X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=d9bac9e16f577d6d58a5b38243d68670c350e3a9;hb=ce039b3f8a0b9a3a266838082a678821507ddcc3;hp=97ff4046126df89a79dddfc75187c6c74d729dbb;hpb=7534e6f358b2bba0db179cb2f496bd2e5a4da43d;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 97ff404..d9bac9e 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -36,11 +36,8 @@ import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.io.DataSourceType; import jalview.jbgui.GStructureChooser; -import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; -import jalview.ws.DBRefFetcher; -import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -71,27 +68,25 @@ public class StructureChooser extends GStructureChooser { private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; - private static int MAX_QLENGTH = 7820; + private static final int MAX_QLENGTH = 7820; - private SequenceI selectedSequence; + protected SequenceI selectedSequence; - private SequenceI[] selectedSequences; + SequenceI[] selectedSequences; private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + protected Collection discoveredStructuresSet; - private FTSRestRequest lastPdbRequest; + protected FTSRestRequest lastPdbRequest; - private FTSRestClientI pdbRestCleint; + protected FTSRestClientI pdbRestClient; - private String selectedPdbFileName; + protected String selectedPdbFileName; - private boolean isValidPBDEntry; + protected boolean isValidPBDEntry; - private boolean cachedPDBExists; - - private static StructureViewer lastTargetedView = null; + protected boolean cachedPDBExists; public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) @@ -146,21 +141,24 @@ public class StructureChooser extends GStructureChooser * structures may be added. If this list is empty then it, and the 'Add' * button, are hidden. */ - private void discoverStructureViews() + protected void discoverStructureViews() { - if (Desktop.instance != null) + Desktop desktop = Desktop.getInstance(); + if (desktop != null) { targetView.removeAllItems(); - if (lastTargetedView != null && !lastTargetedView.isVisible()) + if (desktop.lastTargetedView != null + && !desktop.lastTargetedView.isVisible()) { - lastTargetedView = null; + desktop.lastTargetedView = null; } int linkedViewsAt = 0; - for (StructureViewerBase view : Desktop.instance + for (StructureViewerBase view : desktop .getStructureViewers(null, null)) { - StructureViewer viewHandler = (lastTargetedView != null - && lastTargetedView.sview == view) ? lastTargetedView + StructureViewer viewHandler = (desktop.lastTargetedView != null + && desktop.lastTargetedView.sview == view) + ? desktop.lastTargetedView : StructureViewer.reconfigure(view); if (view.isLinkedWith(ap)) @@ -181,9 +179,9 @@ public class StructureChooser extends GStructureChooser if (targetView.getItemCount() > 0) { targetView.setVisible(true); - if (lastTargetedView != null) + if (desktop.lastTargetedView != null) { - targetView.setSelectedItem(lastTargetedView); + targetView.setSelectedItem(desktop.lastTargetedView); } else { @@ -217,7 +215,7 @@ public class StructureChooser extends GStructureChooser void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); + pdbRestClient = PDBFTSRestClient.getInstance(); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); @@ -239,7 +237,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -337,10 +335,12 @@ public class StructureChooser extends GStructureChooser } } - if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) + List refs = seq.getDBRefs(); + if (refs != null && refs.size() != 0) { - for (DBRefEntry dbRef : seq.getDBRefs()) + for (int ib = 0, nb = refs.size(); ib < nb; ib++) { + DBRefEntry dbRef = refs.get(ib); if (isValidSeqName(getDBRefId(dbRef)) && queryBuilder.length() < MAX_QLENGTH) { @@ -461,7 +461,7 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); + pdbRestClient = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); @@ -497,7 +497,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -872,13 +872,11 @@ public class StructureChooser extends GStructureChooser /** * structure viewer opened by this dialog, or null */ - private StructureViewer sViewer = null; + protected StructureViewer sViewer = null; public void showStructures(boolean waitUntilFinished) { - final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - final int preferredHeight = pnl_filter.getHeight(); Runnable viewStruc = new Runnable() @@ -927,7 +925,7 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ap, pdbEntriesToView, selectedSeqs); } else if (currentView == VIEWS_LOCAL_PDB) @@ -951,7 +949,7 @@ public class StructureChooser extends GStructureChooser } SequenceI[] selectedSeqs = selectedSeqsToView .toArray(new SequenceI[selectedSeqsToView.size()]); - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ap, pdbEntriesToView, selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) @@ -981,7 +979,7 @@ public class StructureChooser extends GStructureChooser } PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, + sViewer = launchStructureViewer(ap, pdbEntriesToView, new SequenceI[] { selectedSequence }); } @@ -993,14 +991,13 @@ public class StructureChooser extends GStructureChooser { selectedSequence = userSelectedSeq; } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() + PDBEntry fileEntry = AssociatePdbFileWithSeq .