X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=2d28a9cb9a072116f2b843785c6930c74d2ef3bb;hb=0353fb50f77f7d60e3c88c297298d04e0b1b80b3;hp=770b564d14dd1c192b59325f5eab5ab74caf474c;hpb=231cba7c0cb9097957cd61ef96aab8e32e2d0337;p=jalview.git

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 770b564..2d28a9c 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,6 +1,26 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.rest.params;
 
 import jalview.datamodel.AlignmentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
@@ -18,6 +38,7 @@ import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
@@ -47,7 +68,7 @@ public class Alignment extends InputType
   /**
    * input data as a file upload rather than inline content
    */
-  public boolean writeAsFile;
+  public boolean writeAsFile=false;
 
   @Override
   public ContentBody formatForInput(RestJob rj)
@@ -165,4 +186,20 @@ public class Alignment extends InputType
     }
     return false;
   }
+  @Override
+  public List<OptionI> getOptions()
+  {
+    List<OptionI> lst = getBaseOptions();
+    lst.add(new BooleanOption("jvsuffix","Append jalview style /start-end suffix to ID", false, false, jvsuffix, null));
+    lst.add(new BooleanOption("writeasfile","Append jalview style /start-end suffix to ID", false, false, writeAsFile, null));
+    
+    lst.add(new Option("format",
+            "Alignment upload format", true, "FASTA",
+            format, Arrays.asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS), null));
+    lst.add(createMolTypeOption("type", "Sequence type", false, type,
+            null));
+    
+    return lst;
+  }
+
 }
\ No newline at end of file