X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=7c386f1a8cf63bd953e20adcaa2d22f2b871ae83;hb=bf97c293ad31f6ed5006a97d3a7d079c032652e8;hp=3e516a621b58bc6421027ef62559ccef480f154f;hpb=b838581d0bef5793a819a317a827d66421ee48a2;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 3e516a6..7c386f1 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -62,8 +62,8 @@ import javax.swing.table.AbstractTableModel; * */ @SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser implements - IProgressIndicator +public class StructureChooser extends GStructureChooser + implements IProgressIndicator { private static int MAX_QLENGTH = 7820; @@ -117,9 +117,8 @@ public class StructureChooser extends GStructureChooser implements .getString("status.loading_cached_pdb_entries"), startTime); loadLocalCachedPDBEntries(); updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager - .getString("status.searching_for_pdb_structures"), - startTime); + updateProgressIndicator(MessageManager.getString( + "status.searching_for_pdb_structures"), startTime); fetchStructuresMetaData(); // revise filter options if no results were found populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); @@ -158,8 +157,8 @@ public class StructureChooser extends GStructureChooser implements Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); - HashSet errors = new HashSet(); + discoveredStructuresSet = new LinkedHashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { FTSRestRequest pdbRequest = new FTSRestRequest(); @@ -197,9 +196,8 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, discoveredStructuresSet)); noOfStructuresFound = discoveredStructuresSet.size(); mainFrame.setTitle(MessageManager.formatMessage( "label.structure_chooser_no_of_structures", @@ -225,7 +223,7 @@ public class StructureChooser extends GStructureChooser implements public void loadLocalCachedPDBEntries() { - ArrayList entries = new ArrayList(); + ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) { if (seq.getDatasetSequence() != null @@ -259,7 +257,7 @@ public class StructureChooser extends GStructureChooser implements boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; StringBuilder queryBuilder = new StringBuilder(); - Set seqRefs = new LinkedHashSet(); + Set seqRefs = new LinkedHashSet<>(); if (seq.getAllPDBEntries() != null && queryBuilder.length() < MAX_QLENGTH) @@ -268,8 +266,8 @@ public class StructureChooser extends GStructureChooser implements { if (isValidSeqName(entry.getId())) { - queryBuilder.append("pdb_id:") - .append(entry.getId().toLowerCase()).append(" OR "); + queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase()) + .append(" OR "); isPDBRefsFound = true; } } @@ -403,8 +401,8 @@ public class StructureChooser extends GStructureChooser implements lbl_loading.setVisible(true); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); - HashSet errors = new HashSet(); + Collection filteredResponse = new HashSet<>(); + HashSet errors = new HashSet<>(); for (SequenceI seq : selectedSequences) { @@ -455,12 +453,11 @@ public class StructureChooser extends GStructureChooser implements if (!filteredResponse.isEmpty()) { final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); + Collection reorderedStructuresSet = new LinkedHashSet<>(); reorderedStructuresSet.addAll(filteredResponse); reorderedStructuresSet.addAll(discoveredStructuresSet); - getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - reorderedStructuresSet)); + getResultTable().setModel(FTSRestResponse + .getTableModel(lastPdbRequest, reorderedStructuresSet)); FTSRestResponse.configureTableColumn(getResultTable(), wantedFields, tempUserPrefs); @@ -484,9 +481,7 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JvOptionPane.showMessageDialog( - null, - errorMsg.toString(), + JvOptionPane.showMessageDialog(null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), JvOptionPane.ERROR_MESSAGE); } @@ -509,9 +504,9 @@ public class StructureChooser extends GStructureChooser implements jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", - selectedSequence.getDisplayId(false))); + chooser.setDialogTitle( + MessageManager.formatMessage("label.select_pdb_file_for", + selectedSequence.getDisplayId(false))); chooser.setToolTipText(MessageManager.formatMessage( "label.load_pdb_file_associate_with_sequence", selectedSequence.getDisplayId(false))); @@ -551,14 +546,14 @@ public class StructureChooser extends GStructureChooser implements cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", "number_of_polymer_residues", VIEWS_FILTER, true)); } - cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID, false)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE, false)); + cmb_filterOption.addItem( + new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false)); + cmb_filterOption.addItem( + new FilterOption("From File", "-", VIEWS_FROM_FILE, false)); if (cachedPDBExists) { - FilterOption cachedOption = new FilterOption("Cached PDB Entries", + FilterOption cachedOption = new FilterOption("Cached Structures", "-", VIEWS_LOCAL_PDB, false); cmb_filterOption.addItem(cachedOption); cmb_filterOption.setSelectedItem(cachedOption); @@ -642,22 +637,20 @@ public class StructureChooser extends GStructureChooser implements lbl_pdbManualFetchStatus.setToolTipText(""); if (txt_search.getText().length() > 0) { - lbl_pdbManualFetchStatus - .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager - .formatMessage("info.no_pdb_entry_found_for", - txt_search.getText()))); + lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("info.no_pdb_entry_found_for", + txt_search.getText()))); } if (errorWarning.length() > 0) { lbl_pdbManualFetchStatus.setIcon(warningImage); - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, errorWarning.toString())); + lbl_pdbManualFetchStatus.setToolTipText( + JvSwingUtils.wrapTooltip(true, errorWarning.toString())); } - if (selectedSequences.length == 1 - || !