X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=14b69972a1276bd20bff2ac2425acb3c1103549f;hb=aa030270d61a25a3417f674c48c2d323ff238277;hp=b1d3f3c01d4b8793588efadda07a65cffa8f1bf3;hpb=92f7b5ee3bbdb5456d498f1c2780d90420491342;p=jalview.git
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index b1d3f3c..14b6997 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,20 +1,20 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
- */
+/*
+ * 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 .
+ */
package jalview.ws;
import jalview.datamodel.Alignment;
@@ -22,7 +22,6 @@ import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
@@ -48,6 +47,10 @@ public class SequenceFetcher extends ASequenceFetcher
*/
public SequenceFetcher()
{
+ this(true);
+ }
+ public SequenceFetcher(boolean addDas)
+ {
addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);
addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
@@ -60,7 +63,9 @@ public class SequenceFetcher extends ASequenceFetcher
// PFAM
addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
- registerDasSequenceSources();
+ if (addDas) {
+ registerDasSequenceSources();
+ }
}
/**
@@ -73,15 +78,18 @@ public class SequenceFetcher extends ASequenceFetcher
ArrayList dassrc = new ArrayList(), nondas = new ArrayList();
for (int i = 0; i < srcs.length; i++)
{
- boolean das = false,skip=false;
+ boolean das = false, skip = false;
String nm;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
- // Skip the alignment databases for the moment - they're not useful for verifying a single sequence against its reference source
+ // Skip the alignment databases for the moment - they're not useful for
+ // verifying a single sequence against its reference source
if (dbs.isA(DBRefSource.ALIGNMENTDB))
{
- skip=true;
- } else {
+ skip = true;
+ }
+ else
+ {
nm = dbs.getDbName();
if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
{
@@ -208,12 +216,22 @@ public class SequenceFetcher extends ASequenceFetcher
{
AlignmentI ds = null;
Vector noProds = new Vector();
- String usage = "SequenceFetcher.main [ ]\n"
+ String usage = "SequenceFetcher.main [-nodas] [ []]\n"
+ "With no arguments, all DbSources will be queried with their test Accession number.\n"
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to and retrieve from it.";
+ + "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"
+ + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to and retrieve from it.\n"
+ + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
+ boolean withDas=true;
+ if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
+ {
+ withDas=false;
+ String targs[] = new String[argv.length-1];
+ System.arraycopy(argv, 1, targs, 0, targs.length);
+ argv=targs;
+ }
if (argv != null && argv.length > 0)
{
- List sps = new SequenceFetcher()
+ List sps = new SequenceFetcher(withDas)
.getSourceProxy(argv[0]);
if (sps != null)
@@ -223,11 +241,11 @@ public class SequenceFetcher extends ASequenceFetcher
AlignmentI al = null;
try
{
- al = sp.getSequenceRecords(argv[1]);
+ al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Error when retrieving " + argv[1]
+ System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
+ " from " + argv[0] + "\nUsage: " + usage);
}
SequenceI[] prod = al.getSequencesArray();
@@ -252,7 +270,7 @@ public class SequenceFetcher extends ASequenceFetcher
System.out.println(usage);
return;
}
- ASequenceFetcher sfetcher = new SequenceFetcher();
+ ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
String[] dbSources = sfetcher.getSupportedDb();
for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
{