implemented embl validation properly

[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 2075a0b..91ffbca 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -29,23 +29,29 @@ import jalview.io.FastaFile;
 import jalview.io.StockholmFile;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
+\r
 /**\r
- * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment\r
- * TODO: create interface to pass alignment properties and tree back to sequence fetcher\r
+ * TODO: later PFAM is a complex datasource - it could return a tree in addition\r
+ * to an alignment TODO: create interface to pass alignment properties and tree\r
+ * back to sequence fetcher\r
+ * \r
  * @author JimP\r
- *\r
+ * \r
  */\r
-abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
+abstract public class Pfam extends DbSourceProxyImpl implements\r
+        DbSourceProxy\r
 {\r
 \r
   public Pfam()\r
   {\r
     super();\r
-    // all extensions of this PFAM source base class are DOMAINDB sources \r
+    // all extensions of this PFAM source base class are DOMAINDB sources\r
     addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
   }\r
 \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
    */\r
   public String getAccessionSeparator()\r
@@ -54,7 +60,9 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return null;\r
   }\r
 \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
    */\r
   public Regex getAccessionValidator()\r
@@ -63,27 +71,28 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return null;\r
   }\r
 \r
-  /* (non-Javadoc)\r
-   * @see jalview.ws.DbSourceProxy#getDbSource()\r
-  public String getDbSource()\r
-  {\r
-    ** this doesn't work - DbSource is key for the hash of DbSourceProxy instances - 1:many mapping for DbSource to proxy will be lost.\r
-    ** suggest : PFAM is an 'alignment' source - means proxy is higher level than a sequence source.\r
-    return jalview.datamodel.DBRefSource.PFAM;\r
-  }\r
+  /*\r
+   * (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
    */\r
 \r
-  \r
-  /* (non-Javadoc)\r
-   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()\r
-  public Hashtable getDbSourceProperties()\r
-  {\r
-    \r
-    return null;\r
-  }\r
- */\r
-  \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
+   * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable\r
+   *      getDbSourceProperties() {\r
+   * \r
+   * return null; }\r
+   */\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getDbVersion()\r
    */\r
   public String getDbVersion()\r
@@ -91,46 +100,55 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub\r
     return null;\r
   }\r
+\r
   /**\r
    * \r
    * @return PFAM URL stub for this DbSource\r
    */\r
   protected abstract String getPFAMURL();\r
-  /* (non-Javadoc)\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
    */\r
   public AlignmentI getSequenceRecords(String queries) throws Exception\r
   {\r
-    // 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. \r
+    // TODO: this is not a perfect implementation. We need to be able to add\r
+    // individual references to each sequence in each family alignment that's\r
+    // retrieved.\r
     startQuery();\r
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");\r
-    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)\r
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()\r
+            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,\r
+            "STH");\r
+    for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)\r
     {\r
-      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,\r
-              // getDbSource(), \r
-              getDbVersion(), queries.trim().toUpperCase()));\r
+      rcds.getSequenceAt(s).addDBRef(\r
+              new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,\r
+              // getDbSource(),\r
+                      getDbVersion(), queries.trim().toUpperCase()));\r
       if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))\r
-      {         // add the specific ref too\r
+      { // add the specific ref too\r
         rcds.getSequenceAt(s).addDBRef(\r
-                new DBRefEntry( getDbSource(), \r
-                        getDbVersion(), queries.trim().toUpperCase()));\r
+                new DBRefEntry(getDbSource(), getDbVersion(), queries\r
+                        .trim().toUpperCase()));\r
       }\r
     }\r
     stopQuery();\r
     return rcds;\r
   }\r
 \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
    */\r
   public boolean isValidReference(String accession)\r
   {\r
-    return accession.indexOf("PF")==0;\r
+    return accession.indexOf("PF") == 0;\r
   }\r
 \r
-\r
-  /*public String getDbName()\r
-  {\r
-    return "PFAM"; // getDbSource();\r
-  } */\r
+  /*\r
+   * public String getDbName() { return "PFAM"; // getDbSource(); }\r
+   */\r
 }\r