X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=2d9028a4620f695bd8ee0225d446aa77e519e79d;hb=64dd25185d2caf389946bb7e70053183d5aa31a6;hp=f38f267926a232310f8f1afa81151afb98ded2ab;hpb=f8563f9a829936e3cf75f36282e4816a3ea6163b;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index f38f267..2d9028a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -26,16 +26,17 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.fts.api.FTSData; +import jalview.fts.api.FTSDataColumnI; +import jalview.fts.api.FTSRestClientI; +import jalview.fts.core.FTSDataColumnPreferences; +import jalview.fts.core.FTSRestRequest; +import jalview.fts.core.FTSRestResponse; +import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.jbgui.GStructureChooser; -import jalview.jbgui.PDBDocFieldPreferences; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.dbsources.PDBRestClient.PDBDocField; import jalview.ws.sifts.SiftsSettings; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; import java.awt.event.ItemEvent; import java.util.ArrayList; @@ -70,11 +71,11 @@ public class StructureChooser extends GStructureChooser implements private IProgressIndicator progressIndicator; - private Collection discoveredStructuresSet; + private Collection discoveredStructuresSet; - private PDBRestRequest lastPdbRequest; + private FTSRestRequest lastPdbRequest; - private PDBRestClient pdbRestCleint; + private FTSRestClientI pdbRestCleint; private String selectedPdbFileName; @@ -146,22 +147,22 @@ public class StructureChooser extends GStructureChooser implements public void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = FTSDataColumnPreferences .getStructureSummaryFields(); - discoveredStructuresSet = new LinkedHashSet(); + discoveredStructuresSet = new LinkedHashSet(); HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(500); pdbRequest.setFieldToSearchBy("("); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setAssociatedSequence(seq); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -185,7 +186,7 @@ public class StructureChooser extends GStructureChooser implements if (discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty()) { - tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest, + tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest, discoveredStructuresSet)); structuresDiscovered = true; noOfStructuresFound = discoveredStructuresSet.size(); @@ -255,7 +256,7 @@ public class StructureChooser extends GStructureChooser implements { if (isValidSeqName(entry.getId())) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) + queryBuilder.append("pdb_id") .append(":") .append(entry.getId().toLowerCase()) .append(" OR "); @@ -274,12 +275,11 @@ public class StructureChooser extends GStructureChooser implements if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION - .getCode()).append(":") +.append("uniprot_accession").append(":") .append(getDBRefId(dbRef)) .append(" OR "); queryBuilder - .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode()) +.append("uniprot_id") .append(":") .append(getDBRefId(dbRef)).append(" OR "); isUniProtRefsFound = true; @@ -287,7 +287,7 @@ public class StructureChooser extends GStructureChooser implements else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) { - queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode()) + queryBuilder.append("pdb_id") .append(":").append(getDBRefId(dbRef).toLowerCase()) .append(" OR "); isPDBRefsFound = true; @@ -341,7 +341,7 @@ public class StructureChooser extends GStructureChooser implements { Objects.requireNonNull(seqName); return seqName.replaceAll("\\[\\d*\\]", "") - .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+"); + .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+"); } @@ -396,14 +396,14 @@ public class StructureChooser extends GStructureChooser implements { long startTime = System.currentTimeMillis(); lbl_loading.setVisible(true); - Collection wantedFields = PDBDocFieldPreferences + Collection wantedFields = FTSDataColumnPreferences .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); + Collection filteredResponse = new HashSet(); HashSet errors = new HashSet(); for (SequenceI seq : selectedSequences) { - PDBRestRequest pdbRequest = new PDBRestRequest(); + FTSRestRequest pdbRequest = new FTSRestRequest(); if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) { System.out.println(">>>>>> Filtering with uniprot coverate"); @@ -428,8 +428,8 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setWantedFields(wantedFields); pdbRequest.setAssociatedSequence(seq); } - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest); @@ -452,13 +452,13 @@ 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); - tbl_summary.setModel(PDBRestResponse.getTableModel( + tbl_summary.setModel(FTSRestResponse.getTableModel( lastPdbRequest, reorderedStructuresSet)); - PDBRestResponse.configureTableColumn(tbl_summary, wantedFields); + FTSRestResponse.configureTableColumn(tbl_summary, wantedFields); tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120); tbl_summary.getColumn("Ref Sequence").setMinWidth(100); tbl_summary.getColumn("Ref Sequence").setMaxWidth(200); @@ -529,17 +529,17 @@ public class StructureChooser extends GStructureChooser implements if (isStructuresDiscovered()) { cmb_filterOption.addItem(new FilterOption("Best Quality", - PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER)); + "overall_quality", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage", - PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER)); + "uniprot_coverage", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Best Resolution", - PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER)); + "resolution", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Protein Chain", - PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER)); + "number_of_protein_chains", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", - PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER)); + "number_of_bound_molecules", VIEWS_FILTER)); cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", - PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER)); + "number_of_polymer_residues", VIEWS_FILTER)); } cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID)); @@ -730,8 +730,8 @@ public class StructureChooser extends GStructureChooser implements String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - int pdbIdColIndex = tbl_summary.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); + int pdbIdColIndex = tbl_summary.getColumn("PDB Id") + .getModelIndex(); int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") .getModelIndex(); int[] selectedRows = tbl_summary.getSelectedRows(); @@ -769,8 +769,8 @@ public class StructureChooser extends GStructureChooser implements int[] selectedRows = tbl_local_pdb.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; - int pdbIdColIndex = tbl_local_pdb.getColumn( - PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); + int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") + .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); ArrayList selectedSeqsToView = new ArrayList(); @@ -927,7 +927,7 @@ public class StructureChooser extends GStructureChooser implements this.structuresDiscovered = structuresDiscovered; } - public Collection getDiscoveredStructuresSet() + public Collection getDiscoveredStructuresSet() { return discoveredStructuresSet; } @@ -944,9 +944,8 @@ public class StructureChooser extends GStructureChooser implements isValidPBDEntry = false; if (txt_search.getText().length() > 0) { - List wantedFields = new ArrayList(); - wantedFields.add(PDBDocField.PDB_ID); - PDBRestRequest pdbRequest = new PDBRestRequest(); + List wantedFields = new ArrayList(); + FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); pdbRequest.setResponseSize(1); pdbRequest.setFieldToSearchBy("(pdb_id:"); @@ -954,8 +953,9 @@ public class StructureChooser extends GStructureChooser implements pdbRequest .setSearchTerm(txt_search.getText().toLowerCase() + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = new PDBRestClient(); - PDBRestResponse resultList; + pdbRestCleint = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + FTSRestResponse resultList; try { resultList = pdbRestCleint.executeRequest(pdbRequest);