X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FAWSThread.java;h=e55761428171003eb8a3746527bd834602b44975;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=a40d27aee25433fb50232774aa2f0db0a005a0e3;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index a40d27a..e557614 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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;
@@ -25,7 +28,11 @@ 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.Set;
public abstract class AWSThread extends Thread
{
@@ -53,7 +60,7 @@ 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.
@@ -83,6 +90,11 @@ 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
*/
@@ -120,8 +132,9 @@ 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.");
@@ -163,30 +176,7 @@ 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
@@ -208,10 +198,40 @@ public abstract class AWSThread extends Thread
{
Cache.log
.debug("WebServiceJob poll loop finished with no jobs created.");
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ 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();
@@ -284,13 +304,12 @@ 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;
}
}
@@ -334,11 +353,12 @@ 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
- * - gui attachment point
+ * - gui attachment point - may be null
* @param alview
* - input data for the calculation
* @param wsurl2
@@ -348,7 +368,7 @@ 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();
@@ -357,13 +377,18 @@ public abstract class AWSThread extends Thread
WsUrl = wsurl2;
if (alframe != null)
{
- AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ Set 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;
+ }
}