From b21e94b5a1885b167c9168f1250cc478cfb6a723 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 21 May 2024 18:16:59 +0100
Subject: [PATCH] JAL-4159 PASiMap currently doesn't support different score
 models

---
 src/jalview/gui/CalculationChooser.java      |   13 +++++++------
 test/jalview/gui/CalculationChooserTest.java |   21 +++++++++++++++------
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 80102cb..6536358 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -538,7 +538,7 @@ public class CalculationChooser extends JPanel
     boolean ssPresent = AlignmentUtils.isSecondaryStructurePresent(alignmentAnnotations);
 
     List<ScoreModelI> models = getApplicableScoreModels(nucleotide, pca.isSelected(),
-            ssPresent);
+            ssPresent, pasimap.isSelected());
 
     /*
      * now we can actually add entries to the combobox,
@@ -591,15 +591,16 @@ public class CalculationChooser extends JPanel
    * @return
    */
   protected static List<ScoreModelI> getApplicableScoreModels(
-          boolean nucleotide, boolean forPca, boolean ssPresent)
+          boolean nucleotide, boolean forPca, boolean ssPresent, boolean forPasimap)
   {
     List<ScoreModelI> filtered = new ArrayList<>();
 
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
-      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
-              || ssPresent && sm.isSecondaryStructure())
+      if (!forPasimap && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
+              || sm.isSecondaryStructure() && ssPresent))
+              
       {
         filtered.add(sm);
       }
@@ -609,7 +610,7 @@ public class CalculationChooser extends JPanel
      * special case: add BLOSUM62 as last option for nucleotide PCA, 
      * for backwards compatibility with Jalview < 2.8 (JAL-2962)
      */
-    if (nucleotide && forPca
+    if (!forPasimap && nucleotide && forPca
             && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
     {
       filtered.add(scoreModels.getBlosum62());
@@ -637,7 +638,7 @@ public class CalculationChooser extends JPanel
   {
     boolean doPCA = pca.isSelected();
     boolean doPaSiMap = pasimap.isSelected();
-    String modelName = modelNames.getSelectedItem().toString();
+    String modelName = modelNames.getSelectedItem() == null ? "" : modelNames.getSelectedItem().toString();
     String ssSource = "";
     Object selectedItem = ssSourceDropdown.getSelectedItem();
     if (selectedItem != null) {
diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
index 23538c2..1fbad1d 100644
--- 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, true);
+            .getApplicableScoreModels(false, true, true,false);
     assertEquals(filtered.size(), 5);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
@@ -66,7 +66,7 @@ public class CalculationChooserTest
     /*
      * peptide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(false, false, true);
+    filtered = CalculationChooser.getApplicableScoreModels(false, false, true,false);
     assertEquals(filtered.size(), 5);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
@@ -77,7 +77,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for PCA
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -86,7 +86,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false, false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false, false,false);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -101,7 +101,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are unchanged
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false, true);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false, true,false);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -111,11 +111,20 @@ public class CalculationChooserTest
     /*
      * nucleotide models for PCA add BLOSUM62 as last option
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
     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);
+    
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, false,true);
+    assertEquals(filtered.size(), 0);
+    for (int i=0; i<=8;i++)
+    {
+      boolean isDna = (i & 1) != 0,isPca = (i & 2) != 0,isSS = (i & 4) != 0;
+     
+      assertEquals(CalculationChooser.getApplicableScoreModels(isDna,isPca,isSS,true).size(), 0);
+    }
   }
 }
-- 
1.7.10.2