JAL-4386 Added further checks for sequences that have no secondary structure.

diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index 7fcee35..0aac7fa 100644 (file)
--- a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
@@ -255,14 +255,19 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel
          int seqPosition = seq.findPosition(columnPosition);
          AlignmentAnnotation[] aa = seq.getRefSeq().getAnnotation("Secondary Structure");
          if (aa != null) {
+           if (aa[0].getAnnotationForPosition(seqPosition) != null) {
              Annotation a = aa[0].getAnnotationForPosition(seqPosition);
              ss = a.secondaryStructure;
              if (ss == ' ') {
-                 ss = 'C'; // In JalView, 'C' is represented as ' ' 
-             }
-             if (ss != '\0') { // Check if ss is not the default null character
-                 secondaryStructure.add(String.valueOf(ss));
+               ss = 'C'; // In JalView, 'C' is represented as ' ' 
              }
+           }
+           else {
+             ss = 'C';
+           }
+           if (ss != '\0') { // Check if ss is not the default null character
+             secondaryStructure.add(String.valueOf(ss));
+           }
          }
          return secondaryStructure;
   }

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index af41e58..25885d7 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -58,7 +58,9 @@ import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
 /**
@@ -430,8 +432,27 @@ public class CalculationChooser extends JPanel
      * select the score models applicable to the alignment type
      */
     boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-    List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
-            pca.isSelected());
+    AlignmentAnnotation[] alignmentAnnotation = af.getViewport().getAlignment().getAlignmentAnnotation();
+
+    boolean ssPresent = false;
+
+    for (AlignmentAnnotation aa : alignmentAnnotation)
+
+    {
+      if(ssPresent) {
+        break;
+      }     
+
+      if (aa.label.equals("Secondary Structure"))
+
+      {
+        ssPresent = true;
+        break;
+      }
+    }
+
+    List<ScoreModelI> models = getApplicableScoreModels(nucleotide, pca.isSelected(),
+            ssPresent);
 
     /*
      * now we can actually add entries to the combobox,
@@ -483,14 +504,15 @@ public class CalculationChooser extends JPanel
    * @return
    */
   protected static List<ScoreModelI> getApplicableScoreModels(
-          boolean nucleotide, boolean forPca)
+          boolean nucleotide, boolean forPca, boolean ssPresent)
   {
     List<ScoreModelI> filtered = new ArrayList<>();
 
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
-      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
+              || ssPresent && sm.isSecondaryStructure())
       {
         filtered.add(sm);
       }
@@ -505,7 +527,7 @@ public class CalculationChooser extends JPanel
     {
       filtered.add(scoreModels.getBlosum62());
     }
-
+    
     return filtered;
   }
 

diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
index 9835189..5e6d57c 100644 (file)
--- a/test/jalview/gui/CalculationChooserTest.java
+++ b/test/jalview/gui/CalculationChooserTest.java
@@ -55,7 +55,7 @@ public class CalculationChooserTest
      * peptide models for PCA
      */
     List<ScoreModelI> filtered = CalculationChooser
-            .getApplicableScoreModels(false, true);
+            .getApplicableScoreModels(false, true, true);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
@@ -65,7 +65,7 @@ public class CalculationChooserTest
     /*
      * peptide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(false, false);
+    filtered = CalculationChooser.getApplicableScoreModels(false, false, true);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
@@ -75,7 +75,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for PCA
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, true);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -84,7 +84,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false, true);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -99,7 +99,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are unchanged
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false, true);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -108,7 +108,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for PCA add BLOSUM62 as last option
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, true);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");