From 5143fe21d91fa16c40be42cc0923be0d6f2f6536 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 28 Feb 2019 16:41:55 +0000
Subject: [PATCH] JAL-3140 confine intervalstore imports to
 jalview.datamodel.features

---
 src/jalview/datamodel/Range.java                   |   72 ++++++++++++++++++++
 src/jalview/datamodel/Sequence.java                |    4 +-
 src/jalview/datamodel/SequenceI.java               |    3 +-
 .../renderer/seqfeatures/FeatureRenderer.java      |    5 +-
 4 files changed, 76 insertions(+), 8 deletions(-)
 create mode 100644 src/jalview/datamodel/Range.java

diff --git a/src/jalview/datamodel/Range.java b/src/jalview/datamodel/Range.java
new file mode 100644
index 0000000..8b6f617
--- /dev/null
+++ b/src/jalview/datamodel/Range.java
@@ -0,0 +1,72 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+/**
+ * An immutable data bean that models a start-end range
+ */
+public class Range implements ContiguousI
+{
+  public final int start;
+
+  public final int end;
+
+  @Override
+  public int getBegin()
+  {
+    return start;
+  }
+
+  @Override
+  public int getEnd()
+  {
+    return end;
+  }
+
+  public Range(int i, int j)
+  {
+    start = i;
+    end = j;
+  }
+
+  @Override
+  public String toString()
+  {
+    return String.valueOf(start) + "-" + String.valueOf(end);
+  }
+
+  @Override
+  public int hashCode()
+  {
+    return start * 31 + end;
+  }
+
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (obj instanceof Range)
+    {
+      Range r = (Range) obj;
+      return (start == r.start && end == r.end);
+    }
+    return false;
+  }
+}
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 674fabe..37e3278 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -40,8 +40,6 @@ import java.util.ListIterator;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
-import intervalstore.api.IntervalI;
-import intervalstore.impl.Range;
 
 /**
  * 
@@ -1071,7 +1069,7 @@ public class Sequence extends ASequence implements SequenceI
    * {@inheritDoc}
    */
   @Override
-  public IntervalI findPositions(int fromColumn, int toColumn)
+  public ContiguousI findPositions(int fromColumn, int toColumn)
   {
     if (toColumn < fromColumn || fromColumn < 1)
     {
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index ed8e8e4..f33132a 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -29,7 +29,6 @@ import java.util.List;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
-import intervalstore.api.IntervalI;
 
 /**
  * Methods for manipulating a sequence, its metadata and related annotation in
@@ -214,7 +213,7 @@ public interface SequenceI extends ASequenceI
    * @param toColumn
    * @return
    */
-  public IntervalI findPositions(int fromColum, int toColumn);
+  public ContiguousI findPositions(int fromColum, int toColumn);
 
   /**
    * Returns an int array where indices correspond to each residue in the
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 9db55d3..13885b4 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,6 +22,7 @@ package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -34,8 +35,6 @@ import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.util.List;
 
-import intervalstore.api.IntervalI;
-
 public class FeatureRenderer extends FeatureRendererModel
 {
   private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
@@ -273,7 +272,7 @@ public class FeatureRenderer extends FeatureRendererModel
     /*
      * if columns are all gapped, or sequence has no features, nothing to do
      */
-    IntervalI visiblePositions = seq.findPositions(start + 1, end + 1);
+    ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
     if (visiblePositions == null || !seq.getFeatures().hasFeatures())
     {
       return null;
-- 
1.7.10.2