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[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentView.java
diff --git
a/src/jalview/datamodel/AlignmentView.java
b/src/jalview/datamodel/AlignmentView.java
index
8e596ce
..
a23aad5
100644
(file)
--- a/
src/jalview/datamodel/AlignmentView.java
+++ b/
src/jalview/datamodel/AlignmentView.java
@@
-21,6
+21,7
@@
import jalview.util.ShiftList;
\r
import java.io.PrintStream;
\r
import java.util.Enumeration;
\r
\r
import java.io.PrintStream;
\r
import java.util.Enumeration;
\r
+import java.util.List;
\r
import java.util.Vector;
\r
\r
/**
\r
import java.util.Vector;
\r
\r
/**
\r
@@
-105,7
+106,7
@@
public class AlignmentView
SequenceI[] selseqs;
\r
if (selection != null)
\r
{
\r
SequenceI[] selseqs;
\r
if (selection != null)
\r
{
\r
- Vector sel = selection.getSequences(null);
\r
+ List<SequenceI> sel = selection.getSequences(null);
\r
this.selected = new Vector();
\r
selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
\r
}
\r
this.selected = new Vector();
\r
selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
\r
}
\r
@@
-116,12
+117,8
@@
public class AlignmentView
\r
// get the alignment's group list and make a copy
\r
Vector grps = new Vector();
\r
\r
// get the alignment's group list and make a copy
\r
Vector grps = new Vector();
\r
- Vector gg = alignment.getGroups();
\r
- Enumeration gge = gg.elements();
\r
- while (gge.hasMoreElements())
\r
- {
\r
- grps.addElement(gge.nextElement());
\r
- }
\r
+ List<SequenceGroup> gg = alignment.getGroups();
\r
+ grps.addAll(gg);
\r
ScGroup[] sgrps = null;
\r
boolean addedgps[] = null;
\r
if (grps != null)
\r
ScGroup[] sgrps = null;
\r
boolean addedgps[] = null;
\r
if (grps != null)
\r
@@
-1047,12
+1044,10
@@
public class AlignmentView
+ " wide and has " + visal.getHeight() + " seqs.");
\r
if (visal.getGroups() != null && visal.getGroups().size() > 0)
\r
{
\r
+ " wide and has " + visal.getHeight() + " seqs.");
\r
if (visal.getGroups() != null && visal.getGroups().size() > 0)
\r
{
\r
- SequenceGroup sg;
\r
- Enumeration en = visal.getGroups().elements();
\r
+
\r
int i = 1;
\r
int i = 1;
\r
- while (en.hasMoreElements())
\r
+ for (SequenceGroup sg:visal.getGroups())
\r
{
\r
{
\r
- sg = (SequenceGroup) en.nextElement();
\r
os.println("Group " + (i++) + " begins at column "
\r
+ sg.getStartRes() + " and ends at " + sg.getEndRes());
\r
}
\r
os.println("Group " + (i++) + " begins at column "
\r
+ sg.getStartRes() + " and ends at " + sg.getEndRes());
\r
}
\r