+/*
+ * 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 <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 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;
import org.apache.http.entity.mime.content.FileBody;
/**
* format an alignment for input to rest service.
+ *
* @author JimP
- *
+ *
*/
-public class Alignment extends InputType {
+public class Alignment extends InputType
+{
public Alignment()
{
- super(new Class[] { AlignmentI.class} );
+ super(new Class[] { AlignmentI.class });
}
- String format="FASTA";
+ String format = "FASTA";
+
molType type;
- boolean jvsuffix=false;
+
+ boolean jvsuffix = false;
+
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile;
+ public boolean writeAsFile = false;
+
@Override
- public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+ public ContentBody formatForInput(RestJob rj)
+ throws UnsupportedEncodingException, NoValidInputDataException
{
- AlignmentI alignment = rj.getAlignmentForInput(token,type);
+ AlignmentI alignment = rj.getAlignmentForInput(token, type);
if (writeAsFile)
{
- try {
- File fa = File.createTempFile("jvmime", ".fa");
- PrintWriter pw = new PrintWriter(new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(fa)), "UTF-8"));
- pw.append(new jalview.io.FormatAdapter().formatSequences(format, alignment, jvsuffix));
- pw.close();
- return new FileBody(fa, "text/plain");
- } catch (Exception ex)
- {
- throw new NoValidInputDataException("Couldn't write out alignment to file.",ex);
+ try
+ {
+ File fa = File.createTempFile("jvmime", ".fa");
+ PrintWriter pw = new PrintWriter(
+ new OutputStreamWriter(new BufferedOutputStream(
+ new FileOutputStream(fa)), "UTF-8"));
+ pw.append(new jalview.io.FormatAdapter().formatSequences(format,
+ alignment, jvsuffix));
+ pw.close();
+ return new FileBody(fa, "text/plain");
+ } catch (Exception ex)
+ {
+ throw new NoValidInputDataException(
+ "Couldn't write out alignment to file.", ex);
+ }
}
- } else {
+ else
+ {
jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
fa.setNewlineString("\r\n");
- return new StringBody((fa.formatSequences(format, alignment, jvsuffix)));
- //,
- //"text/plain",Charset.forName("UTF-8"));
+ return new StringBody(
+ (fa.formatSequences(format, alignment, jvsuffix)));
+ // ,
+ // "text/plain",Charset.forName("UTF-8"));
// , "text/plain", Charset.forName("UTF-8"));
- // sb.getContentTypeParameters().put("filename", "alignment.fa");
+ // sb.getContentTypeParameters().put("filename", "alignment.fa");
+ }
+ }
+
+ @Override
+ public List<String> getURLEncodedParameter()
+ {
+ ArrayList<String> prms = new ArrayList<String>();
+ prms.add("format='" + format + "'");
+ if (type != null)
+ {
+ prms.add("type='" + type.toString() + "'");
+ }
+ if (jvsuffix)
+ {
+ prms.add("jvsuffix");
+ }
+ ;
+ if (writeAsFile)
+ {
+ prms.add("writeasfile");
+ }
+ ;
+ return prms;
+ }
+
+ @Override
+ public String getURLtokenPrefix()
+ {
+ return "ALIGNMENT";
+ }
+
+ @Override
+ public boolean configureProperty(String tok, String val,
+ StringBuffer warnings)
+ {
+ if (tok.startsWith("jvsuffix"))
+ {
+ jvsuffix = true;
+ return true;
+ }
+ if (tok.startsWith("writeasfile"))
+ {
+ writeAsFile = true;
+ return true;
}
+
+ if (tok.startsWith("format"))
+ {
+ for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ {
+ if (val.equalsIgnoreCase(fmt))
+ {
+ format = fmt;
+ return true;
+ }
+ }
+ warnings.append("Invalid alignment format '" + val
+ + "'. Must be one of (");
+ for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ {
+ warnings.append(" " + fmt);
+ }
+ warnings.append(")\n");
+ }
+ if (tok.startsWith("type"))
+ {
+ 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(" " + v);
+ }
+ warnings.append(")\n");
+ }
+ }
+ return false;
+ }
+
+ @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;
}
-}
\ No newline at end of file
+
+}
git://source.jalview.org / jalview.git / blobdiff