X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FAWSThread.java;h=2074f9f54c99870a05f1a61b0803e110bc327906;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=4f604802d7a6d26633fba80790f5d1d2424bb4c1;hpb=add30afdc46a14e61ccf55881fa91b9ca9abfe80;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 4f60480..2074f9f 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws;
import jalview.bin.Cache;
@@ -8,7 +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
{
@@ -17,47 +41,62 @@ public abstract class AWSThread extends Thread
* view that this job was associated with
*/
protected AlignmentI currentView = null;
+
/**
* feature settings from view that job was associated with
*/
protected FeatureRendererSettings featureSettings = null;
+
/**
* metadata about this web service
*/
protected WebserviceInfo wsInfo = null;
+
/**
* original input data for this job
*/
protected AlignmentView input = null;
+
/**
* 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.
*/
protected boolean jobComplete = false;
+
/**
* one or more jobs being managed by this thread.
*/
protected AWsJob jobs[] = null;
+
/**
* full name of service
*/
protected String WebServiceName = null;
+
protected char defGapChar = '-';
+
/**
* header prepended to all output from job
*/
protected String OutputHeader;
/**
- * only used when reporting a web service out of memory error - the job ID will be concatenated to the URL
+ * only used when reporting a web service out of memory error - the job ID
+ * will be concatenated to the URL
*/
protected String WsUrl = null;
+ /*
+ * The AlignFrame from which the service was requested.
+ */
+ private AlignFrame alignFrame;
+
/**
- * generic web service job/subjob poll loop
+ * generic web service job/subjob poll loop
*/
public void run()
{
@@ -93,8 +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.");
@@ -136,30 +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
@@ -181,10 +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()
{
@@ -247,8 +294,8 @@ public abstract class AWSThread extends Thread
/**
* helper function to conserve dataset references to sequence objects returned
* from web services 1. Propagates AlCodonFrame data from
- * codonframe to al
- * TODO: refactor to datamodel
+ * codonframe to al TODO: refactor to datamodel
+ *
* @param al
*/
public void propagateDatasetMappings(Alignment al)
@@ -258,13 +305,12 @@ 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;
}
}
@@ -308,11 +354,12 @@ 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
@@ -322,7 +369,7 @@ 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();
@@ -331,13 +378,18 @@ 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;
+ }
}