/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
*
*/
package jalview.ws.dbsources;
-import com.stevesoft.pat.Regex;
+import java.util.Locale;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
* @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";
+
+ 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;
+ private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download";
+
+ 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);
+ }
+
+
+ String getURL(String queries)
+ {
+ return getPfamDownloadURL(
+ queries.trim().toUpperCase(Locale.ROOT), alignmentType);
}
/*
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
- // TODO Auto-generated method stub
return null;
}
@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);
}
/*
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
return accession.indexOf("PF") == 0;
* public String getDbName() { return "PFAM"; // getDbSource(); }
*/
+ @Override
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.PFAM;
+ return DBRefSource.PFAM;
}
-
}