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imports and formatting
author
Jim Procter
<jprocter@dundee.ac.uk>
Mon, 17 Nov 2014 14:42:21 +0000
(14:42 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Mon, 17 Nov 2014 14:42:21 +0000
(14:42 +0000)
src/jalview/ws/jws1/JPredThread.java
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diff --git
a/src/jalview/ws/jws1/JPredThread.java
b/src/jalview/ws/jws1/JPredThread.java
index
dc245ae
..
72274de
100644
(file)
--- a/
src/jalview/ws/jws1/JPredThread.java
+++ b/
src/jalview/ws/jws1/JPredThread.java
@@
-20,17
+20,26
@@
*/
package jalview.ws.jws1;
*/
package jalview.ws.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.List;
+
import vamsas.objects.simple.JpredResult;
class JPredThread extends JWS1Thread implements WSClientI
import vamsas.objects.simple.JpredResult;
class JPredThread extends JWS1Thread implements WSClientI
@@
-138,7
+147,7
@@
class JPredThread extends JWS1Thread implements WSClientI
sqs[i] = al.getSequenceAt(i);
}
if (!jalview.analysis.SeqsetUtils.deuniquify(
sqs[i] = al.getSequenceAt(i);
}
if (!jalview.analysis.SeqsetUtils.deuniquify(
- (Hashtable) SequenceInfo, sqs))
+ SequenceInfo, sqs))
{
throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
}
{
throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
}
@@
-169,8
+178,8
@@
class JPredThread extends JWS1Thread implements WSClientI
if (predMap != null)
{
char gc = getGapChar();
if (predMap != null)
{
char gc = getGapChar();
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
- .getAlignmentAndColumnSelection(gc))[0];
+ SequenceI[] sqs = (SequenceI[]) input
+ .getAlignmentAndColumnSelection(gc)[0];
if (this.msaIndex >= sqs.length)
{
throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
if (this.msaIndex >= sqs.length)
{
throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
@@
-428,7
+437,7
@@
class JPredThread extends JWS1Thread implements WSClientI
{
if (job.getJobId().startsWith("Broken"))
{
{
if (job.getJobId().startsWith("Broken"))
{
- job.result = (vamsas.objects.simple.Result) new JpredResult();
+ job.result = new JpredResult();
job.result.setInvalid(true);
job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
throw new Exception(job.getJobId());
job.result.setInvalid(true);
job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
throw new Exception(job.getJobId());