X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=ec2ebe3355b58eedce3aa77f3a0963bad1eb1a73;hb=9c16178c0601ea3169d7a5d5d623dafa45c54f85;hp=3350f6cc62327c338415713360233537290d1a83;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 3350f6c..ec2ebe3 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; @@ -32,6 +34,7 @@ import jalview.fts.api.FTSRestClientI; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.io.DataSourceType; import jalview.jbgui.GStructureChooser; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; @@ -52,7 +55,8 @@ import java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; -import javax.swing.JOptionPane; +import javax.swing.JTable; +import javax.swing.SwingUtilities; import javax.swing.table.AbstractTableModel; /** @@ -62,9 +66,13 @@ import javax.swing.table.AbstractTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser implements - IProgressIndicator +public class StructureChooser extends GStructureChooser + implements IProgressIndicator { + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + + private static int MAX_QLENGTH = 7820; + private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -83,6 +91,8 @@ public class StructureChooser extends GStructureChooser implements private boolean cachedPDBExists; + private static StructureViewer lastTargetedView = null; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -96,13 +106,15 @@ public class StructureChooser extends GStructureChooser implements /** * Initializes parameters used by the Structure Chooser Panel */ - public void init() + protected void init() { if (!Jalview.isHeadlessMode()) { 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() @@ -115,12 +127,12 @@ public class StructureChooser extends GStructureChooser implements .getString("status.loading_cached_pdb_entries"), startTime); loadLocalCachedPDBEntries(); updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager - .getString("status.searching_for_pdb_structures"), - startTime); + updateProgressIndicator(MessageManager.getString( + "status.searching_for_pdb_structures"), startTime); fetchStructuresMetaData(); // revise filter options if no results were found populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); + discoverStructureViews(); updateProgressIndicator(null, startTime); mainFrame.setVisible(true); updateCurrentView(); @@ -130,6 +142,59 @@ public class StructureChooser extends GStructureChooser implements } /** + * Builds a drop-down choice list of existing structure viewers to which new + * structures may be added. If this list is empty then it, and the 'Add' + * button, are hidden. + */ + private void discoverStructureViews() + { + if (Desktop.instance != null) + { + targetView.removeAllItems(); + if (lastTargetedView != null && !lastTargetedView.isVisible()) + { + lastTargetedView = null; + } + int linkedViewsAt = 0; + 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); + } + } + + /* + * show option to Add to viewer if at least 1 viewer found + */ + targetView.setVisible(false); + if (targetView.getItemCount() > 0) + { + targetView.setVisible(true); + if (lastTargetedView != null) + { + targetView.setSelectedItem(lastTargetedView); + } + else + { + targetView.setSelectedIndex(0); + } + } + btn_add.setVisible(targetView.isVisible()); + } + } + + /** * Updates the progress indicator with the specified message * * @param message @@ -137,7 +202,7 @@ public class StructureChooser extends GStructureChooser implements * @param id * unique handle for this indicator */ - public void updateProgressIndicator(String message, long id) + protected void updateProgressIndicator(String message, long id) { if (progressIndicator != null) { @@ -149,15 +214,15 @@ public class StructureChooser extends GStructureChooser implements * Retrieve meta-data for all the structure(s) for a given sequence(s) in a * selection group */ - public void fetchStructuresMetaData() + void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); pdbRestCleint = PDBFTSRestClient.getInstance(); 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(); @@ -195,9 +260,8 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -214,16 +278,16 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(this, errorMsg.toString(), + JvOptionPane.showMessageDialog(this, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { - ArrayList entries = new ArrayList(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null @@ -252,23 +316,29 @@ public class StructureChooser extends GStructureChooser implements * @return the built query string */ - public static String buildQuery(SequenceI seq) + static String buildQuery(SequenceI seq) { boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - Set seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet<>(); + + /* + * note PDBs as DBRefEntry so they are not duplicated in query + */ + Set pdbids = new HashSet<>(); - if (seq.getAllPDBEntries() != null) + if (seq.getAllPDBEntries() != null + && queryBuilder.length() < MAX_QLENGTH) { for (PDBEntry entry : seq.getAllPDBEntries()) { if (isValidSeqName(entry.getId())) { - queryBuilder.append("pdb_id:") - .append(entry.getId().toLowerCase()).append(" OR "); + String id = entry.getId().toLowerCase(); + queryBuilder.append("pdb_id:").append(id).append(" OR "); isPDBRefsFound = true; - // seqRefs.add(entry.getId()); + pdbids.add(id); } } } @@ -277,7 +347,8 @@ public class StructureChooser extends GStructureChooser implements { for (DBRefEntry dbRef : seq.getDBRefs()) { - if (isValidSeqName(getDBRefId(dbRef))) + if (isValidSeqName(getDBRefId(dbRef)) + && queryBuilder.length() < MAX_QLENGTH) { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { @@ -290,9 +361,13 @@ public class StructureChooser extends GStructureChooser implements else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) { - queryBuilder.append("pdb_id:") - .append(getDBRefId(dbRef).toLowerCase()).append(" OR "); - isPDBRefsFound = true; + String id = getDBRefId(dbRef).toLowerCase(); + if (!pdbids.contains(id)) + { + queryBuilder.append("pdb_id:").append(id).append(" OR "); + isPDBRefsFound = true; + pdbids.add(id); + } } else { @@ -353,7 +428,7 @@ public class StructureChooser extends GStructureChooser implements * @param seqName * @return */ - public static boolean isValidSeqName(String seqName) + static boolean isValidSeqName(String seqName) { // System.out.println("seqName : " + seqName); String ignoreList = "pdb,uniprot,swiss-prot"; @@ -376,7 +451,7 @@ public class StructureChooser extends GStructureChooser implements return true; } - public static String getDBRefId(DBRefEntry dbRef) + static String getDBRefId(DBRefEntry dbRef) { String ref = dbRef.getAccessionId().replaceAll("GO:", ""); return ref; @@ -388,7 +463,7 @@ public class StructureChooser extends GStructureChooser implements * @param fieldToFilterBy * the field to filter by */ - public void filterResultSet(final String fieldToFilterBy) + void filterResultSet(final String fieldToFilterBy) { Thread filterThread = new Thread(new Runnable() { @@ -400,8 +475,8 @@ public class StructureChooser extends GStructureChooser implements 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) { @@ -452,12 +527,11 @@ public class StructureChooser extends GStructureChooser implements 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.getTableModel(lastPdbRequest, - reorderedStructuresSet)); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, reorderedStructuresSet)); FTSRestResponse.configureTableColumn(getResultTable(), wantedFields, tempUserPrefs); @@ -481,11 +555,9 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog( - null, - errorMsg.toString(), + JvOptionPane.showMessageDialog(null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -501,14 +573,14 @@ public class StructureChooser extends GStructureChooser implements * Handles action event for btn_pdbFromFile */ @Override - public void pdbFromFile_actionPerformed() + protected void pdbFromFile_actionPerformed() { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", - selectedSequence.getDisplayId(false))); + chooser.setDialogTitle( + MessageManager.formatMessage("label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( "label.load_pdb_file_associate_with_sequence", selectedSequence.getDisplayId(false))); @@ -527,7 +599,7 @@ public class StructureChooser extends GStructureChooser implements * structures */ protected void populateFilterComboBox(boolean haveData, - boolean cachedPDBExists) + boolean cachedPDBExist) { /* * temporarily suspend the change listener behaviour @@ -537,27 +609,35 @@ public class StructureChooser extends GStructureChooser implements cmb_filterOption.removeAllItems(); if (haveData) { - cmb_filterOption.addItem(new FilterOption("Best Quality", - "overall_quality", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Best Resolution", - "resolution", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most Protein Chain", - "number_of_protein_chains", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", - "number_of_bound_molecules", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", - "number_of_polymer_residues", VIEWS_FILTER)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_quality"), + "overall_quality", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.best_resolution"), + "resolution", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_protein_chain"), + "number_of_protein_chains", VIEWS_FILTER, false)); + cmb_filterOption.addItem(new FilterOption( + MessageManager.getString("label.most_bound_molecules"), + "number_of_bound_molecules", VIEWS_FILTER, false)); + 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)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB); - cmb_filterOption.addItem(cachedOption); - - if (/*!haveData &&*/cachedPDBExists) + cmb_filterOption.addItem( + new FilterOption(MessageManager.getString("label.enter_pdb_id"), + "-", VIEWS_ENTER_ID, false)); + cmb_filterOption.addItem( + new FilterOption(MessageManager.getString("label.from_file"), + "-", VIEWS_FROM_FILE, false)); + + if (cachedPDBExist) { + FilterOption cachedOption = new FilterOption( + MessageManager.getString("label.cached_structures"), + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); cmb_filterOption.setSelectedItem(cachedOption); } @@ -594,28 +674,37 @@ public class StructureChooser extends GStructureChooser implements } /** - * Validates user selection and activates the view button if all parameters - * are correct + * Validates user selection and enables the 'Add' and 'New View' buttons if + * all parameters are correct (the Add button will only be visible if there is + * at least one existing structure viewer open). This basically means at least + * one structure selected and no error messages. + *

