From 0ad352a33dee2be3c35a875475e504a29a8b3ad6 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 6 Oct 2022 12:21:28 +0100
Subject: [PATCH] JAL-4073 Pfam retrieval now works via a template including
 $PFAMID$ and $ALTYPE$ (full, seed, etc). Also changed name
 of PFAM_BASEURL_KEY to PFAM_INTERPRO_URL_TEMPLATE to avoid
 misconfiguration

---
 src/jalview/ws/dbsources/Pfam.java          |   29 +++++++++++++++++++--------
 src/jalview/ws/dbsources/PfamFull.java      |    7 +------
 src/jalview/ws/dbsources/PfamSeed.java      |    7 +------
 test/jalview/ws/dbsources/PfamFullTest.java |    4 ++--
 4 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 2587bac..0c21d42 100644
--- 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;
   }
-
 }
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index d71892b..ffb5e41 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -29,12 +29,7 @@ public class PfamFull extends Pfam
   public PfamFull()
   {
     super();
-  }
-
-  @Override
-  public String getURLSuffix()
-  {
-    return "/alignment/full" + GZIPPED;
+    alignmentType=FULL;
   }
 
   /*
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index f64d07f..6d486e8 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -31,12 +31,7 @@ public class PfamSeed extends Pfam
   public PfamSeed()
   {
     super();
-  }
-
-  @Override
-  public String getURLSuffix()
-  {
-    return "/alignment/seed" + GZIPPED;
+    alignmentType=SEED;
   }
 
   /*
diff --git a/test/jalview/ws/dbsources/PfamFullTest.java b/test/jalview/ws/dbsources/PfamFullTest.java
index 23cceb2..eb2f147 100644
--- a/test/jalview/ws/dbsources/PfamFullTest.java
+++ b/test/jalview/ws/dbsources/PfamFullTest.java
@@ -38,14 +38,14 @@ public class PfamFullTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "pfam.xfam.org/family/ABC/alignment/full/gzipped";
+      String path = "www.ebi.ac.uk/interpro/wwwapi/entry/pfam/ABC/?annotation=alignment:full&download";
 
     // with default value for domain
     String url = new PfamFull().getURL(" abc ");
     assertEquals(url, "https://" + path);
 
     // with override in properties
-    Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://pfam.xfam.org");
+    Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download");
     url = new PfamFull().getURL(" abc ");
     assertEquals(url, "http://" + path);
   }
-- 
1.7.10.2