X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=97b0cfb9a3d17cd5b658609452ffa6defc64d132;hb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;hp=da10e3f7a786cbae94500dc4d6579979008b3d2a;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index da10e3f..97b0cfb 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,25 +21,6 @@ package jalview.gui; -import jalview.bin.Jalview; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.fts.api.FTSData; -import jalview.fts.api.FTSDataColumnI; -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; -import jalview.util.MessageManager; -import jalview.ws.DBRefFetcher; -import jalview.ws.sifts.SiftsSettings; - import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; @@ -53,8 +34,27 @@ 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; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +import jalview.fts.api.FTSDataColumnI; +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.util.MessageManager; + /** * Provides the behaviors for the Structure chooser Panel * @@ -65,6 +65,8 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { + static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -77,7 +79,7 @@ public class StructureChooser extends GStructureChooser private FTSRestRequest lastPdbRequest; - private FTSRestClientI pdbRestCleint; + private FTSRestClientI pdbRestClient; private String selectedPdbFileName; @@ -85,6 +87,8 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; + static StructureViewer lastTargetedView = null; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -98,13 +102,15 @@ public class StructureChooser extends GStructureChooser /** * 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() @@ -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(); @@ -131,6 +138,58 @@ public class StructureChooser extends GStructureChooser } /** + * 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.getInstance() != null) + { + targetView.removeAllItems(); + if (lastTargetedView != null && !lastTargetedView.isVisible()) + { + lastTargetedView = null; + } + int linkedViewsAt = 0; + for (StructureViewerBase view : Desktop.getInstance() + .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 @@ -138,7 +197,7 @@ public class StructureChooser extends GStructureChooser * @param id * unique handle for this indicator */ - public void updateProgressIndicator(String message, long id) + protected void updateProgressIndicator(String message, long id) { if (progressIndicator != null) { @@ -150,15 +209,15 @@ public class StructureChooser extends GStructureChooser * 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(); + pdbRestClient = 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(); @@ -175,7 +234,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -221,9 +280,9 @@ public class StructureChooser extends GStructureChooser } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { - ArrayList entries = new ArrayList(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null @@ -252,12 +311,17 @@ public class StructureChooser extends GStructureChooser * @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 && queryBuilder.length() < MAX_QLENGTH) @@ -266,17 +330,20 @@ public class StructureChooser extends GStructureChooser { 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; + pdbids.add(id); } } } - if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) + List refs = seq.getDBRefs(); + if (refs != null && refs.size() != 0) { - for (DBRefEntry dbRef : seq.getDBRefs()) + for (int ib = 0, nb = refs.size(); ib < nb; ib++) { + DBRefEntry dbRef = refs.get(ib); if (isValidSeqName(getDBRefId(dbRef)) && queryBuilder.length() < MAX_QLENGTH) { @@ -291,9 +358,13 @@ public class StructureChooser extends GStructureChooser 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 { @@ -354,7 +425,7 @@ public class StructureChooser extends GStructureChooser * @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"; @@ -377,7 +448,7 @@ public class StructureChooser extends GStructureChooser return true; } - public static String getDBRefId(DBRefEntry dbRef) + static String getDBRefId(DBRefEntry dbRef) { String ref = dbRef.getAccessionId().replaceAll("GO:", ""); return ref; @@ -389,7 +460,7 @@ public class StructureChooser extends GStructureChooser * @param fieldToFilterBy * the field to filter by */ - public void filterResultSet(final String fieldToFilterBy) + void filterResultSet(final String fieldToFilterBy) { Thread filterThread = new Thread(new Runnable() { @@ -397,12 +468,12 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); + pdbRestClient = PDBFTSRestClient.getInstance(); 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) { @@ -433,7 +504,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -453,7 +524,7 @@ 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 @@ -499,8 +570,11 @@ public class StructureChooser extends GStructureChooser * Handles action event for btn_pdbFromFile */ @Override - public void pdbFromFile_actionPerformed() + protected void