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); + DataSourceType.FILE, selectedSequence, true); sViewer = launchStructureViewer( - ssm, new PDBEntry[] - { fileEntry }, ap, + ap, new PDBEntry[] + { fileEntry }, new SequenceI[] { selectedSequence }); } @@ -1034,7 +1031,7 @@ public class StructureChooser extends GStructureChooser } } - private PDBEntry getFindEntry(String id, Vector pdbEntries) + protected PDBEntry getFindEntry(String id, Vector pdbEntries) { Objects.requireNonNull(id); Objects.requireNonNull(pdbEntries); @@ -1053,13 +1050,12 @@ public class StructureChooser extends GStructureChooser * Answers a structure viewer (new or existing) configured to superimpose * added structures or not according to the user's choice * - * @param ssm * @return */ - StructureViewer getTargetedStructureViewer( - StructureSelectionManager ssm) + StructureViewer getTargetedStructureViewer() { - Object sv = targetView.getSelectedItem(); + final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + Object sv = (targetView == null ? null : targetView.getSelectedItem()); return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; } @@ -1067,93 +1063,24 @@ public class StructureChooser extends GStructureChooser /** * Adds PDB structures to a new or existing structure viewer * - * @param ssm + * @param ap * @param pdbEntriesToView - * @param alignPanel * @param sequences - * @return + * @param superimpose + * @return viewer */ - private StructureViewer launchStructureViewer( - StructureSelectionManager ssm, - final PDBEntry[] pdbEntriesToView, - final AlignmentPanel alignPanel, SequenceI[] sequences) + protected StructureViewer launchStructureViewer( + AlignmentPanel ap, PDBEntry[] pdbEntriesToView, + SequenceI[] selectedSeqs) { - 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; + return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs, + superimpose, getTargetedStructureViewer(), progressBar); } /** @@ -1192,52 +1119,61 @@ public class StructureChooser extends GStructureChooser && !discoveredStructuresSet.isEmpty(); } + protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this. + // Doing a search for "1" or "1c" is valuable? + // Those work but are enormously slow. + @Override protected void txt_search_ActionPerformed() { - new Thread() + String text = txt_search.getText().trim(); + if (text.length() >= PDB_ID_MIN) { - @Override - public void run() + new Thread() { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + + @Override + public void run() { - String searchTerm = txt_search.getText().toLowerCase(); - searchTerm = searchTerm.split(":")[0]; - // System.out.println(">>>>> search term : " + searchTerm); - List wantedFields = new ArrayList<>(); - FTSRestRequest pdbRequest = new FTSRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(pdb_id:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(searchTerm + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = PDBFTSRestClient.getInstance(); - wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); - FTSRestResponse resultList; - try + errorWarning.setLength(0); + isValidPBDEntry = false; + if (text.length() > 0) { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - errorWarning.append(e.getMessage()); - return; - } finally - { - validateSelections(); - } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) - { - isValidPBDEntry = true; + String searchTerm = text.toLowerCase(); + searchTerm = searchTerm.split(":")[0]; + // System.out.println(">>>>> search term : " + searchTerm); + List wantedFields = new ArrayList<>(); + FTSRestRequest pdbRequest = new FTSRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(1); + pdbRequest.setFieldToSearchBy("(pdb_id:"); + pdbRequest.setWantedFields(wantedFields); + pdbRequest.setSearchTerm(searchTerm + ")"); + pdbRequest.setAssociatedSequence(selectedSequence); + pdbRestClient = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); + FTSRestResponse resultList; + try + { + resultList = pdbRestClient.executeRequest(pdbRequest); + } catch (Exception e) + { + errorWarning.append(e.getMessage()); + return; + } finally + { + validateSelections(); + } + if (resultList.getSearchSummary() != null + && resultList.getSearchSummary().size() > 0) + { + isValidPBDEntry = true; + } } + validateSelections(); } - validateSelections(); - } - }.start(); + }.start(); + } } @Override @@ -1365,7 +1301,10 @@ public class StructureChooser extends GStructureChooser @Override public void setProgressBar(String message, long id) { - progressBar.setProgressBar(message, id); + if (progressBar != null) + { + progressBar.setProgressBar(message, id); + } } @Override