X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=316c1aac7d3e7711ddd38598a87fc1343838d09d;hb=c41398473f1493a06f28da53be50630a0f6e6f6d;hp=b2443e8338cee2980efa996c5fee3db8706a705a;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index b2443e8..316c1aa 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,28 +1,32 @@
/*
- * 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 java.util.Locale;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
@@ -32,15 +36,43 @@ import jalview.ws.seqfetcher.DbSourceProxy;
* @author JimP
*
*/
-abstract public class Pfam extends Xfam implements DbSourceProxy
+abstract public class Pfam extends Xfam
{
+ public static final String FULL = "full", RP35 = "rp35", RP15 = "rp15",
+ RP75 = "rp75", RP55 = "rp55", SEED = "seed", UNIPROT = "uniprot";
+
+ public String getPfamDownloadURL(String id, String alType)
+ {
+ String url = Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
+ url = url.replace("$PFAMID$", id);
+ url = url.replace("$ALTYPE$", alType);
+ return url;
+ }
+
+ static final String PFAM_BASEURL_KEY = "PFAM_INTERPRO_URL_TEMPLATE";
+
+ protected String alignmentType;
+
+ /**
+ * docs are http://www.ebi.ac.uk/interpro/api/
+ */
+ private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$";
+
+ static
+ {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
+ }
public Pfam()
{
super();
- // all extensions of this PFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
+ }
+
+ @Override
+ String getURL(String queries)
+ {
+ return getPfamDownloadURL(queries.trim().toUpperCase(Locale.ROOT),
+ alignmentType);
}
/*
@@ -48,9 +80,9 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
@@ -59,9 +91,9 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
- // TODO Auto-generated method stub
return null;
}
@@ -92,47 +124,13 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
@Override
public String getDbVersion()
{
- // TODO Auto-generated method stub
return null;
}
- /**
- * Returns base URL for selected Pfam alignment type
- *
- * @return PFAM URL stub for this DbSource
- */
@Override
- protected abstract String getXFAMURL();
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
- */
- public AlignmentI getSequenceRecords(String queries) throws Exception
+ protected String getURLPrefix()
{
- // TODO: this is not a perfect implementation. We need to be able to add
- // individual references to each sequence in each family alignment that's
- // retrieved.
- startQuery();
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
- for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
- {
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
- if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
- { // add the specific ref too
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(getDbSource(), getDbVersion(), queries
- .trim().toUpperCase()));
- }
- }
- stopQuery();
- return rcds;
+ return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
}
/*
@@ -140,6 +138,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
return accession.indexOf("PF") == 0;
@@ -149,9 +148,9 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
* public String getDbName() { return "PFAM"; // getDbSource(); }
*/
+ @Override
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.PFAM;
+ return DBRefSource.PFAM;
}
-
}