X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FAWSThread.java;h=7f05e9065a29420f1899458b7971e6394b880a73;hb=759d83a940b86333a264437462a2b0c8bc662d97;hp=73004625ab76ed7f9fe3da4d5ffa4b9e5780c8a3;hpb=338fec5009a92d5cedc15612a13313bdb3f42756;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 7300462..7f05e90 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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;
@@ -24,8 +27,9 @@ import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
public abstract class AWSThread extends Thread
{
@@ -120,8 +124,8 @@ 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 String[]{WebServiceName,ex.getMessage()}));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
@@ -163,30 +167,7 @@ public abstract class AWSThread extends Thread
jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
}
// Decide on overall state based on collected jobs[] states
- if (jstate.running > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- }
- else if (jstate.queuing > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- }
- else
- {
- jobComplete = true;
- if (jstate.finished > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (jstate.error > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
- else if (jstate.serror > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
+ updateGlobalStatus(jstate);
if (!jobComplete)
{
try
@@ -209,11 +190,39 @@ 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.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
+ protected void updateGlobalStatus(JobStateSummary jstate)
+ {
+ if (jstate.running > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ else if (jstate.queuing > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+ else
+ {
+ jobComplete = true;
+ if (jstate.finished > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (jstate.error > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ else if (jstate.serror > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ }
+ }
+
public AWSThread()
{
super();
@@ -288,10 +297,11 @@ public abstract class AWSThread extends Thread
{
for (int i = 0; i < codonframe.length; i++)
{
- if (codonframe[i] != null
- && codonframe[i].involvesSequence(alignment[sq]))
+ AlignedCodonFrame acf = codonframe[i];
+ final SequenceI seq = alignment[sq];
+ if (acf != null && acf.involvesSequence(seq))
{
- al.addCodonFrame(codonframe[i]);
+ al.addCodonFrame(new AlignedCodonFrame(acf, alignment));
codonframe[i] = null;
break;
}
@@ -337,6 +347,7 @@ public abstract class AWSThread extends Thread
/**
* Extracts additional info from alignment view's context.
+ *
* @param alframe
* - reference for copying mappings and display styles across
* @param wsinfo2