X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5e4226ad816c90aa90be64debe734b92e31a1347;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=af5f8a4ad710c266d4b8a60e96a8aa770c35d951;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index af5f8a4..5e4226a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -44,6 +44,7 @@ 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; @@ -79,8 +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; @@ -111,7 +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) @@ -197,6 +202,7 @@ public class StructureChooser extends GStructureChooser Executors.defaultThreadFactory().newThread(new Runnable() { + @Override public void run() { populateSeqsWithoutSourceDBRef(); @@ -263,6 +269,7 @@ public class StructureChooser extends GStructureChooser 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 @@ -270,7 +277,7 @@ public class StructureChooser extends GStructureChooser previousWantedFields = null; lastSelected = (FilterOption) cmb_filterOption.getSelectedItem(); cmb_filterOption.setSelectedItem(null); - cachedPDBExists = false; // reset to initial + cachedPDBExists=false; // reset to initial initialStructureDiscovery(); if (!isStructuresDiscovered()) { @@ -280,11 +287,13 @@ public class StructureChooser extends GStructureChooser 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); @@ -294,7 +303,7 @@ public class StructureChooser extends GStructureChooser final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() { - + @Override public void finished() { @@ -302,16 +311,17 @@ 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() { + btn_queryTDB.setEnabled(false); populateSeqsWithoutSourceDBRef(); final int y = seqsWithoutSourceDBRef.size(); @@ -336,6 +346,7 @@ public class StructureChooser extends GStructureChooser }; final Runnable revertview = new Runnable() { + @Override public void run() { if (lastSelected != null) @@ -344,15 +355,18 @@ public class StructureChooser extends GStructureChooser } }; }; - 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(); + 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) @@ -361,12 +375,13 @@ 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"), MessageManager.getString("action.cancel") }, - MessageManager.getString("action.ok")); + MessageManager.getString("action.ok"), false); } /** @@ -376,7 +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()) @@ -384,7 +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 @@ -707,6 +722,7 @@ public class StructureChooser extends GStructureChooser if (canQueryTDB && notQueriedTDBYet) { btn_queryTDB.setVisible(true); + pnl_queryTDB.setVisible(true); } if (cachedPDBExist) @@ -734,7 +750,7 @@ public class StructureChooser extends GStructureChooser { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - + if (lastSelected == selectedFilterOpt) { // don't need to do anything, probably @@ -749,7 +765,7 @@ public class StructureChooser extends GStructureChooser String filterTitle = mainFrame.getTitle(); mainFrame.setTitle(frameTitle); chk_invertFilter.setVisible(false); - + if (selectedFilterOpt.getView() == VIEWS_FILTER) { mainFrame.setTitle(filterTitle); @@ -840,11 +856,9 @@ public class StructureChooser extends GStructureChooser 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); @@ -862,6 +876,7 @@ public class StructureChooser extends GStructureChooser popup.add(viewUrl); SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { popup.show(getResultTable(), x, y); @@ -872,7 +887,6 @@ public class StructureChooser extends GStructureChooser // event not handled by us return false; } - /** * Validates inputs from the Manual PDB entry panel */ @@ -944,9 +958,7 @@ 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 @@ -1035,7 +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() @@ -1059,8 +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) { @@ -1084,8 +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) { @@ -1103,8 +1116,7 @@ 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 { @@ -1115,9 +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) { @@ -1127,14 +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() { @@ -1181,98 +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. */ @@ -1372,6 +1291,7 @@ public class StructureChooser extends GStructureChooser { if (selectedSequences != null) { + lbl_loading.setVisible(true); Thread refreshThread = new Thread(new Runnable() { @Override @@ -1383,6 +1303,7 @@ public class StructureChooser extends GStructureChooser filterResultSet( ((FilterOption) cmb_filterOption.getSelectedItem()) .getValue()); + lbl_loading.setVisible(false); } }); refreshThread.start(); @@ -1505,6 +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) @@ -1541,7 +1474,6 @@ public class StructureChooser extends GStructureChooser && mainFrame.isVisible() && cmb_filterOption.getSelectedItem() != null; } - /** * * @return true if the 3D-Beacons query button will/has been displayed