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Merge branch 'develop' into trialMerge
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceFetcher.java
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
a9df882
..
8e1d549
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-28,6
+28,7
@@
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.fts.service.uniprot.UniprotFTSPanel;
import jalview.datamodel.SequenceI;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
@@
-116,8
+117,6
@@
public class SequenceFetcher extends JPanel implements Runnable
private static Thread initingThread = null;
private static Thread initingThread = null;
- int debounceTrap = 0;
-
public JTextArea getTextArea()
{
return textArea;
public JTextArea getTextArea()
{
return textArea;
@@
-169,9
+168,8
@@
public class SequenceFetcher extends JPanel implements Runnable
if (sfetch == null
|| dasRegistry != Cache.getDasSourceRegistry()
|| lastDasSourceRegistry != (Cache.getDasSourceRegistry()
if (sfetch == null
|| dasRegistry != Cache.getDasSourceRegistry()
|| lastDasSourceRegistry != (Cache.getDasSourceRegistry()
- .getDasRegistryURL() + Cache
- .getDasSourceRegistry().getLocalSourceString())
- .hashCode())
+ .getDasRegistryURL() + Cache.getDasSourceRegistry()
+ .getLocalSourceString()).hashCode())
{
_initingFetcher = true;
initingThread = Thread.currentThread();
{
_initingFetcher = true;
initingThread = Thread.currentThread();
@@
-215,7
+213,7
@@
public class SequenceFetcher extends JPanel implements Runnable
public SequenceFetcher(IProgressIndicator guiIndic,
final String selectedDb, final String queryString)
{
public SequenceFetcher(IProgressIndicator guiIndic,
final String selectedDb, final String queryString)
{
- this._isConstructing=true;
+ this._isConstructing = true;
this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
@@
-228,7
+226,7
@@
public class SequenceFetcher extends JPanel implements Runnable
if (getSequenceFetcherSingleton(progressIndicator) != null)
{
us.initGui(progressIndicator, selectedDb, queryString);
if (getSequenceFetcherSingleton(progressIndicator) != null)
{
us.initGui(progressIndicator, selectedDb, queryString);
- us._isConstructing=false;
+ us._isConstructing = false;
}
else
{
}
else
{
@@
-237,14
+235,14
@@
public class SequenceFetcher extends JPanel implements Runnable
@Override
public void run()
{
@Override
public void run()
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("warn.couldnt_create_sequence_fetcher_client"),
MessageManager
.getString("label.couldnt_create_sequence_fetcher"),
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("warn.couldnt_create_sequence_fetcher_client"),
MessageManager
.getString("label.couldnt_create_sequence_fetcher"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
});
}
});
@@
-254,17
+252,23
@@
public class SequenceFetcher extends JPanel implements Runnable
});
sf.start();
}
});
sf.start();
}
+
/**
/**
- * blocking call which creates a new sequence fetcher panel, configures it and presses the OK button with the given database and query.
+ * blocking call which creates a new sequence fetcher panel, configures it and
+ * presses the OK button with the given database and query.
+ *
* @param database
* @param query
*/
public static List<AlignFrame> fetchAndShow(String database, String query)
{
* @param database
* @param query
*/
public static List<AlignFrame> fetchAndShow(String database, String query)
{
- final SequenceFetcher sf = new SequenceFetcher(Desktop.instance, database, query);
+ final SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
+ database, query);
while (sf._isConstructing)
{
while (sf._isConstructing)
{
- try { Thread.sleep(50);
+ try
+ {
+ Thread.sleep(50);
} catch (Exception q)
{
return Collections.emptyList();
} catch (Exception q)
{
return Collections.emptyList();
@@
-284,7
+288,7
@@
public class SequenceFetcher extends JPanel implements Runnable
{
};
{
};
-
+
/**
* initialise the database and query for this fetcher panel
*
/**
* initialise the database and query for this fetcher panel
*
@@
-303,13
+307,21
@@
public class SequenceFetcher extends JPanel implements Runnable
try
{
List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
try
{
List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
- if (sp == null || sp.size() != 1)
+ for (DbSourceProxy sourcep : sp)
+ {
+ if (sourcep.getTier() == 0)
+ {
+ database.selection = Arrays
+ .asList(new DbSourceProxy[] { sourcep });
+ break;
+ }
+ }
+ if (database.selection == null || database.selection.size() == 0)
{
System.err.println("Ignoring fetch parameter db='" + selectedDb
+ "'");
return false;
}
{
System.err.println("Ignoring fetch parameter db='" + selectedDb
+ "'");
return false;
}
- database.selection = sp;
textArea.setText(queryString);
} catch (Exception q)
{
textArea.setText(queryString);
} catch (Exception q)
{
@@
-445,7
+457,6
@@
public class SequenceFetcher extends JPanel implements Runnable
jPanel1.add(example);
jPanel1.add(clear);
jPanel1.add(close);
jPanel1.add(example);
jPanel1.add(clear);
jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
databaseButt = /*database.getDatabaseSelectorButton();
final JButton viewdbs =*/new JButton(
jPanel2.setLayout(borderLayout3);
databaseButt = /*database.getDatabaseSelectorButton();
final JButton viewdbs =*/new JButton(
@@
-466,7
+477,6
@@
public class SequenceFetcher extends JPanel implements Runnable
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- debounceTrap++;
String currentSelection = database.getSelectedItem();
if (currentSelection == null)
{
String currentSelection = database.getSelectedItem();
if (currentSelection == null)
{
@@
-475,13
+485,11
@@
public class SequenceFetcher extends JPanel implements Runnable
showPanel();
showPanel();
- if (currentSelection.equalsIgnoreCase("pdb")
- && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ if ("pdb".equalsIgnoreCase(currentSelection))
{
pdbSourceAction();
}
{
pdbSourceAction();
}
- else if (currentSelection.equalsIgnoreCase("uniprot")
- && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
{
uniprotSourceAction();
}
{
uniprotSourceAction();
}
@@
-521,6
+529,7
@@
public class SequenceFetcher extends JPanel implements Runnable
new UniprotFTSPanel(this);
frame.dispose();
}
new UniprotFTSPanel(this);
frame.dispose();
}
+
private void otherSourceAction()
{
try
private void otherSourceAction()
{
try
@@
-910,8
+919,8
@@
public class SequenceFetcher extends JPanel implements Runnable
} catch (Exception e)
{
Cache.log.info(
} catch (Exception e)
{
Cache.log.info(
- "Error retrieving " + accession
- + " from " + proxy.getDbName(), e);
+ "Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
return success;
}
}
return success;
}
@@
-970,7
+979,7
@@
public class SequenceFetcher extends JPanel implements Runnable
}
AlignmentI parseResult(AlignmentI al, String title,
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat,
+ FileFormatI currentFileFormat,
FeatureSettingsModelI preferredFeatureColours)
{
FeatureSettingsModelI preferredFeatureColours)
{
@@
-1030,8
+1039,7
@@
public class SequenceFetcher extends JPanel implements Runnable
try
{
try
{
- af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
} catch (Exception ex)
{
}
@@
-1052,9
+1060,9
@@
public class SequenceFetcher extends JPanel implements Runnable
@Override
public void run()
{
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
MessageManager.getString("label.error_retrieving_data"),
MessageManager.getString("label.error_retrieving_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
}
});
}