X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxyImpl.java;h=5bed7209772625e4ab6f29a60ba12ed5012a3eb5;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=44de157bc9a7216b8f59b2b4ebdaee251a6f76a7;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 44de157..5bed720 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,131 +1,158 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * 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/>.
- */
-package jalview.ws.seqfetcher;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.DBRefSource;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-
-import java.util.Hashtable;
-
-/**
- * common methods for implementations of the DbSourceProxy interface.
- * 
- * @author JimP
- * 
- */
-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;
-  }
-
-  protected void addDbSourceProperty(Object propname)
-  {
-    addDbSourceProperty(propname, propname);
-  }
-
-  protected void addDbSourceProperty(Object propname, Object propvalue)
-  {
-    if (props == null)
-    {
-      props = new Hashtable();
-    }
-    props.put(propname, propvalue);
-  }
-
-  boolean queryInProgress = false;
-
-  protected StringBuffer results = null;
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getRawRecords()
-   */
-  public StringBuffer getRawRecords()
-  {
-    return results;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#queryInProgress()
-   */
-  public boolean queryInProgress()
-  {
-    return queryInProgress;
-  }
-
-  /**
-   * call to set the queryInProgress flag
-   * 
-   */
-  protected void startQuery()
-  {
-    queryInProgress = true;
-  }
-
-  /**
-   * call to clear the queryInProgress flag
-   * 
-   */
-  protected void stopQuery()
-  {
-    queryInProgress = false;
-  }
-
-  /**
-   * create an alignment from raw text file...
-   * 
-   * @param result
-   * @return null or a valid alignment
-   * @throws Exception
-   */
-  protected Alignment parseResult(String result) throws Exception
-  {
-    Alignment sequences = null;
-    String format = new IdentifyFile().Identify(result, "Paste");
-    if (FormatAdapter.isValidFormat(format))
-    {
-      sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-              format);
-    }
-    return sequences;
-  }
-
-}
+/*
+ * 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.
+ *  
+ * 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.seqfetcher;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+
+/**
+ * common methods for implementations of the DbSourceProxy interface.
+ * 
+ * @author JimP
+ * 
+ */
+public abstract class DbSourceProxyImpl implements DbSourceProxy
+{
+
+  boolean queryInProgress = false;
+
+  protected StringBuffer results = null;
+
+  public DbSourceProxyImpl()
+  {
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getRawRecords()
+   */
+  @Override
+  public StringBuffer getRawRecords()
+  {
+    return results;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#queryInProgress()
+   */
+  @Override
+  public boolean queryInProgress()
+  {
+    return queryInProgress;
+  }
+
+  /**
+   * call to set the queryInProgress flag
+   * 
+   */
+  protected void startQuery()
+  {
+    queryInProgress = true;
+  }
+
+  /**
+   * call to clear the queryInProgress flag
+   * 
+   */
+  protected void stopQuery()
+  {
+    queryInProgress = false;
+  }
+
+  /**
+   * create an alignment from raw text file...
+   * 
+   * @param result
+   * @return null or a valid alignment
+   * @throws Exception
+   */
+  protected AlignmentI parseResult(String result) throws Exception
+  {
+    AlignmentI sequences = null;
+    String format = new IdentifyFile().identify(result, "Paste");
+    if (FormatAdapter.isValidFormat(format))
+    {
+      sequences = new FormatAdapter().readFile(result.toString(), "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)
+  {
+    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;
+  }
+}