+ * The 'Superpose Structures' option is enabled if either more than one + * structure is selected, or the 'Add' to existing view option is enabled, and + * disabled if the only option is to open a new view of a single structure. */ @Override - public void validateSelections() + protected void validateSelections() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - btn_view.setEnabled(false); + btn_add.setEnabled(false); String currentView = selectedFilterOpt.getView(); + int selectedCount = 0; if (currentView == VIEWS_FILTER) { - if (getResultTable().getSelectedRows().length > 0) + selectedCount = getResultTable().getSelectedRows().length; + if (selectedCount > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); } } else if (currentView == VIEWS_LOCAL_PDB) { - if (tbl_local_pdb.getSelectedRows().length > 0) + selectedCount = tbl_local_pdb.getSelectedRows().length; + if (selectedCount > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); } } else if (currentView == VIEWS_ENTER_ID) @@ -626,12 +715,21 @@ public class StructureChooser extends GStructureChooser implements { validateAssociationFromFile(); } + + btn_newView.setEnabled(btn_add.isEnabled()); + + /* + * enable 'Superpose' option if more than one structure is selected, + * or there are view(s) available to add structure(s) to + */ + chk_superpose + .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); } /** * Validates inputs from the Manual PDB entry panel */ - public void validateAssociationEnterPdb() + protected void validateAssociationEnterPdb() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel .getCmb_assSeq().getSelectedItem(); @@ -639,27 +737,25 @@ public class StructureChooser extends GStructureChooser implements lbl_pdbManualFetchStatus.setToolTipText(""); if (txt_search.getText().length() > 0) { - lbl_pdbManualFetchStatus - .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager - .formatMessage("info.no_pdb_entry_found_for", - txt_search.getText()))); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); } if (errorWarning.length() > 0) { lbl_pdbManualFetchStatus.setIcon(warningImage); - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, errorWarning.toString())); + lbl_pdbManualFetchStatus.setToolTipText( + JvSwingUtils.wrapTooltip(true, errorWarning.toString())); } - if (selectedSequences.length == 1 - || !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-")) + if (selectedSequences.length == 1 || !assSeqOpt.getName() + .equalsIgnoreCase("-Select Associated Seq-")) { txt_search.setEnabled(true); if (isValidPBDEntry) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } @@ -674,19 +770,18 @@ public class StructureChooser extends GStructureChooser implements /** * Validates inputs for the manual PDB file selection options */ - public void validateAssociationFromFile() + protected void validateAssociationFromFile() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); lbl_fromFileStatus.setIcon(errorImage); - if (selectedSequences.length == 1 - || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-"))) + if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt + .getName().equalsIgnoreCase("-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_fromFileStatus.setIcon(goodImage); } } @@ -698,7 +793,7 @@ public class StructureChooser extends GStructureChooser implements } @Override - public void cmbAssSeqStateChanged() + protected void cmbAssSeqStateChanged() { validateSelections(); } @@ -725,17 +820,76 @@ public class StructureChooser extends GStructureChooser implements } /** - * Handles action event for btn_ok + * 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 the 'New View' action + */ + @Override + protected void newView_ActionPerformed() + { + targetView.setSelectedItem(null); + showStructures(false); + } + + /** + * Handles the 'Add to existing viewer' action */ @Override - public void ok_ActionPerformed() + protected void add_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() @@ -743,21 +897,24 @@ public class StructureChooser extends GStructureChooser implements 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; - ArrayList selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { - String pdbIdStr = getResultTable().getValueAt(row, - pdbIdColIndex).toString(); - SequenceI selectedSeq = (SequenceI) getResultTable() + String pdbIdStr = restable + .getValueAt(row, pdbIdColIndex).toString(); + SequenceI selectedSeq = (SequenceI) restable .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); @@ -766,6 +923,7 @@ public class StructureChooser extends GStructureChooser implements pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } + if (pdbEntry == null) { pdbEntry = new PDBEntry(); @@ -777,7 +935,8 @@ public class StructureChooser extends GStructureChooser implements } 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) { @@ -788,19 +947,20 @@ public class StructureChooser extends GStructureChooser implements .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, pdbIdColIndex); pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt( - row, refSeqColIndex); + SequenceI selectedSeq = (SequenceI) tbl_local_pdb + .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); } 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) { @@ -810,7 +970,6 @@ public class StructureChooser extends GStructureChooser implements { selectedSequence = userSelectedSeq; } - String pdbIdStr = txt_search.getText(); PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); if (pdbEntry == null) @@ -830,8 +989,9 @@ public class StructureChooser extends GStructureChooser implements } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, - new SequenceI[] { selectedSequence }); + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + new SequenceI[] + { selectedSequence }); } else if (currentView == VIEWS_FROM_FILE) { @@ -843,15 +1003,43 @@ public class StructureChooser extends GStructureChooser implements } PDBEntry fileEntry = new AssociatePdbFileWithSeq() .