X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5e4226ad816c90aa90be64debe734b92e31a1347;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=694b0639043d4309544a69e3a2959c3aa79c5c7e;hpb=752f89e5730d804d1982ce4a09ab0f9266dde03d;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 694b063..5e4226a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -37,12 +37,14 @@ import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuItem; +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; @@ -78,13 +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"; /** - * transient combo box choice for initiating 3db fetch + * warn user if need to fetch more than this many uniprot records at once */ - private static final String VIEWS_QUERYING_TDB = "QUERY_3DB"; - + private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20; private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -115,7 +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) @@ -172,7 +173,8 @@ public class StructureChooser extends GStructureChooser canQueryTDB = true; if (needCanonical) { - notQueriedTDBYet = false; + // triggers display of the 'Query TDB' button + notQueriedTDBYet = true; } } }; @@ -188,9 +190,19 @@ public class StructureChooser extends GStructureChooser } chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); + btn_queryTDB.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + promptForTDBFetch(false); + } + }); Executors.defaultThreadFactory().newThread(new Runnable() { + @Override public void run() { populateSeqsWithoutSourceDBRef(); @@ -236,7 +248,13 @@ public class StructureChooser extends GStructureChooser updateCurrentView(); } - private void promptForTDBFetch() + /** + * raises dialog for Uniprot fetch followed by 3D beacons search + * + * @param ignoreGui + * - when true, don't ask, just fetch + */ + public void promptForTDBFetch(boolean ignoreGui) { final long progressId = System.currentTimeMillis(); @@ -246,13 +264,40 @@ public class StructureChooser extends GStructureChooser @Override public void run() { + mainFrame.setEnabled(false); + cmb_filterOption.setEnabled(false); + 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; - + 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")); + btn_queryTDB.setEnabled(false); + 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); + cmb_filterOption.setEnabled(true); } }; @@ -276,6 +321,7 @@ public class StructureChooser extends GStructureChooser @Override public void run() { + btn_queryTDB.setEnabled(false); populateSeqsWithoutSourceDBRef(); final int y = seqsWithoutSourceDBRef.size(); @@ -289,23 +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); } }; }; + 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' - JvOptionPane.newOptionDialog(this) + // 'cancel' TODO: mock should be OK + StructureChooser thisSC = this; + JvOptionPane.newOptionDialog(thisSC.getFrame()) .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs) .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) @@ -320,7 +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); } /** @@ -330,7 +391,7 @@ public class StructureChooser extends GStructureChooser */ private void discoverStructureViews() { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { targetView.removeAllItems(); if (lastTargetedView != null && !lastTargetedView.isVisible()) @@ -338,7 +399,7 @@ public class StructureChooser extends GStructureChooser lastTargetedView = null; } int linkedViewsAt = 0; - for (StructureViewerBase view : Desktop.instance + for (StructureViewerBase view : Desktop.getInstance() .getStructureViewers(null, null)) { StructureViewer viewHandler = (lastTargetedView != null @@ -592,7 +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", @@ -605,7 +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(); } } @@ -660,10 +721,8 @@ public class StructureChooser extends GStructureChooser "-", VIEWS_FROM_FILE, false, null)); if (canQueryTDB && notQueriedTDBYet) { - FilterOption queryTDBOption = new FilterOption( - MessageManager.getString("label.search_3dbeacons"), "-", - VIEWS_QUERYING_TDB, false, null); - cmb_filterOption.addItem(queryTDBOption); + btn_queryTDB.setVisible(true); + pnl_queryTDB.setVisible(true); } if (cachedPDBExist) @@ -692,12 +751,6 @@ public class StructureChooser extends GStructureChooser FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - // first check if we need to rebuild dialog - if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB) - { - promptForTDBFetch(); - return; - } if (lastSelected == selectedFilterOpt) { // don't need to do anything, probably @@ -798,38 +851,36 @@ public class StructureChooser extends GStructureChooser } @Override - protected boolean showPopupFor(int selectedRow) + protected boolean showPopupFor(int selectedRow, int x, int y) { 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=null; - - int i=1; - for (FTSData el:discoveredStructuresSet) { - if (i==selectedRow) { - row = (TDB_FTSData) el; - break; - } - i++; - } - String pageUrl = row.getModelViewUrl(); - JMenu popup = new JMenu("3D Beacons"); + 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.setVisible(true); } + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + popup.show(getResultTable(), x, y); + } }); return true; } @@ -996,7 +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() @@ -1020,8 +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) { @@ -1045,8 +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) { @@ -1075,9 +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) { @@ -1087,14 +1140,12 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); - - 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() { @@ -1141,98 +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. */ @@ -1332,6 +1291,7 @@ public class StructureChooser extends GStructureChooser { if (selectedSequences != null) { + lbl_loading.setVisible(true); Thread refreshThread = new Thread(new Runnable() { @Override @@ -1343,6 +1303,7 @@ public class StructureChooser extends GStructureChooser filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); + lbl_loading.setVisible(false); } }); refreshThread.start(); @@ -1465,6 +1426,18 @@ public class StructureChooser extends GStructureChooser { progressBar.setProgressBar(message, id); } + + @Override + public void addProgressBar(long id, String message) + { + progressBar.addProgressBar(id, message); + } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(long id, IProgressIndicatorHandler handler) @@ -1501,4 +1474,17 @@ public class StructureChooser extends GStructureChooser && mainFrame.isVisible() && cmb_filterOption.getSelectedItem() != null; } + /** + * + * @return true if the 3D-Beacons query button will/has been displayed + */ + public boolean isCanQueryTDB() + { + return canQueryTDB; + } + + public boolean isNotQueriedTDBYet() + { + return notQueriedTDBYet; + } }