X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=a1b67e72df49e314a3dec16116018d9adf08e7cc;hb=9f327c52e2dc32b445f87c1852b7f5ffa0196870;hp=8c8f228a745e0e8dc65ac9f23f6abf3cffb3d736;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 8c8f228..a1b67e7 100644
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -38,7 +38,6 @@ import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
@@ -52,8 +51,8 @@ import org.biodas.jdas.schema.sources.COORDINATES;
import org.biodas.jdas.schema.sources.PROP;
import org.biodas.jdas.schema.sources.VERSION;
-public class DasSourceBrowser extends GDasSourceBrowser implements
- Runnable, ListSelectionListener
+public class DasSourceBrowser extends GDasSourceBrowser
+ implements Runnable, ListSelectionListener
{
DasSourceRegistryI sourceRegistry = null;
@@ -125,7 +124,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
{
if (sourceRegistry == null)
{
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "PaintDasThread");
worker.start();
}
}
@@ -138,8 +137,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
for (int i = 0; i < dSize; i++)
{
data[i][0] = sources.get(i).getTitle(); // what's equivalent of nickname
- data[i][1] = new Boolean(selectedSources.contains(sources.get(i)
- .getTitle()));
+ data[i][1] = new Boolean(
+ selectedSources.contains(sources.get(i).getTitle()));
}
refreshTableData(data);
@@ -177,9 +176,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
if (nickName == null)
{
- fullDetails.setText(text
- + MessageManager
- .getString("label.select_das_service_from_table"));
+ fullDetails.setText(text + MessageManager
+ .getString("label.select_das_service_from_table"));
return;
}
@@ -192,8 +190,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
}
VERSION latest = ds.getVersion();
- text.append("Id: " + ds.getUri()
- + "
");
+ text.append(
+ "Id: " + ds.getUri() + "
");
text.append("Nickname: "
+ ds.getTitle() + "
");
@@ -212,8 +210,10 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
text.append("Description: "
+ ds.getDescription() + "
");
- text.append("Admin Email: " + ds.getEmail() + "" + "
");
+ text.append(
+ "Admin Email: " + ds.getEmail() + ""
+ + "
");
text.append("Registered at: "
+ latest.getCreated() + "
");
@@ -351,7 +351,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
}
}
- Vector selected = new Vector();
+ Vector selected = new Vector<>();
for (String source : selectedSources)
{
jalviewSourceI srce = sourceRegistry.getSource(source);
@@ -368,16 +368,16 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
{
saveProperties(jalview.bin.Cache.applicationProperties);
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "RepaintDasThread");
worker.start();
}
private void setCapabilities(DasSourceRegistryI sourceRegistry2)
{
- Vector authority = new Vector();
- Vector type = new Vector();
- Vector label = new Vector();
- Vector taxIds = new Vector();
+ Vector authority = new Vector<>();
+ Vector type = new Vector<>();
+ Vector label = new Vector<>();
+ Vector taxIds = new Vector<>();
authority.add("Any");
type.add("Any");
label.add("Any");
@@ -453,15 +453,14 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
pane12.add(nametf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.url")),
+ pane12.add(new JLabel(MessageManager.getString("label.url:")),
BorderLayout.NORTH);
pane12.add(seqs, BorderLayout.SOUTH);
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.SOUTH);
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- panel,
- MessageManager.getString("label.enter_local_das_source"),
+ panel, MessageManager.getString("label.enter_local_das_source"),
JvOptionPane.OK_CANCEL_OPTION);
if (reply != JvOptionPane.OK_OPTION)
@@ -474,19 +473,21 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
urltf.setText(urltf.getText() + "/");
}
- jalviewSourceI local = sourceRegistry.createLocalSource(
- urltf.getText(), nametf.getText(), seqs.isSelected(), true);
+ jalviewSourceI local = sourceRegistry.createLocalSource(urltf.getText(),
+ nametf.getText(), seqs.isSelected(), true);
List sources = sourceRegistry.getSources();
int osize = sources.size();
int size = osize + (newSource ? 1 : 0);
Object[][] data = new Object[size][2];
- DASTableModel dtm = (table != null) ? (DASTableModel) ((TableSorter) table
- .getModel()).getTableModel() : null;
+ DASTableModel dtm = (table != null)
+ ? (DASTableModel) ((TableSorter) table.getModel())
+ .getTableModel()
+ : null;
for (int i = 0; i < osize; i++)
{
- String osrc = (dtm == null || i >= osize) ? null : (String) dtm
- .getValueAt(i, 0);
+ String osrc = (dtm == null || i >= osize) ? null
+ : (String) dtm.getValueAt(i, 0);
if (!newSource && osrc != null
&& dtm.getValueAt(i, 0).equals(nickname))
{
@@ -514,8 +515,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
@Override
public void run()
{
- scrollPane.getVerticalScrollBar().setValue(
- scrollPane.getVerticalScrollBar().getMaximum());
+ scrollPane.getVerticalScrollBar()
+ .setValue(scrollPane.getVerticalScrollBar().getMaximum());
}
});
@@ -534,13 +535,11 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
if (!sourceRegistry.getSource(nickname).isLocal())
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_can_only_edit_or_remove_local_das_sources"),
- MessageManager.getString("label.public_das_source"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.you_can_only_edit_or_remove_local_das_sources"),
+ MessageManager.getString("label.public_das_source"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@@ -548,8 +547,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
int choice = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
"Do you want to edit or remove " + nickname + "?",
"Edit / Remove Local DAS Source",
- JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.QUESTION_MESSAGE,
- null, options, options[2]);
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.QUESTION_MESSAGE, null, options, options[2]);
switch (choice)
{
@@ -560,8 +559,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
sourceRegistry.removeLocalSource(sourceRegistry.getSource(nickname));
selectedSources.remove(nickname);
Object[][] data = new Object[sourceRegistry.getSources().size()][2];
- int index = 0,
- l = table.getRowCount();
+ int index = 0, l = table.getRowCount();
for (int i = 0; i < l; i++)
{
@@ -583,8 +581,8 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
@Override
public void run()
{
- scrollPane.getVerticalScrollBar().setValue(
- scrollPane.getVerticalScrollBar().getMaximum());
+ scrollPane.getVerticalScrollBar()
+ .setValue(scrollPane.getVerticalScrollBar().getMaximum());
}
});
@@ -618,11 +616,10 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
VERSION v = ds.getVersion();
List coords = v.getCOORDINATES();
- if (ds.isLocal()
- || ((coords == null || coords.size() == 0)
- && filter1.getSelectedIndex() == 0
- && filter2.getSelectedIndex() == 0 && filter3
- .getSelectedIndex() == 0))
+ if (ds.isLocal() || ((coords == null || coords.size() == 0)
+ && filter1.getSelectedIndex() == 0
+ && filter2.getSelectedIndex() == 0
+ && filter3.getSelectedIndex() == 0))
{
// THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
// HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
@@ -642,12 +639,14 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
for (int j = 0; j < coords.size(); j++)
{
if (selectedInList(filter1.getSelectedValues(),
- new String[] { coords.get(j).getAuthority() })
+ new String[]
+ { coords.get(j).getAuthority() })
&& selectedInList(filter2.getSelectedValues(), new String[]
{ coords.get(j).getSource() }))
{
names.add(ds.getTitle());
- selected.add(new Boolean(selectedSources.contains(ds.getTitle())));
+ selected.add(
+ new Boolean(selectedSources.contains(ds.getTitle())));
break;
}
}