JAL-2962 option to offer BLOSUM62 for nucleotide PCA

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f674c7e..f0d9521 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -25,6 +25,7 @@ import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
@@ -103,7 +104,7 @@ public class CalculationChooser extends JPanel
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 
-  List<String> tips = new ArrayList<String>();
+  List<String> tips = new ArrayList<>();
 
   /*
    * the most recently opened PCA results panel
@@ -375,7 +376,7 @@ public class CalculationChooser extends JPanel
    */
   protected JComboBox<String> buildModelOptionsList()
   {
-    final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+    final JComboBox<String> scoreModelsCombo = new JComboBox<>();
     scoreModelsCombo.setRenderer(renderer);
 
     /*
@@ -418,39 +419,42 @@ public class CalculationChooser extends JPanel
   {
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
-    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+
+    /*
+     * select the score models applicable to the alignment type
+     */
+    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+    List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+            pca.isSelected());
 
     /*
      * now we can actually add entries to the combobox,
      * remembering their descriptions for tooltips
      */
-    ScoreModels scoreModels = ScoreModels.getInstance();
     boolean selectedIsPresent = false;
-    for (ScoreModelI sm : scoreModels.getModels())
+    for (ScoreModelI sm : models)
     {
-      boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-      if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+      if (curSel != null && sm.getName().equals(curSel))
+      {
+        selectedIsPresent = true;
+        curSel = sm.getName();
+      }
+      model.addElement(sm.getName());
+
+      /*
+       * tooltip is description if provided, else text lookup with
+       * fallback on the model name
+       */
+      String tooltip = sm.getDescription();
+      if (tooltip == null)
       {
-        if (curSel != null && sm.getName().equals(curSel))
-        {
-          selectedIsPresent = true;
-          curSel = sm.getName();
-        }
-        model.addElement(sm.getName());
-
-        /*
-         * tooltip is description if provided, else text lookup with
-         * fallback on the model name
-         */
-        String tooltip = sm.getDescription();
-        if (tooltip == null)
-        {
-          tooltip = MessageManager.getStringOrReturn("label.score_model_",
-                  sm.getName());
-        }
-        toolTips.add(tooltip);
+        tooltip = MessageManager.getStringOrReturn("label.score_model_",
+                sm.getName());
       }
+      toolTips.add(tooltip);
     }
+
     if (selectedIsPresent)
     {
       model.setSelectedItem(curSel);
@@ -460,6 +464,47 @@ public class CalculationChooser extends JPanel
   }
 
   /**
+   * Builds a list of score models which are applicable for the alignment and
+   * calculation type (peptide or generic models for protein, nucleotide or
+   * generic models for nucleotide).
+   * <p>
+   * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA.
+   * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62
+   * was the only score matrix supported. This is included if property
+   * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file.
+   * 
+   * @param nucleotide
+   * @param forPca
+   * @return
+   */
+  protected static List<ScoreModelI> getApplicableScoreModels(
+          boolean nucleotide, boolean forPca)
+  {
+    List<ScoreModelI> filtered = new ArrayList<>();
+
+    ScoreModels scoreModels = ScoreModels.getInstance();
+    for (ScoreModelI sm : scoreModels.getModels())
+    {
+      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+      {
+        filtered.add(sm);
+      }
+    }
+
+    /*
+     * special case: add BLOSUM62 as last option for nucleotide PCA, 
+     * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+     */
+    if (nucleotide && forPca
+            && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+    {
+      filtered.add(scoreModels.getBlosum62());
+    }
+
+    return filtered;
+  }
+
+  /**
    * Open and calculate the selected tree or PCA on 'OK'
    */
   protected void calculate_actionPerformed()

diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
new file mode 100644 (file)
index 0000000..6c2e777
--- /dev/null
+++ b/test/jalview/gui/CalculationChooserTest.java
@@ -0,0 +1,98 @@
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertSame;
+
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.bin.Cache;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CalculationChooserTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    // read-only Jalview properties
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+            Boolean.FALSE.toString());
+  }
+
+  @Test(groups = "Functional")
+  public void testGetApplicableScoreModels()
+  {
+    ScoreModels models = ScoreModels.getInstance();
+    ScoreModelI blosum62 = models.getBlosum62();
+    ScoreModelI pam250 = models.getPam250();
+    ScoreModelI dna = models.getDefaultModel(false);
+
+    /*
+     * peptide models for PCA
+     */
+    List<ScoreModelI> filtered = CalculationChooser
+            .getApplicableScoreModels(false, true);
+    assertEquals(filtered.size(), 4);
+    assertSame(filtered.get(0), blosum62);
+    assertSame(filtered.get(1), pam250);
+    assertEquals(filtered.get(2).getName(), "PID");
+    assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+
+    /*
+     * peptide models for Tree are the same
+     */
+    filtered = CalculationChooser.getApplicableScoreModels(false, false);
+    assertEquals(filtered.size(), 4);
+    assertSame(filtered.get(0), blosum62);
+    assertSame(filtered.get(1), pam250);
+    assertEquals(filtered.get(2).getName(), "PID");
+    assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+
+    /*
+     * nucleotide models for PCA
+     */
+    filtered = CalculationChooser.getApplicableScoreModels(true, true);
+    assertEquals(filtered.size(), 3);
+    assertSame(filtered.get(0), dna);
+    assertEquals(filtered.get(1).getName(), "PID");
+    assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+    /*
+     * nucleotide models for Tree are the same
+     */
+    filtered = CalculationChooser.getApplicableScoreModels(true, false);
+    assertEquals(filtered.size(), 3);
+    assertSame(filtered.get(0), dna);
+    assertEquals(filtered.get(1).getName(), "PID");
+    assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+    /*
+     * enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962)
+     */
+    Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+            Boolean.TRUE.toString());
+
+    /*
+     * nucleotide models for Tree are unchanged
+     */
+    filtered = CalculationChooser.getApplicableScoreModels(true, false);
+    assertEquals(filtered.size(), 3);
+    assertSame(filtered.get(0), dna);
+    assertEquals(filtered.get(1).getName(), "PID");
+    assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+    /*
+     * nucleotide models for PCA add BLOSUM62 as last option
+     */
+    filtered = CalculationChooser.getApplicableScoreModels(true, true);
+    assertEquals(filtered.size(), 4);
+    assertSame(filtered.get(0), dna);
+    assertEquals(filtered.get(1).getName(), "PID");
+    assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+    assertSame(filtered.get(3), blosum62);
+  }
+}