Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / datamodel / SearchResults.java

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 880f970..9d357c8 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -35,13 +35,14 @@ public class SearchResults implements SearchResultsI
 {
   private int count;
 
-  private List<SearchResultMatchI> matches = new ArrayList<>();
+  private ArrayList<SearchResultMatchI> matches = new ArrayList<>();
 
   /**
    * One match consists of a sequence reference, start and end positions.
    * Discontiguous ranges in a sequence require two or more Match objects.
    */
-  public class Match implements SearchResultMatchI
+  public class Match
+          implements SearchResultMatchI, Comparable<SearchResultMatchI>
   {
     final SequenceI sequence;
 
@@ -160,6 +161,42 @@ public class SearchResults implements SearchResultsI
     {
       return (sequence == seq && start <= from && end >= to);
     }
+
+    @Override
+    public boolean adjacent(SequenceI seq, int from, int to)
+    {
+      return (sequence == seq && ((start <= from && end >= to)
+              || (from <= (end + 1) && to >= (end + 1))
+              || (from <= (start - 1) && to >= (start - 1))));
+    }
+
+    @Override
+    public int compareTo(SearchResultMatchI o)
+    {
+      if (start < o.getStart())
+      {
+        return -1;
+      }
+      if (start > o.getStart())
+      {
+        return +1;
+      }
+      if (end < o.getEnd())
+      {
+        return -1;
+      }
+      if (end > o.getEnd())
+      {
+        return +1;
+      }
+      if (sequence != o.getSequence())
+      {
+        int hashc = sequence.hashCode(), oseq = o.getSequence().hashCode();
+        return (hashc < oseq) ? -1 : 1;
+      }
+      return 0;
+    }
+
   }
 
   @Override
@@ -193,6 +230,58 @@ public class SearchResults implements SearchResultsI
   }
 
   @Override
+  public boolean appendResult(SequenceI sequence, int start, int end)
+  {
+
+    Match m = new Match(sequence, start, end);
+
+    boolean appending = false;
+
+    // we dynamically maintain an interval to add as we test each range in the
+    // list
+
+    int cstart = start, cend = end;
+    List<SearchResultMatchI> toRemove = new ArrayList<>();
+    for (SearchResultMatchI thatm : matches)
+    {
+      if (thatm.getSequence() == sequence)
+      {
+        if (thatm.contains(sequence, cstart, cend))
+        {
+          // found a match containing the current range. nothing else to do
+          // except report if we operated on the list
+          return appending;
+        }
+        if (thatm.adjacent(sequence, cstart, cend))
+        {
+          // update the match to add with the adjacent start/end
+          start = Math.min(m.start, thatm.getStart());
+          end = Math.max(m.end, thatm.getEnd());
+          // and check if we keep or remove the old one
+          if (thatm.getStart() != start || thatm.getEnd() != end)
+          {
+            toRemove.add(thatm);
+            count--;
+            cstart = start;
+            cend = end;
+            appending = true;
+          }
+          else
+          {
+            return false;
+          }
+        }
+      }
+    }
+    matches.removeAll(toRemove);
+    {
+      matches.add(new Match(sequence, cstart, cend));
+      count++;
+    }
+    return appending;
+  }
+
+  @Override
   public boolean involvesSequence(SequenceI sequence)
   {
     final int start = sequence.getStart();
@@ -269,7 +358,8 @@ public class SearchResults implements SearchResultsI
         else
         {
           // debug
-          // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+          // jalview.bin.Console.errPrintln("Outwith bounds!" +
+          // matchStart+">"+end +" or "
           // + matchEnd+"<"+start);
         }
       }
@@ -370,4 +460,28 @@ public class SearchResults implements SearchResultsI
   {
     matches.addAll(toAdd.getResults());
   }
+
+  @Override
+  public List<SequenceI> getMatchingSubSequences()
+  {
+    List<SequenceI> seqs = new ArrayList<>();
+
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    for (SearchResultMatchI match : matches)
+    {
+      SequenceI seq = match.getSequence();
+      while (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
+      // getSubSequence is index-base0, findIndex returns index-base1
+      seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1,
+              seq.findIndex(match.getEnd())));
+    }
+    return seqs;
+  }
+
 }