X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FRfam.java;h=12f2d2728ce7a275ef315e14b32d505ef6f88a8e;hb=ab58313e7bb31264ddb2715a1c548cdc789d7fa6;hp=11cdc024e9f72c03772c994ac62757677ba8a7f6;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 11cdc02..12f2d27 100644
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -1,40 +1,61 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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.
+ * 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 .
+ * 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;
-import com.stevesoft.pat.Regex;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
/**
* Contains methods for fetching sequences from Rfam database
*
* @author Lauren Michelle Lui
*/
-abstract public class Rfam extends Xfam implements DbSourceProxy
+abstract public class Rfam extends Xfam
{
+ static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
+
+ private static final String DEFAULT_RFAM_BASEURL = "https://rfam.org";
+
+ static
+ {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_RFAM_BASEURL);
+ }
+
+ /*
+ * append to URLs to retrieve as a gzipped file
+ */
+ protected static final String GZIPPED = "?gzip=1&download=1";
+
+ @Override
+ protected String getURLPrefix()
+ {
+ return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
+ }
public Rfam()
{
super();
- // all extensions of this RFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
}
/*
@@ -43,9 +64,9 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
* @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
* consistency with Pfam class
*/
+ @Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
@@ -54,9 +75,9 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
*/
+ @Override
public Regex getAccessionValidator()
{
- // TODO Auto-generated method stub
return null;
}
@@ -80,23 +101,15 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
@Override
public String getDbVersion()
{
- // TODO Auto-generated method stub
return null;
}
- /**
- * Returns base URL for selected Rfam alignment type
- *
- * @return RFAM URL stub for this DbSource
- */
- @Override
- protected abstract String getXFAMURL();
-
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
return accession.indexOf("RF") == 0;
@@ -107,9 +120,10 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.dbsources.Xfam#getXfamSource()
*/
+ @Override
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.RFAM;
+ return DBRefSource.RFAM;
}
}