JAL-2418 source formatting

[jalview.git] / src / jalview / ws / seqfetcher / DbSourceProxyImpl.java

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 1e1468f..ab4644e 100644 (file)
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -20,12 +20,13 @@
  */
 package jalview.ws.seqfetcher;
 
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 
-import com.stevesoft.pat.Regex;
-
 /**
  * common methods for implementations of the DbSourceProxy interface.
  * 
@@ -93,32 +94,30 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
   protected AlignmentI parseResult(String result) throws Exception
   {
     AlignmentI sequences = null;
-    String format = new IdentifyFile().identify(result, "Paste");
-    if (FormatAdapter.isValidFormat(format))
+    FileFormatI format = new IdentifyFile().identify(result,
+            DataSourceType.PASTE);
+    if (format != null)
     {
-      sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-              format);
+      sequences = new FormatAdapter().readFile(result.toString(),
+              DataSourceType.PASTE, format);
     }
     return sequences;
   }
 
+  /**
+   * Returns the first accession id in the query (up to the first accession id
+   * separator), or the whole query if there is no separator or it is not found
+   */
   @Override
   public String getAccessionIdFromQuery(String query)
   {
-    Regex vgr = getAccessionValidator();
-    if (vgr == null)
+    String sep = getAccessionSeparator();
+    if (sep == null)
     {
       return query;
     }
-    vgr.search(query);
-    if (vgr.numSubs() > 0)
-    {
-      return (vgr.stringMatched(1));
-    }
-    else
-    {
-      return (vgr.stringMatched());
-    }
+    int sepPos = query.indexOf(sep);
+    return sepPos == -1 ? query : query.substring(0, sepPos);
   }
 
   /**
@@ -147,4 +146,16 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
   {
     return false;
   }
+
+  @Override
+  public String getDescription()
+  {
+    return "";
+  }
+
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return null;
+  }
 }