X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqVector.java;h=55ca3ffa05e23fd563060a7006447a471c3f799e;hb=9811278f9e18ee6cb88470dbae98da046734a0af;hp=040e000d88397b7a40809969a693ac2a8f297cf5;hpb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;p=jalview.git
diff --git a/src/jalview/ws/rest/params/SeqVector.java b/src/jalview/ws/rest/params/SeqVector.java
index 040e000..55ca3ff 100644
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
@@ -7,8 +27,6 @@ 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.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
@@ -17,45 +35,50 @@ import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
-import org.jmol.util.ArrayUtil;
/**
- * input a list of sequences separated by some separator
+ * input a list of sequences separated by some separator
+ *
* @author JimP
- *
+ *
*/
-public class SeqVector extends InputType {
+public class SeqVector extends InputType
+{
String sep;
+
molType type;
+
public SeqVector()
{
- super(new Class[] { AlignmentI.class} );
+ super(new Class[] { AlignmentI.class });
}
@Override
- public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+ public ContentBody formatForInput(RestJob rj)
+ throws UnsupportedEncodingException, NoValidInputDataException
{
StringBuffer idvector = new StringBuffer();
- boolean list=false;
- for (SequenceI seq:rj.getSequencesForInput(token, type))
+ boolean list = false;
+ for (SequenceI seq : rj.getSequencesForInput(token, type))
{
if (list)
{
idvector.append(sep);
}
- idvector.append(seq.getSequence());
+ idvector.append(seq.getSequenceAsString());
}
return new StringBody(idvector.toString());
}
+
@Override
public List getURLEncodedParameter()
{
ArrayList prms = new ArrayList();
super.addBaseParams(prms);
- prms.add("sep='"+ sep+"'");
- if (type!=null)
+ prms.add("sep='" + sep + "'");
+ if (type != null)
{
- prms.add("type='"+type+"'");
+ prms.add("type='" + type + "'");
}
return prms;
}
@@ -73,20 +96,22 @@ public class SeqVector extends InputType {
if (tok.startsWith("sep"))
{
- sep=val;
+ sep = val;
return true;
}
if (tok.startsWith("type"))
{
- try {
- type=molType.valueOf(val);
+ try
+ {
+ type = molType.valueOf(val);
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
- for (molType v:molType.values())
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
+ for (molType v : molType.values())
{
- warnings.append(" "+v);
+ warnings.append(" " + v);
}
warnings.append(")\n");
}
@@ -104,8 +129,8 @@ public class SeqVector extends InputType {
{ " ", ",", ";", "\t", "|" }), null));
lst.add(createMolTypeOption("type", "Sequence type", false, type,
molType.MIX));
-
+
return lst;
}
-}
\ No newline at end of file
+}