X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAnnotationFile.java;fp=src%2Fjalview%2Fws%2Frest%2Fparams%2FAnnotationFile.java;h=84dcfb951c6f18336e6e96999929e6efb5399bcc;hb=c762d9525db36ffd5d3fca49fb5e7d506d13401a;hp=0000000000000000000000000000000000000000;hpb=f2c8e788b0c86c77ac4e62f6f6e2da13fdf43fc0;p=jalview.git

diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
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+++ b/src/jalview/ws/rest/params/AnnotationFile.java
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+package jalview.ws.rest.params;
+
+import jalview.datamodel.AlignmentI;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.NoValidInputDataException;
+import jalview.ws.rest.RestJob;
+import jalview.ws.rest.InputType.molType;
+
+import java.io.UnsupportedEncodingException;
+
+import org.apache.http.entity.mime.content.ContentBody;
+import org.apache.http.entity.mime.content.StringBody;
+
+/**
+ * format a jalview annotation file for input to a rest service.
+ * @author JimP
+ *
+ */
+public class AnnotationFile extends InputType {
+  public AnnotationFile()
+  {
+    super(new Class[] { AlignmentI.class} );
+  }
+  /**
+   * standard jalview annotation file
+   */
+  final String JVANNOT="JalviewAnnotation";
+  /**
+   * export annotation row as simple csv
+   */
+  final String CSVANNOT="CsvAnnotationRow";
+  /**
+   * format of annotation file
+   */
+  String format=JVANNOT;
+  // TODO verify annotation file format enumeration
+  @Override
+  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+  {
+    AlignmentI al = rj.getAlignmentForInput(token,molType.MIX);
+    if (format.equals(JVANNOT))
+      {return new StringBody(new jalview.io.AnnotationFile().printAnnotations(al.getAlignmentAnnotation(),
+            al.getGroups(),al.getProperties()));
+      } else {
+        if (!format.equals(CSVANNOT))
+        {
+          throw new UnsupportedEncodingException("Unrecognised format for exporting Annotation ("+format+")");
+        }
+        return new StringBody(new jalview.io.AnnotationFile().printCSVAnnotations(al.getAlignmentAnnotation()));
+      }
+  }
+}
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