pdbFromFile_actionPerformed() { + // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and + // StructureChooser + // works jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); @@ -525,7 +599,7 @@ public class StructureChooser extends GStructureChooser * structures */ protected void populateFilterComboBox(boolean haveData, - boolean cachedPDBExists) + boolean cachedPDBExist) { /* * temporarily suspend the change listener behaviour @@ -535,26 +609,34 @@ 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", - "-", VIEWS_LOCAL_PDB, false); + FilterOption cachedOption = new FilterOption( + MessageManager.getString("label.cached_structures"), "-", + VIEWS_LOCAL_PDB, false); cmb_filterOption.addItem(cachedOption); cmb_filterOption.setSelectedItem(cachedOption); } @@ -592,28 +674,37 @@ public class StructureChooser extends GStructureChooser } /** - * 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) @@ -624,12 +715,21 @@ public class StructureChooser extends GStructureChooser { 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(); @@ -655,7 +755,7 @@ public class StructureChooser extends GStructureChooser txt_search.setEnabled(true); if (isValidPBDEntry) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } @@ -670,7 +770,7 @@ public class StructureChooser extends GStructureChooser /** * Validates inputs for the manual PDB file selection options */ - public void validateAssociationFromFile() + protected void validateAssociationFromFile() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); @@ -681,7 +781,7 @@ public class StructureChooser extends GStructureChooser btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_fromFileStatus.setIcon(goodImage); } } @@ -693,7 +793,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void cmbAssSeqStateChanged() + protected void cmbAssSeqStateChanged() { validateSelections(); } @@ -720,17 +820,77 @@ public class StructureChooser extends GStructureChooser } /** - * 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() + { + showStructures(false); + } + + /** + * structure viewer opened by this dialog, or null + */ + private StructureViewer sViewer = null; + + public void showStructures(boolean waitUntilFinished) { - final long progressSessionId = System.currentTimeMillis(); - final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + final int preferredHeight = pnl_filter.getHeight(); - ssm.setProgressIndicator(this); - ssm.setProgressSessionId(progressSessionId); - new Thread(new Runnable() + + final StructureViewer theViewer = getTargetedStructureViewer(); + boolean superimpose = chk_superpose.isSelected(); + + Runnable viewStruc = new Runnable() { @Override public void run() @@ -738,22 +898,24 @@ 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 = restable.getColumn("Ref Sequence") .getModelIndex(); - int refSeqColIndex = getResultTable().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() - .getValueAt(row, pdbIdColIndex).toString(); - SequenceI selectedSeq = (SequenceI) getResultTable() - .getValueAt(row, refSeqColIndex); + String pdbIdStr = restable.getValueAt(row, pdbIdColIndex) + .toString(); + SequenceI selectedSeq = (SequenceI) restable.getValueAt(row, + refSeqColIndex); selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); if (pdbEntry == null) @@ -761,18 +923,18 @@ public class StructureChooser extends GStructureChooser pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } + if (pdbEntry == null) { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); + pdbEntry = new PDBEntry(pdbIdStr, null, "pdb"); selectedSeq.getDatasetSequence().addPDBId(pdbEntry); } pdbEntriesToView[count++] = pdbEntry; } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + selectedSeqs, superimpose, theViewer, progressBar); } else if (currentView == VIEWS_LOCAL_PDB) { @@ -783,7 +945,7 @@ 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 +957,8 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + selectedSeqs, superimpose, theViewer, progressBar); } else if (currentView == VIEWS_ENTER_ID) { @@ -805,7 +968,6 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - String pdbIdStr = txt_search.getText(); PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); if (pdbEntry == null) @@ -825,9 +987,10 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, new SequenceI[] - { selectedSequence }); + { selectedSequence }, superimpose, theViewer, + progressBar); } else if (currentView == VIEWS_FROM_FILE) { @@ -837,18 +1000,41 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); - - launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, + PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true); + sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry }, new SequenceI[] - { selectedSequence }); + { selectedSequence }, superimpose, theViewer, + progressBar); + } + 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) + { + } - closeAction(preferredHeight); } - }).start(); + } } private PDBEntry getFindEntry(String id, Vector pdbEntries) @@ -866,82 +1052,16 @@ public class StructureChooser extends