X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5ea68fb5e2f825d838b7dc0233fc008eb08ca0ba;hp=694b0639043d4309544a69e3a2959c3aa79c5c7e;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hpb=752f89e5730d804d1982ce4a09ab0f9266dde03d diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 694b063..5ea68fb 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -37,6 +37,7 @@ 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; @@ -80,11 +81,6 @@ public class StructureChooser extends GStructureChooser { private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; - /** - * transient combo box choice for initiating 3db fetch - */ - private static final String VIEWS_QUERYING_TDB = "QUERY_3DB"; - private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -172,7 +168,8 @@ public class StructureChooser extends GStructureChooser canQueryTDB = true; if (needCanonical) { - notQueriedTDBYet = false; + // triggers display of the 'Query TDB' button + notQueriedTDBYet = true; } } }; @@ -188,6 +185,15 @@ 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() { @@ -236,7 +242,13 @@ 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(); @@ -246,19 +258,46 @@ 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() { @@ -266,12 +305,12 @@ 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() @@ -289,22 +328,33 @@ 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() + { + public void run() + { + if (lastSelected != null) + { cmb_filterOption.setSelectedItem(lastSelected); } }; }; + if (ignoreGui) + { + 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) @@ -314,8 +364,7 @@ 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"), @@ -592,7 +641,7 @@ 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 +654,7 @@ 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 +709,8 @@ 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) @@ -691,13 +738,7 @@ 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 @@ -712,7 +753,7 @@ public class StructureChooser extends GStructureChooser String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); - + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); @@ -798,44 +839,44 @@ 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() + { + 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 */ @@ -907,7 +948,9 @@ 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 @@ -1064,7 +1107,8 @@ 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 { @@ -1501,4 +1545,18 @@ 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; + } }