X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=d7b1fc711d08353610064dfbd793bd4d9a6b5a4d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=dc6e6e8e1be0e015cde914855a2b1d02a2b173b5;hpb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;p=jalview.git
diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index dc6e6e8..d7b1fc7 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
@@ -7,19 +27,13 @@ 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;
@@ -38,8 +52,7 @@ public class Alignment extends InputType
{
public Alignment()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
String format = "FASTA";
@@ -51,7 +64,7 @@ public class Alignment extends InputType
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile=false;
+ public boolean writeAsFile = false;
@Override
public ContentBody formatForInput(RestJob rj)
@@ -169,20 +182,25 @@ public class Alignment extends InputType
}
return false;
}
+
@Override
public List getOptions()
{
List 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,
+ 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
+}