JAL-3116 Uniprot XML unmarshalled using JAXB not Castor

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblSequence.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java
index c68bcc5..92c424b 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblSequence.java
+++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java
@@ -1,43 +1,49 @@
+/*
+ * 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.datamodel.xdb.embl;
 
-public class EmblSequence {
-    String version;
-    String sequence;
-    String type;
-    /**
-     * @return the sequence
-     */
-    public String getSequence() {
-        return sequence;
-    }
-    /**
-     * @param sequence the sequence to set
-     */
-    public void setSequence(String sequence) {
-        this.sequence = sequence;
-    }
-    /**
-     * @return the type
-     */
-    public String getType() {
-        return type;
-    }
-    /**
-     * @param type the type to set
-     */
-    public void setType(String type) {
-        this.type = type;
-    }
-    /**
-     * @return the version
-     */
-    public String getVersion() {
-        return version;
-    }
-    /**
-     * @param version the version to set
-     */
-    public void setVersion(String version) {
-        this.version = version;
-    }
+/**
+ * Data model for the sequence extracted from an EMBL query reply
+ * 
+ * @see embl_mapping.xml
+ */
+public class EmblSequence
+{
+  String sequence;
+
+  /**
+   * @return the sequence
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * @param sequence
+   *          the sequence to set
+   */
+  public void setSequence(String sequence)
+  {
+    // remove spaces introduced by unmarshalling of newline characters
+    this.sequence = sequence.replace(" ", "");
+  }
 }