X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=1b69989952864235bfd1b4cdd3d6378393268014;hb=39a640a77b531e7b4801eebf6c43502cc9821180;hp=217f653bf5e403979f0ebedc0890895288499262;hpb=6c118f968f6e8f726fdbb6ce6c24d870b22419bb;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 217f653..1b69989 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,6 +21,8 @@ package jalview.gui; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; @@ -53,6 +55,8 @@ import java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; +import javax.swing.JTable; +import javax.swing.SwingUtilities; import javax.swing.table.AbstractTableModel; /** @@ -105,6 +109,8 @@ public class StructureChooser extends GStructureChooser progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + chk_superpose.setSelected(Cache.getDefault("AUTOSUPERIMPOSE", true)); + // ensure a filter option is in force for search populateFilterComboBox(true, cachedPDBExists); Thread discoverPDBStructuresThread = new Thread(new Runnable() @@ -122,6 +128,7 @@ public class StructureChooser extends GStructureChooser fetchStructuresMetaData(); // revise filter options if no results were found populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); + discoverStructureViews(); updateProgressIndicator(null, startTime); mainFrame.setVisible(true); updateCurrentView(); @@ -130,6 +137,47 @@ public class StructureChooser extends GStructureChooser discoverPDBStructuresThread.start(); } + private void discoverStructureViews() + { + if (Desktop.instance != null) + { + targetView.removeAllItems(); + targetView.addItem( + new StructureViewer(ap.getStructureSelectionManager())); + if (lastTargetedView != null && !lastTargetedView.isVisible()) + { + lastTargetedView = null; + } + int linkedViewsAt = 1; + for (StructureViewerBase view : Desktop.instance + .getStructureViewers(null, null)) + { + StructureViewer viewHandler = (lastTargetedView != null + && lastTargetedView.sview == view) ? lastTargetedView + : StructureViewer.reconfigure(view); + + if (view.isLinkedWith(ap)) + { + targetView.insertItemAt(viewHandler, + linkedViewsAt++); + } + else + { + targetView.addItem(viewHandler); + } + } + targetView.setVisible(targetView.getItemCount() > 1); + + // finally, restore last targeted view by default. + if (lastTargetedView != null) + { + targetView.setSelectedItem(lastTargetedView); + } + } + } + + private static StructureViewer lastTargetedView = null; + /** * Updates the progress indicator with the specified message * @@ -728,16 +776,65 @@ public class StructureChooser extends GStructureChooser } /** + * select structures for viewing by their PDB IDs + * + * @param pdbids + * @return true if structures were found and marked as selected + */ + public boolean selectStructure(String... pdbids) + { + boolean found = false; + + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption + .getSelectedItem()); + String currentView = selectedFilterOpt.getView(); + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null; + + if (restable == null) + { + // can't select (enter PDB ID, or load file - need to also select which + // sequence to associate with) + return false; + } + + int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex(); + for (int r = 0; r < restable.getRowCount(); r++) + { + for (int p = 0; p < pdbids.length; p++) + { + if (String.valueOf(restable.getValueAt(r, pdbIdColIndex)) + .equalsIgnoreCase(pdbids[p])) + { + restable.setRowSelectionInterval(r, r); + found = true; + } + } + } + return found; + } + /** * Handles action event for btn_ok */ @Override public void ok_ActionPerformed() { + showStructures(false); + } + + /** + * structure viewer opened by this dialog, or null + */ + private StructureViewer sViewer = null; + + public void showStructures(boolean waitUntilFinished) + { + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); final int preferredHeight = pnl_filter.getHeight(); - new Thread(new Runnable() + Runnable viewStruc = new Runnable() { @Override public void run() @@ -745,21 +842,24 @@ public class StructureChooser extends GStructureChooser FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); String currentView = selectedFilterOpt.getView(); + JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() + : tbl_local_pdb; + if (currentView == VIEWS_FILTER) { - int pdbIdColIndex = getResultTable().getColumn("PDB Id") + int pdbIdColIndex = restable.getColumn("PDB Id") .getModelIndex(); - int refSeqColIndex = getResultTable().getColumn("Ref Sequence") + int refSeqColIndex = restable.getColumn("Ref Sequence") .getModelIndex(); - int[] selectedRows = getResultTable().getSelectedRows(); + int[] selectedRows = restable.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { - String pdbIdStr = getResultTable() + String pdbIdStr = restable .getValueAt(row, pdbIdColIndex).toString(); - SequenceI selectedSeq = (SequenceI) getResultTable() + SequenceI selectedSeq = (SequenceI) restable .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); @@ -780,7 +880,8 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + selectedSeqs); } else if (currentView == VIEWS_LOCAL_PDB) { @@ -803,7 +904,8 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) { @@ -832,7 +934,7 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } @@ -849,14 +951,40 @@ public class StructureChooser extends GStructureChooser DataSourceType.FILE, selectedSequence, true, Desktop.instance); - launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + sViewer = launchStructureViewer( + ssm, new PDBEntry[] + { fileEntry }, ap, new SequenceI[] { selectedSequence }); } - closeAction(preferredHeight); - mainFrame.dispose(); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + closeAction(preferredHeight); + mainFrame.dispose(); + } + }); } - }).start(); + }; + Thread runner = new Thread(viewStruc); + runner.start(); + if (waitUntilFinished) + { + while (sViewer == null ? runner.isAlive() + : (sViewer.sview == null ? true + : !sViewer.sview.hasMapping())) + { + try + { + Thread.sleep(300); + } catch (InterruptedException ie) + { + + } + } + } } private PDBEntry getFindEntry(String id, Vector pdbEntries) @@ -874,16 +1002,37 @@ public class StructureChooser extends GStructureChooser return foundEntry; } - private void launchStructureViewer(StructureSelectionManager ssm, + /** + * @param ssm + * @return targetted structure view (new or existing) configured according to + * superpose checkbox + */ + public StructureViewer getTargetedStructureViewer( + StructureSelectionManager ssm) + { + Object _sv = targetView.getSelectedItem(); + StructureViewer sv; + if (_sv == null) + { + sv = new StructureViewer(ssm); + } else { + sv = (StructureViewer) _sv; + } + sv.setSuperpose(chk_superpose.isSelected()); + return sv; + } + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { long progressId = sequences.hashCode(); setProgressBar(MessageManager .getString("status.launching_3d_structure_viewer"), progressId); - final StructureViewer sViewer = new StructureViewer(ssm); - setProgressBar(null, progressId); + final StructureViewer sViewer = getTargetedStructureViewer(ssm); + sViewer.setSuperpose(chk_superpose.isSelected()); + setProgressBar(null, progressId); if (SiftsSettings.isMapWithSifts()) { List seqsWithoutSourceDBRef = new ArrayList<>(); @@ -948,6 +1097,9 @@ public class StructureChooser extends GStructureChooser sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } setProgressBar(null, progressId); + // remember the last viewer we used... + lastTargetedView = sViewer; + return sViewer; } /** @@ -1178,4 +1330,9 @@ public class StructureChooser extends GStructureChooser { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }