X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSThread.java;h=a28494cb7a26ce92f667c5d4ca02e4a0389a6dd0;hb=48d771634c20c172ba99d675a2f8277ccc252333;hp=d080c4a3271edfb5f531bbf6ab0dad4618aa25e4;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index d080c4a..a28494c 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -1,32 +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.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
import jalview.io.NewickFile;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
+
import vamsas.objects.simple.MsaResult;
import vamsas.objects.simple.SeqSearchResult;
@@ -58,7 +70,7 @@ class SeqSearchWSThread 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"));
}
}
@@ -82,7 +94,8 @@ class SeqSearchWSThread 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++)
{
@@ -123,8 +136,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
if (submitGaps)
@@ -158,7 +170,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
- public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ public Object[] getAlignment(Alignment dataset, Map featureColours)
{
if (result != null && result.isFinished())
@@ -256,8 +268,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
* trigger a 'fetchDBids' to annotate sequences with database ids...
*/
- return new Object[]
- { al, nf };
+ return new Object[] { al, nf };
}
return null;
}
@@ -443,8 +454,9 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
{
if (!(job instanceof SeqSearchWSJob))
{
- 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() }));
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
@@ -462,7 +474,8 @@ class SeqSearchWSThread 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
@@ -481,10 +494,9 @@ class SeqSearchWSThread 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());
@@ -502,11 +514,8 @@ class SeqSearchWSThread 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
}
@@ -544,8 +553,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
.getAlignment();
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++)
{
@@ -603,7 +612,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Hashtable featureColours = new Hashtable();
+ Map featureColours = new HashMap();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
@@ -645,7 +654,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (nf != null)
{
- af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+ af.ShowNewickTree(nf, MessageManager.formatMessage(
+ "label.tree_from", new String[] { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);