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JAL-2428 Javadoc
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeBuilder.java
diff --git
a/src/jalview/analysis/TreeBuilder.java
b/src/jalview/analysis/TreeBuilder.java
index
5347ba2
..
5381880
100644
(file)
--- a/
src/jalview/analysis/TreeBuilder.java
+++ b/
src/jalview/analysis/TreeBuilder.java
@@
-253,6
+253,12
@@
public abstract class TreeBuilder
findMaxDist(top);
}
findMaxDist(top);
}
+ /**
+ * Returns the minimum distance between two clusters, and also sets the
+ * indices of the clusters in fields mini and minj
+ *
+ * @return
+ */
protected abstract double findMinDistance();
/**
protected abstract double findMinDistance();
/**
@@
-295,10
+301,10
@@
public abstract class TreeBuilder
}
/**
}
/**
- * DOCUMENT ME!
+ * Finds the node, at or below the given node, with the maximum distance, and
+ * saves the node and the distance value
*
* @param nd
*
* @param nd
- * DOCUMENT ME!
*/
void findMaxDist(SequenceNode nd)
{
*/
void findMaxDist(SequenceNode nd)
{
@@
-325,14
+331,12
@@
public abstract class TreeBuilder
}
/**
}
/**
- * DOCUMENT ME!
+ * Calculates and returns r, whatever that is
*
* @param i
*
* @param i
- * DOCUMENT ME!
* @param j
* @param j
- * DOCUMENT ME!
*
*
- * @return DOCUMENT ME!
+ * @return
*/
protected double findr(int i, int j)
{
*/
protected double findr(int i, int j)
{
@@
-428,8
+432,12
@@
public abstract class TreeBuilder
done.set(j);
}
done.set(j);
}
- protected abstract void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- double dist);
+ /*
+ * Computes and stores new distances for nodei and nodej, given the previous
+ * distance between them
+ */
+ protected abstract void findNewDistances(SequenceNode nodei,
+ SequenceNode nodej, double previousDistance);
/**
* Calculates and saves the distance between the combination of cluster(i) and
/**
* Calculates and saves the distance between the combination of cluster(i) and