+/*
+ * 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 <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.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+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;
+import java.util.Arrays;
import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
/**
- * input a list of sequence IDs separated by some separator
+ * input a list of sequence IDs separated by some separator
+ *
* @author JimP
- *
+ *
*/
-public class SeqIdVector extends InputType {
+public class SeqIdVector extends InputType
+{
public SeqIdVector()
{
- super(new Class[] { AlignmentI.class} );
+ super(new Class[] { AlignmentI.class });
}
/**
* separator for list of sequence IDs - default is ','
*/
- String sep=",";
+ String sep = ",";
+
molType type;
+
@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(seq.getName());
}
return new StringBody(idvector.toString());
- }
+ }
+
@Override
public List<String> getURLEncodedParameter()
{
ArrayList<String> prms = new ArrayList<String>();
super.addBaseParams(prms);
- prms.add("sep='"+ sep+"'");
- prms.add("type='"+type+"'");
+ prms.add("sep='" + sep + "'");
+ if (type != null)
+ {
+ prms.add("type='" + type + "'");
+ }
return prms;
}
+
@Override
public String getURLtokenPrefix()
{
return "SEQIDS";
}
+
@Override
- public boolean configureProperty(String tok, String val, StringBuffer warnings)
+ public boolean configureProperty(String tok, String val,
+ StringBuffer warnings)
{
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");
}
}
return false;
}
+
+ @Override
+ public List<OptionI> getOptions()
+ {
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new Option("sep",
+ "Separator character between elements of vector", true, ",",
+ sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+ null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
+ return lst;
+ }
}