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JAL-3865 isolate PDB and TDB clients and last query records in their query objects
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 3 Sep 2021 16:01:04 +0000
(17:01 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 3 Sep 2021 16:01:04 +0000
(17:01 +0100)
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
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src/jalview/gui/structurechooser/StructureChooserQuerySource.java
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src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
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diff --git
a/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
b/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
index
4dede2e
..
3d1b982
100644
(file)
--- a/
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
+++ b/
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
@@
-37,6
+37,10
@@
public class PDBStructureChooserQuerySource
private static int MAX_QLENGTH = 7820;
private static int MAX_QLENGTH = 7820;
+ protected FTSRestRequest lastPdbRequest;
+
+ protected FTSRestClientI pdbRestClient;
+
public PDBStructureChooserQuerySource()
{
pdbRestClient = PDBFTSRestClient.getInstance();
public PDBStructureChooserQuerySource()
{
pdbRestClient = PDBFTSRestClient.getInstance();
@@
-344,4
+348,11
@@
public class PDBStructureChooserQuerySource
return pdbEntriesToView;
}
return pdbEntriesToView;
}
+
+ @Override
+ protected FTSRestRequest getLastFTSRequest()
+ {
+ return lastPdbRequest;
+ }
+
}
\ No newline at end of file
}
\ No newline at end of file
diff --git
a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
index
4faa2de
..
96b67e4
100644
(file)
--- a/
src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/
src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@
-28,9
+28,6
@@
import jalview.jbgui.FilterOption;
*/
public abstract class StructureChooserQuerySource
{
*/
public abstract class StructureChooserQuerySource
{
- protected FTSRestRequest lastPdbRequest;
-
- protected FTSRestClientI pdbRestClient;
protected FTSDataColumnPreferences docFieldPrefs;
protected FTSDataColumnPreferences docFieldPrefs;
@@
-191,10
+188,12
@@
public abstract class StructureChooserQuerySource
public TableModel getTableModel(
Collection<FTSData> discoveredStructuresSet)
{
public TableModel getTableModel(
Collection<FTSData> discoveredStructuresSet)
{
- return FTSRestResponse.getTableModel(lastPdbRequest,
+ return FTSRestResponse.getTableModel(getLastFTSRequest(),
discoveredStructuresSet);
}
discoveredStructuresSet);
}
+ protected abstract FTSRestRequest getLastFTSRequest();
+
public abstract PDBEntry[] collectSelectedRows(JTable restable,
int[] selectedRows, List<SequenceI> selectedSeqsToView);
public abstract PDBEntry[] collectSelectedRows(JTable restable,
int[] selectedRows, List<SequenceI> selectedSeqsToView);
diff --git
a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index
e188b23
..
0bf9fdb
100644
(file)
--- a/
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@
-14,6
+14,7
@@
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSDataColumnI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
@@
-23,7
+24,7
@@
import jalview.jbgui.FilterOption;
import jalview.util.MessageManager;
/**
import jalview.util.MessageManager;
/**
- * logic for querying the PDBe API for structures of sequences
+ * logic for querying the 3DBeacons API for structures of sequences
*
* @author jprocter
*/
*
* @author jprocter
*/
@@
-33,9
+34,13
@@
public class ThreeDBStructureChooserQuerySource
private static int MAX_QLENGTH = 7820;
private static int MAX_QLENGTH = 7820;
+ protected FTSRestRequest lastTdbRequest;
+
+ protected FTSRestClientI tdbRestClient;
+
public ThreeDBStructureChooserQuerySource()
{
public ThreeDBStructureChooserQuerySource()
{
- pdbRestClient = TDBeaconsFTSRestClient.getInstance();
+ tdbRestClient = TDBeaconsFTSRestClient.getInstance();
docFieldPrefs = new FTSDataColumnPreferences(
PreferenceSource.STRUCTURE_CHOOSER,
TDBeaconsFTSRestClient.getInstance());
docFieldPrefs = new FTSDataColumnPreferences(
PreferenceSource.STRUCTURE_CHOOSER,
TDBeaconsFTSRestClient.getInstance());
@@
-143,10
+148,10
@@
public class ThreeDBStructureChooserQuerySource
FilterOption selectedFilterOpt, boolean b) throws Exception
{
FTSRestResponse resultList;
FilterOption selectedFilterOpt, boolean b) throws Exception
{
FTSRestResponse resultList;
- FTSRestRequest pdbRequest = getTDBeaconsRequest(seq, wantedFields);
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
+ resultList = tdbRestClient.executeRequest(tdbRequest);
- lastPdbRequest = pdbRequest;
+ lastTdbRequest = tdbRequest;
return resultList;
}
return resultList;
}
@@
-214,11
+219,11
@@
public class ThreeDBStructureChooserQuerySource
return null;
}
pdbRequest.setResponseSize(1);
return null;
}
pdbRequest.setResponseSize(1);
- resultList = pdbRestClient.executeRequest(pdbRequest);
+ resultList = tdbRestClient.executeRequest(pdbRequest);
// TODO: client side filtering - sort results and pick top one (or N)
// TODO: client side filtering - sort results and pick top one (or N)
- lastPdbRequest = pdbRequest;
+ lastTdbRequest = pdbRequest;
return resultList;
}
return resultList;
}
@@
-271,4
+276,11
@@
public class ThreeDBStructureChooserQuerySource
}
return pdbEntriesToView;
}
}
return pdbEntriesToView;
}
+
+
+ @Override
+ protected FTSRestRequest getLastFTSRequest()
+ {
+ return lastTdbRequest;
+ }
}
\ No newline at end of file
}
\ No newline at end of file