X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FJalviewSource.java;h=b3bb342e9d7da3293fc652295be44ab8986a338a;hb=28fda83cbef0c9c82cd09a343af4e1721085c104;hp=139bafeb0b2fd150102f127a5d3e8d4ef0dc2e20;hpb=7243db3d99cc1760c2d4802f3005b4f86d1b4bd6;p=jalview.git
diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index 139bafe..b3bb342 100644
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources.das.datamodel;
import java.text.ParseException;
@@ -10,7 +30,6 @@ import java.util.Map;
import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
import org.biodas.jdas.dassources.Capabilities;
import org.biodas.jdas.dassources.utils.DasTimeFormat;
-import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
import org.biodas.jdas.schema.sources.CAPABILITY;
import org.biodas.jdas.schema.sources.COORDINATES;
import org.biodas.jdas.schema.sources.MAINTAINER;
@@ -18,16 +37,20 @@ import org.biodas.jdas.schema.sources.PROP;
import org.biodas.jdas.schema.sources.SOURCE;
import org.biodas.jdas.schema.sources.VERSION;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.DbSourceProxy;
public class JalviewSource implements jalviewSourceI
{
SOURCE source;
+
MultipleConnectionPropertyProviderI connprov;
- public JalviewSource(SOURCE local2, MultipleConnectionPropertyProviderI connprov, boolean local)
+
+ public JalviewSource(SOURCE local2,
+ MultipleConnectionPropertyProviderI connprov, boolean local)
{
- this.connprov=connprov;
+ this.connprov = connprov;
this.local = local;
source = local2;
}
@@ -311,22 +334,26 @@ public class JalviewSource implements jalviewSourceI
{
try
{
- // kind of dumb, since org.biodas.jdas.dassources.utils.VersionAdapter.getSourceUriFromQueryUri() does this,
- // but this way, we can access non DAS 1.6 compliant sources (which have to have a URL like /das/ and cause a validation exception)
-
+ // kind of dumb, since
+ // org.biodas.jdas.dassources.utils.VersionAdapter.getSourceUriFromQueryUri()
+ // does this,
+ // but this way, we can access non DAS 1.6 compliant sources (which have
+ // to have a URL like /das/ and cause a validation exception)
+
for (CAPABILITY cap : getVersion().getCAPABILITY())
{
String capname = cap.getType().substring(
cap.getType().indexOf(":") + 1);
- int p=cap.getQueryUri().lastIndexOf(capname);
- if (p<-1) {
- throw new Exception("Invalid das source: "+source.getUri());
- }
- if (cap.getQueryUri().charAt(p)=='/')
+ int p = cap.getQueryUri().lastIndexOf(capname);
+ if (p < -1)
+ {
+ throw new Exception(MessageManager.formatMessage("exception.invalid_das_source", new String[]{source.getUri()}));
+ }
+ if (cap.getQueryUri().charAt(p) == '/')
{
p--;
}
- return cap.getQueryUri().substring(0,p);
+ return cap.getQueryUri().substring(0, p);
}
} catch (Exception x)
{
@@ -343,4 +370,12 @@ public class JalviewSource implements jalviewSourceI
return isLaterThan(getVersion().getCreated(), other.getVersion()
.getCreated());
}
+
+ @Override
+ public boolean isReferenceSource()
+ {
+ // TODO check source object for indication that we are the primary for a DAS
+ // coordinate system
+ return false;
+ }
}