X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FNCNode.java;h=b9917501717f0379283545fc67fe84ebe32a8bd8;hb=8c5cefb3ac80bd094a8dab7ce6735a11583b1772;hp=ab10f67aaec0ca7c5fdb17b1efcf1251d4820718;hpb=0ea61b395605ecf1854406f8e0c9a0be04404cb1;p=jalview.git
diff --git a/src/jalview/datamodel/features/NCNode.java b/src/jalview/datamodel/features/NCNode.java
index ab10f67..b991750 100644
--- a/src/jalview/datamodel/features/NCNode.java
+++ b/src/jalview/datamodel/features/NCNode.java
@@ -1,5 +1,27 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel.features;
+import jalview.datamodel.ContiguousI;
+
import java.util.ArrayList;
import java.util.List;
@@ -9,7 +31,7 @@ import java.util.List;
*
* @param
*/
-class NCNode
+class NCNode implements ContiguousI
{
/*
* deep size (number of ranges included)
@@ -18,6 +40,9 @@ class NCNode
private V region;
+ /*
+ * null, or an object holding contained subregions of this nodes region
+ */
private NCList subregions;
/**
@@ -37,7 +62,7 @@ class NCNode
*/
NCNode(V range)
{
- List ranges = new ArrayList();
+ List ranges = new ArrayList<>();
ranges.add(range);
build(ranges);
}
@@ -46,7 +71,7 @@ class NCNode
{
region = entry;
subregions = newNCList;
- // size = 1 + newNCList.size();
+ size = 1 + newNCList.size();
}
/**
@@ -66,12 +91,14 @@ class NCNode
}
}
- int getStart()
+ @Override
+ public int getBegin()
{
return region.getBegin();
}
- int getEnd()
+ @Override
+ public int getEnd()
{
return region.getEnd();
}
@@ -112,7 +139,7 @@ class NCNode
* @param to
* @param result
*/
- void addOverlaps(long from, long to, List result)
+ void findOverlaps(long from, long to, List result)
{
if (region.getBegin() <= to && region.getEnd() >= from)
{
@@ -145,6 +172,7 @@ class NCNode
{
subregions.add(entry);
}
+ size++;
}
/**
@@ -155,10 +183,93 @@ class NCNode
*/
boolean isValid()
{
+ /*
+ * we don't handle reverse ranges
+ */
+ if (region != null && region.getBegin() > region.getEnd())
+ {
+ return false;
+ }
if (subregions == null)
{
return true;
}
- return subregions.isValid(getStart(), getEnd());
+ return subregions.isValid(getBegin(), getEnd());
+ }
+
+ /**
+ * Adds all contained entries to the given list
+ *
+ * @param entries
+ */
+ void getEntries(List entries)
+ {
+ entries.add(region);
+ if (subregions != null)
+ {
+ subregions.getEntries(entries);
+ }
+ }
+
+ /**
+ * Answers true if this object contains the given entry (by object equals
+ * test), else false
+ *
+ * @param entry
+ * @return
+ */
+ boolean contains(V entry)
+ {
+ if (entry == null)
+ {
+ return false;
+ }
+ if (entry.equals(region))
+ {
+ return true;
+ }
+ return subregions == null ? false : subregions.contains(entry);
+ }
+
+ /**
+ * Answers the 'root' region modelled by this object
+ *
+ * @return
+ */
+ V getRegion()
+ {
+ return region;
+ }
+
+ /**
+ * Answers the (possibly null) contained regions within this object
+ *
+ * @return
+ */
+ NCList getSubRegions()
+ {
+ return subregions;
+ }
+
+ /**
+ * Nulls the subregion reference if it is empty (after a delete entry
+ * operation)
+ */
+ void deleteSubRegionsIfEmpty()
+ {
+ if (subregions != null && subregions.size() == 0)
+ {
+ subregions = null;
+ }
+ }
+
+ /**
+ * Answers the (deep) size of this node i.e. the number of ranges it models
+ *
+ * @return
+ */
+ int size()
+ {
+ return size;
}
}