From 435792460e417edc981c308f917f2ff5a7829971 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Nov 2016 21:32:48 +0000
Subject: [PATCH] JAL-966 JAL-345 JAL-1738 decontaminate SearchResultI with
 references to Match

---
 src/jalview/datamodel/SearchResults.java  |   32 +++++++++++++++++------------
 src/jalview/datamodel/SearchResultsI.java |    3 +--
 2 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 3cb34de..58f8517 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -35,7 +35,7 @@ import java.util.List;
 public class SearchResults implements SearchResultsI
 {
 
-  private List<Match> matches = new ArrayList<Match>();
+  private List<SearchResultMatchI> matches = new ArrayList<SearchResultMatchI>();
 
   /**
    * One match consists of a sequence reference, start and end positions.
@@ -164,12 +164,13 @@ public class SearchResults implements SearchResultsI
     @Override
     public boolean equals(Object obj)
     {
-      if (obj == null || !(obj instanceof Match))
+      if (obj == null || !(obj instanceof SearchResultMatchI))
       {
         return false;
       }
-      Match m = (Match) obj;
-      return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
+      SearchResultMatchI m = (SearchResultMatchI) obj;
+      return (sequence == m.getSequence() && start == m.getStart() && end == m
+              .getEnd());
     }
   }
 
@@ -189,8 +190,10 @@ public class SearchResults implements SearchResultsI
   public boolean involvesSequence(SequenceI sequence)
   {
     SequenceI ds = sequence.getDatasetSequence();
-    for (Match m : matches)
+    Match m;
+    for (SearchResultMatchI _m : matches)
     {
+      m = (Match) _m;
       if (m.sequence != null
               && (m.sequence == sequence || m.sequence == ds))
       {
@@ -215,8 +218,11 @@ public class SearchResults implements SearchResultsI
     int[] tmp = null;
     int resultLength, matchStart = 0, matchEnd = 0;
     boolean mfound;
-    for (Match m : matches)
+    Match m;
+    for (SearchResultMatchI _m : matches)
     {
+      m = (Match) _m;
+
       mfound = false;
       if (m.sequence == sequence)
       {
@@ -311,7 +317,7 @@ public class SearchResults implements SearchResultsI
   @Override
   public SequenceI getResultSequence(int index)
   {
-    return matches.get(index).sequence;
+    return matches.get(index).getSequence();
   }
 
   /* (non-Javadoc)
@@ -320,7 +326,7 @@ public class SearchResults implements SearchResultsI
   @Override
   public int getResultStart(int i)
   {
-    return matches.get(i).start;
+    return matches.get(i).getStart();
   }
 
   /* (non-Javadoc)
@@ -329,7 +335,7 @@ public class SearchResults implements SearchResultsI
   @Override
   public int getResultEnd(int i)
   {
-    return matches.get(i).end;
+    return matches.get(i).getEnd();
   }
 
   /* (non-Javadoc)
@@ -345,7 +351,7 @@ public class SearchResults implements SearchResultsI
    * @see jalview.datamodel.SearchResultsI#getResults()
    */
   @Override
-  public List<Match> getResults()
+  public List<SearchResultMatchI> getResults()
   {
     return matches;
   }
@@ -403,11 +409,11 @@ public class SearchResults implements SearchResultsI
   @Override
   public boolean equals(Object obj)
   {
-    if (obj == null || !(obj instanceof SearchResults))
+    if (obj == null || !(obj instanceof SearchResultsI))
     {
       return false;
     }
-    SearchResults sr = (SearchResults) obj;
-    return ((ArrayList<Match>) this.matches).equals(sr.matches);
+    SearchResultsI sr = (SearchResultsI) obj;
+    return matches.equals(sr.getResults());
   }
 }
diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index d59f453..bc62a66 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -1,6 +1,5 @@
 package jalview.datamodel;
 
-import jalview.datamodel.SearchResults.Match;
 
 import java.util.BitSet;
 import java.util.List;
@@ -78,7 +77,7 @@ public interface SearchResultsI
    * 
    * @return
    */
-  public abstract List<Match> getResults();
+  public abstract List<SearchResultMatchI> getResults();
 
   /**
    * Set bits in a bitfield for all columns in the given sequence collection
-- 
1.7.10.2