JAL-2282 Changed DB accession id token to $DB_ACCESSION$; updated

messages

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index c3cf90a..bce538c 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -787,9 +787,9 @@ label.hide_columns_containing = Hide columns containing
 label.hide_columns_not_containing = Hide columns that do not contain
 option.trim_retrieved_seqs = Trim retrieved sequences
 label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
-label.use_sequence_id_1 = Use $ACCESSION_ID$ or $ACCESSION_ID=/<regex>/=$
+label.use_sequence_id_1 = Use $DB_ACCESSION$ or $DB_ACCESSION=/<regex>/=$
 label.use_sequence_id_2 = to embed accession id in URL
-label.use_sequence_id_3 = Use $SEQUENCE_ID$ similarly to embed sequence name
+label.use_sequence_id_3 = Use $SEQUENCE_ID$ similarly to embed sequence id
 label.use_sequence_id_4 = 
 label.ws_parameters_for = Parameters for {0}
 label.switch_server = Switch server
@@ -1268,3 +1268,7 @@ status.exporting_alignment_as_x_file = Exporting alignment as {0} file
 label.column = Column
 label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
 label.operation_failed = Operation failed
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB accessions
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in Tools | Preferences | Connections:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
+label.do_not_display_again = Do not display this message again

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index e92483f..535abba 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -720,10 +720,10 @@ label.select_columns_containing = Seleccione las columnas que contengan
 label.select_columns_not_containing = Seleccione las columnas que no contengan
 option.trim_retrieved_seqs = Ajustar las secuencias recuperadas
 label.trim_retrieved_sequences = Cuando la secuencia de referencia es más larga que la secuencia con la que está trabajando, sólo se mantienen las subsecuencias relevantes.
-label.use_sequence_id_1 = Utilice $ACCESSION_ID$ o $ACCESSION_ID=/<regex>/=$
+label.use_sequence_id_1 = Utilice $DB_ACCESSION$ o $DB_ACCESSION=/<regex>/=$
 label.use_sequence_id_2 = para embeber el accession id en una URL
 label.use_sequence_id_3 = Utilice $SEQUENCE_ID$ de manera similar para embeber
-label.use_sequence_id_4 = el nombre de la secuencia
+label.use_sequence_id_4 = el ID de la secuencia
 label.ws_parameters_for = Parámetros para {0}
 label.switch_server = Cambiar servidor
 label.open_jabaws_web_page = Abra el página principal del servidor JABAWS en un navegador web
@@ -1269,3 +1269,7 @@ status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo
 label.column = Columna
 label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos
 label.operation_failed = Operación fallada
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ no se utiliza más para los DB accessions
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Por favor, revise sus URL links en Tools | Preferences | Connections:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
+label.do_not_display_again = No mostrar este mensaje de nuevo
\ No newline at end of file

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 3f457ea..b1b913b 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -82,9 +82,12 @@ import java.util.concurrent.Executors;
 import java.util.concurrent.Semaphore;
 
 import javax.swing.AbstractAction;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
 import javax.swing.DefaultDesktopManager;
 import javax.swing.DesktopManager;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JComponent;
 import javax.swing.JDesktopPane;
@@ -382,6 +385,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     showNews.setVisible(false);
 
+    checkURLLinks();
+
     this.addWindowListener(new WindowAdapter()
     {
       @Override
@@ -2256,6 +2261,55 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     new Thread(jvq).start();
   }
 
+  public void checkURLLinks()
+  {
+    // Thread off the URL link checker
+    addDialogThread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        if (Cache.getDefault("CHECKURLLINKS", true))
+        {
+          // check in case URL links use old style tokens ($SEQUENCE_ID$ for
+          // sequence id _or_ accession id)
+          JPanel msgPanel = new JPanel();
+          msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
+          msgPanel.add(Box.createVerticalGlue());
+          JLabel msg = new JLabel(
+                  MessageManager
+                          .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+          JLabel msg2 = new JLabel(
+                  MessageManager
+                          .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+          msgPanel.add(msg);
+          msgPanel.add(msg2);
+
+          final JCheckBox jcb = new JCheckBox(
+                  MessageManager.getString("label.do_not_display_again"));
+          jcb.addActionListener(new ActionListener()
+          {
+
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // update Cache settings if checkbox is selected
+              if (jcb.isSelected())
+              {
+                Cache.setProperty("CHECKURLLINKS", "false");
+              }
+            }
+          });
+          msgPanel.add(jcb);
+
+          JOptionPane.showMessageDialog(null, msgPanel, MessageManager
+                  .getString("label.SEQUENCE_ID_no_longer_used"),
+                  JOptionPane.WARNING_MESSAGE);
+        }
+      }
+    });
+    }
+
   /**
    * Proxy class for JDesktopPane which optionally displays the current memory
    * usage and highlights the desktop area with a red bar if free memory runs

diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java
index b511b8c..b70edf5 100644 (file)
--- a/src/jalview/util/UrlConstants.java
+++ b/src/jalview/util/UrlConstants.java
@@ -29,7 +29,7 @@ public class UrlConstants
   /*
    * Sequence ID string
    */
-  public static final String SEQUENCE_ID = "ACCESSION_ID";
+  public static final String SEQUENCE_ID = "DB_ACCESSION";
 
   /*
    * Sequence Name string