X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FAWSThread.java;h=b158448ab65ab93f138bc3ff5fd42279eff5fa0b;hb=2c11e91e2917eed2c65ff7c06ff2ab70a88c3914;hp=0167690aa3db669b5dc359e14792c4eed3f691f7;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 0167690..b158448 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,19 +1,21 @@
/*
- * 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.
*
* 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;
@@ -26,7 +28,12 @@ import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Set;
public abstract class AWSThread extends Thread
{
@@ -54,7 +61,7 @@ public abstract class AWSThread extends Thread
/**
* dataset sequence relationships to be propagated onto new results
*/
- protected AlignedCodonFrame[] codonframe = null;
+ protected Set codonframe = null;
/**
* are there jobs still running in this thread.
@@ -84,9 +91,15 @@ public abstract class AWSThread extends Thread
*/
protected String WsUrl = null;
+ /*
+ * The AlignFrame from which the service was requested.
+ */
+ private AlignFrame alignFrame;
+
/**
* generic web service job/subjob poll loop
*/
+ @Override
public void run()
{
JobStateSummary jstate = null;
@@ -121,8 +134,9 @@ public abstract class AWSThread extends Thread
} catch (Exception ex)
{
// Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
+ wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
+ .formatMessage("info.server_exception", new Object[] {
+ WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
@@ -186,8 +200,9 @@ public abstract class AWSThread extends Thread
{
Cache.log
.debug("WebServiceJob poll loop finished with no jobs created.");
- wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText("No jobs ran.");
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendProgressText(MessageManager
+ .getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
@@ -292,13 +307,12 @@ public abstract class AWSThread extends Thread
SequenceI[] alignment = al.getSequencesArray();
for (int sq = 0; sq < alignment.length; sq++)
{
- for (int i = 0; i < codonframe.length; i++)
+ for (AlignedCodonFrame acf : codonframe)
{
- if (codonframe[i] != null
- && codonframe[i].involvesSequence(alignment[sq]))
+ final SequenceI seq = alignment[sq];
+ if (acf != null && acf.involvesSequence(seq))
{
- al.addCodonFrame(codonframe[i]);
- codonframe[i] = null;
+ al.addCodonFrame(acf);
break;
}
}
@@ -357,7 +371,7 @@ public abstract class AWSThread extends Thread
AlignmentView alview, String wsurl2)
{
super();
- // this.alignFrame = alframe;
+ this.alignFrame = alframe;
currentView = alframe.getCurrentView().getAlignment();
featureSettings = alframe.getFeatureRenderer().getSettings();
defGapChar = alframe.getViewport().getGapCharacter();
@@ -366,13 +380,18 @@ public abstract class AWSThread extends Thread
WsUrl = wsurl2;
if (alframe != null)
{
- AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ List cf = alframe.getViewport().getAlignment()
.getCodonFrames();
if (cf != null)
{
- codonframe = new AlignedCodonFrame[cf.length];
- System.arraycopy(cf, 0, codonframe, 0, cf.length);
+ codonframe = new LinkedHashSet();
+ codonframe.addAll(cf);
}
}
}
+
+ protected AlignFrame getRequestingAlignFrame()
+ {
+ return this.alignFrame;
+ }
}