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JAL-2674 Rationalising iterators and retesting
[jalview.git]
/
src
/
jalview
/
ws
/
rest
/
RestJob.java
diff --git
a/src/jalview/ws/rest/RestJob.java
b/src/jalview/ws/rest/RestJob.java
index
770824a
..
824af90
100644
(file)
--- a/
src/jalview/ws/rest/RestJob.java
+++ b/
src/jalview/ws/rest/RestJob.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,13
+20,6
@@
*/
package jalview.ws.rest;
*/
package jalview.ws.rest;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Hashtable;
-import java.util.Map;
-import java.util.Set;
-import java.util.Vector;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
@@
-37,6
+30,13
@@
import jalview.ws.AWsJob;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.SeqGroupIndexVector;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.SeqGroupIndexVector;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
public class RestJob extends AWsJob
{
public class RestJob extends AWsJob
{
@@
-77,8
+77,8
@@
public class RestJob extends AWsJob
* @param viscontigs
* visible contigs of an alignment view from which _input was derived
*/
* @param viscontigs
* visible contigs of an alignment view from which _input was derived
*/
- public RestJob(int jobNum, RestJobThread restJobThread,
- AlignmentI _input, int[] viscontigs)
+ public RestJob(int jobNum, RestJobThread restJobThread, AlignmentI _input,
+ int[] viscontigs)
{
rsd = restJobThread.restClient.service;
jobnum = jobNum;
{
rsd = restJobThread.restClient.service;
jobnum = jobNum;
@@
-90,13
+90,15
@@
public class RestJob extends AWsJob
// get sequences for the alignmentI
// get groups trimmed to alignment columns
// get any annotation trimmed to start/end columns, too.
// get sequences for the alignmentI
// get groups trimmed to alignment columns
// get any annotation trimmed to start/end columns, too.
- squniq = jalview.analysis.SeqsetUtils.uniquify(_input.getSequencesArray(), true);
+ squniq = jalview.analysis.SeqsetUtils
+ .uniquify(_input.getSequencesArray(), true);
// prepare input
// form alignment+groups+annotation,preprocess and then record references
// for formatters
ArrayList<InputType> alinp = new ArrayList<InputType>();
int paramsWithData = 0;
// prepare input
// form alignment+groups+annotation,preprocess and then record references
// for formatters
ArrayList<InputType> alinp = new ArrayList<InputType>();
int paramsWithData = 0;
- // TODO: JAL-715 - generalise the following validation logic for all parameter types
+ // TODO: JAL-715 - generalise the following validation logic for all
+ // parameter types
// we cheat for moment - since we know a-priori what data is available and
// what inputs we have implemented so far
for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
// we cheat for moment - since we know a-priori what data is available and
// what inputs we have implemented so far
for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
@@
-113,13
+115,15
@@
public class RestJob extends AWsJob
&& _input.getGroups() != null
&& _input.getGroups().size() >= -1 + prm.getValue().min)
{
&& _input.getGroups() != null
&& _input.getGroups().size() >= -1 + prm.getValue().min)
{
- // the test above is not rigorous but fixes JAL-1298, since submission will fail if the partition set doesn't contain at least one partition
+ // the test above is not rigorous but fixes JAL-1298, since
+ // submission will fail if the partition set doesn't contain at
+ // least one partition
alinp.add(prm.getValue());
}
else
{
alinp.add(prm.getValue());
}
else
{
- statMessage = ("Not enough groups defined on the alignment - need at least " + prm
- .getValue().min);
+ statMessage = ("Not enough groups defined on the alignment - need at least "
+ + prm.getValue().min);
}
}
}
}
}
}