/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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.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 java.util.Map;
import java.util.Vector;
+import javax.swing.JInternalFrame;
+
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(
+ 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;
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)
{
{
return validInput;
}
+
public boolean isCancellable()
{
return true;
// boiler plate template
if (!(job instanceof MsaWSJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called",
+ new String[] { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
}
else
{
- throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[] { WsUrl }));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
- 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.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(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.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(), MessageManager.getString("warn.invalid_job_param_set"));
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
+ 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(),
- MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+ 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);
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"),
+ progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
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