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-")) + if (selectedSequences.length == 1 || !assSeqOpt.getName() + .equalsIgnoreCase("-Select Associated Seq-")) { txt_search.setEnabled(true); if (isValidPBDEntry) @@ -682,9 +675,8 @@ public class StructureChooser extends GStructureChooser implements AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); lbl_fromFileStatus.setIcon(errorImage); - if (selectedSequences.length == 1 - || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-"))) + if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt + .getName().equalsIgnoreCase("-Select Associated Seq-"))) { btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) @@ -733,11 +725,10 @@ public class StructureChooser extends GStructureChooser implements @Override public void ok_ActionPerformed() { - final long progressSessionId = System.currentTimeMillis(); final StructureSelectionManager ssm = ap.getStructureSelectionManager(); + final int preferredHeight = pnl_filter.getHeight(); - ssm.setProgressIndicator(this); - ssm.setProgressSessionId(progressSessionId); + new Thread(new Runnable() { @Override @@ -755,11 +746,11 @@ public class StructureChooser extends GStructureChooser implements int[] selectedRows = getResultTable().getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; - List selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { - String pdbIdStr = getResultTable().getValueAt(row, - pdbIdColIndex).toString(); + String pdbIdStr = getResultTable() + .getValueAt(row, pdbIdColIndex).toString(); SequenceI selectedSeq = (SequenceI) getResultTable() .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); @@ -769,6 +760,7 @@ public class StructureChooser extends GStructureChooser implements pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } + if (pdbEntry == null) { pdbEntry = new PDBEntry(); @@ -791,14 +783,14 @@ public class StructureChooser extends GStructureChooser implements .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); - List selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList<>(); for (int row : selectedRows) { PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, pdbIdColIndex); pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt( - row, refSeqColIndex); + SequenceI selectedSeq = (SequenceI) tbl_local_pdb + .getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); } SequenceI[] selectedSeqs = selectedSeqsToView @@ -813,7 +805,6 @@ public class StructureChooser extends GStructureChooser implements { selectedSequence = userSelectedSeq; } - String pdbIdStr = txt_search.getText(); PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); if (pdbEntry == null) @@ -834,25 +825,28 @@ public class StructureChooser extends GStructureChooser implements PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ssm, pdbEntriesToView, ap, - new SequenceI[] { selectedSequence }); - } - else if (currentView == VIEWS_FROM_FILE) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, - selectedSequence, true, Desktop.instance); + new SequenceI[] + { selectedSequence }); + } + else if (currentView == VIEWS_FROM_FILE) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, selectedSequence, true, + Desktop.instance); launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); + new SequenceI[] + { selectedSequence }); } closeAction(preferredHeight); + mainFrame.dispose(); } }).start(); } @@ -876,13 +870,15 @@ public class StructureChooser extends GStructureChooser implements final PDBEntry[] pdbEntriesToView, final AlignmentPanel alignPanel, SequenceI[] sequences) { - ssm.setProgressBar(MessageManager - .getString("status.launching_3d_structure_viewer")); + long progressId = sequences.hashCode(); + setProgressBar(MessageManager + .getString("status.launching_3d_structure_viewer"), progressId); final StructureViewer sViewer = new StructureViewer(ssm); + setProgressBar(null, progressId); if (SiftsSettings.isMapWithSifts()) { - List seqsWithoutSourceDBRef = new ArrayList(); + 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 @@ -913,41 +909,37 @@ public class StructureChooser extends GStructureChooser implements if (!seqsWithoutSourceDBRef.isEmpty()) { int y = seqsWithoutSourceDBRef.size(); - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_dbrefs_for_sequences_without_valid_refs", - y)); + y), progressId); SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; int x = 0; for (SequenceI fSeq : seqsWithoutSourceDBRef) { seqWithoutSrcDBRef[x++] = fSeq; } + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); + + setProgressBar("Fetch complete.", progressId); // todo i18n } } if (pdbEntriesToView.length > 1) { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) - { - seqsMap.add(new SequenceI[] { seq }); - } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager - .getString("status.fetching_3d_structures_for_selected_entries")); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + setProgressBar(MessageManager.getString( + "status.fetching_3d_structures_for_selected_entries"), + progressId); + sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( + setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId())); + pdbEntriesToView[0].getId()),progressId); sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } + setProgressBar(null, progressId); } /** @@ -956,11 +948,12 @@ public class StructureChooser extends GStructureChooser implements */ @Override public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) + JComboBox cmb_assSeq, + JLabel lbl_associateSeq) { cmb_assSeq.removeAllItems(); - cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-", - null)); + cmb_assSeq.addItem( + new AssociateSeqOptions("-Select Associated Seq-", null)); lbl_associateSeq.setVisible(false); if (selectedSequences.length > 1) { @@ -1005,7 +998,7 @@ public class StructureChooser extends GStructureChooser implements String searchTerm = txt_search.getText().toLowerCase(); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); - List wantedFields = new ArrayList(); + List wantedFields = new ArrayList<>(); FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); @@ -1049,8 +1042,9 @@ public class StructureChooser extends GStructureChooser implements public void run() { fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); + filterResultSet( + ((FilterOption) cmb_filterOption.getSelectedItem()) + .getValue()); } }); refreshThread.start(); @@ -1059,13 +1053,14 @@ public class StructureChooser extends GStructureChooser implements public class PDBEntryTableModel extends AbstractTableModel { - String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; + String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", + "File" }; private List pdbEntries; public PDBEntryTableModel(List pdbEntries) { - this.pdbEntries = new ArrayList(pdbEntries); + this.pdbEntries = new ArrayList<>(pdbEntries); } @Override @@ -1106,8 +1101,8 @@ public class StructureChooser extends GStructureChooser implements value = entry.getPdbEntry(); break; case 2: - value = entry.getPdbEntry().getChainCode() == null ? "_" : entry - .getPdbEntry().getChainCode(); + value = entry.getPdbEntry().getChainCode() == null ? "_" + : entry.getPdbEntry().getChainCode(); break; case 3: value = entry.getPdbEntry().getType();