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Only calculate consenus from start to end
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentView.java
diff --git
a/src/jalview/datamodel/AlignmentView.java
b/src/jalview/datamodel/AlignmentView.java
index
a76e90e
..
e668470
100644
(file)
--- a/
src/jalview/datamodel/AlignmentView.java
+++ b/
src/jalview/datamodel/AlignmentView.java
@@
-40,6
+40,7
@@
public class AlignmentView
private SeqCigar[] sequences = null;
private int[] contigs = null;
private int width=0;
private SeqCigar[] sequences = null;
private int[] contigs = null;
private int width=0;
+ private int firstCol=0;
public AlignmentView(CigarArray seqcigararray)
{
if (!seqcigararray.isSeqCigarArray())
public AlignmentView(CigarArray seqcigararray)
{
if (!seqcigararray.isSeqCigarArray())
@@
-49,6
+50,15
@@
public class AlignmentView
sequences = seqcigararray.getSeqCigarArray();
width = seqcigararray.getWidth(); // visible width
}
sequences = seqcigararray.getSeqCigarArray();
width = seqcigararray.getWidth(); // visible width
}
+ /**
+ * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
+ * @param sdata
+ * @param firstcol
+ */
+ public AlignmentView(CigarArray sdata, int firstcol) {
+ this(sdata);
+ firstCol=firstcol;
+ }
public void setSequences(SeqCigar[] sequences)
{
public void setSequences(SeqCigar[] sequences)
{
@@
-431,4
+441,12
@@
public class AlignmentView
return new int[] { 0, width};
}
}
return new int[] { 0, width};
}
}
+ /**
+ *
+ * @return position of first visible column of AlignmentView within its parent's alignment reference frame
+ */
+ public int getAlignmentOrigin() {
+ // TODO Auto-generated method stub
+ return firstCol;
+ }
}
}