From d879fd713c06451d655f312840a610f2bae7eda5 Mon Sep 17 00:00:00 2001
From: MorellThomas <morellth@yahoo.co.jp>
Date: Wed, 6 Mar 2024 15:29:15 +0100
Subject: [PATCH] Fix PaSiMap on selected sequences

---
 src/jalview/analysis/Connectivity.java |    9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/jalview/analysis/Connectivity.java b/src/jalview/analysis/Connectivity.java
index 0f849e3..a9cd46c 100644
--- a/src/jalview/analysis/Connectivity.java
+++ b/src/jalview/analysis/Connectivity.java
@@ -45,7 +45,14 @@ public class Connectivity
    */
   public static Hashtable<SequenceI, Integer> getConnectivity(AlignmentViewport av, float[][] scores, byte dim) throws RuntimeException
   {
-    SequenceI[] sequences = av.getAlignment().getSequencesArray();
+    boolean isSelection = av.getSelectionGroup() != null && av.getSelectionGroup().getSize() > 0;
+    SequenceI[] sequences;
+    if (isSelection)
+    {
+      sequences = (SequenceI[]) av.getAlignmentView(isSelection).getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
+    } else {
+      sequences = av.getAlignment().getSequencesArray();
+    }
 
     Hashtable<SequenceI, Integer> connectivity = new Hashtable<SequenceI, Integer>();
     // for each unique connection
-- 
1.7.10.2