JAL-1894 update year/version in copyright

[jalview.git] / src / jalview / ws / rest / params / AnnotationFile.java

diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index 5abf0fc..a8bf2d1 100644 (file)
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -1,14 +1,35 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.rest.params;
 
 import jalview.datamodel.AlignmentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
@@ -16,55 +37,73 @@ import org.apache.http.entity.mime.content.StringBody;
 
 /**
  * format a jalview annotation file for input to a rest service.
+ * 
  * @author JimP
- *
+ * 
  */
-public class AnnotationFile extends InputType {
+public class AnnotationFile extends InputType
+{
   public AnnotationFile()
   {
-    super(new Class[] { AlignmentI.class} );
+    super(new Class[] { AlignmentI.class });
   }
+
   /**
    * standard jalview annotation file
    */
-  final String JVANNOT="JalviewAnnotation";
+  final String JVANNOT = "JalviewAnnotation";
+
   /**
    * export annotation row as simple csv
    */
-  final String CSVANNOT="CsvAnnotationRow";
+  final String CSVANNOT = "CsvAnnotationRow";
+
   /**
    * format of annotation file
    */
-  String format=JVANNOT;
+  String format = JVANNOT;
+
   // TODO verify annotation file format enumeration
   @Override
-  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+  public ContentBody formatForInput(RestJob rj)
+          throws UnsupportedEncodingException, NoValidInputDataException
   {
-    AlignmentI al = rj.getAlignmentForInput(token,molType.MIX);
+    AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
     if (format.equals(JVANNOT))
-      {return new StringBody(new jalview.io.AnnotationFile().printAnnotations(al.getAlignmentAnnotation(),
-            al.getGroups(),al.getProperties()));
-      } else {
-        if (!format.equals(CSVANNOT))
-        {
-          throw new UnsupportedEncodingException("Unrecognised format for exporting Annotation ("+format+")");
-        }
-        return new StringBody(new jalview.io.AnnotationFile().printCSVAnnotations(al.getAlignmentAnnotation()));
+    {
+      return new StringBody(
+              new jalview.io.AnnotationFile()
+                      .printAnnotationsForAlignment(al));
+    }
+    else
+    {
+      if (!format.equals(CSVANNOT))
+      {
+        throw new UnsupportedEncodingException(
+                "Unrecognised format for exporting Annotation (" + format
+                        + ")");
       }
+      return new StringBody(
+              new jalview.io.AnnotationFile().printCSVAnnotations(al
+                      .getAlignmentAnnotation()));
+    }
   }
+
   @Override
   public List<String> getURLEncodedParameter()
   {
     ArrayList<String> prms = new ArrayList<String>();
     super.addBaseParams(prms);
-    prms.add("format='"+format+"'");
-    return prms;     
+    prms.add("format='" + format + "'");
+    return prms;
   }
+
   @Override
   public String getURLtokenPrefix()
   {
     return "ALANNOTATION";
   }
+
   @Override
   public boolean configureProperty(String tok, String val,
           StringBuffer warnings)
@@ -72,7 +111,7 @@ public class AnnotationFile extends InputType {
 
     if (tok.startsWith("format"))
     {
-      for (String fmt : new String[] { CSVANNOT, JVANNOT})
+      for (String fmt : new String[] { CSVANNOT, JVANNOT })
       {
         if (val.equalsIgnoreCase(fmt))
         {
@@ -82,7 +121,7 @@ public class AnnotationFile extends InputType {
       }
       warnings.append("Invalid annotation file format '" + val
               + "'. Must be one of (");
-      for (String fmt : new String[] { CSVANNOT, JVANNOT})
+      for (String fmt : new String[] { CSVANNOT, JVANNOT })
       {
         warnings.append(" " + fmt);
       }
@@ -90,4 +129,15 @@ public class AnnotationFile extends InputType {
     }
     return false;
   }
+
+  @Override
+  public List<OptionI> getOptions()
+  {
+    // TODO - consider disregarding base options here.
+    List<OptionI> lst = getBaseOptions();
+    lst.add(new Option("format", "Alignment annotation upload format",
+            true, JVANNOT, format, Arrays.asList(new String[] { JVANNOT,
+                CSVANNOT }), null));
+    return lst;
+  }
 }