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Merge branch 'develop' into features/JAL-1793VCF
[jalview.git]
/
src
/
jalview
/
ws
/
rest
/
params
/
SeqVector.java
diff --git
a/src/jalview/ws/rest/params/SeqVector.java
b/src/jalview/ws/rest/params/SeqVector.java
index
7632067
..
55ca3ff
100644
(file)
--- a/
src/jalview/ws/rest/params/SeqVector.java
+++ b/
src/jalview/ws/rest/params/SeqVector.java
@@
-1,20
+1,23
@@
-/*******************************************************************************
- * 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
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* This file is part of Jalview.
* 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
* 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.
- *
+ * 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.
* 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/>.
- *******************************************************************************/
+ *
+ * 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;
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
@@
-24,8
+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.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;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
@@
-34,45
+35,50
@@
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
import org.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
* @author JimP
- *
+ *
*/
*/
-public class SeqVector extends InputType {
+public class SeqVector extends InputType
+{
String sep;
String sep;
+
molType type;
molType type;
+
public SeqVector()
{
public SeqVector()
{
- super(new Class[] { AlignmentI.class} );
+ super(new Class[] { AlignmentI.class });
}
@Override
}
@Override
- public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+ public ContentBody formatForInput(RestJob rj)
+ throws UnsupportedEncodingException, NoValidInputDataException
{
StringBuffer idvector = new StringBuffer();
{
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);
}
{
if (list)
{
idvector.append(sep);
}
- idvector.append(seq.getSequence());
+ idvector.append(seq.getSequenceAsString());
}
return new StringBody(idvector.toString());
}
}
return new StringBody(idvector.toString());
}
+
@Override
public List<String> getURLEncodedParameter()
{
ArrayList<String> prms = new ArrayList<String>();
super.addBaseParams(prms);
@Override
public List<String> getURLEncodedParameter()
{
ArrayList<String> prms = new ArrayList<String>();
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;
}
}
return prms;
}
@@
-90,20
+96,22
@@
public class SeqVector extends InputType {
if (tok.startsWith("sep"))
{
if (tok.startsWith("sep"))
{
- sep=val;
+ sep = val;
return true;
}
if (tok.startsWith("type"))
{
return true;
}
if (tok.startsWith("type"))
{
- try {
- type=molType.valueOf(val);
+ try
+ {
+ type = molType.valueOf(val);
return true;
} catch (Exception x)
{
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");
}
}
warnings.append(")\n");
}
@@
-121,8
+129,8
@@
public class SeqVector extends InputType {
{ " ", ",", ";", "\t", "|" }), null));
lst.add(createMolTypeOption("type", "Sequence type", false, type,
molType.MIX));
{ " ", ",", ";", "\t", "|" }), null));
lst.add(createMolTypeOption("type", "Sequence type", false, type,
molType.MIX));
-
+
return lst;
}
return lst;
}
-}
\ No newline at end of file
+}