JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 b8f7eab..5bed720 100644 (file)
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,28 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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.seqfetcher;
 
-import jalview.datamodel.Alignment;
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 
-import java.util.Hashtable;
-
 /**
  * common methods for implementations of the DbSourceProxy interface.
  * 
@@ -31,50 +33,21 @@ import java.util.Hashtable;
  */
 public abstract class DbSourceProxyImpl implements DbSourceProxy
 {
-  public DbSourceProxyImpl()
-  {
-    // default constructor - do nothing probably.
-  }
 
-  private Hashtable props = null;
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
-   */
-  public Hashtable getDbSourceProperties()
-  {
-    if (props == null)
-    {
-      props = new Hashtable();
-    }
-    return props;
-  }
+  boolean queryInProgress = false;
 
-  protected void addDbSourceProperty(Object propname)
-  {
-    addDbSourceProperty(propname, propname);
-  }
+  protected StringBuffer results = null;
 
-  protected void addDbSourceProperty(Object propname, Object propvalue)
+  public DbSourceProxyImpl()
   {
-    if (props == null)
-    {
-      props = new Hashtable();
-    }
-    props.put(propname, propvalue);
   }
 
-  boolean queryInProgress = false;
-
-  protected StringBuffer results = null;
-
   /*
    * (non-Javadoc)
    * 
    * @see jalview.ws.DbSourceProxy#getRawRecords()
    */
+  @Override
   public StringBuffer getRawRecords()
   {
     return results;
@@ -85,6 +58,7 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#queryInProgress()
    */
+  @Override
   public boolean queryInProgress()
   {
     return queryInProgress;
@@ -115,10 +89,10 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
    * @return null or a valid alignment
    * @throws Exception
    */
-  protected Alignment parseResult(String result) throws Exception
+  protected AlignmentI parseResult(String result) throws Exception
   {
-    Alignment sequences = null;
-    String format = new IdentifyFile().Identify(result, "Paste");
+    AlignmentI sequences = null;
+    String format = new IdentifyFile().identify(result, "Paste");
     if (FormatAdapter.isValidFormat(format))
     {
       sequences = new FormatAdapter().readFile(result.toString(), "Paste",
@@ -127,11 +101,58 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
     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 boolean isA(Object dbsourceproperty)
+  public String getAccessionIdFromQuery(String query)
   {
-    assert (dbsourceproperty != null);
-    return (props == null) ? false : props.containsKey(dbsourceproperty);
+    String sep = getAccessionSeparator();
+    if (sep == null)
+    {
+      return query;
+    }
+    int sepPos = query.indexOf(sep);
+    return sepPos == -1 ? query : query.substring(0, sepPos);
+  }
+
+  /**
+   * Default is only one accession id per query - override if more are allowed.
+   */
+  @Override
+  public int getMaximumQueryCount()
+  {
+    return 1;
+  }
+
+  /**
+   * Returns false - override to return true for DNA coding data sources
+   */
+  @Override
+  public boolean isDnaCoding()
+  {
+    return false;
   }
 
+  /**
+   * Answers false - override as required in subclasses
+   */
+  @Override
+  public boolean isAlignmentSource()
+  {
+    return false;
+  }
+
+  @Override
+  public String getDescription()
+  {
+    return "";
+  }
+
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return null;
+  }
 }