From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 5 Aug 2024 17:41:40 +0000 (+0100)
Subject: JAL-4446 .. missing methods for cancellable pasimap
X-Git-Tag: Release_2_11_4_0~14^2~6^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1a09df2fbacbdaf9a76ee5fe3b25925742bc78d9;p=jalview.git

JAL-4446 .. missing methods for cancellable pasimap
---

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 5be8c7b..b2a17ac 100755
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -60,6 +60,8 @@ public class PaSiMap implements Runnable
    * outputs
    */
   final private PairwiseAlignPanel alignment;
+  
+  private boolean cancelled=false;
 
   private MatrixI pairwiseScores;
 
@@ -230,6 +232,11 @@ public class PaSiMap implements Runnable
     {
       // alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
       alignment.calculate(scoreMatrix);
+      if (alignment.isCancelled())
+      {
+        cancel();
+        return;
+      }
       float[][] scores = alignment.getAlignmentScores(); // bigger index first
                                                          // -- eg scores[14][13]
       SequenceI[] iseqs = alignment.getInputSequences();
@@ -249,6 +256,22 @@ public class PaSiMap implements Runnable
       q.printStackTrace();
     }
   }
+  
+  
+
+  public void cancel()
+  {
+    if (alignment!=null)
+    {
+      alignment.cancel();
+    }
+    cancelled=true;
+  }
+  
+  public boolean isCancelled()
+  {
+    return cancelled;
+  }
 
   /**
    * Returns a PrintStream that wraps (appends its output to) the given