From cf8e95cb72c90c73963816ca71856ba1ab7e1d99 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 9 Dec 2010 15:28:45 +0000
Subject: [PATCH] javadoc and additional convenience method for JAL-716
---
src/jalview/datamodel/SequenceGroup.java | 26 ++++++++++++++++++++------
1 file changed, 20 insertions(+), 6 deletions(-)
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index be40bce..f045555 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -627,10 +627,9 @@ public class SequenceGroup
}
/**
- * DOCUMENT ME!
+ * Set the first column selected by this group. Runs from 0<=i<N_cols
*
* @param i
- * DOCUMENT ME!
*/
public void setStartRes(int i)
{
@@ -638,10 +637,9 @@ public class SequenceGroup
}
/**
- * DOCUMENT ME!
+ * Set the groups last selected column. Runs from 0<=i<N_cols
*
* @param i
- * DOCUMENT ME!
*/
public void setEndRes(int i)
{
@@ -794,23 +792,39 @@ public class SequenceGroup
*/
public SequenceI[] getSequencesInOrder(AlignmentI al)
{
+ return getSequencesInOrder(al, true);
+ }
+ /**
+ * return an array representing the intersection of the group with al, optionally returning an array the size of al.getHeight()
+ * where nulls mark the non-intersected sequences
+ * @param al
+ * @param trim
+ * @return null or array
+ */
+ public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
+ {
int sSize = sequences.size();
int alHeight = al.getHeight();
- SequenceI[] seqs = new SequenceI[sSize];
+ SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
int index = 0;
for (int i = 0; i < alHeight && index < sSize; i++)
{
if (sequences.contains(al.getSequenceAt(i)))
{
- seqs[index++] = al.getSequenceAt(i);
+ seqs[(trim) ? index : i] = al.getSequenceAt(i);
+ index++;
}
}
if (index == 0)
{
return null;
}
+ if (!trim)
+ {
+ return seqs;
+ }
if (index < seqs.length)
{
SequenceI[] dummy = seqs;
--
1.7.10.2