Merge branch 'test/progressBar' into feature/JAL-4159_pasimap

diff --cc src/jalview/analysis/Connectivity.java
Simple merge

diff --cc src/jalview/analysis/PaSiMap.java
index 96f1e15,c776701..7c1c24a
--- 1/src/jalview/analysis/PaSiMap.java
--- 2/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@@ -50,10 -47,12 +47,12 @@@ public class PaSiMap implements Runnabl
  
    final private ScoreModelI scoreModel;
  
-   final private SimilarityParamsI similarityParams;
- 
 -  final private byte dim = 3;
 +  final private byte dim = 8;
  
+   final private int openCost = 100;
+ 
+   final private int extendCost = 5;
+ 
    /*
     * outputs
     */

diff --cc src/jalview/gui/PaSiMapPanel.java
Simple merge

diff --cc src/jalview/viewmodel/PaSiMapModel.java
Simple merge