continue;\r
+ }\r
+ if (das)\r
+ {\r
+ dassrc.add(srcs[i]);\r
+ }\r
+ else\r
+ {\r
+ nondas.add(srcs[i]);\r
+ }\r
+ }\r
+ String[] tosort = nondas.toArray(new String[0]), sorted = nondas\r
+ .toArray(new String[0]);\r
+ for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
+ {\r
+ tosort[j] = tosort[j].toLowerCase();\r
+ }\r
+ jalview.util.QuickSort.sort(tosort, sorted);\r
+ // construct array with all sources listed\r
+\r
+ srcs = new String[sorted.length + dassrc.size()];\r
+ int i = 0;\r
+ for (int j = sorted.length - 1; j >= 0; j--, i++)\r
+ {\r
+ srcs[i] = sorted[j];\r
+ sorted[j] = null;\r
+ }\r
+\r
+ sorted = dassrc.toArray(new String[0]);\r
+ tosort = dassrc.toArray(new String[0]);\r
+ for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
+ {\r
+ tosort[j] = tosort[j].toLowerCase();\r
+ }\r
+ jalview.util.QuickSort.sort(tosort, sorted);\r
+ for (int j = sorted.length - 1; j >= 0; j--, i++)\r
+ {\r
+ srcs[i] = sorted[j];\r
+ }\r
+ return srcs;\r
+ }\r
+\r
+ /**\r
+ * return plaintext databse list suitable for using in a GUI element\r
+ */\r
+ public String[] _getOrderedSupportedSources()\r
+ {\r
+ String[] srcs = this.getSupportedDb();\r
ArrayList dassrc = new ArrayList(), nondas = new ArrayList();\r
for (int i = 0; i < srcs.length; i++)\r
{\r
{\r
AlignmentI ds = null;\r
Vector noProds = new Vector();\r
- String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"\r
+ String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"\r
+ "With no arguments, all DbSources will be queried with their test Accession number.\n"\r
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";\r
+ + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"\r
+ + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"\r
+ + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";\r
+ boolean withDas=true;\r
+ if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))\r
+ {\r
+ withDas=false;\r
+ String targs[] = new String[argv.length-1];\r
+ System.arraycopy(argv, 1, targs, 0, targs.length);\r
+ argv=targs;\r
+ }\r
if (argv != null && argv.length > 0)\r
{\r
- List<DbSourceProxy> sps = new SequenceFetcher()\r
+ List<DbSourceProxy> sps = new SequenceFetcher(withDas)\r
.getSourceProxy(argv[0]);\r
\r
if (sps != null)\r
AlignmentI al = null;\r
try\r
{\r
- al = sp.getSequenceRecords(argv[1]);\r
+ al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());\r
} catch (Exception e)\r
{\r
e.printStackTrace();\r
- System.err.println("Error when retrieving " + argv[1]\r
+ System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())\r
+ " from " + argv[0] + "\nUsage: " + usage);\r
}\r
SequenceI[] prod = al.getSequencesArray();\r
System.out.println(usage);\r
return;\r
}\r
- ASequenceFetcher sfetcher = new SequenceFetcher();\r
+ ASequenceFetcher sfetcher = new SequenceFetcher(withDas);\r
String[] dbSources = sfetcher.getSupportedDb();\r
for (int dbsource = 0; dbsource < dbSources.length; dbsource++)\r
{\r
}\r
}\r
}\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff