X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSThread.java;h=72d41c945532c1baea49d9108b50002cafb3adb5;hb=c70905eb5589c7622a2c7cf8a008ba0863b5c010;hp=363296ecbd4b9c9974a977c2e0bea72e48fcbc87;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index 363296e..72d41c9 100644
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -1,31 +1,44 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
import vamsas.objects.simple.MsaResult;
class MsaWSThread extends JWS1Thread implements WSClientI
@@ -60,7 +73,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
subjobComplete = true;
result = new MsaResult();
result.setFinished(true);
- result.setStatus("Job never ran - input returned to user.");
+ result.setStatus(MessageManager.getString("label.job_never_ran"));
}
}
@@ -84,7 +97,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
if (minlen < 0)
{
throw new Error(
- "Implementation error: minlen must be zero or more.");
+ MessageManager
+ .getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
@@ -122,8 +136,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
this.seqs = new vamsas.objects.simple.SequenceSet();
@@ -135,6 +148,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
*
* @return true if getAlignment will return a valid alignment result.
*/
+ @Override
public boolean hasResults()
{
if (subjobComplete && result != null && result.isFinished()
@@ -242,8 +256,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
// account for any missing sequences
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[]
- { alseqs, msaorder };
+ return new Object[] { alseqs, msaorder };
}
return null;
}
@@ -262,6 +275,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
*
* @return boolean true if job can be submitted.
*/
+ @Override
public boolean hasValidInput()
{
if (seqs.getSeqs() != null)
@@ -274,7 +288,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
String alTitle; // name which will be used to form new alignment window.
- Alignment dataset; // dataset to which the new alignment will be
+ AlignmentI dataset; // dataset to which the new alignment will be
// associated.
@@ -316,7 +330,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
String wsname, String title, AlignmentView _msa, boolean subgaps,
- boolean presorder, Alignment seqset)
+ boolean presorder, AlignmentI seqset)
{
this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
OutputHeader = wsInfo.getProgressText();
@@ -348,11 +362,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
}
}
+ @Override
public boolean isCancellable()
{
return true;
}
+ @Override
public void cancelJob()
{
if (!jobComplete && jobs != null)
@@ -419,17 +435,20 @@ class MsaWSThread extends JWS1Thread implements WSClientI
}
}
+ @Override
public void pollJob(AWsJob job) throws Exception
{
((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId());
}
+ @Override
public void StartJob(AWsJob job)
{
if (!(job instanceof MsaWSJob))
{
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
- + job.getClass());
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called",
+ new String[] { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
@@ -447,7 +466,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus("Empty Alignment Job");
+ j.result.setStatus(MessageManager
+ .getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
@@ -465,10 +485,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
{
if (jobsubmit == null)
{
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null object, it probably cannot be contacted. Try again later ?");
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
@@ -486,11 +505,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.appendProgressText(
- j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .getString("info.failed_to_submit_sequences_for_alignment"));
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
@@ -512,6 +528,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
return msa;
}
+ @Override
public void parseResult()
{
int results = 0; // number of result sets received
@@ -535,8 +552,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
.getMsa();
if (valign != null)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(),
- "\nAlignment Object Method Notes\n");
+ wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
+ .getString("info.alignment_object_method_notes"));
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
@@ -562,6 +579,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
@@ -570,6 +588,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
@@ -613,7 +632,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
orders[j] = null;
}
SequenceI[] alignment = (SequenceI[]) newview[0];
- ColumnSelection columnselection = (ColumnSelection) newview[1];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
Alignment al = new Alignment(alignment);
// TODO: add 'provenance' property to alignment from the method notes
// accompanying each subjob
@@ -627,7 +646,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
if (newFrame)
{
- AlignFrame af = new AlignFrame(al, columnselection,
+ AlignFrame af = new AlignFrame(al, hidden,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// initialise with same renderer settings as in parent alignframe.
@@ -651,8 +670,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
while (j < l)
{
- if (((AlignmentOrder) alorders.get(i))
- .equals(((AlignmentOrder) alorders.get(j))))
+ if (((AlignmentOrder) alorders.get(i)).equals((alorders
+ .get(j))))
{
alorders.remove(j);
l--;
@@ -695,6 +714,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
}
}
+ @Override
public boolean canMergeResults()
{
return false;