/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
-import java.util.*;
+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.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.SplitFrame;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.Preset;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.ws.AWsJob;
-import jalview.ws.WSClientI;
-import jalview.ws.JobStateSummary;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.params.WsParamSetI;
-
class MsaWSThread extends AWS2Thread implements WSClientI
{
boolean submitGaps = false; // pass sequences including gaps to alignment
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++)
{
.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
return valid;
int ow = w, nw = w;
for (i = 0, w = emptySeqs.size(); i < w; i++)
{
- String[] es = (String[]) emptySeqs.get(i);
+ String[] es = emptySeqs.get(i);
if (es != null && es[1] != null)
{
int sw = es[1].length();
}
for (i = 0, w = emptySeqs.size(); i < w; i++)
{
- String[] es = (String[]) emptySeqs.get(i);
+ String[] es = emptySeqs.get(i);
if (es[1] == null)
{
t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
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;
}
* @param presorder
* boolean
*/
- MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
+ private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, AlignmentView alview,
String wsname, boolean subgaps, boolean presorder)
{
SequenceI[][] conmsa = _msa.getVisibleContigs('-');
if (conmsa != null)
{
- int njobs = conmsa.length;
+ int nvalid = 0, njobs = conmsa.length;
jobs = new MsaWSJob[njobs];
for (int j = 0; j < njobs; j++)
{
{
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
+ if (((MsaWSJob) jobs[j]).hasValidInput())
+ {
+ nvalid++;
+ }
((MsaWSJob) jobs[j]).preset = preset;
((MsaWSJob) jobs[j]).arguments = paramset;
((MsaWSJob) jobs[j]).alignmentProgram = wsname;
}
wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
}
+ validInput = nvalid > 0;
}
}
+ boolean validInput = false;
+
+ /**
+ *
+ * @return true if the thread will perform a calculation
+ */
+ public boolean hasValidInput()
+ {
+ return validInput;
+ }
+
public boolean isCancellable()
{
return true;
try
{
boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
- if (cancelledJob || true)
+ if (true) // cancelledJob || true)
{
// CANCELLED_JOB
// if the Jaba server indicates the job can't be cancelled, its
wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ cancelledMessage + "\n");
}
+ else
+ {
+ // if we hadn't submitted then just mark the job as cancelled.
+ jobs[job].setSubjobComplete(true);
+ wsInfo.setStatus(jobs[job].getJobnum(),
+ WebserviceInfo.STATE_CANCELLED_OK);
+
+ }
}
if (cancelled)
{
{
StringBuffer response = j.jobProgress;
long lastchunk = j.getLastChunk();
- boolean changed=false;
+ boolean changed = false;
do
{
j.setLastChunk(lastchunk);
.pullExecStatistics(j.getJobId(), lastchunk);
if (chunk != null)
{
- changed=chunk.getChunk().length()>0;
+ changed |= chunk.getChunk().length() > 0;
response.append(chunk.getChunk());
lastchunk = chunk.getNextPosition();
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
}
;
} while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
// boiler plate template
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())
{
// special case - selection consisted entirely of empty sequences...
j.setjobStatus(JobStatus.FINISHED);
- j.setStatus("Empty Alignment Job");
+ j.setStatus(MessageManager.getString("label.empty_alignment_job"));
}
try
{
}
else if (j.hasArguments())
{
- j.setJobId(server.customAlign(j.seqs,j.getJabaArguments()));
+ j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
}
else
{
}
else
{
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null string for job id, it probably cannot be contacted. Try again later ?");
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
- wsInfo.appendProgressText("Job could not be run because the server doesn't support this program.\n"
- + _lex.getMessage());
- wsInfo.warnUser(_lex.getMessage(), "Service not supported!");
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_server_doesnt_support_program",
+ new String[] { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
} catch (compbio.metadata.LimitExceededException _lex)
{
lex = _lex;
- wsInfo.appendProgressText("Job could not be run because it exceeded a hard limit on the server.\n"
- + _lex.getMessage());
- wsInfo.warnUser(_lex.getMessage(), "Input is too big!");
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_exceeded_hard_limit",
+ new String[] { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (compbio.metadata.WrongParameterException _lex)
{
lex = _lex;
- wsInfo.warnUser(_lex.getMessage(), "Invalid job parameter set!");
- wsInfo.appendProgressText("Job could not be run because some of the parameter settings are not supported by the server.\n"
- + _lex.getMessage()
- + "\nPlease check to make sure you have used the correct parameter set for this service!\n");
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.invalid_job_param_set"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_incorrect_param_setting",
+ new String[] { _lex.getMessage() }));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
// TODO: JBPNote catch timeout or other fault types explicitly
j.setAllowedServerExceptions(0);
- wsInfo.appendProgressText(j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "Just close the window\n");
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .getString("info.failed_to_submit_sequences_for_alignment"));
}
}
}
public void parseResult()
{
+ long progbar = System.currentTimeMillis();
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"),
+ progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
MsaWSJob msjob = ((MsaWSJob) jobs[j]);
if (jobs[j].isFinished() && msjob.alignment == null)
{
- boolean jpchanged=false,jpex=false;
- do {
+ int nunchanged = 3, nexcept = 3;
+ boolean jpchanged = false, jpex = false;
+ do
+ {
try
{
jpchanged = updateJobProgress(msjob);
- jpex=false;
+ jpex = false;
+ if (jpchanged)
+ {
+ nexcept = 3;
+ }
} catch (Exception e)
{
-
+
Cache.log
.warn("Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
- if (jpex) {
- // give up polling after two consecutive exceptions
- jpchanged=false;
- } else {
- jpchanged=true;
- }
+ nexcept--;
+ nunchanged = 3;
// set flag remember that we've had an exception.
