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JAL-3807 Fix SlivkaWSInstance not fetching alignments.
author
Mateusz Warowny
<mmzwarowny@dundee.ac.uk>
Fri, 9 Jul 2021 14:44:53 +0000
(16:44 +0200)
committer
Mateusz Warowny
<mmzwarowny@dundee.ac.uk>
Fri, 9 Jul 2021 14:44:53 +0000
(16:44 +0200)
src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
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src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
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src/jalview/ws/slivkaws/SlivkaWSInstance.java
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diff --git
a/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
b/src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
index
a614f02
..
00843fc
100644
(file)
--- a/
src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
+++ b/
src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
@@
-36,7
+36,11
@@
public class SlivkaJPredServiceInstance extends SlivkaWSInstance
try {
files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files) {
try {
files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files) {
- return readAlignment(f);
+ if (f.getMimeType().equals("application/clustal")
+ || f.getMimeType().equals("application/fasta"))
+ {
+ return readAlignment(f);
+ }
}
}
catch (IOException e) {
}
}
catch (IOException e) {
diff --git
a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index
a04cff5
..
93c0bdb
100644
(file)
--- a/
src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/
src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@
-1,17
+1,22
@@
package jalview.ws.slivkaws;
package jalview.ws.slivkaws;
-import java.io.IOError;
-import java.io.IOException;
-import java.rmi.ServerError;
-import java.util.List;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;
+
+import java.io.IOError;
+import java.io.IOException;
+import java.rmi.ServerError;
+import java.util.List;
+
+import compbio.data.msa.Category;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
@@
-32,13
+37,16
@@
public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements Multip
@Override
public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
{
@Override
public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
{
- List<RemoteFile> files;
try
{
try
{
- files = client.getJobResults(jobId.getJobId());
+ List<RemoteFile> files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files)
{
for (RemoteFile f : files)
{
- return readAlignment(f);
+ if (f.getMimeType().equals("application/clustal")
+ || f.getMimeType().equals("application/fasta"))
+ {
+ return readAlignment(f);
+ }
}
} catch (IOException e)
{
}
} catch (IOException e)
{
diff --git
a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index
8aa56fa
..
138b432
100644
(file)
--- a/
src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/
src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@
-252,9
+252,9
@@
public abstract class SlivkaWSInstance extends ServiceWithParameters
{
final var mimetype = f.getMimeType();
FileFormat format;
{
final var mimetype = f.getMimeType();
FileFormat format;
- if (mimetype == "application/clustal")
+ if (mimetype.equals("application/clustal"))
format = FileFormat.Clustal;
format = FileFormat.Clustal;
- else if (mimetype == "application/fasta")
+ else if (mimetype.equals("application/fasta"))
format = FileFormat.Fasta;
else
return null;
format = FileFormat.Fasta;
else
return null;