src/jalview/ws/rest/params/Alignment.java

   1 package jalview.ws.rest.params;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.ws.rest.InputType;
   5 import jalview.ws.rest.NoValidInputDataException;
   6 import jalview.ws.rest.RestJob;
   7 import jalview.ws.rest.InputType.molType;
   8
   9 import java.io.BufferedOutputStream;
  10 import java.io.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.FileOutputStream;
  13 import java.io.OutputStreamWriter;
  14 import java.io.PrintWriter;
  15 import java.io.StringWriter;
  16 import java.io.UnsupportedEncodingException;
  17 import java.net.URLEncoder;
  18 import java.nio.charset.Charset;
  19
  20 import org.apache.http.entity.mime.content.ContentBody;
  21 import org.apache.http.entity.mime.content.FileBody;
  22 import org.apache.http.entity.mime.content.StringBody;
  23
  24 /**
  25  * format an alignment for input to rest service.
  26  * @author JimP
  27  *
  28  */
  29 public class Alignment extends InputType {
  30   public Alignment()
  31   {
  32     super(new Class[] { AlignmentI.class} );
  33   }
  34
  35   String format="FASTA";
  36   molType type;
  37   boolean jvsuffix=false;
  38   /**
  39    * input data as a file upload rather than inline content
  40    */
  41   public boolean writeAsFile;
  42   @Override
  43   public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
  44   {
  45     AlignmentI alignment = rj.getAlignmentForInput(token,type);
  46     if (writeAsFile)
  47     {
  48     try {
  49       File fa = File.createTempFile("jvmime", ".fa");
  50       PrintWriter pw = new PrintWriter(new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(fa)), "UTF-8"));
  51       pw.append(new jalview.io.FormatAdapter().formatSequences(format, alignment, jvsuffix));
  52       pw.close();
  53       return new FileBody(fa, "text/plain");
  54     } catch (Exception ex)
  55     {
  56       throw new NoValidInputDataException("Couldn't write out alignment to file.",ex);
  57     }
  58     } else {
  59       jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
  60       fa.setNewlineString("\r\n");
  61       return new StringBody((fa.formatSequences(format, alignment, jvsuffix)));
  62       //,
  63       //"text/plain",Charset.forName("UTF-8"));
  64       // , "text/plain", Charset.forName("UTF-8"));
  65     // sb.getContentTypeParameters().put("filename", "alignment.fa");
  66     }
  67   }
  68 }