From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 28 Oct 2020 16:04:52 +0000 (+0000)
Subject: Merge branch 'portforward/JAL-3765_patch_to_2112' into develop
X-Git-Tag: Develop-2_11_2_0-d20201215~22
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d33e7a8955a620936a9419bb40763922898c597e;hp=2d41cbfe3c25373256501a298b98c25f774aa72b;p=jalview.git

Merge branch 'portforward/JAL-3765_patch_to_2112' into develop
---

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index c545c7f..d52e42a 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -417,7 +417,7 @@ public class Finder implements FinderI
      * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    residueIndex += offset + 1;
+    residueIndex = searchPattern.matchedFrom()+1;
 
     /*
      * return false if the match is entirely in a hidden region
diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 95e6c0d..1f45f70 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -123,6 +123,19 @@ public class FinderTest
     assertEquals(matches.get(1).getEnd(), 6);
   }
 
+  @Test(groups = "Functional")
+  public void testFind_findAll()
+  {
+    /*
+     * simple JAL-3765 test
+     * single symbol should find *all* matching symbols 
+     */
+    Finder f = new Finder(av);
+    f.findAll("M", false,false,false);
+    SearchResultsI sr = f.getSearchResults();
+    assertEquals(sr.getCount(),5);
+    
+  }
   /**
    * Test for (undocumented) find residue by position
    */