X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=9ff181b6f274e636785290f83c1dcd64cbee3d92;hp=9f9de6ea386372cea19dc89eb1f90b301c2c7250;hb=299d07a9554a3661d44395aa2c6bad9cecd10bf0;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7 diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 9f9de6e..9ff181b 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -21,25 +21,29 @@ package jalview.gui; -import java.util.Locale; - +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; +import java.util.Locale; import java.util.concurrent.Executors; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; +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; @@ -50,6 +54,7 @@ import jalview.fts.core.FTSDataColumnPreferences; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.fts.service.threedbeacons.TDB_FTSData; import jalview.gui.structurechooser.PDBStructureChooserQuerySource; import jalview.gui.structurechooser.StructureChooserQuerySource; import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; @@ -77,9 +82,9 @@ public class StructureChooser extends GStructureChooser private 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; @@ -168,7 +173,8 @@ public class StructureChooser extends GStructureChooser canQueryTDB = true; if (needCanonical) { - notQueriedTDBYet = false; + // triggers display of the 'Query TDB' button + notQueriedTDBYet = true; } } }; @@ -184,9 +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(); @@ -232,7 +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(); @@ -242,19 +264,46 @@ 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); } }; final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() { - + @Override public void finished() { @@ -262,12 +311,12 @@ public class StructureChooser extends GStructureChooser notQueriedTDBYet = false; // new thread to discover structures - via 3d beacons Executors.defaultThreadFactory().newThread(strucDiscovery).start(); - + } }; - + // fetch db refs if OK pressed - final Runnable discoverCanonicalDBrefs = new Runnable() + final Runnable discoverCanonicalDBrefs = new Runnable() { @Override public void run() @@ -285,38 +334,56 @@ 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("THRESHOLD_WARN_UNIPROT_FETCH", + THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); + Console.debug("Using Uniprot fetch threshold of " + threshold); + boolean runThread = false; + if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) + { + runThread = true; + } // need cancel and no to result in the discoverPDB action - mocked is - // 'cancel' - JvOptionPane.newOptionDialog(this) - .setResponseHandler(JvOptionPane.OK_OPTION, - discoverCanonicalDBrefs) - .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) - .setResponseHandler(JvOptionPane.NO_OPTION, revertview) - .showDialog( - MessageManager.formatMessage( - "label.fetch_references_for_3dbeacons", - seqsWithoutSourceDBRef.size()), - MessageManager - .getString("label.3dbeacons"), - JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE, - null, new Object[] - { MessageManager.getString("action.ok"), - MessageManager.getString("action.cancel") }, - MessageManager.getString("action.ok")); + // 'cancel' TODO: mock should be OK + if (!runThread) + { + int answer = JvOptionPane.showConfirmDialog(this, + MessageManager.formatMessage( + "label.fetch_references_for_3dbeacons", + seqsWithoutSourceDBRef.size()), + MessageManager.getString("label.3dbeacons"), + JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE); + runThread = (answer == JvOptionPane.OK_OPTION); + } + if (runThread) + { + Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs) + .start(); + return; + } + else + { + revertview.run(); + } } /** @@ -588,7 +655,7 @@ 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", @@ -601,7 +668,7 @@ 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(); } } @@ -656,10 +723,8 @@ 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) @@ -687,13 +752,7 @@ 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 @@ -708,7 +767,7 @@ public class StructureChooser extends GStructureChooser String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); - + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); @@ -793,6 +852,46 @@ public class StructureChooser extends GStructureChooser .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); } + @Override + 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) + { + + 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); + } + }); + popup.add(viewUrl); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + popup.show(getResultTable(), x, y); + } + }); + return true; + } + // event not handled by us + return false; + } + /** * Validates inputs from the Manual PDB entry panel */ @@ -864,7 +963,9 @@ public class StructureChooser extends GStructureChooser { validateSelections(); } - private FilterOption lastSelected=null; + + private FilterOption lastSelected = null; + /** * Handles the state change event for the 'filter' combo-box and 'invert' * check-box @@ -1021,7 +1122,8 @@ public class StructureChooser extends GStructureChooser if (pdbIdStr.split(":").length > 1) { pdbEntry.setId(pdbIdStr.split(":")[0]); - pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); + pdbEntry.setChainCode( + pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); } else { @@ -1458,4 +1560,18 @@ 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; + } }