X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=b2d3dc98a50d1f62de92b7eb5d1c3b7f7f92113d;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d935db92629803b4e07ec5d860409f12f781d582;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d935db9..b2d3dc9 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,112 +1,159 @@
-/**
- * 
- */
-package jalview.ws.dbsources;
-
-import java.util.Hashtable;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.io.FastaFile;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-/**
- * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.
- * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment
- * TODO: HP: Incorporate jalview.gui.SequenceFetcher retrieval code here.
- * @author JimP
- *
- */
-public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
-{
-
-  public Pfam()
-  {
-    super();
-    
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  public String getAccessionSeparator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  public Regex getAccessionValidator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSource()
-   */
-  public String getDbSource()
-  {
-    return jalview.datamodel.DBRefSource.PFAM;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
-   */
-  public Hashtable getDbSourceProperties()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  public String getDbVersion()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-  public static String PFAMURL = "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=";
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
-  public AlignmentI getSequenceRecords(String queries) throws Exception
-  {
-    // 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();
-    results = new StringBuffer();
-    // split queries into many little ones.
-    results.append(new FastaFile(
-                PFAMURL+queries.trim().toUpperCase(), "URL").print());
-    stopQuery();
-    AlignmentI rcds = parseResult(results.toString());
-    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)
-    {
-      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), getDbVersion(), queries.trim().toUpperCase()));
-    }
-    return rcds;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  public boolean isValidReference(String accession)
-  {
-    return accession.indexOf("PF")==0;
-  }
-
-  public String getTestQuery()
-  {
-    return "PF00535";
-  }
-
-  public String getDbName()
-  {
-    return getDbSource();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * 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
+ * back to sequence fetcher
+ * 
+ * @author JimP
+ * 
+ */
+abstract public class Pfam extends Xfam implements DbSourceProxy
+{
+
+  public Pfam()
+  {
+    super();
+    // all extensions of this PFAM source base class are DOMAINDB sources
+    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
+    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+   */
+  public String getAccessionSeparator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+   */
+  public Regex getAccessionValidator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
+   * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
+   * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
+   * 'alignment' source - means proxy is higher level than a sequence source.
+   * return jalview.datamodel.DBRefSource.PFAM; }
+   */
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+   * getDbSourceProperties() {
+   * 
+   * return null; }
+   */
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbVersion()
+   */
+  @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
+  {
+    // 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;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+   */
+  public boolean isValidReference(String accession)
+  {
+    return accession.indexOf("PF") == 0;
+  }
+
+  /*
+   * public String getDbName() { return "PFAM"; // getDbSource(); }
+   */
+
+  public String getXfamSource()
+  {
+    return jalview.datamodel.DBRefSource.PFAM;
+  }
+
+}