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); + + sViewer = launchStructureViewer( + ssm, new PDBEntry[] + { fileEntry }, ap, + new SequenceI[] + { selectedSequence }); + } + 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) + { - launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); } - closeAction(preferredHeight); } - }).start(); + } } private PDBEntry getFindEntry(String id, Vector pdbEntries) @@ -869,17 +1057,52 @@ public class StructureChooser extends GStructureChooser implements return foundEntry; } - private void launchStructureViewer(StructureSelectionManager ssm, + /** + * Answers a structure viewer (new or existing) configured to superimpose + * added structures or not according to the user's choice + * + * @param ssm + * @return + */ + StructureViewer getTargetedStructureViewer( + StructureSelectionManager ssm) + { + Object sv = targetView.getSelectedItem(); + + return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; + } + + /** + * Adds PDB structures to a new or existing structure viewer + * + * @param ssm + * @param pdbEntriesToView + * @param alignPanel + * @param sequences + * @return + */ + private StructureViewer launchStructureViewer( + StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { - ssm.setProgressBar(MessageManager - .getString("status.launching_3d_structure_viewer")); - final StructureViewer sViewer = new StructureViewer(ssm); + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); + final StructureViewer theViewer = getTargetedStructureViewer(ssm); + boolean superimpose = chk_superpose.isSelected(); + theViewer.setSuperpose(superimpose); + + /* + * remember user's choice of superimpose or not + */ + Cache.setProperty(AUTOSUPERIMPOSE, + Boolean.valueOf(superimpose).toString()); + 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 @@ -901,7 +1124,7 @@ public class StructureChooser extends GStructureChooser implements } } } - if (seq.getPrimaryDBRefs().size() == 0) + if (seq.getPrimaryDBRefs().isEmpty()) { seqsWithoutSourceDBRef.add(seq); continue; @@ -910,41 +1133,35 @@ public class StructureChooser extends GStructureChooser implements 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)); - SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; - int x = 0; - for (SequenceI fSeq : seqsWithoutSourceDBRef) - { - seqWithoutSrcDBRef[x++] = fSeq; - } + y), progressId); + SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n } } if (pdbEntriesToView.length > 1) { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) - { - seqsMap.add(new SequenceI[] { seq }); - } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager - .getString("status.fetching_3d_structures_for_selected_entries")); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId())); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + pdbEntriesToView[0].getId()),progressId); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } + setProgressBar(null, progressId); + // remember the last viewer we used... + lastTargetedView = theViewer; + return theViewer; } /** @@ -952,12 +1169,13 @@ public class StructureChooser extends GStructureChooser implements * a unique sequence when more than one sequence selection is made. */ @Override - public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) + protected void populateCmbAssociateSeqOptions( + JComboBox cmb_assSeq, + JLabel lbl_associateSeq) { cmb_assSeq.removeAllItems(); - cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-", - null)); + cmb_assSeq.addItem( + new AssociateSeqOptions("-Select Associated Seq-", null)); lbl_associateSeq.setVisible(false); if (selectedSequences.length > 1) { @@ -976,17 +1194,12 @@ public class StructureChooser extends GStructureChooser implements } } - public boolean isStructuresDiscovered() + protected boolean isStructuresDiscovered() { return discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() - { - return discoveredStructuresSet; - } - @Override protected void txt_search_ActionPerformed() { @@ -1002,7 +1215,7 @@ public class StructureChooser extends GStructureChooser implements 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); @@ -1036,7 +1249,7 @@ public class StructureChooser extends GStructureChooser implements } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) { @@ -1046,8 +1259,9 @@ public class StructureChooser extends GStructureChooser implements public void run() { fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); } }); refreshThread.start(); @@ -1056,13 +1270,14 @@ public class StructureChooser extends GStructureChooser implements public class PDBEntryTableModel extends AbstractTableModel { - String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", + "File" }; private List pdbEntries; public PDBEntryTableModel(List pdbEntries) { - this.pdbEntries = new ArrayList(pdbEntries); + this.pdbEntries = new ArrayList<>(pdbEntries); } @Override @@ -1103,8 +1318,8 @@ public class StructureChooser extends GStructureChooser implements value = entry.getPdbEntry(); break; case 2: - value = entry.getPdbEntry().getChainCode() == null ? "_" : entry - .getPdbEntry().getChainCode(); + value = entry.getPdbEntry().getChainCode() == null ? "_" + : entry.getPdbEntry().getChainCode(); break; case 3: value = entry.getPdbEntry().getType(); @@ -1172,4 +1387,9 @@ public class StructureChooser extends GStructureChooser implements { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }