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JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
09eb7af
..
34fa751
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-168,7
+168,8
@@
public class StructureChooser extends GStructureChooser
canQueryTDB = true;
if (needCanonical)
{
canQueryTDB = true;
if (needCanonical)
{
- notQueriedTDBYet = false;
+ // triggers display of the 'Query TDB' button
+ notQueriedTDBYet = true;
}
}
};
}
}
};
@@
-190,7
+191,7
@@
public class StructureChooser extends GStructureChooser
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- promptForTDBFetch();
+ promptForTDBFetch(false);
}
});
}
});
@@
-241,7
+242,11
@@
public class StructureChooser extends GStructureChooser
updateCurrentView();
}
updateCurrentView();
}
- private void promptForTDBFetch()
+ /**
+ * raises dialog for Uniprot fetch followed by 3D beacons search
+ * @param ignoreGui - when true, don't ask, just fetch
+ */
+ public void promptForTDBFetch(boolean ignoreGui)
{
final long progressId = System.currentTimeMillis();
{
final long progressId = System.currentTimeMillis();
@@
-259,6
+264,9
@@
public class StructureChooser extends GStructureChooser
// redo initial discovery - this time with 3d beacons
// Executors.
previousWantedFields=null;
// redo initial discovery - this time with 3d beacons
// Executors.
previousWantedFields=null;
+ lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+ cmb_filterOption.setSelectedItem(null);
+ cachedPDBExists=false; // reset to initial
initialStructureDiscovery();
if (!isStructuresDiscovered())
{
initialStructureDiscovery();
if (!isStructuresDiscovered())
{
@@
-266,6
+274,7
@@
public class StructureChooser extends GStructureChooser
btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
btn_queryTDB.setEnabled(false);
} else {
btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
btn_queryTDB.setEnabled(false);
} else {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
btn_queryTDB.setVisible(false);
progressBar.setProgressBar(null, progressId);
}
btn_queryTDB.setVisible(false);
progressBar.setProgressBar(null, progressId);
}
@@
-321,8
+330,13
@@
public class StructureChooser extends GStructureChooser
}
};
};
}
};
};
+ if (ignoreGui)
+ {
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ return;
+ }
// need cancel and no to result in the discoverPDB action - mocked is
// need cancel and no to result in the discoverPDB action - mocked is
- // 'cancel'
+ // 'cancel' TODO: mock should be OK
JvOptionPane.newOptionDialog(this)
.setResponseHandler(JvOptionPane.OK_OPTION,
discoverCanonicalDBrefs)
JvOptionPane.newOptionDialog(this)
.setResponseHandler(JvOptionPane.OK_OPTION,
discoverCanonicalDBrefs)
@@
-610,7
+624,7
@@
public class StructureChooser extends GStructureChooser
// StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
// StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
@@
-623,7
+637,7
@@
public class StructureChooser extends GStructureChooser
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
validateSelections();
}
}
@@
-1503,4
+1517,16
@@
public class StructureChooser extends GStructureChooser
&& mainFrame.isVisible()
&& cmb_filterOption.getSelectedItem() != null;
}
&& mainFrame.isVisible()
&& cmb_filterOption.getSelectedItem() != null;
}
+ /**
+ *
+ * @return true if the 3D-Beacons query button will/has been displayed
+ */
+ public boolean isCanQueryTDB() {
+ return canQueryTDB;
+ }
+
+ public boolean isNotQueriedTDBYet()
+ {
+ return notQueriedTDBYet;
+ }
}
}