X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=36d98915a11341da8e5059603d6cc78b0c55fb5d;hb=ab58313e7bb31264ddb2715a1c548cdc789d7fa6;hp=dd2d155ef2c21afa723966393b92cdd8ca40800c;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index dd2d155..36d9891 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -1,25 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 java.util.Locale;
+
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
/**
@@ -30,18 +38,24 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
*/
public abstract class Xfam extends DbSourceProxyImpl
{
-
public Xfam()
{
super();
}
- protected abstract String getXFAMURL();
+ /**
+ * the base URL for this Xfam-like service
+ *
+ * @return
+ */
+ protected abstract String getURLPrefix();
+ @Override
public abstract String getDbVersion();
abstract String getXfamSource();
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
// TODO: this is not a perfect implementation. We need to be able to add
@@ -49,23 +63,51 @@ public abstract class Xfam extends DbSourceProxyImpl
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
+ String xfamUrl = getURL(queries);
+
+ Console.debug("XFAM URL for retrieval is: " + xfamUrl);
+
+ AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
+ DataSourceType.URL, FileFormat.Stockholm);
+
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ // getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(getDbSource(), getDbVersion(), queries
- .trim().toUpperCase()));
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
}
}
stopQuery();
return rcds;
}
+ String getURL(String queries)
+ {
+ return getURLPrefix() + "/family/"
+ + queries.trim().toUpperCase(Locale.ROOT) + getURLSuffix();
+ }
+
+ /**
+ * Pfam and Rfam provide alignments
+ */
+ @Override
+ public boolean isAlignmentSource()
+ {
+ return true;
+ }
+
+ /**
+ * default suffix to append the retrieval URL for this source.
+ *
+ * @return "" for most Xfam sources
+ */
+ public String getURLSuffix()
+ {
+ return "";
+ }
+
}