X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=0709dbb434318d4808e4c8ca91244253cfbba31a;hb=4ffa5161216adc501b127408f1596f507b9c7b92;hp=20f4a49a3492dca874b489d470e2e860d7d219df;hpb=75db7abd6c89a9465861dc7604faca4893c52101;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 20f4a49..0709dbb 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; /** @@ -65,6 +69,8 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -85,6 +91,8 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; + private static StructureViewer lastTargetedView = null; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -98,13 +106,15 @@ 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 +132,7 @@ 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 +142,59 @@ 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.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 @@ -138,7 +202,7 @@ 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) { @@ -150,7 +214,7 @@ 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(); @@ -221,7 +285,7 @@ public class StructureChooser extends GStructureChooser } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) @@ -252,12 +316,17 @@ 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<>(); + + /* + * note PDBs as DBRefEntry so they are not duplicated in query + */ + Set pdbids = new HashSet<>(); if (seq.getAllPDBEntries() != null && queryBuilder.length() < MAX_QLENGTH) @@ -266,9 +335,10 @@ 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); } } } @@ -291,9 +361,13 @@ 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 +428,7 @@ 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 +451,7 @@ 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 +463,7 @@ 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() { @@ -499,7 +573,7 @@ public class StructureChooser extends GStructureChooser * 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")); @@ -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 @@ -535,25 +609,33 @@ 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); @@ -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(); } @@ -720,16 +820,76 @@ 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 - public void ok_ActionPerformed() + protected void newView_ActionPerformed() { + targetView.setSelectedItem(null); + showStructures(false); + } + + /** + * Handles the 'Add to existing viewer' action + */ + @Override + protected void add_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 +897,24 @@ 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 +935,8 @@ 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 +959,8 @@ 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 +989,7 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); } @@ -839,16 +1004,42 @@ public class StructureChooser extends GStructureChooser PDBEntry fileEntry = new AssociatePdbFileWithSeq() .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE, selectedSequence, true, - Desktop.instance); + Desktop.instance, true); - 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(); + } + }); + } + }; + 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) @@ -866,16 +1057,49 @@ public class StructureChooser extends GStructureChooser 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) { long progressId = sequences.hashCode(); setProgressBar(MessageManager .getString("status.launching_3d_structure_viewer"), progressId); - final StructureViewer sViewer = new StructureViewer(ssm); - setProgressBar(null, 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<>(); @@ -900,7 +1124,7 @@ public class StructureChooser extends GStructureChooser } } } - if (seq.getPrimaryDBRefs().size() == 0) + if (seq.getPrimaryDBRefs().isEmpty()) { seqsWithoutSourceDBRef.add(seq); continue; @@ -912,13 +1136,8 @@ public class StructureChooser extends GStructureChooser setProgressBar(MessageManager.formatMessage( "status.fetching_dbrefs_for_sequences_without_valid_refs", y), progressId); - SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; - int x = 0; - for (SequenceI fSeq : seqsWithoutSourceDBRef) - { - seqWithoutSrcDBRef[x++] = fSeq; - } - + SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); @@ -927,25 +1146,22 @@ public class StructureChooser extends GStructureChooser } 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]); - - setProgressBar(MessageManager - .getString("status.fetching_3d_structures_for_selected_entries"), progressId); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", pdbEntriesToView[0].getId()),progressId); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } setProgressBar(null, progressId); + // remember the last viewer we used... + lastTargetedView = theViewer; + return theViewer; } /** @@ -953,7 +1169,7 @@ 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) { @@ -978,17 +1194,12 @@ public class StructureChooser extends GStructureChooser } } - public boolean isStructuresDiscovered() + protected boolean isStructuresDiscovered() { return discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() - { - return discoveredStructuresSet; - } - @Override protected void txt_search_ActionPerformed() { @@ -1038,7 +1249,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) { @@ -1176,4 +1387,9 @@ public class StructureChooser extends GStructureChooser { return progressBar.operationInProgress(); } + + public JalviewStructureDisplayI getOpenedStructureViewer() + { + return sViewer == null ? null : sViewer.sview; + } }