X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=4fb9e22c521b735fae3fa9852acba615e1f85cff;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=a8ce65971d1cef0164e2555711857ddbfa8566ac;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index a8ce659..4fb9e22 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -41,8 +41,10 @@ import javax.swing.JPopupMenu; 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.Console; import jalview.bin.Jalview; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; @@ -78,8 +80,12 @@ import jalview.ws.sifts.SiftsSettings; public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + protected static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + /** + * warn user if need to fetch more than this many uniprot records at once + */ + private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20; private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -110,7 +116,7 @@ public class StructureChooser extends GStructureChooser List seqsWithoutSourceDBRef = null; - private static StructureViewer lastTargetedView = null; + protected static StructureViewer lastTargetedView = null; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) @@ -118,11 +124,13 @@ public class StructureChooser extends GStructureChooser // which FTS engine to use data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); initDialog(); + this.ap = ap; this.selectedSequence = selectedSeq; this.selectedSequences = selectedSeqs; this.progressIndicator = (ap == null) ? null : ap.alignFrame; init(); + } /** @@ -194,6 +202,7 @@ public class StructureChooser extends GStructureChooser Executors.defaultThreadFactory().newThread(new Runnable() { + @Override public void run() { populateSeqsWithoutSourceDBRef(); @@ -212,6 +221,7 @@ public class StructureChooser extends GStructureChooser // ensure a filter option is in force for search populateFilterComboBox(true, cachedPDBExists); + // looks for any existing structures already loaded // for the sequences (the cached ones) // then queries the StructureChooserQuerySource to @@ -240,7 +250,9 @@ public class StructureChooser extends GStructureChooser /** * raises dialog for Uniprot fetch followed by 3D beacons search - * @param ignoreGui - when true, don't ask, just fetch + * + * @param ignoreGui + * - when true, don't ask, just fetch */ public void promptForTDBFetch(boolean ignoreGui) { @@ -254,24 +266,34 @@ public class StructureChooser extends GStructureChooser { mainFrame.setEnabled(false); cmb_filterOption.setEnabled(false); - progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId); + progressBar.setProgressBar( + MessageManager.getString("status.searching_3d_beacons"), + progressId); + btn_queryTDB.setEnabled(false); // TODO: warn if no accessions discovered populateSeqsWithoutSourceDBRef(); // redo initial discovery - this time with 3d beacons // Executors. - previousWantedFields=null; - lastSelected=(FilterOption) cmb_filterOption.getSelectedItem(); + previousWantedFields = null; + lastSelected = (FilterOption) cmb_filterOption.getSelectedItem(); cmb_filterOption.setSelectedItem(null); cachedPDBExists=false; // reset to initial initialStructureDiscovery(); if (!isStructuresDiscovered()) { - progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId); - btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons")); + progressBar.setProgressBar(MessageManager.getString( + "status.no_structures_discovered_from_3d_beacons"), + progressId); + btn_queryTDB.setToolTipText(MessageManager.getString( + "status.no_structures_discovered_from_3d_beacons")); btn_queryTDB.setEnabled(false); - } else { + pnl_queryTDB.setVisible(false); + } + else + { cmb_filterOption.setSelectedIndex(0); // select 'best' btn_queryTDB.setVisible(false); + pnl_queryTDB.setVisible(false); progressBar.setProgressBar(null, progressId); } mainFrame.setEnabled(true); @@ -299,6 +321,7 @@ public class StructureChooser extends GStructureChooser @Override public void run() { + btn_queryTDB.setEnabled(false); populateSeqsWithoutSourceDBRef(); final int y = seqsWithoutSourceDBRef.size(); @@ -312,28 +335,38 @@ public class StructureChooser extends GStructureChooser dbRefFetcher.addListener(afterDbRefFetch); // ideally this would also gracefully run with callbacks dbRefFetcher.fetchDBRefs(true); - } else { + } + else + { // call finished action directly afterDbRefFetch.finished(); } } }; - final Runnable revertview = new Runnable() { - public void run() { - if (lastSelected!=null) { + final Runnable revertview = new Runnable() + { + @Override + public void run() + { + if (lastSelected != null) + { cmb_filterOption.setSelectedItem(lastSelected); } }; }; - if (ignoreGui) + int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD", + THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); + Console.debug("Using Uniprot fetch threshold of " + threshold); + if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) { Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start(); return; } // need cancel and no to result in the discoverPDB action - mocked is // 'cancel' TODO: mock should be OK - JvOptionPane.newOptionDialog(this) + StructureChooser thisSC = this; + JvOptionPane.newOptionDialog(thisSC.getFrame()) .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs) .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) @@ -348,7 +381,7 @@ public class StructureChooser extends GStructureChooser null, new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }, - MessageManager.getString("action.ok")); + MessageManager.getString("action.ok"), false); } /** @@ -431,10 +464,13 @@ public class StructureChooser extends GStructureChooser discoveredStructuresSet = new LinkedHashSet<>(); HashSet errors = new HashSet<>(); + FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); + for (SequenceI seq : selectedSequences) { + FTSRestResponse resultList; try { @@ -468,6 +504,7 @@ public class StructureChooser extends GStructureChooser { getResultTable() .setModel(data.getTableModel(discoveredStructuresSet)); + noOfStructuresFound = discoveredStructuresSet.size(); lastDiscoveredStructuresSet = discoveredStructuresSet; mainFrame.setTitle(MessageManager.formatMessage( @@ -525,6 +562,7 @@ public class StructureChooser extends GStructureChooser { Thread filterThread = new Thread(new Runnable() { + @Override public void run() { @@ -537,12 +575,14 @@ public class StructureChooser extends GStructureChooser for (SequenceI seq : selectedSequences) { + FTSRestResponse resultList; try { resultList = data.selectFirstRankedQuery(seq, discoveredStructuresSet, wantedFields, fieldToFilterBy, !chk_invertFilter.isSelected()); + } catch (Exception e) { e.printStackTrace(); @@ -613,7 +653,7 @@ public class StructureChooser extends GStructureChooser // StructureChooser // works jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle( MessageManager.formatMessage("label.select_pdb_file_for", @@ -626,7 +666,7 @@ public class StructureChooser extends GStructureChooser if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); + Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); validateSelections(); } } @@ -648,11 +688,11 @@ public class StructureChooser extends GStructureChooser protected void populateFilterComboBox(boolean haveData, boolean cachedPDBExist, FilterOption lastSel) { + /* * temporarily suspend the change listener behaviour */ cmb_filterOption.removeItemListener(this); - int selSet = -1; cmb_filterOption.removeAllItems(); if (haveData) @@ -672,6 +712,7 @@ public class StructureChooser extends GStructureChooser cmb_filterOption.addItem(filter); } } + cmb_filterOption.addItem( new FilterOption(MessageManager.getString("label.enter_pdb_id"), "-", VIEWS_ENTER_ID, false, null)); @@ -681,6 +722,7 @@ public class StructureChooser extends GStructureChooser if (canQueryTDB && notQueriedTDBYet) { btn_queryTDB.setVisible(true); + pnl_queryTDB.setVisible(true); } if (cachedPDBExist) @@ -694,7 +736,6 @@ public class StructureChooser extends GStructureChooser cmb_filterOption.setSelectedItem(cachedOption); } } - if (selSet > -1) { cmb_filterOption.setSelectedIndex(selSet); @@ -718,6 +759,7 @@ public class StructureChooser extends GStructureChooser // otherwise, record selection // and update the layout and dialog accordingly lastSelected = selectedFilterOpt; + layout_switchableViews.show(pnl_switchableViews, selectedFilterOpt.getView()); String filterTitle = mainFrame.getTitle(); @@ -814,26 +856,31 @@ public class StructureChooser extends GStructureChooser FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); String currentView = selectedFilterOpt.getView(); - - if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource) + if (currentView == VIEWS_FILTER + && data instanceof ThreeDBStructureChooserQuerySource) { - - TDB_FTSData row=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet); - String pageUrl = row.getModelViewUrl(); + TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data) + .getFTSDataFor(getResultTable(), selectedRow, + discoveredStructuresSet); + String pageUrl = row.getModelViewUrl(); JPopupMenu