X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAnnotationFile.java;h=b610fca46fb04694abe1b8dca685c36d2a73a2b4;hb=2eaab3084d84daa55785c0c288592d2a7f603742;hp=b1681a06f75cd3eff3d32c1cf486c67f48fff869;hpb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;p=jalview.git

diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index b1681a0..b610fca 100644
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -1,3 +1,23 @@
+/*
+ * 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.rest.params;
 
 import jalview.datamodel.AlignmentI;
@@ -6,8 +26,6 @@ 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;
@@ -19,55 +37,71 @@ 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)
@@ -75,7 +109,7 @@ 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))
         {
@@ -85,7 +119,7 @@ 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);
       }
@@ -93,15 +127,15 @@ 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));
+    lst.add(new Option("format", "Alignment annotation upload format", true,
+            JVANNOT, format, Arrays.asList(new String[]
+            { JVANNOT, CSVANNOT }), null));
     return lst;
   }
 }