JAL-4469 Added a checkbox to remove version numbers from accession ids enabled/visibl...

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 9df42b9..a2960db 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1490,3 +1490,4 @@ warning.the_following_errors = The following errors and warnings occurred whilst
 action.show_hetatm = Show Ligands (HETATM)
 warning.running_from_installer_volume_title = Running from Installer
 warning.running_from_installer_volume_message = You appear to be launching {0} from the Installer volume.\nPlease drag and drop the "{0}" icon into the Applications folder or your user Applications folder, and launch from there.
+label.remove_version_numbers_from_ids = Remove version numbers from IDs ("." and following number)

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index b8200fa..a67f238 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1452,3 +1452,4 @@ warning.using_mixed_command_line_arguments = Jalview no puede utilizar argumento
 warning.the_following_errors = Se produjeron los siguientes errores y advertencias al procesar archivos:
 warning.running_from_installer_volume_title = Ejecutando desde el instalador
 warning.running_from_installer_volume_message = Parece que está iniciando {0} desde el Volumen del instalador.\nArrastre y suelte el ícono "{0}" en la carpeta Aplicaciones o en la carpeta Aplicaciones de su usuario e inícielo desde allí.
+label.remove_version_numbers_from_ids = Eliminar la versión del identificador ("." y los números siguientes)

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 137655f..252c855 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -113,6 +113,8 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   JComboBox<StringPair> database;
 
+  JCheckBox removeVersions = null;
+
   JCheckBox replacePunctuation;
 
   JButton okBtn;
@@ -203,6 +205,16 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     this.setLayout(new BorderLayout());
 
+    removeVersions = new JCheckBox(MessageManager
+            .getString("label.remove_version_numbers_from_ids"));
+    removeVersions.setHorizontalAlignment(SwingConstants.LEFT);
+    removeVersions.setFont(new Font("Verdana", Font.ITALIC, 11));
+    boolean removeVersionsDefault = Cache
+            .getDefault("REMOVE_VERSION_FROM_IDENTIFIERS_DEFAULT", true);
+    removeVersions.setSelected(removeVersionsDefault);
+    removeVersions.setEnabled(false);
+    removeVersions.setVisible(false);
+
     database = new JComboBox<>();
     database.setFont(JvSwingUtils.getLabelFont());
     StringPair instructionItem = new StringPair(
@@ -238,6 +250,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 .getKey();
         updateExampleQuery(currentSelection);
 
+        boolean showRemoveVersions = false;
         if ("pdb".equalsIgnoreCase(currentSelection))
         {
           frame.dispose();
@@ -247,6 +260,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           frame.dispose();
           new UniprotFTSPanel(SequenceFetcher.this);
+          showRemoveVersions = true;
         }
         else if ("3d-beacons".equalsIgnoreCase(currentSelection))
         {
@@ -257,6 +271,9 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           otherSourceAction();
         }
+
+        removeVersions.setEnabled(showRemoveVersions);
+        removeVersions.setVisible(showRemoveVersions);
       }
     });
 
@@ -348,6 +365,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     databasePanel.add(exampleAccession, BorderLayout.CENTER);
     JPanel jPanel2a = new JPanel(new BorderLayout());
     jPanel2a.add(jLabel1, BorderLayout.NORTH);
+    jPanel2a.add(removeVersions, BorderLayout.CENTER);
     jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
     databasePanel.add(jPanel2a, BorderLayout.SOUTH);
 
@@ -490,12 +508,10 @@ public class SequenceFetcher extends JPanel implements Runnable
      * tidy inputs and check there is something to search for
      */
     String t0 = textArea.getText();
-    String text = t0.trim();
-    if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
-    {
-      text = text.replace(",", ";");
-    }
-    text = text.replaceAll("(\\s|[; ])+", ";");
+    String text = replaceQueryText(t0,
+            replacePunctuation.isEnabled()
+                    && replacePunctuation.isSelected(),
+            removeVersions.isEnabled() && removeVersions.isSelected());
     if (!t0.equals(text))
     {
       textArea.setText(text);
@@ -526,6 +542,30 @@ public class SequenceFetcher extends JPanel implements Runnable
     worker.start();
   }
 
