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