+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.BooleanOption;
+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.InputType.molType;
-import jalview.ws.rest.RestServiceDescription;
import java.io.BufferedOutputStream;
-import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.io.StringWriter;
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;
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile;
+ public boolean writeAsFile = false;
@Override
public ContentBody formatForInput(RestJob rj)
}
return false;
}
-}
\ No newline at end of file
+
+ @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;
+ }
+
+}