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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
3ecca9b
..
34fa751
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-81,11
+81,6
@@
public class StructureChooser extends GStructureChooser
{
private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
{
private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
- /**
- * transient combo box choice for initiating 3db fetch
- */
- private static final String VIEWS_QUERYING_TDB = "QUERY_3DB";
-
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
@@
-173,7
+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;
}
}
};
}
}
};
@@
-189,6
+185,15
@@
public class StructureChooser extends GStructureChooser
}
chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
}
chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+ btn_queryTDB.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ promptForTDBFetch(false);
+ }
+ });
Executors.defaultThreadFactory().newThread(new Runnable()
{
Executors.defaultThreadFactory().newThread(new Runnable()
{
@@
-237,7
+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();
@@
-247,19
+256,30
@@
public class StructureChooser extends GStructureChooser
@Override
public void run()
{
@Override
public void run()
{
- progressBar.setProgressBar("status.searching_3d_beacons", progressId);
+ mainFrame.setEnabled(false);
+ cmb_filterOption.setEnabled(false);
+ progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId);
// TODO: warn if no accessions discovered
populateSeqsWithoutSourceDBRef();
// redo initial discovery - this time with 3d beacons
// Executors.
previousWantedFields=null;
// TODO: warn if no accessions discovered
populateSeqsWithoutSourceDBRef();
// 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())
{
- progressBar.setProgressBar("status.no_structures_discovered_from_3d_beacons", progressId);
+ progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId);
+ btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
+ btn_queryTDB.setEnabled(false);
} else {
} else {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
+ btn_queryTDB.setVisible(false);
progressBar.setProgressBar(null, progressId);
}
progressBar.setProgressBar(null, progressId);
}
+ mainFrame.setEnabled(true);
+ cmb_filterOption.setEnabled(true);
}
};
}
};
@@
-310,8
+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)
@@
-599,7
+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",
@@
-612,7
+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();
}
}
@@
-667,10
+692,7
@@
public class StructureChooser extends GStructureChooser
"-", VIEWS_FROM_FILE, false, null));
if (canQueryTDB && notQueriedTDBYet)
{
"-", VIEWS_FROM_FILE, false, null));
if (canQueryTDB && notQueriedTDBYet)
{
- FilterOption queryTDBOption = new FilterOption(
- MessageManager.getString("label.search_3dbeacons"), "-",
- VIEWS_QUERYING_TDB, false, null);
- cmb_filterOption.addItem(queryTDBOption);
+ btn_queryTDB.setVisible(true);
}
if (cachedPDBExist)
}
if (cachedPDBExist)
@@
-699,12
+721,6
@@
public class StructureChooser extends GStructureChooser
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
- // first check if we need to rebuild dialog
- if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB)
- {
- promptForTDBFetch();
- return;
- }
if (lastSelected == selectedFilterOpt)
{
// don't need to do anything, probably
if (lastSelected == selectedFilterOpt)
{
// don't need to do anything, probably
@@
-1501,4
+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;
+ }
}
}