Hi Thomas, I found this bug was a bit deeper - the items in the tree were generated only when peak list was added to the tree, but were not regenerated when the peak list was modified. I just committed a fix to the SVN, please check if it works for you.
Best, Tomas On Oct 31, 2014, at 16:20, TFRD (Thomas Franck Dyrlund) <t...@steno.dk<mailto:t...@steno.dk>> wrote: It doesn’t work for me – the new peak is still not added. I tried the following: Index: src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/manual/ManualPickerTask.java =================================================================== --- src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/manual/ManualPickerTask.java (revision 3423) +++ src/main/java/net/sf/mzmine/modules/rawdatamethods/peakpicking/manual/ManualPickerTask.java (working copy) @@ -30,8 +30,10 @@ import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.Scan; import net.sf.mzmine.datamodel.impl.SimpleDataPoint; +import net.sf.mzmine.desktop.impl.projecttree.PeakListTreeModel; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.modules.visualization.peaklist.table.PeakListTable; +import net.sf.mzmine.project.impl.MZmineProjectImpl; import net.sf.mzmine.taskcontrol.AbstractTask; import net.sf.mzmine.taskcontrol.TaskStatus; import net.sf.mzmine.util.Range; @@ -129,7 +131,13 @@ } // Notify the GUI that peaklist contents have changed - if (peakList != null) { MZmineCore.getCurrentProject().notifyObjectChanged(peakList, true); } + if (peakList != null) { + MZmineCore.getCurrentProject().notifyObjectChanged(peakList, true); + MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getCurrentProject(); + PeakListTreeModel treeModel = project.getPeakListTreeModel(); + treeModel.notifyObjectChanged(peakList, true); + } if (table != null) { ((AbstractTableModel) table.getModel()).fireTableDataChanged(); } logger.finest("Finished manual peak picker" + processedScans Also, if I call treeModel.reload(); after treeModel.notifyObjectChanged(peakList, true); I can see that the peak list view is reloaded but when I expand the peak list again the new peak is still not there. /Thomas From: Tomas Pluskal [mailto:plus...@oist.jp] Sent: 31. oktober 2014 01:42 To: Developer discussion Subject: Re: [Mzmine-devel] Error with adding a new peak to the peak list table Hi Thomas, I think instead of adding the row manually to the tree model, you should just let the tree model know that the peak list structure has changed, by calling treeModel.notifyObjectChanged(peakList, true); That should result in updating the peak list rows in the tree. Cheers, Tomas On Oct 30, 2014, at 19:05, TFRD (Thomas Franck Dyrlund) <t...@steno.dk<mailto:t...@steno.dk>> wrote: Hi everyone I need your help to fix a bug in MZmine. The problem is that after adding a new peak to the peak list table, it is not shown in the tree if the peak list is expanded in the main window. When a user then deletes this row, an error is returned in SimplePeakList.java l. 246. Based on what I can see, the problem is that the project tree model is not updated after adding the row in SimplePeakList.java: public void addRow(PeakListRow row) { List<RawDataFile> myFiles = Arrays.asList(this.getRawDataFiles()); for (RawDataFile testFile : row.getRawDataFiles()) { if (!myFiles.contains(testFile)) throw (new IllegalArgumentException("Data file " + testFile+ " is not in this peak list")); } peakListRows.add(row); ... } Deleting a non-user added row works fine and I have therefore tried adding the following to addRow(): // We have to update the project tree model MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getCurrentProject(); PeakListTreeModel treeModel = project.getPeakListTreeModel(); treeModel.addObject(row); However, I get the following error when loading a project and also a new row is not added to the peak list tree: java.lang.IllegalStateException: This method must be called from Swing thread Can anyone please help solve this bug? Best regards, Thomas ------------------------------------------------------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net<mailto:Mzmine-devel@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890 ------------------------------------------------------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net<mailto:Mzmine-devel@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890
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