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JAL-1632 remove unused check for sequences aligned
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 12 Apr 2017 13:43:39 +0000
(14:43 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 12 Apr 2017 13:43:39 +0000
(14:43 +0100)
src/jalview/gui/PCAPanel.java
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diff --git
a/src/jalview/gui/PCAPanel.java
b/src/jalview/gui/PCAPanel.java
index
f75c756
..
482dff3
100644
(file)
--- a/
src/jalview/gui/PCAPanel.java
+++ b/
src/jalview/gui/PCAPanel.java
@@
-30,7
+30,6
@@
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
import jalview.util.MessageManager;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
import jalview.util.MessageManager;
@@
-129,18
+128,6
@@
public class PCAPanel extends GPCAPanel implements Runnable,
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- // TODO can we allow PCA on unaligned data given choice of
- // similarity measure parameters?
- if (!checkAligned(seqstrings))
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
params);
PaintRefresher.Register(this, av.getSequenceSetId());
pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
params);
PaintRefresher.Register(this, av.getSequenceSetId());
@@
-152,28
+139,6
@@
public class PCAPanel extends GPCAPanel implements Runnable,
}
/**
}
/**
- * Answers true if all sequences have the same aligned length, else false
- *
- * @param seqstrings
- * @return
- */
- protected boolean checkAligned(AlignmentView seqstrings)
- {
- SeqCigar sq[] = seqstrings.getSequences();
- int length = sq[0].getWidth();
- boolean sameLength = true;
- for (int i = 0; i < sq.length; i++)
- {
- if (sq[i].getWidth() != length)
- {
- sameLength = false;
- break;
- }
- }
- return sameLength;
- }
-
- /**
* Ensure references to potentially very large objects (the PCA matrices) are
* nulled when the frame is closed
*/
* Ensure references to potentially very large objects (the PCA matrices) are
* nulled when the frame is closed
*/