JAL-2416 add score model description field for tooltip in PCA panel

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 0e30064..6ca43b0 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -177,6 +177,8 @@ label.select_score_model = Select score model
 label.score_model_pid = % Identity
 label.score_model_blosum62 = BLOSUM62
 label.score_model_pam250 = PAM 250
+label.score_model_smithwatermanscore = Score between two sequences aligned with Smith-Waterman with default Peptide/Nucleotide matrix
+label.score_model_sequencefeaturesimilarity = Distance measure of average number of features not shared at sequence positions 
 label.score_model_conservation = Physicochemical property conservation
 label.score_model_enhconservation = Physicochemical property conservation
 label.status_bar = Status bar

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index b44b4cf..5bf4b11 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -41,8 +41,19 @@ import java.util.Set;
 public class FeatureDistanceModel implements DistanceScoreModelI,
         ViewBasedAnalysisI
 {
+  private static final String NAME = "Sequence Feature Similarity";
+
+  private String description;
+
   FeatureRenderer fr;
 
+  /**
+   * Constructor
+   */
+  public FeatureDistanceModel()
+  {
+  }
+
   @Override
   public boolean configureFromAlignmentView(AlignmentViewPanel view)
 
@@ -183,7 +194,13 @@ public class FeatureDistanceModel implements DistanceScoreModelI,
   @Override
   public String getName()
   {
-    return "Sequence Feature Similarity";
+    return NAME;
+  }
+
+  @Override
+  public String getDescription()
+  {
+    return description;
   }
 
   @Override

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index a3358aa..3e940af 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -14,11 +14,27 @@ import jalview.util.Comparison;
 public class PIDModel implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
+  private static final String NAME = "PID";
+
+  private String description;
+
+  /**
+   * Constructor
+   */
+  public PIDModel()
+  {
+  }
 
   @Override
   public String getName()
   {
-    return "% Identity (PID)";
+    return NAME;
+  }
+
+  @Override
+  public String getDescription()
+  {
+    return description;
   }
 
   @Override

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 6a74dfc..b73f826 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -51,10 +51,16 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
   /*
    * the name of the model as shown in menus
+   * each score model in use should have a unique name
    */
   private String name;
 
   /*
+   * a description for the model as shown in tooltips
+   */
+  private String description;
+
+  /*
    * the characters that the model provides scores for
    */
   private char[] symbols;
@@ -165,6 +171,12 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   @Override
+  public String getDescription()
+  {
+    return description;
+  }
+
+  @Override
   public boolean isDNA()
   {
     return !peptide;
@@ -487,4 +499,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   {
     return new String(symbols);
   }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
 }

diff --git a/src/jalview/analysis/scoremodels/SmithWatermanModel.java b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
index eec08ed..190b88f 100644 (file)
--- a/src/jalview/analysis/scoremodels/SmithWatermanModel.java
+++ b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
@@ -37,6 +37,15 @@ public class SmithWatermanModel implements SimilarityScoreModelI
 {
   private static final String NAME = "Smith Waterman Score";
 
+  private String description;
+
+  /**
+   * Constructor
+   */
+  public SmithWatermanModel()
+  {
+  }
+
   @Override
   public MatrixI findSimilarities(AlignmentView seqData,
           SimilarityParamsI options)
@@ -88,8 +97,8 @@ public class SmithWatermanModel implements SimilarityScoreModelI
   }
 
   @Override
-  public String toString()
+  public String getDescription()
   {
-    return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+    return description;
   }
 }

diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java
index 4433cea..7352a71 100644 (file)
--- a/src/jalview/api/analysis/ScoreModelI.java
+++ b/src/jalview/api/analysis/ScoreModelI.java
@@ -12,6 +12,15 @@ public interface ScoreModelI
   String getName();
 
   /**
+   * Answers an informative description of the model, suitable for use in
+   * tooltips. Descriptions may be internationalised, and need not be unique
+   * (but should be).
+   * 
+   * @return
+   */
+  String getDescription();
+
+  /**
    * Answers true if this model is applicable for nucleotide data (so should be
    * shown in menus in that context)
    * 

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 3b73c5a..885c3bf 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -195,10 +195,19 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
       final String name = sm.getName();
-      // create an entry for this score matrix for use in PCA
-      JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
-      jm.setText(MessageManager.getStringOrReturn("label.score_model_",
-              name));
+      JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
+
+      /*
+       * if the score model doesn't provide a description, try to look one
+       * up in the text bundle, falling back on its name
+       */
+      String tooltip = sm.getDescription();
+      if (tooltip == null)
+      {
+        tooltip = MessageManager.getStringOrReturn("label.score_model_",
+                name);
+      }
+      jm.setToolTipText(tooltip);
       jm.setSelected(pcaModel.getScoreModelName().equals(name));
       if ((pcaModel.isNucleotide() && sm.isDNA())
               || (!pcaModel.isNucleotide() && sm.isProtein()))

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index 8265cd8..03513f1 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -47,7 +47,7 @@ public class ScoreModelsTest
     assertTrue(sm instanceof SimilarityScoreModelI);
     assertTrue(sm instanceof PairwiseScoreModelI);
     assertFalse(sm instanceof DistanceScoreModelI);
-    assertEquals(sm.getName(), "% Identity (PID)");
+    assertEquals(sm.getName(), "PID");
     assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
     assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);