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JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequ...
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
b32e435
..
07eec2b
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-43,6
+43,7
@@
import javax.swing.table.AbstractTableModel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.bin.Jalview;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
@@
-320,6
+321,7
@@
public class StructureChooser extends GStructureChooser
@Override
public void run()
{
@Override
public void run()
{
+ btn_queryTDB.setEnabled(false);
populateSeqsWithoutSourceDBRef();
final int y = seqsWithoutSourceDBRef.size();
populateSeqsWithoutSourceDBRef();
final int y = seqsWithoutSourceDBRef.size();
@@
-332,6
+334,7
@@
public class StructureChooser extends GStructureChooser
{ new jalview.ws.dbsources.Uniprot() }, null, false);
dbRefFetcher.addListener(afterDbRefFetch);
// ideally this would also gracefully run with callbacks
{ new jalview.ws.dbsources.Uniprot() }, null, false);
dbRefFetcher.addListener(afterDbRefFetch);
// ideally this would also gracefully run with callbacks
+
dbRefFetcher.fetchDBRefs(true);
}
else
dbRefFetcher.fetchDBRefs(true);
}
else
@@
-353,8
+356,10
@@
public class StructureChooser extends GStructureChooser
}
};
};
}
};
};
- if (ignoreGui || seqsWithoutSourceDBRef
- .size() < THRESHOLD_WARN_UNIPROT_FETCH_NEEDED)
+ int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
+ THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
+ Console.debug("Using Uniprot fetch threshold of " + threshold);
+ if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
{
Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
.start();
{
Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
.start();
@@
-362,7
+367,9
@@
public class StructureChooser extends GStructureChooser
}
// need cancel and no to result in the discoverPDB action - mocked is
// 'cancel' TODO: mock should be OK
}
// need cancel and no to result in the discoverPDB action - mocked is
// 'cancel' TODO: mock should be OK
- JvOptionPane.newOptionDialog(this)
+
+ StructureChooser thisSC = this;
+ JvOptionPane.newOptionDialog(thisSC.getFrame())
.setResponseHandler(JvOptionPane.OK_OPTION,
discoverCanonicalDBrefs)
.setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
.setResponseHandler(JvOptionPane.OK_OPTION,
discoverCanonicalDBrefs)
.setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
@@
-376,7
+383,7
@@
public class StructureChooser extends GStructureChooser
null, new Object[]
{ MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") },
null, new Object[]
{ MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") },
- MessageManager.getString("action.ok"));
+ MessageManager.getString("action.ok"), false);
}
/**
}
/**
@@
-1384,6
+1391,7
@@
public class StructureChooser extends GStructureChooser
{
if (selectedSequences != null)
{
{
if (selectedSequences != null)
{
+ lbl_loading.setVisible(true);
Thread refreshThread = new Thread(new Runnable()
{
@Override
Thread refreshThread = new Thread(new Runnable()
{
@Override
@@
-1395,6
+1403,7
@@
public class StructureChooser extends GStructureChooser
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
+ lbl_loading.setVisible(false);
}
});
refreshThread.start();
}
});
refreshThread.start();