X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=198aa626baa97f7b4e470ebcb59396cac130cb1f;hb=f8eadd61b07375a6aada36b2b4b2aa8c3423510e;hp=cf8c190ef74eeb17ce1506d1997210b6a25c88d1;hpb=cfa72c2cceb390460b4f08c320146bd6910d8484;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index cf8c190..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; /** @@ -157,8 +160,8 @@ public class StructureChooser extends GStructureChooser Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); - HashSet errors = new HashSet(); + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { FTSRestRequest pdbRequest = new FTSRestRequest(); @@ -223,7 +226,7 @@ public class StructureChooser extends GStructureChooser public void loadLocalCachedPDBEntries() { - ArrayList entries = new ArrayList(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null @@ -257,7 +260,7 @@ public class StructureChooser extends GStructureChooser boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - Set seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet<>(); if (seq.getAllPDBEntries() != null && queryBuilder.length() < MAX_QLENGTH) @@ -401,8 +404,8 @@ public class StructureChooser extends GStructureChooser lbl_loading.setVisible(true); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); - HashSet errors = new HashSet(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { @@ -453,7 +456,7 @@ public class StructureChooser extends GStructureChooser if (!filteredResponse.isEmpty()) { final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); + Collection reorderedStructuresSet = new LinkedHashSet<>(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); getResultTable().setModel(FTSRestResponse @@ -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); @@ -720,17 +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() { - final long progressSessionId = System.currentTimeMillis(); + 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(); - ssm.setProgressIndicator(this); - ssm.setProgressSessionId(progressSessionId); - new Thread(new Runnable() + + Runnable viewStruc = new Runnable() { @Override public void run() @@ -738,21 +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(); + 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); @@ -761,6 +823,7 @@ public class StructureChooser extends GStructureChooser pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } + if (pdbEntry == null) { pdbEntry = new PDBEntry(); @@ -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) { @@ -783,7 +847,7 @@ public class StructureChooser extends GStructureChooser .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); - List selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, @@ -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) { @@ -805,7 +870,6 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - String pdbIdStr = txt_search.getText(); PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); if (pdbEntry == null) @@ -825,7 +889,7 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } @@ -842,13 +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); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + closeAction(preferredHeight); + mainFrame.dispose(); + } + }); + } + }; + 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) + { + + } } - }).start(); + } } private PDBEntry getFindEntry(String id, Vector pdbEntries) @@ -866,17 +957,20 @@ 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) { - ssm.setProgressBar(MessageManager - .getString("status.launching_3d_structure_viewer")); + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); final StructureViewer sViewer = new StructureViewer(ssm); + setProgressBar(null, progressId); if (SiftsSettings.isMapWithSifts()) { - List seqsWithoutSourceDBRef = new ArrayList(); + List seqsWithoutSourceDBRef = new ArrayList<>(); int p = 0; // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a // real PDB ID. For moment, we can also safely do this if there is already @@ -907,35 +1001,38 @@ public class StructureChooser extends GStructureChooser if (!seqsWithoutSourceDBRef.isEmpty()) { int y = seqsWithoutSourceDBRef.size(); - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_dbrefs_for_sequences_without_valid_refs", - y)); + y), progressId); SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; int x = 0; for (SequenceI fSeq : seqsWithoutSourceDBRef) { seqWithoutSrcDBRef[x++] = fSeq; } + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n } } if (pdbEntriesToView.length > 1) { - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.getString( - "status.fetching_3d_structures_for_selected_entries")); + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId())); + pdbEntriesToView[0].getId()),progressId); sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } + setProgressBar(null, progressId); + return sViewer; } /** @@ -994,7 +1091,7 @@ public class StructureChooser extends GStructureChooser String searchTerm = txt_search.getText().toLowerCase(); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); - List wantedFields = new ArrayList(); + List wantedFields = new ArrayList<>(); FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); @@ -1056,7 +1153,7 @@ public class StructureChooser extends GStructureChooser public PDBEntryTableModel(List pdbEntries) { - this.pdbEntries = new ArrayList(pdbEntries); + this.pdbEntries = new ArrayList<>(pdbEntries); } @Override @@ -1166,4 +1263,9 @@ public class StructureChooser extends GStructureChooser { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }