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JAL-2326 updated references of JOptionPane to JvOptionPane
[jalview.git]
/
src
/
jalview
/
gui
/
Preferences.java
diff --git
a/src/jalview/gui/Preferences.java
b/src/jalview/gui/Preferences.java
index
b36a73d
..
b293e6f
100755
(executable)
--- a/
src/jalview/gui/Preferences.java
+++ b/
src/jalview/gui/Preferences.java
@@
-20,8
+20,8
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.EMBLEBI_STRING;
import static jalview.util.UrlConstants.EMBLEBI_STRING;
-import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import static jalview.util.UrlConstants.SRS_STRING;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import static jalview.util.UrlConstants.SRS_STRING;
@@
-126,7
+126,11
@@
public class Preferences extends GPreferences
String name = st.nextToken();
String url = st.nextToken();
// check for '|' within a regex
String name = st.nextToken();
String url = st.nextToken();
// check for '|' within a regex
- int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+ int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
+ if (rxstart == -1)
+ {
+ rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+ }
while (rxstart == -1 && url.indexOf("/=$") == -1)
{
url = url + "|" + st.nextToken();
while (rxstart == -1 && url.indexOf("/=$") == -1)
{
url = url + "|" + st.nextToken();
@@
-144,12
+148,6
@@
public class Preferences extends GPreferences
{
sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
}
{
sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
}
- // upgrade old EMBL-EBI link
- int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
- if (emblPos > -1)
- {
- sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
- }
}
/**
}
/**
@@
-569,6
+567,7
@@
public class Preferences extends GPreferences
else
{
Cache.applicationProperties.remove("SEQUENCE_LINKS");
else
{
Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ sequenceURLLinks.clear();
}
Cache.applicationProperties.setProperty("USE_PROXY",
}
Cache.applicationProperties.setProperty("USE_PROXY",
@@
-755,9
+754,9
@@
public class Preferences extends GPreferences
boolean valid = false;
while (!valid)
{
boolean valid = false;
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
MessageManager.getString("label.new_sequence_url_link"),
- JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
{
if (link.checkValid())
{
@@
-782,10
+781,10
@@
public class Preferences extends GPreferences
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
return;
}
@@
-796,9
+795,9
@@
public class Preferences extends GPreferences
while (!valid)
{
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
MessageManager.getString("label.new_sequence_url_link"),
- JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
{
if (link.checkValid())
{
@@
-822,10
+821,10
@@
public class Preferences extends GPreferences
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
nameLinks.removeElementAt(index);
return;
}
nameLinks.removeElementAt(index);
@@
-917,10
+916,10
@@
public class Preferences extends GPreferences
}
} catch (NumberFormatException x)
{
}
} catch (NumberFormatException x)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
}
userIdWidth.setText("");
}
}
@@
-943,10
+942,10
@@
public class Preferences extends GPreferences
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
return false;
}
}
return false;
}
}
@@
-982,13
+981,13
@@
public class Preferences extends GPreferences
if (!found)
{
String[] options = { "OK", "Help" };
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JOptionPane.showInternalOptionDialog(
+ int showHelp = JvOptionPane.showInternalOptionDialog(
Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
- "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
null, options, options[0]);
- if (showHelp == JOptionPane.NO_OPTION)
+ if (showHelp == JvOptionPane.NO_OPTION)
{
try
{
{
try
{