Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka...

diff --combined src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 75e5722,138b432..fa54cf0
--- 1/src/jalview/ws/slivkaws/SlivkaWSInstance.java
--- 2/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@@ -1,7 -1,21 +1,21 @@@
  package jalview.ws.slivkaws;
  
+ import java.io.ByteArrayInputStream;
+ import java.io.ByteArrayOutputStream;
+ import java.io.IOError;
+ import java.io.IOException;
+ import java.io.InputStream;
+ import java.util.Arrays;
+ import java.util.EnumMap;
+ import java.util.HashSet;
+ import java.util.List;
+ import java.util.Optional;
+ import java.util.Set;
+ 
+ import jalview.datamodel.AlignmentI;
  import jalview.datamodel.SequenceI;
  import jalview.gui.WebserviceInfo;
+ import jalview.io.DataSourceType;
  import jalview.io.FileFormat;
  import jalview.io.FormatAdapter;
  import jalview.ws.api.JalviewServiceEndpointProviderI;
@@@ -13,21 -27,7 +27,8 @@@ import jalview.ws.params.ArgumentI
  import jalview.ws.params.ParamDatastoreI;
  import jalview.ws.params.ParamManager;
  import jalview.ws.params.WsParamSetI;
- 
- import java.io.ByteArrayInputStream;
- import java.io.ByteArrayOutputStream;
- import java.io.IOError;
- import java.io.IOException;
- import java.io.InputStream;
- import java.util.Arrays;
- import java.util.EnumMap;
- import java.util.HashSet;
- import java.util.List;
- import java.util.Optional;
- import java.util.Set;
- 
  import uk.ac.dundee.compbio.slivkaclient.FieldType;
 +import uk.ac.dundee.compbio.slivkaclient.FileField;
  import uk.ac.dundee.compbio.slivkaclient.FormField;
  import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  import uk.ac.dundee.compbio.slivkaclient.JobState;
@@@ -76,34 -76,21 +77,34 @@@ public abstract class SlivkaWSInstance 
            WsParamSetI preset, List<ArgumentI> args) throws Throwable
    {
      SlivkaForm form = service.getForm();
 -    Optional<FormField> inputField = form.getFields().stream()
 -            .filter(f -> f.getType() == FieldType.FILE).findFirst();
 -    if (inputField.isPresent())
 +    for (FormField field : form.getFields())
      {
 -      StringBuilder builder = new StringBuilder();
 -      for (SequenceI seq : sequences)
 +      if (field.getType() == FieldType.FILE)
        {
 -        builder.append(">").append(seq.getName()).append("\n")
 -                .append(seq.getSequence()).append("\n");
 +        FormatAdapter fa = new FormatAdapter();
 +        fa.setNewlineString("\r\n");
 +        FileField fileField = (FileField) field;
 +        FileFormat format;
 +        switch (fileField.getMediaType())
 +        {
 +        case "application/pfam":
 +          format = FileFormat.Pfam;
 +          break;
 +        case "application/stockholm":
 +          format = FileFormat.Stockholm;
 +          break;
 +        default:
 +        case "application/fasta":
 +          format = FileFormat.Fasta;
 +          break;
 +        }
 +        InputStream stream = new ByteArrayInputStream(
 +            fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
 +                .getBytes());
 +        RemoteFile rf = client.uploadFile(stream, "input",
 +            fileField.getMediaType());
 +        form.insert(field.getName(), rf);
        }
 -      InputStream stream = new ByteArrayInputStream(
 -              builder.toString().getBytes());
 -      RemoteFile file = client.uploadFile(stream, "input.fa",
 -              "application/fasta");
 -      form.insert(inputField.get().getName(), file);
      }
      if (args != null)
      {
@@@ -260,5 -247,19 +261,19 @@@
      }
      return store;
    }
+   
+   public static AlignmentI readAlignment(RemoteFile f) throws IOException
+   {
+     final var mimetype = f.getMimeType();
+     FileFormat format;
+     if (mimetype.equals("application/clustal"))
+       format = FileFormat.Clustal;
+     else if (mimetype.equals("application/fasta"))
+       format = FileFormat.Fasta;
+     else
+       return null;
+     return new FormatAdapter().readFile(f.getURL().toString(),
+         DataSourceType.URL, format);
+   }
  
  }