import java.util.Locale;
+import com.stevesoft.pat.Regex;
+
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import jalview.util.Platform;
-import com.stevesoft.pat.Regex;
-
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
* to an alignment TODO: create interface to pass alignment properties and tree
*/
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;
- }
+ 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
super();
}
-
- String getURL(String queries)
+ @Override
+ String getURL(String queries)
{
- return getPfamDownloadURL(
- queries.trim().toUpperCase(Locale.ROOT), alignmentType);
+ return getPfamDownloadURL(queries.trim().toUpperCase(Locale.ROOT),
+ alignmentType);
}
/*