- jpex=true;
+ jpex = true;
+ jpchanged = false;
}
- if (jpchanged)
+ if (!jpchanged)
{
try
{
- Thread.sleep(jpex ? 400 : 200); // wait a bit longer if we experienced an exception.
+ Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
+ // experienced an exception.
} catch (Exception ex)
{
}
;
+ nunchanged--;
}
- } while (jpchanged);
-
+ } while (nunchanged > 0 && nexcept > 0);
+
if (Cache.log.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
Cache.log
.debug("Results not available for finished job - marking as broken job.",
e);
+ msjob.jobProgress
+ .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ + e.getLocalizedMessage());
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
}
else
{
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setFinishedNoResults();
}
+ updateGlobalStatus(finalState);
+ wsInfo.setProgressBar(null, progbar);
}
+ /**
+ * Display alignment results in a new frame (or - not currently supported -
+ * added to an existing alignment).
+ *
+ * @param newFrame
+ */
void displayResults(boolean newFrame)
{
// view input or result data for each block
- Vector alorders = new Vector();
+ List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
msjob = (MsaWSJob) jobs[j];
Object[] res = msjob.getAlignment();
lastProgram = msjob.getAlignmentProgram();
- alorders.add(res[1]);
+ alorders.add((AlignmentOrder) res[1]);
results[j] = (SequenceI[]) res[0];
orders[j] = (AlignmentOrder) res[1];
if (newFrame)
{
- AlignFrame af = new AlignFrame(al, columnselection,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ displayInNewFrame(al, alorders, columnselection);
- // initialise with same renderer settings as in parent alignframe.
- af.getFeatureRenderer().transferSettings(this.featureSettings);
- // update orders
- if (alorders.size() > 0)
- {
- if (alorders.size() == 1)
- {
- af.addSortByOrderMenuItem(WebServiceName + " Ordering",
- (AlignmentOrder) alorders.get(0));
- }
- else
- {
- // construct a non-redundant ordering set
- Vector names = new Vector();
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- String orderName = new String(" Region " + i);
- int j = i + 1;
+ }
+ else
+ {
+ // TODO 2.9.x feature
+ System.out.println("MERGE WITH OLD FRAME");
+ // TODO: modify alignment in original frame, replacing old for new
+ // alignment using the commands.EditCommand model to ensure the update can
+ // be undone
+ }
+ }
- while (j < l)
- {
- if (((AlignmentOrder) alorders.get(i))
- .equals(((AlignmentOrder) alorders.get(j))))
- {
- alorders.remove(j);
- l--;
- orderName += "," + j;
- }
- else
- {
- j++;
- }
- }
+ /**
+ * Display the alignment result in a new frame.
+ *
+ * @param al
+ * @param alorders
+ * @param columnselection
+ */
+ protected void displayInNewFrame(AlignmentI al,
+ List<AlignmentOrder> alorders, ColumnSelection columnselection)
+ {
+ AlignFrame af = new AlignFrame(al, columnselection,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- if (i == 0 && j == 1)
- {
- names.add(new String(""));
- }
- else
- {
- names.add(orderName);
- }
- }
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- af.addSortByOrderMenuItem(
- WebServiceName + ((String) names.get(i)) + " Ordering",
- (AlignmentOrder) alorders.get(i));
- }
- }
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+
+ if (alorders.size() > 0)
+ {
+ addSortByMenuItems(af, alorders);
+ }
+
+ // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = getRequestingAlignFrame();
+ if (requestedBy != null
+ && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer().getComplement(
+ requestedBy) != null)
+ {
+ AlignmentI complement = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
+ AlignmentI copyComplement = new Alignment(complement);
+ copyComplement.alignAs(al);
+ if (copyComplement.getHeight() > 0)
+ {
+ af.setTitle(alTitle);
+ AlignFrame af2 = new AlignFrame(copyComplement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af2.setTitle(complementTitle);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(al.isNucleotide() ? af
+ : af2, al.isNucleotide() ? af2 : af);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+ return;
}
+ }
- Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ /*
+ * Not from SplitFrame, or failed to created a complementary alignment
+ */
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ /**
+ * Add sort order options to the AlignFrame menus.
+ *
+ * @param af
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame af,
+ List<AlignmentOrder> alorders)
+ {
+ // update orders
+ if (alorders.size() == 1)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+ alorders.get(0));
}
else
{
- System.out.println("MERGE WITH OLD FRAME");
- // TODO: modify alignment in original frame, replacing old for new
- // alignment using the commands.EditCommand model to ensure the update can
- // be undone
+ // construct a non-redundant ordering set
+ List<String> names = new ArrayList<String>();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = " Region " + i;
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add("");
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + (names.get(i))
+ + " Ordering", alorders.get(i));
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff