X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=456236a02efd63d3b5954230320e0aa5f646ab77;hb=1724567f3dfc3b4637aac7bdeb6633628e6a8335;hp=941bf1afa2330f293781c7df61cc1afe903ef3fc;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 941bf1a..456236a 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -20,12 +20,9 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
+import jalview.util.Platform;
 
 import com.stevesoft.pat.Regex;
 
@@ -39,6 +36,17 @@ 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";
+
+  private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
+  static {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
+  }
 
   public Pfam()
   {
@@ -53,7 +61,6 @@ abstract public class Pfam extends Xfam
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -65,7 +72,6 @@ abstract public class Pfam extends Xfam
   @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -96,47 +102,13 @@ abstract public class Pfam extends Xfam
   @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[])
-   */
   @Override
-  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 FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), DataSourceType.URL,
-            FileFormat.Stockholm);
-    for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
-    {
-      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
-      // getDbSource(),
-              getDbVersion(), queries.trim().toUpperCase()));
-      if (!getDbSource().equals(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);
   }
 
   /*