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JAL-2085 JAL-2086 fix hiddenRepSequence and new referenceSeq getter
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
f38f267
..
d924e73
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-26,16
+26,16
@@
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
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.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.jbgui.GStructureChooser;
import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
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.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;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
@@
-70,11
+70,11
@@
public class StructureChooser extends GStructureChooser implements
private IProgressIndicator progressIndicator;
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet;
+ private Collection<FTSData> discoveredStructuresSet;
- private PDBRestRequest lastPdbRequest;
+ private FTSRestRequest lastPdbRequest;
- private PDBRestClient pdbRestCleint;
+ private FTSRestClientI pdbRestCleint;
private String selectedPdbFileName;
private String selectedPdbFileName;
@@
-146,22
+146,22
@@
public class StructureChooser extends GStructureChooser implements
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
- discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ discoveredStructuresSet = new LinkedHashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
HashSet<String> errors = new HashSet<String>();
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);
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
@@
-185,7
+185,7
@@
public class StructureChooser extends GStructureChooser implements
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+ tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
@@
-255,7
+255,7
@@
public class StructureChooser extends GStructureChooser implements
{
if (isValidSeqName(entry.getId()))
{
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
+ queryBuilder.append("pdb_id")
.append(":")
.append(entry.getId().toLowerCase())
.append(" OR ");
.append(":")
.append(entry.getId().toLowerCase())
.append(" OR ");
@@
-274,12
+274,11
@@
public class StructureChooser extends GStructureChooser implements
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
queryBuilder
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(getDBRefId(dbRef))
.append(" OR ");
queryBuilder
- .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode())
+.append("uniprot_id")
.append(":")
.append(getDBRefId(dbRef)).append(" OR ");
isUniProtRefsFound = true;
.append(":")
.append(getDBRefId(dbRef)).append(" OR ");
isUniProtRefsFound = true;
@@
-287,7
+286,7
@@
public class StructureChooser extends GStructureChooser implements
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
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;
.append(":").append(getDBRefId(dbRef).toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
@@
-341,7
+340,7
@@
public class StructureChooser extends GStructureChooser implements
{
Objects.requireNonNull(seqName);
return seqName.replaceAll("\\[\\d*\\]", "")
{
Objects.requireNonNull(seqName);
return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+");
+ .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+");
}
}
@@
-395,15
+394,16
@@
public class StructureChooser extends GStructureChooser implements
public void run()
{
long startTime = System.currentTimeMillis();
public void run()
{
long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
lbl_loading.setVisible(true);
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
+ Collection<FTSData> filteredResponse = new HashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
System.out.println(">>>>>> Filtering with uniprot coverate");
if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
System.out.println(">>>>>> Filtering with uniprot coverate");
@@
-428,8
+428,7
@@
public class StructureChooser extends GStructureChooser implements
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq);
}
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq);
}
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
@@
-452,13
+451,13
@@
public class StructureChooser extends GStructureChooser implements
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(PDBRestResponse.getTableModel(
+ tbl_summary.setModel(FTSRestResponse.getTableModel(
lastPdbRequest, reorderedStructuresSet));
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);
tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
@@
-529,17
+528,17
@@
public class StructureChooser extends GStructureChooser implements
if (isStructuresDiscovered())
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
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",
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",
cmb_filterOption.addItem(new FilterOption("Best Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ "resolution", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
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",
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",
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));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
VIEWS_ENTER_ID));
@@
-730,8
+729,8
@@
public class StructureChooser extends GStructureChooser implements
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
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();
int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
.getModelIndex();
int[] selectedRows = tbl_summary.getSelectedRows();
@@
-769,8
+768,8
@@
public class StructureChooser extends GStructureChooser implements
int[] selectedRows = tbl_local_pdb.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
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<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
@@
-927,7
+926,7
@@
public class StructureChooser extends GStructureChooser implements
this.structuresDiscovered = structuresDiscovered;
}
this.structuresDiscovered = structuresDiscovered;
}
- public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ public Collection<FTSData> getDiscoveredStructuresSet()
{
return discoveredStructuresSet;
}
{
return discoveredStructuresSet;
}
@@
-944,9
+943,8
@@
public class StructureChooser extends GStructureChooser implements
isValidPBDEntry = false;
if (txt_search.getText().length() > 0)
{
isValidPBDEntry = false;
if (txt_search.getText().length() > 0)
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
@@
-954,8
+952,9
@@
public class StructureChooser extends GStructureChooser implements
pdbRequest
.setSearchTerm(txt_search.getText().toLowerCase() + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
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);
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);