+  protected static String replaceQueryText(String text0,
+          boolean replaceSemiColons, boolean removeVersions)
+  {
+    String text = text0.trim();
+    if (replaceSemiColons)
+    {
+      text = text.replace(",", ";");
+    }
+    text = text.replaceAll("(\\s|[; ])+", ";");
+    if (removeVersions)
+    {
+      Console.debug("search text was '" + text + "'");
+      // remove all *last* .123 from an ID. (ID is terminated just before a
+      // non-alphanumeric-or-dot [which is replaced] or end of string)
+      text = text.replaceAll("\\.[0-9]+([^0-9a-zA-Z\\.]|$)", "$1");
+      /* or do we want:
+      // remove everything after a first .123.45.6 in an ID
+      text = text.replaceAll("\\.[0-9\\.]+", "");
+      */
+      Console.debug("search text now '" + text + "'");
+    }
+    return text;
+  }
+
   private void resetDialog()
   {
     exampleBtn.setEnabled(true);

diff --git a/test/jalview/gui/SequenceFetcherTest.java b/test/jalview/gui/SequenceFetcherTest.java
new file mode 100644 (file)
index 0000000..34c7956
--- /dev/null
+++ b/test/jalview/gui/SequenceFetcherTest.java
@@ -0,0 +1,62 @@
+package jalview.gui;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+public class SequenceFetcherTest
+{
+  @Test(groups = { "Functional" }, dataProvider = "queryConversions")
+  public void testQueryConversions(String query0, boolean replaceSemiColons,
+          boolean removeVersions, String result)
+  {
+    Assert.assertEquals(
+            SequenceFetcher.replaceQueryText(query0, replaceSemiColons,
+                    removeVersions),
+            result, "Converted query string isn't as expected");
+  }
+
+  @DataProvider(name = "queryConversions")
+  public Object[][] queryConversions()
+  {
+    /**
+     * String typedInQuery, replaceSemiColons, removeVersions, resultantQuery
+     */
+    return new Object[][] {
+        //
+
+        { "P12345", false, false, "P12345" },
+        { "P12345", true, false, "P12345" },
+        { "P12345", false, true, "P12345" },
+        { "P12345", true, true, "P12345" },
+        //
+        { "P12345.1", false, false, "P12345.1" },
+        { "P12345.1", true, false, "P12345.1" },
+        { "P12345.1", false, true, "P12345" },
+        { "P12345.1", true, true, "P12345" },
+        //
+        { "P12345.1 P22222.2", false, false, "P12345.1;P22222.2" },
+        { "P12345.1 P22222.2", true, false, "P12345.1;P22222.2" },
+        { "P12345.1 P22222.2", false, true, "P12345;P22222" },
+        { "P12345.1 P22222.2", true, true, "P12345;P22222" },
+        //
+        { "P12345.1,P22222.2", false, false, "P12345.1,P22222.2" },
+        { "P12345.1,P22222.2", true, false, "P12345.1;P22222.2" },
+        { "P12345.1,P22222.2", false, true, "P12345,P22222" },
+        { "P12345.1,P22222.2", true, true, "P12345;P22222" },
+        //
+        { "P12345.1.9; P22222.2", false, false, "P12345.1.9;P22222.2" },
+        { "P12345.1.9; P22222.2", true, false, "P12345.1.9;P22222.2" },
+        { "P12345.1.9; P22222.2", false, true, "P12345.1;P22222" },
+        { "P12345.1.9; P22222.2", true, true, "P12345.1;P22222" },
+        //
+        { "P12345.1x; P22222.2", false, false, "P12345.1x;P22222.2" },
+        { "P12345.1x; P22222.2", true, false, "P12345.1x;P22222.2" },
+        { "P12345.1x; P22222.2", false, true, "P12345.1x;P22222" },
+        { "P12345.1x; P22222.2", true, true, "P12345.1x;P22222" },
+
+        //
+    };
+  }
+
+}