X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=9c4f6c8a344da84879d98232331eddfa94b5df84;hb=60541afc96ff3a4f5b79b78009922f373cbc29c3;hp=cd1cfc37fa79a5487548d5a9f2476fec86d72ccc;hpb=f7775ab8e5622ab365c1e178c79ec78a707aad1f;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index cd1cfc3..9c4f6c8 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -36,11 +36,8 @@ 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; @@ -69,25 +66,27 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private static int MAX_QLENGTH = 7820; + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; - private SequenceI selectedSequence; + private static final int MAX_QLENGTH = 7820; - private SequenceI[] selectedSequences; + protected SequenceI selectedSequence; + + public SequenceI[] selectedSequences; private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + protected Collection discoveredStructuresSet; - private FTSRestRequest lastPdbRequest; + protected FTSRestRequest lastPdbRequest; - private FTSRestClientI pdbRestCleint; + protected FTSRestClientI pdbRestClient; - private String selectedPdbFileName; + protected String selectedPdbFileName; - private boolean isValidPBDEntry; + protected boolean isValidPBDEntry; - private boolean cachedPDBExists; + protected boolean cachedPDBExists; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) @@ -102,14 +101,14 @@ 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)); + chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); // ensure a filter option is in force for search populateFilterComboBox(true, cachedPDBExists); @@ -137,21 +136,29 @@ public class StructureChooser extends GStructureChooser discoverPDBStructuresThread.start(); } - private void discoverStructureViews() + /** + * 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. + */ + protected void discoverStructureViews() { - if (Desktop.instance != null) + Desktop desktop = Desktop.getInstance(); + if (desktop != null) { targetView.removeAllItems(); - if (lastTargetedView != null && !lastTargetedView.isVisible()) + if (desktop.lastTargetedView != null + && !desktop.lastTargetedView.isVisible()) { - lastTargetedView = null; + desktop.lastTargetedView = null; } int linkedViewsAt = 0; - for (StructureViewerBase view : Desktop.instance + for (StructureViewerBase view : desktop .getStructureViewers(null, null)) { - StructureViewer viewHandler = (lastTargetedView != null - && lastTargetedView.sview == view) ? lastTargetedView + StructureViewer viewHandler = (desktop.lastTargetedView != null + && desktop.lastTargetedView.sview == view) + ? desktop.lastTargetedView : StructureViewer.reconfigure(view); if (view.isLinkedWith(ap)) @@ -164,22 +171,27 @@ public class StructureChooser extends GStructureChooser targetView.addItem(viewHandler); } } - targetView.setVisible(targetView.getItemCount() > 0); - btn_view.setVisible(targetView.isVisible()); - if (targetView.isVisible()) { - // finally, restore last targeted view by default. - if (lastTargetedView != null) + + /* + * show option to Add to viewer if at least 1 viewer found + */ + targetView.setVisible(false); + if (targetView.getItemCount() > 0) + { + targetView.setVisible(true); + if (desktop.lastTargetedView != null) + { + targetView.setSelectedItem(desktop.lastTargetedView); + } + else { - targetView.setSelectedItem(lastTargetedView); - } else { targetView.setSelectedIndex(0); } } + btn_add.setVisible(targetView.isVisible()); } } - private static StructureViewer lastTargetedView = null; - /** * Updates the progress indicator with the specified message * @@ -188,7 +200,7 @@ 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) { @@ -200,10 +212,10 @@ 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(); @@ -225,7 +237,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -271,7 +283,7 @@ public class StructureChooser extends GStructureChooser } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) @@ -302,7 +314,7 @@ 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; @@ -323,10 +335,12 @@ public class StructureChooser extends GStructureChooser } } - 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) { @@ -404,7 +418,7 @@ 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"; @@ -427,7 +441,7 @@ 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; @@ -439,7 +453,7 @@ 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() { @@ -447,7 +461,7 @@ 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(); @@ -483,7 +497,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -549,8 +563,10 @@ 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()); @@ -650,28 +666,37 @@ 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) @@ -682,12 +707,21 @@ 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(); @@ -713,7 +747,7 @@ 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); } @@ -728,7 +762,7 @@ 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(); @@ -739,7 +773,7 @@ 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); } } @@ -751,7 +785,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void cmbAssSeqStateChanged() + protected void cmbAssSeqStateChanged() { validateSelections(); } @@ -815,21 +849,22 @@ public class StructureChooser extends