From 6e8e0af46a13c3a314754245ff27273f7a11eb18 Mon Sep 17 00:00:00 2001
From: MorellThomas <morellth@yahoo.co.jp>
Date: Thu, 23 May 2024 14:50:03 +0200
Subject: [PATCH] Fix PaSiMap taking scoreModels input and allow
 AlignSeq/PairwiseAlignPanel to take a ScoreMatrix

---
 src/jalview/analysis/AlignSeq.java      |   33 ++-----------------------------
 src/jalview/analysis/PaSiMap.java       |   20 +++++++++++++++----
 src/jalview/gui/CalculationChooser.java |   11 ++++++++++-
 src/jalview/gui/PairwiseAlignPanel.java |    7 +++++++
 4 files changed, 35 insertions(+), 36 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 22cffb1..ae8638d 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1466,37 +1466,8 @@ public class AlignSeq
     this.alignmentScore = (score <= minScore) ? Float.NaN : score;
   }
 
-  public void clear()
+  public void setScoreMatrix(ScoreMatrix sm)
   {
-    score = null;
-    alignmentScore = 0f;
-    E = null;
-    F = null;
-    traceback = null; // todo is this actually used?
-    seq1 = null;
-    seq2 = null;
-    s1 = null;
-    s2 = null;
-    s1str = null;
-    s2str = null;
-    maxi = 0;
-    maxj = 0;
-    aseq1 = null;
-    aseq2 = null;
-    astr1 = "";
-    astr2 = "";
-    indelfreeAstr1 = "";
-    indelfreeAstr2 = "";
-    seq1start = 0;
-    seq1end = 0;
-    seq2start = 0;
-    seq2end = 0;
-    count = 0;
-    maxscore = 0f;
-    meanScore = 0f;	//needed for PaSiMap
-    hypotheticMaxScore = 0; 	// needed for PaSiMap
-    prev = 0;
-    StringBuffer output = new StringBuffer();
-    String type = null; // AlignSeq.PEP or AlignSeq.DNA
+    this.scoreMatrix = sm;
   }
 }
diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 86888ee..fd20465 100755
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -22,6 +22,8 @@ package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.bin.Console;
 import jalview.datamodel.Point;
 import jalview.datamodel.SequenceI;
@@ -45,7 +47,7 @@ public class PaSiMap implements Runnable
    */
   final private AlignmentViewport seqs;
 
-  final private ScoreModelI scoreModel;
+  final private ScoreMatrix scoreMatrix;
 
   final private byte dim = 8;
 
@@ -73,7 +75,17 @@ public class PaSiMap implements Runnable
   public PaSiMap(AlignmentViewport sequences, ScoreModelI sm, PairwiseAlignPanel pap)
   {
     this.seqs = sequences;
-    this.scoreModel = sm;
+
+    //convert ScoreModel name into score matrix, use default if not Blosum or Pam
+    if (sm.getName().equals("BLOSUM62"))
+    {
+      this.scoreMatrix = ScoreModels.getInstance().getBlosum62();
+    } else if (sm.getName().equals("PAM250")) {
+      this.scoreMatrix = ScoreModels.getInstance().getPam250();
+    } else {
+      this.scoreMatrix = null;
+    }
+
     this.alignment = pap;
   }
 
@@ -163,7 +175,7 @@ public class PaSiMap implements Runnable
   public String getDetails()
   {
     StringBuilder sb = new StringBuilder(1024);
-    sb.append("PaSiMap calculation using ").append(scoreModel.getName())
+    sb.append("PaSiMap calculation using ").append(scoreMatrix.getName())
             .append(" sequence similarity matrix\n========\n\n");
     PrintStream ps = wrapOutputBuffer(sb);
 
@@ -203,7 +215,7 @@ public class PaSiMap implements Runnable
     try
     {
       //alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
-      alignment.calculate();
+      alignment.calculate(scoreMatrix);
       float[][] scores = alignment.getAlignmentScores();	//bigger index first -- eg scores[14][13]
       SequenceI[] iseqs = alignment.getInputSequences();
       Connectivity.getConnectivity(iseqs, scores, dim);
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 3b7ca81..0053547 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -601,13 +601,22 @@ public class CalculationChooser extends JPanel
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
-      if ((!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
+      if (!forPasimap && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
               || sm.isSecondaryStructure() && ssPresent))
               
       {
         filtered.add(sm);
       }
     }
+    
+    /*
+     * make PaSiMap only use Blosum62 and Pam250
+     */
+    if (forPasimap && !nucleotide && !forPca)
+    {
+      filtered.add(scoreModels.getBlosum62());
+      filtered.add(scoreModels.getPam250());
+    }
 
     /*
      * special case: add BLOSUM62 as last option for nucleotide PCA, 
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 6800b0c..65f1c6d 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
@@ -115,6 +116,10 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
   
   public void calculate()
   {
+    calculate(null);
+  }
+  public void calculate (ScoreMatrix sm)
+  {
 
     StringBuilder sb = new StringBuilder(1024);
 
@@ -176,6 +181,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       {
         AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
                 seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
+        if (sm != null)
+	  as.setScoreMatrix(sm);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
-- 
1.7.10.2