JAL-4073 Pfam retrieval now works via a template including $PFAMID$ and $ALTYPE$...

[jalview.git] / src / jalview / ws / dbsources / Pfam.java

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 2587bac..0c21d42 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
 import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
 import jalview.util.Platform;
@@ -36,14 +38,19 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Pfam extends Xfam
 {
-  /*
-   * 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";
 
-  private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
   static
   {
     Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
@@ -54,6 +61,13 @@ abstract public class Pfam extends Xfam
     super();
   }
 
+    
+    String getURL(String queries)
+  {
+      return getPfamDownloadURL(
+                                queries.trim().toUpperCase(Locale.ROOT), alignmentType);
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -132,5 +146,4 @@ abstract public class Pfam extends Xfam
   {
     return DBRefSource.PFAM;
   }
-
 }