GStructureChooser } return found; } + /** - * Handles action event for btn_ok + * Handles the 'New View' action */ @Override - public void newview_ActionPerformed() + protected void newView_ActionPerformed() { targetView.setSelectedItem(null); showStructures(false); } /** - * Handles action event for btn_ok + * Handles the 'Add to existing viewer' action */ @Override - public void view_ActionPerformed() + protected void add_ActionPerformed() { showStructures(false); } @@ -837,13 +872,11 @@ public class StructureChooser extends GStructureChooser /** * structure viewer opened by this dialog, or null */ - private StructureViewer sViewer = null; + protected StructureViewer sViewer = null; public void showStructures(boolean waitUntilFinished) { - final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - final int preferredHeight = pnl_filter.getHeight(); Runnable viewStruc = new Runnable() @@ -892,7 +925,7 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ap, pdbEntriesToView, selectedSeqs); } else if (currentView == VIEWS_LOCAL_PDB) @@ -916,7 +949,7 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ap, pdbEntriesToView, selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) @@ -946,7 +979,7 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ap, pdbEntriesToView, new SequenceI[] { selectedSequence }); } @@ -958,14 +991,13 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() + PDBEntry fileEntry = AssociatePdbFileWithSeq .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); + DataSourceType.FILE, selectedSequence, true); sViewer = launchStructureViewer( - ssm, new PDBEntry[] - { fileEntry }, ap, + ap, new PDBEntry[] + { fileEntry }, new SequenceI[] { selectedSequence }); } @@ -999,7 +1031,7 @@ public class StructureChooser extends GStructureChooser } } - private PDBEntry getFindEntry(String id, Vector pdbEntries) + protected PDBEntry getFindEntry(String id, Vector pdbEntries) { Objects.requireNonNull(id); Objects.requireNonNull(pdbEntries); @@ -1015,103 +1047,40 @@ public class StructureChooser extends GStructureChooser } /** - * @param ssm - * @return targetted structure view (new or existing) configured according to - * superpose checkbox + * Answers a structure viewer (new or existing) configured to superimpose + * added structures or not according to the user's choice + * + * @return */ - public StructureViewer getTargetedStructureViewer( - StructureSelectionManager ssm) + StructureViewer getTargetedStructureViewer() { - Object _sv = targetView.getSelectedItem(); - StructureViewer sv; - if (_sv == null) - { - sv = new StructureViewer(ssm); - } else { - sv = (StructureViewer) _sv; - } - sv.setSuperpose(chk_superpose.isSelected()); - return sv; - } - 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 = getTargetedStructureViewer(ssm); - sViewer.setSuperpose(chk_superpose.isSelected()); - - setProgressBar(null, progressId); - 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(); - 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; - } + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + Object sv = (targetView == null ? null : targetView.getSelectedItem()); - DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); - dbRefFetcher.fetchDBRefs(true); + return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; + } - setProgressBar("Fetch complete.", progressId); // todo i18n - } - } - if (pdbEntriesToView.length > 1) - { - setProgressBar(MessageManager.getString( - "status.fetching_3d_structures_for_selected_entries"), - progressId); - sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); - } - else - { - setProgressBar(MessageManager.formatMessage( - "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId()),progressId); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } - setProgressBar(null, progressId); - // remember the last viewer we used... - lastTargetedView = sViewer; - return sViewer; + /** + * Adds PDB structures to a new or existing structure viewer + * + * @param ap + * @param pdbEntriesToView + * @param sequences + * @param superimpose + * @return viewer + */ + protected StructureViewer launchStructureViewer( + AlignmentPanel ap, PDBEntry[] pdbEntriesToView, + SequenceI[] selectedSeqs) + { + boolean superimpose = chk_superpose.isSelected(); + /* + * remember user's choice of superimpose or not + */ + Cache.setProperty(AUTOSUPERIMPOSE, + Boolean.valueOf(superimpose).toString()); + return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs, + superimpose, getTargetedStructureViewer(), progressBar); } /** @@ -1119,7 +1088,7 @@ 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) { @@ -1144,30 +1113,33 @@ 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<>(); @@ -1178,12 +1150,12 @@ 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()); @@ -1202,9 +1174,10 @@ public class StructureChooser extends GStructureChooser } }.start(); } + } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) { @@ -1328,7 +1301,10 @@ public class StructureChooser extends GStructureChooser @Override public void setProgressBar(String message, long id) { - progressBar.setProgressBar(message, id); + if (progressBar != null) + { + progressBar.setProgressBar(message, id); + } } @Override