formatting

[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 91ffbca..576509c 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
  * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.ws.dbsources;\r
 \r
@@ -38,8 +37,7 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  * @author JimP\r
  * \r
  */\r
-abstract public class Pfam extends DbSourceProxyImpl implements\r
-        DbSourceProxy\r
+abstract public class Pfam extends Xfam implements DbSourceProxy\r
 {\r
 \r
   public Pfam()\r
@@ -47,6 +45,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     super();\r
     // all extensions of this PFAM source base class are DOMAINDB sources\r
     addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
+    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);\r
   }\r
 \r
   /*\r
@@ -75,17 +74,17 @@ abstract public class Pfam extends DbSourceProxyImpl implements
    * (non-Javadoc)\r
    * \r
    * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *\r
-   *      this doesn't work - DbSource is key for the hash of DbSourceProxy\r
-   *      instances - 1:many mapping for DbSource to proxy will be lost. *\r
-   *      suggest : PFAM is an 'alignment' source - means proxy is higher level\r
-   *      than a sequence source. return jalview.datamodel.DBRefSource.PFAM; }\r
+   * this doesn't work - DbSource is key for the hash of DbSourceProxy instances\r
+   * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an\r
+   * 'alignment' source - means proxy is higher level than a sequence source.\r
+   * return jalview.datamodel.DBRefSource.PFAM; }\r
    */\r
 \r
   /*\r
    * (non-Javadoc)\r
    * \r
    * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable\r
-   *      getDbSourceProperties() {\r
+   * getDbSourceProperties() {\r
    * \r
    * return null; }\r
    */\r
@@ -95,6 +94,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
    * \r
    * @see jalview.ws.DbSourceProxy#getDbVersion()\r
    */\r
+  @Override\r
   public String getDbVersion()\r
   {\r
     // TODO Auto-generated method stub\r
@@ -102,10 +102,12 @@ abstract public class Pfam extends DbSourceProxyImpl implements
   }\r
 \r
   /**\r
+   * Returns base URL for selected Pfam alignment type\r
    * \r
    * @return PFAM URL stub for this DbSource\r
    */\r
-  protected abstract String getPFAMURL();\r
+  @Override\r
+  protected abstract String getXFAMURL();\r
 \r
   /*\r
    * (non-Javadoc)\r
@@ -118,7 +120,7 @@ abstract public class Pfam extends DbSourceProxyImpl implements
     // individual references to each sequence in each family alignment that's\r
     // retrieved.\r
     startQuery();\r
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()\r
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()\r
             + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,\r
             "STH");\r
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)\r
@@ -151,4 +153,10 @@ abstract public class Pfam extends DbSourceProxyImpl implements
   /*\r
    * public String getDbName() { return "PFAM"; // getDbSource(); }\r
    */\r
+\r
+  public String getXfamSource()\r
+  {\r
+    return jalview.datamodel.DBRefSource.PFAM;\r
+  }\r
+\r
 }\r