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First patch for * JAL-493
[jalview.git]
/
src
/
jalview
/
ws
/
MsaWSThread.java
diff --git
a/src/jalview/ws/MsaWSThread.java
b/src/jalview/ws/MsaWSThread.java
index
7142e5c
..
ab3dfbe
100644
(file)
--- a/
src/jalview/ws/MsaWSThread.java
+++ b/
src/jalview/ws/MsaWSThread.java
@@
-22,7
+22,6
@@
import java.util.*;
import jalview.analysis.*;
\r
import jalview.bin.*;
\r
import jalview.datamodel.*;
\r
import jalview.analysis.*;
\r
import jalview.bin.*;
\r
import jalview.datamodel.*;
\r
-import jalview.datamodel.Alignment;
\r
import jalview.gui.*;
\r
import vamsas.objects.simple.MsaResult;
\r
\r
import jalview.gui.*;
\r
import vamsas.objects.simple.MsaResult;
\r
\r
@@
-46,7
+45,7
@@
import vamsas.objects.simple.MsaResult;
* @author not attributable
\r
* @version 1.0
\r
*/
\r
* @author not attributable
\r
* @version 1.0
\r
*/
\r
-class MsaWSThread extends WSThread implements WSClientI
\r
+class MsaWSThread extends JWS1Thread implements WSClientI
\r
{
\r
boolean submitGaps = false; // pass sequences including gaps to alignment
\r
\r
{
\r
boolean submitGaps = false; // pass sequences including gaps to alignment
\r
\r
@@
-56,7
+55,7
@@
class MsaWSThread extends WSThread implements WSClientI
\r
// order
\r
\r
\r
// order
\r
\r
- class MsaWSJob extends WSThread.WSJob
\r
+ class MsaWSJob extends WSJob
\r
{
\r
// hold special input for this
\r
vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
\r
{
\r
// hold special input for this
\r
vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
\r
@@
-280,7
+279,7
@@
class MsaWSThread extends WSThread implements WSClientI
*
\r
* @return boolean true if job can be submitted.
\r
*/
\r
*
\r
* @return boolean true if job can be submitted.
\r
*/
\r
- boolean hasValidInput()
\r
+ public boolean hasValidInput()
\r
{
\r
if (seqs.getSeqs() != null)
\r
{
\r
{
\r
if (seqs.getSeqs() != null)
\r
{
\r
@@
-438,12
+437,12
@@
class MsaWSThread extends WSThread implements WSClientI
}
\r
}
\r
\r
}
\r
}
\r
\r
- void pollJob(WSJob job) throws Exception
\r
+ public void pollJob(AWsJob job) throws Exception
\r
{
\r
((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
\r
}
\r
\r
{
\r
((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
\r
}
\r
\r
- void StartJob(WSJob job)
\r
+ public void StartJob(AWsJob job)
\r
{
\r
if (!(job instanceof MsaWSJob))
\r
{
\r
{
\r
if (!(job instanceof MsaWSJob))
\r
{
\r
@@
-531,7
+530,7
@@
class MsaWSThread extends WSThread implements WSClientI
return msa;
\r
}
\r
\r
return msa;
\r
}
\r
\r
- void parseResult()
\r
+ public void parseResult()
\r
{
\r
int results = 0; // number of result sets received
\r
JobStateSummary finalState = new JobStateSummary();
\r
{
\r
int results = 0; // number of result sets received
\r
JobStateSummary finalState = new JobStateSummary();
\r
@@
-544,7
+543,7
@@
class MsaWSThread extends WSThread implements WSClientI
&& jobs[j].hasResults())
\r
{
\r
results++;
\r
&& jobs[j].hasResults())
\r
{
\r
results++;
\r
- vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result)
\r
+ vamsas.objects.simple.Alignment valign = ((MsaResult)((MsaWSJob) jobs[j]).result)
\r
.getMsa();
\r
if (valign != null)
\r
{
\r
.getMsa();
\r
if (valign != null)
\r
{
\r