X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3f5f39c64dd685f9f5b3146f6449adccdef1ade2;hb=052516c9711a49bc5cafbc1145f696febc4ccc74;hp=e400b51226b339d03936abe493276f943fea2fa3;hpb=ee942237fe5155b25f5419ece71a4084a47e2f41;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index e400b51..3f5f39c 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -35,7 +35,6 @@ import java.util.concurrent.Executors; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; -import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; import javax.swing.JTable; @@ -44,6 +43,7 @@ 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; @@ -81,6 +81,11 @@ public class StructureChooser extends GStructureChooser { private 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; @@ -191,12 +196,13 @@ public class StructureChooser extends GStructureChooser @Override public void actionPerformed(ActionEvent e) { - promptForTDBFetch(); + promptForTDBFetch(false); } }); Executors.defaultThreadFactory().newThread(new Runnable() { + @Override public void run() { populateSeqsWithoutSourceDBRef(); @@ -242,7 +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(); @@ -254,20 +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; + 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); @@ -277,7 +303,7 @@ public class StructureChooser extends GStructureChooser final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() { - + @Override public void finished() { @@ -285,12 +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() @@ -308,22 +334,37 @@ 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); + if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) + { + Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs) + .start(); + return; + } // need cancel and no to result in the discoverPDB action - mocked is - // 'cancel' + // 'cancel' TODO: mock should be OK JvOptionPane.newOptionDialog(this) .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs) @@ -333,8 +374,7 @@ public class StructureChooser extends GStructureChooser MessageManager.formatMessage( "label.fetch_references_for_3dbeacons", seqsWithoutSourceDBRef.size()), - MessageManager - .getString("label.3dbeacons"), + MessageManager.getString("label.3dbeacons"), JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE, null, new Object[] { MessageManager.getString("action.ok"), @@ -611,7 +651,7 @@ 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", @@ -624,7 +664,7 @@ 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(); } } @@ -680,6 +720,7 @@ public class StructureChooser extends GStructureChooser if (canQueryTDB && notQueriedTDBYet) { btn_queryTDB.setVisible(true); + pnl_queryTDB.setVisible(true); } if (cachedPDBExist) @@ -707,7 +748,7 @@ public class StructureChooser extends GStructureChooser { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - + if (lastSelected == selectedFilterOpt) { // don't need to do anything, probably @@ -722,7 +763,7 @@ public class StructureChooser extends GStructureChooser String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); - + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); @@ -813,32 +854,40 @@ 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; } // event not handled by us return false; } + /** * Validates inputs from the Manual PDB entry panel */ @@ -910,7 +959,9 @@ 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 @@ -1067,7 +1118,8 @@ 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 { @@ -1504,12 +1556,14 @@ 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 isCanQueryTDB() + { + return canQueryTDB; } public boolean isNotQueriedTDBYet()