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(JAL-1013) specify sequence type to ensure PCA calculation employs correct substituti...
[jalview.git]
/
src
/
jalview
/
appletgui
/
PCAPanel.java
diff --git
a/src/jalview/appletgui/PCAPanel.java
b/src/jalview/appletgui/PCAPanel.java
index
23286db
..
3e87f17
100755
(executable)
--- a/
src/jalview/appletgui/PCAPanel.java
+++ b/
src/jalview/appletgui/PCAPanel.java
@@
-40,6
+40,12
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
SequenceI[] seqs;
SequenceI[] seqs;
+
+ /**
+ * use the identity matrix for calculating similarity between sequences.
+ */
+ private boolean useidentity=false;
+
public PCAPanel(AlignViewport av)
{
public PCAPanel(AlignViewport av)
{
@@
-60,6
+66,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
this.av = av;
seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
this.av = av;
seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+ useidentity=av.getAlignment().isNucleotide();
if (av.getSelectionGroup() == null)
{
seqs = av.alignment.getSequencesArray();
if (av.getSelectionGroup() == null)
{
seqs = av.alignment.getSequencesArray();
@@
-97,7
+104,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
*/
public void run()
{
*/
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '));
+ pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
pca.run();
// Now find the component coordinates
pca.run();
// Now find the component coordinates