X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=97dfa861e11d0d5f64bada916f506703b80404a6;hb=b87512d6e28a2a93ea2f08dcfbee320856c5c8de;hp=5de3082d1a6f66f163c38cb82ec14014457b9781;hpb=2cf5d7bb20203f70d6839b579a7a205f49a46f1d;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 5de3082..97dfa86 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -22,6 +22,7 @@ package jalview.gui; import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; @@ -55,6 +56,7 @@ 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; /** @@ -67,6 +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; @@ -79,7 +83,7 @@ public class StructureChooser extends GStructureChooser private FTSRestRequest lastPdbRequest; - private FTSRestClientI pdbRestCleint; + private FTSRestClientI pdbRestClient; private String selectedPdbFileName; @@ -87,6 +91,8 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; + private static StructureViewer lastTargetedView = null; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -100,13 +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() @@ -124,6 +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(); @@ -133,6 +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.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 @@ -140,7 +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) { @@ -152,10 +214,10 @@ 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(); @@ -177,7 +239,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -223,7 +285,7 @@ public class StructureChooser extends GStructureChooser } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) @@ -254,12 +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) @@ -268,17 +335,20 @@ 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) { @@ -293,9 +363,13 @@ 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 { @@ -356,7 +430,7 @@ 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"; @@ -379,7 +453,7 @@ 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; @@ -391,7 +465,7 @@ 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() { @@ -399,7 +473,7 @@ 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(); @@ -435,7 +509,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -501,8 +575,10 @@ 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()); @@ -602,28 +678,37 @@ 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) @@ -634,12 +719,21 @@ 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(); @@ -665,7 +759,7 @@ 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); } @@ -680,7 +774,7 @@ 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(); @@ -691,7 +785,7 @@ 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); } } @@ -703,7 +797,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void cmbAssSeqStateChanged() + protected void cmbAssSeqStateChanged() { validateSelections(); } @@ -767,11 +861,22 @@ public class StructureChooser extends GStructureChooser } return found; } + /** - * Handles action event for btn_ok + * 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); } @@ -903,7 +1008,7 @@ public class StructureChooser extends GStructureChooser PDBEntry fileEntry = new AssociatePdbFileWithSeq() .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE, selectedSequence, true, - Desktop.instance); + Desktop.getInstance()); sViewer = launchStructureViewer( ssm, new PDBEntry[] @@ -911,8 +1016,15 @@ public class StructureChooser extends GStructureChooser new SequenceI[] { selectedSequence }); } - closeAction(preferredHeight); - mainFrame.dispose(); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + closeAction(preferredHeight); + mainFrame.dispose(); + } + }); } }; Thread runner = new Thread(viewStruc); @@ -949,6 +1061,30 @@ public class StructureChooser extends GStructureChooser return foundEntry; } + /** + * 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, @@ -957,9 +1093,17 @@ public class StructureChooser extends GStructureChooser 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<>(); @@ -984,7 +1128,7 @@ public class StructureChooser extends GStructureChooser } } } - if (seq.getPrimaryDBRefs().size() == 0) + if (seq.getPrimaryDBRefs().isEmpty()) { seqsWithoutSourceDBRef.add(seq); continue; @@ -996,13 +1140,8 @@ 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); @@ -1014,17 +1153,19 @@ public class StructureChooser extends GStructureChooser setProgressBar(MessageManager.getString( "status.fetching_3d_structures_for_selected_entries"), progressId); - sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + 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); - return sViewer; + // remember the last viewer we used... + lastTargetedView = theViewer; + return theViewer; } /** @@ -1032,7 +1173,7 @@ 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) { @@ -1057,30 +1198,32 @@ 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() { + String text = txt_search.getText().trim(); + if (text.length() >= PDB_ID_MIN) new Thread() { - @Override + + @Override public void run() { errorWarning.setLength(0); isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + if (text.length() > 0) { - String searchTerm = txt_search.getText().toLowerCase(); + String searchTerm = text.toLowerCase(); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); List wantedFields = new ArrayList<>(); @@ -1091,12 +1234,12 @@ public class StructureChooser extends GStructureChooser pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = PDBFTSRestClient.getInstance(); - wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + pdbRestClient = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { errorWarning.append(e.getMessage()); @@ -1117,7 +1260,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) {