- /*
- * append to URLs to retrieve as a gzipped file
- */
- protected static final String GZIPPED = "/gzipped";
-
- static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
+ 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";