formatting

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

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 770b564..7782c20 100644 (file)
--- 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 +186,25 @@ 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;
+  }
+
 }
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