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 579a6fe..0c21d42 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,29 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.dbsources;
 
+import java.util.Locale;
 
-import com.stevesoft.pat.Regex;
+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
@@ -33,15 +36,36 @@ import jalview.ws.seqfetcher.DbSourceProxy;
  * @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);
   }
 
   /*
@@ -49,9 +73,9 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -60,9 +84,9 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -93,47 +117,13 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
   @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);
   }
 
   /*
@@ -141,6 +131,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     return accession.indexOf("PF") == 0;
@@ -150,9 +141,9 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * public String getDbName() { return "PFAM"; // getDbSource(); }
    */
 
+  @Override
   public String getXfamSource()
   {
-    return jalview.datamodel.DBRefSource.PFAM;
+    return DBRefSource.PFAM;
   }
-
 }