X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestJobThread.java;h=0592426797c2ca9e60f3a064a5525849e22b01a0;hb=8a0c21a00b4ac6925f6b6a04d1ea43cff44eea50;hp=2aa071dd95e6c84bc95fc06756df546cb263093a;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 2aa071d..0592426 100644
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest;
@@ -24,7 +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;
@@ -34,6 +36,7 @@ import jalview.gui.WebserviceInfo;
import jalview.io.NewickFile;
import jalview.io.packed.JalviewDataset;
import jalview.io.packed.JalviewDataset.AlignmentSet;
+import jalview.util.MessageManager;
import jalview.ws.AWSThread;
import jalview.ws.AWsJob;
@@ -105,8 +108,7 @@ public class RestJobThread extends AWSThread
jobs = new RestJob[viscontigals.length];
for (int j = 0; j < jobs.length; j++)
{
- int[] visc = new int[]
- { viscontig[j * 2], viscontig[j * 2 + 1] };
+ int[] visc = new int[] { viscontig[j * 2], viscontig[j * 2 + 1] };
if (j != 0)
{
jobs[j] = new RestJob(j, this, viscontigals[j], visc);
@@ -171,9 +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 ");
}
@@ -607,7 +613,7 @@ 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
@@ -713,7 +719,7 @@ 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())
{
@@ -729,7 +735,7 @@ public class RestJobThread extends AWSThread
if (!restClient.isAlignmentModified() && merge)
{
destAl = restClient.av.getAlignment();
- destCs = restClient.av.getColumnSelection();
+ destHCs = restClient.av.getAlignment().getHiddenColumns();
resultDest
.add(restClient.isShowResultsInNewView() ? AddDataTo.newView
: AddDataTo.currentView);
@@ -740,15 +746,15 @@ 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
@@ -767,7 +773,7 @@ public class RestJobThread extends AWSThread
// 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
{
@@ -796,14 +802,17 @@ 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("Impl. Error! TODO: ");
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error")
+ + "TODO: ");
}
}
/**
@@ -1038,10 +1047,11 @@ public class RestJobThread extends AWSThread
for (AddDataTo action : resultDest)
{
AlignmentI destal;
- ColumnSelection destcs;
- String alTitle = restClient.service.details.Action + " using "
- + restClient.service.details.Name + " on "
- + restClient.viewTitle;
+ 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)
{
case newAlignment: