X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=198aa626baa97f7b4e470ebcb59396cac130cb1f;hb=f8eadd61b07375a6aada36b2b4b2aa8c3423510e;hp=37632efb08a455ed744e2ea12b7654453e858ea8;hpb=0efc6021e63ff62bb2e275501586c1900561b303;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 37632ef..198aa62 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,6 +21,7 @@ package jalview.gui; +import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Jalview; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; @@ -53,6 +54,8 @@ 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; /** @@ -525,7 +528,7 @@ public class StructureChooser extends GStructureChooser * structures */ protected void populateFilterComboBox(boolean haveData, - boolean cachedPDBExists) + boolean cachedPDBExist) { /* * temporarily suspend the change listener behaviour @@ -535,25 +538,33 @@ public class StructureChooser extends GStructureChooser cmb_filterOption.removeAllItems(); if (haveData) { - cmb_filterOption.addItem(new FilterOption("Best Quality", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_quality"), "overall_quality", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Best Resolution", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_resolution"), "resolution", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Most Protein Chain", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_protein_chain"), "number_of_protein_chains", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_bound_molecules"), "number_of_bound_molecules", VIEWS_FILTER, false)); - cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_polymer_residues"), "number_of_polymer_residues", VIEWS_FILTER, true)); } cmb_filterOption.addItem( - new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false)); + new FilterOption(MessageManager.getString("label.enter_pdb_id"), + "-", VIEWS_ENTER_ID, false)); cmb_filterOption.addItem( - new FilterOption("From File", "-", VIEWS_FROM_FILE, false)); + new FilterOption(MessageManager.getString("label.from_file"), + "-", VIEWS_FROM_FILE, false)); - if (cachedPDBExists) + if (cachedPDBExist) { - FilterOption cachedOption = new FilterOption("Cached PDB Entries", + FilterOption cachedOption = new FilterOption( + MessageManager.getString("label.cached_structures"), "-", VIEWS_LOCAL_PDB, false); cmb_filterOption.addItem(cachedOption); cmb_filterOption.setSelectedItem(cachedOption); @@ -720,16 +731,65 @@ 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() @@ -737,21 +797,24 @@ 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); @@ -772,7 +835,8 @@ 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) { @@ -795,7 +859,8 @@ 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) { @@ -824,7 +889,7 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } @@ -841,14 +906,40 @@ 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) @@ -866,7 +957,8 @@ public class StructureChooser extends GStructureChooser return foundEntry; } - private void launchStructureViewer(StructureSelectionManager ssm, + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { @@ -940,6 +1032,7 @@ public class StructureChooser extends GStructureChooser sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } setProgressBar(null, progressId); + return sViewer; } /** @@ -1170,4 +1263,9 @@ public class StructureChooser extends GStructureChooser { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }