X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=dc6e6e8e1be0e015cde914855a2b1d02a2b173b5;hb=7c28880430765f06ccd5ec8ad3caf17871336e97;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..dc6e6e8 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,6 +1,9 @@
 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 +21,7 @@ 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 +51,7 @@ 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 +169,20 @@ 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