GStructureChooser return foundEntry; } - private void launchStructureViewer(StructureSelectionManager ssm, - final PDBEntry[] pdbEntriesToView, - final AlignmentPanel alignPanel, SequenceI[] sequences) + /** + * 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() { - ssm.setProgressBar(MessageManager - .getString("status.launching_3d_structure_viewer")); - final StructureViewer sViewer = new StructureViewer(ssm); - - if (SiftsSettings.isMapWithSifts()) - { - 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 - // a known mapping between the PDBEntry and the sequence. - for (SequenceI seq : sequences) - { - PDBEntry pdbe = pdbEntriesToView[p++]; - if (pdbe != null && pdbe.getFile() != null) - { - StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); - if (smm != null && smm.length > 0) - { - for (StructureMapping sm : smm) - { - if (sm.getSequence() == seq) - { - continue; - } - } - } - } - if (seq.getPrimaryDBRefs().size() == 0) - { - seqsWithoutSourceDBRef.add(seq); - continue; - } - } - if (!seqsWithoutSourceDBRef.isEmpty()) - { - int y = seqsWithoutSourceDBRef.size(); - ssm.setProgressBar(null); - ssm.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; - } - DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); - dbRefFetcher.fetchDBRefs(true); - } - } - 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); - } - else - { - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( - "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId())); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } + return (StructureViewer) targetView.getSelectedItem(); } /** @@ -949,7 +1069,7 @@ public class StructureChooser extends GStructureChooser * a unique sequence when more than one sequence selection is made. */ @Override - public void populateCmbAssociateSeqOptions( + protected void populateCmbAssociateSeqOptions( JComboBox cmb_assSeq, JLabel lbl_associateSeq) { @@ -974,67 +1094,70 @@ public class StructureChooser extends GStructureChooser } } - public boolean isStructuresDiscovered() + protected boolean isStructuresDiscovered() { return discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() - { - return discoveredStructuresSet; - } + protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes + // this. + // Doing a search for "1" or "1c" is valuable? + // Those work but are enormously slow. @Override protected void txt_search_ActionPerformed() { - new Thread() - { - @Override - public void run() + String text = txt_search.getText().trim(); + if (text.length() >= PDB_ID_MIN) + new Thread() { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + + @Override + public void run() { - String searchTerm = txt_search.getText().toLowerCase(); - searchTerm = searchTerm.split(":")[0]; - // System.out.println(">>>>> search term : " + searchTerm); - List wantedFields = new ArrayList(); - FTSRestRequest pdbRequest = new FTSRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(pdb_id:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(searchTerm + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = PDBFTSRestClient.getInstance(); - wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); - FTSRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - errorWarning.append(e.getMessage()); - return; - } finally - { - validateSelections(); - } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) + errorWarning.setLength(0); + isValidPBDEntry = false; + if (text.length() > 0) { - isValidPBDEntry = true; + String searchTerm = text.toLowerCase(); + searchTerm = searchTerm.split(":")[0]; + // System.out.println(">>>>> search term : " + searchTerm); + List wantedFields = new ArrayList<>(); + FTSRestRequest pdbRequest = new FTSRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(pdb_id:"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setSearchTerm(searchTerm + ")"); + pdbRequest.setAssociatedSequence(selectedSequence); + pdbRestClient = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); + FTSRestResponse resultList; + try + { + resultList = pdbRestClient.executeRequest(pdbRequest); + } catch (Exception e) + { + errorWarning.append(e.getMessage()); + return; + } finally + { + validateSelections(); + } + if (resultList.getSearchSummary() != null + && resultList.getSearchSummary().size() > 0) + { + isValidPBDEntry = true; + } } + validateSelections(); } - validateSelections(); - } - }.start(); + }.start(); } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) { @@ -1062,7 +1185,7 @@ public class StructureChooser extends GStructureChooser public PDBEntryTableModel(List pdbEntries) { - this.pdbEntries = new ArrayList(pdbEntries); + this.pdbEntries = new ArrayList<>(pdbEntries); } @Override @@ -1160,6 +1283,12 @@ public class StructureChooser extends GStructureChooser { progressBar.setProgressBar(message, id); } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(long id, IProgressIndicatorHandler handler) @@ -1172,4 +1301,10 @@ public class StructureChooser extends GStructureChooser { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } + }