X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Frest%2FRestJobThread.java;h=acb7904a002390587dc5c9e6c21c000f1b3508bb;hb=8ab24374eabe70d3d55bc92bcbbae401c743baa5;hp=2d5a83abb2f7e7e2b611595ad4f97d01b0782361;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git
diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 2d5a83a..acb7904 100644
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
*
@@ -26,7 +26,7 @@ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@@ -90,8 +90,8 @@ public class RestJobThread extends AWSThread
{
jobs = new RestJob[1];
jobs[0] = new RestJob(0, this,
- restClient._input.getVisibleAlignment(restClient.service
- .getGapCharacter()),
+ restClient._input.getVisibleAlignment(
+ restClient.service.getGapCharacter()),
restClient._input.getVisibleContigs());
// need a function to get a range on a view/alignment and return both
// annotation, groups and selection subsetted to just that region.
@@ -101,8 +101,8 @@ public class RestJobThread extends AWSThread
{
int[] viscontig = restClient._input.getVisibleContigs();
AlignmentI[] viscontigals = restClient._input
- .getVisibleContigAlignments(restClient.service
- .getGapCharacter());
+ .getVisibleContigAlignments(
+ restClient.service.getGapCharacter());
if (viscontigals != null && viscontigals.length > 0)
{
jobs = new RestJob[viscontigals.length];
@@ -173,9 +173,13 @@ public class RestJobThread extends AWSThread
private String getStage(Stage stg)
{
if (stg == Stage.SUBMIT)
+ {
return "submitting ";
+ }
if (stg == Stage.POLL)
+ {
return "checking status of ";
+ }
return (" being confused about ");
}
@@ -229,8 +233,8 @@ public class RestJobThread extends AWSThread
{
if (input.getValue().validFor(rj))
{
- postentity.addPart(input.getKey(), input.getValue()
- .formatForInput(rj));
+ postentity.addPart(input.getKey(),
+ input.getValue().formatForInput(rj));
}
else
{
@@ -285,10 +289,7 @@ public class RestJobThread extends AWSThread
break;
case 202:
rj.statMessage = "
Job submitted successfully. Results available at this URL:\n"
- + ""
- + rj.getJobId()
+ + "" + rj.getJobId()
+ "
";
rj.running = true;
break;
@@ -301,11 +302,9 @@ public class RestJobThread extends AWSThread
{
if (loc.length > 1)
{
- Cache.log
- .warn("Ignoring additional "
- + (loc.length - 1)
- + " location(s) provided in response header ( next one is '"
- + loc[1].getValue() + "' )");
+ Cache.log.warn("Ignoring additional " + (loc.length - 1)
+ + " location(s) provided in response header ( next one is '"
+ + loc[1].getValue() + "' )");
}
rj.setJobId(loc[0].getValue());
rj.setSubmitted(true);
@@ -319,8 +318,8 @@ public class RestJobThread extends AWSThread
rj.setSubjobComplete(true);
rj.error = true;
rj.running = false;
- completeStatus(rj, response, "" + getStage(stg)
- + "failed. Reason below:\n");
+ completeStatus(rj, response,
+ "" + getStage(stg) + "failed. Reason below:\n");
break;
default:
// Some other response. Probably need to pop up the content in a window.
@@ -333,16 +332,10 @@ public class RestJobThread extends AWSThread
rj.setSubmitted(true);
try
{
- completeStatus(
- rj,
- response,
- ""
- + getStage(stg)
- + " resulted in an unexpected server response.
Url concerned was "
- + request.getURI()
- + "
Filtered response content below:
");
+ completeStatus(rj, response, "" + getStage(stg)
+ + " resulted in an unexpected server response.
Url concerned was " + request.getURI()
+ + "
Filtered response content below:
");
} catch (IOException e)
{
Cache.log.debug("IOException when consuming unhandled response",
@@ -480,21 +473,19 @@ public class RestJobThread extends AWSThread
} catch (Error ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
rj.error = true;
rj.statMessage = "Error whilst parsing data for this job.
URL for job response is :"
- + rj.resSet.getUrl()
+ + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl()
+ "
";
}
}
@@ -609,7 +600,7 @@ public class RestJobThread extends AWSThread
// total number of distinct alignment sets generated by job set.
int numAlSets = 0, als = 0;
List destAls = new ArrayList();
- List destColsel = new ArrayList();
+ List destColsel = new ArrayList();
List> trees = new ArrayList>();
do
@@ -715,7 +706,7 @@ public class RestJobThread extends AWSThread
RestJob rj = (RestJob) jobs[nrj];
int contigs[] = input.getVisibleContigs();
AlignmentI destAl = null;
- jalview.datamodel.ColumnSelection destCs = null;
+ jalview.datamodel.HiddenColumns destHCs = null;
// Resolve destAl for this data.
if (als == 0 && rj.isInputContextModified())
{
@@ -731,10 +722,10 @@ public class RestJobThread extends AWSThread
if (!restClient.isAlignmentModified() && merge)
{
destAl = restClient.av.getAlignment();
- destCs = restClient.av.getColumnSelection();
- resultDest
- .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
- : AddDataTo.currentView);
+ destHCs = restClient.av.getAlignment().getHiddenColumns();
+ resultDest.add(restClient.isShowResultsInNewView()
+ ? AddDataTo.newView
+ : AddDataTo.currentView);
destPanels.add(restClient.recoverAlignPanelForView());
}
else
@@ -742,15 +733,15 @@ public class RestJobThread extends AWSThread
newAlignment = true;
// recreate the input alignment data
Object[] idat = input
- .getAlignmentAndColumnSelection(gapCharacter);
+ .getAlignmentAndHiddenColumns(gapCharacter);
destAl = new Alignment((SequenceI[]) idat[0]);
- destCs = (ColumnSelection) idat[1];
+ destHCs = (HiddenColumns) idat[1];
resultDest.add(AddDataTo.newAlignment);
// but do not add to the alignment panel list - since we need to
// create a whole new alignFrame set.
}
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
}
}
else
@@ -763,13 +754,13 @@ public class RestJobThread extends AWSThread
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log
- .warn("dealing with multiple alignment products returned by non-vertically separable service.");
+ Cache.log.warn(
+ "dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
// ready for extension
destAl = destAls.get(als);
- destCs = destColsel.get(als);
+ destHCs = destColsel.get(als);
}
else
{
@@ -798,16 +789,15 @@ public class RestJobThread extends AWSThread
newview = input.getUpdatedView(rseqs, orders, gapCharacter);
}
destAl = new Alignment((SequenceI[]) newview[0]);
- destCs = (ColumnSelection) newview[1];
+ destHCs = (HiddenColumns) newview[1];
newAlignment = true;
// TODO create alignment from result data with propagated
// references.
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
resultDest.add(AddDataTo.newAlignment);
throw new Error(
- MessageManager
- .getString("error.implementation_error")
+ MessageManager.getString("error.implementation_error")
+ "TODO: ");
}
}
@@ -878,8 +868,8 @@ public class RestJobThread extends AWSThread
}
else
{
- Cache.log
- .warn("Couldn't resolve original sequence for new sequence.");
+ Cache.log.warn(
+ "Couldn't resolve original sequence for new sequence.");
}
}
if (sg.hasSeqrep())
@@ -901,8 +891,8 @@ public class RestJobThread extends AWSThread
{
// adjust boundaries of recovered group w.r.t. new group being
// merged on to original alignment.
- int start = sg.getStartRes() + contigs[ncnt], end = sg
- .getEndRes() + contigs[ncnt];
+ int start = sg.getStartRes() + contigs[ncnt],
+ end = sg.getEndRes() + contigs[ncnt];
if (start < exsg.getStartRes())
{
exsg.setStartRes(start);
@@ -956,8 +946,8 @@ public class RestJobThread extends AWSThread
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log
- .error("Couldn't relocate group referemce for group "
+ Cache.log.error(
+ "Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
}
@@ -983,7 +973,8 @@ public class RestJobThread extends AWSThread
visan.sequenceRef = sqass;
visAlAn.add(visan);
}
- if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
+ if (contigs[ncnt]
+ + alan[nrj][an].annotations.length > visan.annotations.length)
{
// increase width of annotation row
Annotation[] newannv = new Annotation[contigs[ncnt]
@@ -1006,8 +997,8 @@ public class RestJobThread extends AWSThread
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log
- .error("Tree recovery from restjob not yet implemented.");
+ Cache.log.error(
+ "Tree recovery from restjob not yet implemented.");
}
}
}
@@ -1043,10 +1034,10 @@ public class RestJobThread extends AWSThread
for (AddDataTo action : resultDest)
{
AlignmentI destal;
- ColumnSelection destcs;
- String alTitle = MessageManager.formatMessage(
- "label.webservice_job_title_on", new String[] {
- restClient.service.details.Action,
+ HiddenColumns destcs;
+ String alTitle = MessageManager
+ .formatMessage("label.webservice_job_title_on", new String[]
+ { restClient.service.details.Action,
restClient.service.details.Name, restClient.viewTitle });
switch (action)
{
@@ -1055,8 +1046,8 @@ public class RestJobThread extends AWSThread
destcs = destColsel.get(als);
destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- PaintRefresher.Refresh(destaf, destaf.getViewport()
- .getSequenceSetId());
+ PaintRefresher.Refresh(destaf,
+ destaf.getViewport().getSequenceSetId());
// todo transfer any feature settings and colouring
/*
* destaf.getFeatureRenderer().transferSettings(this.featureSettings);
@@ -1184,8 +1175,8 @@ public class RestJobThread extends AWSThread
{
if (start + width < end)
{
- blocks[c][s] = sequenceIs[s].getSubSequence(start, start
- + width);
+ blocks[c][s] = sequenceIs[s].getSubSequence(start,
+ start + width);
}
else
{