popup = new JPopupMenu("3D Beacons"); JMenuItem viewUrl = new JMenuItem("View model web page"); - viewUrl.addActionListener( - new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) - { - Desktop.showUrl(pageUrl); - } - } - ); + viewUrl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(pageUrl); + } + }); popup.add(viewUrl); - SwingUtilities.invokeLater(new Runnable() { - public void run() { popup.show(getResultTable(), x, y); } + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + popup.show(getResultTable(), x, y); + } }); return true; } @@ -911,7 +958,6 @@ public class StructureChooser extends GStructureChooser { validateSelections(); } - private FilterOption lastSelected=null; /** * Handles the state change event for the 'filter' combo-box and 'invert' @@ -972,6 +1018,7 @@ public class StructureChooser extends GStructureChooser } return found; } + /** * Handles the 'New View' action */ @@ -1000,7 +1047,8 @@ public class StructureChooser extends GStructureChooser { final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - + final StructureViewer theViewer = getTargetedStructureViewer(ssm); + boolean superimpose = chk_superpose.isSelected(); final int preferredHeight = pnl_filter.getHeight(); Runnable viewStruc = new Runnable() @@ -1024,8 +1072,8 @@ public class StructureChooser extends GStructureChooser SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + selectedSeqs, superimpose, theViewer, progressBar); } else if (currentView == VIEWS_LOCAL_PDB) { @@ -1041,6 +1089,7 @@ public class StructureChooser extends GStructureChooser { PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb .getModel()).getPDBEntryAt(row).getPdbEntry(); + pdbEntriesToView[count++] = pdbEntry; SequenceI selectedSeq = (SequenceI) tbl_local_pdb .getValueAt(row, refSeqColIndex); @@ -1048,8 +1097,8 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + selectedSeqs, superimpose, theViewer, progressBar); } else if (currentView == VIEWS_ENTER_ID) { @@ -1078,9 +1127,10 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, - new SequenceI[] - { selectedSequence }); + sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, + new SequenceI[] + { selectedSequence }, superimpose, theViewer, + progressBar); } else if (currentView == VIEWS_FROM_FILE) { @@ -1090,14 +1140,12 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.getInstance()); - - sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, - ap, new SequenceI[] - { selectedSequence }); + PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true); + + sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry }, + new SequenceI[] { selectedSequence }, superimpose, theViewer, + progressBar); } SwingUtilities.invokeLater(new Runnable() { @@ -1144,98 +1192,6 @@ public class StructureChooser extends GStructureChooser } /** - * 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 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<>(); - 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().isEmpty()) - { - 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 = seqsWithoutSourceDBRef - .toArray(new SequenceI[y]); - DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); - dbRefFetcher.fetchDBRefs(true); - - setProgressBar("Fetch complete.", progressId); // todo i18n - } - } - if (pdbEntriesToView.length > 1) - { - 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); - theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } - setProgressBar(null, progressId); - // remember the last viewer we used... - lastTargetedView = theViewer; - return theViewer; - } - - /** * Populates the combo-box used in associating manually fetched structures to * a unique sequence when more than one sequence selection is made. */ @@ -1335,6 +1291,7 @@ public class StructureChooser extends GStructureChooser { if (selectedSequences != null) { + lbl_loading.setVisible(true); Thread refreshThread = new Thread(new Runnable() { @Override @@ -1342,9 +1299,11 @@ public class StructureChooser extends GStructureChooser { fetchStructuresMetaData(); // populateFilterComboBox(true, cachedPDBExists); + filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); + lbl_loading.setVisible(false); } }); refreshThread.start(); @@ -1513,8 +1472,9 @@ public class StructureChooser extends GStructureChooser * * @return true if the 3D-Beacons query button will/has been displayed */ - public boolean isCanQueryTDB() { - return canQueryTDB; + public boolean isCanQueryTDB() + { + return canQueryTDB; } public boolean isNotQueriedTDBYet()