package jalview.renderer;
import jalview.api.AlignViewportI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
/**
*/
public class ScaleRenderer
{
+ /**
+ * Represents one major or minor scale mark
+ */
public final class ScaleMark
{
+ /**
+ * true for a major scale mark, false for minor
+ */
public final boolean major;
+ /**
+ * visible column position (0..) e.g. 19
+ */
public final int column;
+ /**
+ * text (if any) to show e.g. "20"
+ */
public final String text;
ScaleMark(boolean isMajor, int col, String txt)
int scalestartx = (startx / 10) * 10;
SequenceI refSeq = av.getAlignment().getSeqrep();
- int refSp = 0, refStartI = 0, refEndI = -1;
+ int refSp = 0;
+ int refStartI = 0;
+ int refEndI = -1;
+
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+
if (refSeq != null)
{
- // find bounds and set origin appopriately
- // locate first visible position for this sequence
- int[] refbounds = av.getAlignment().getHiddenColumns()
- .locateVisibleBoundsOfSequence(refSeq);
+ // find bounds and set origin appropriately
+ // locate first residue in sequence which is not hidden
+ Iterator<int[]> it = hc.iterator();
+ int index = refSeq.firstResidueOutsideIterator(it);
+ refSp = hc.absoluteToVisibleColumn(index);
+
+ refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
+
+ int seqlength = refSeq.getLength();
+ // get sequence position past the end of the sequence
+ int pastEndPos = refSeq.findPosition(seqlength + 1);
+ refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
- refSp = refbounds[0];
- refStartI = refbounds[1];
- refEndI = refbounds[2];
scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
}
String string;
int refN, iadj;
// todo: add a 'reference origin column' to set column number relative to
- for (int i = scalestartx; i < endx; i += 5)
+ for (int i = scalestartx; i <= endx; i += 5)
{
if (((i - refSp) % 10) == 0)
{
if (refSeq == null)
{
- iadj = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(i - 1) + 1;
+ iadj = hc.visibleToAbsoluteColumn(i - 1) + 1;
string = String.valueOf(iadj);
}
else
{
- iadj = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(i - 1);
+ iadj = hc.visibleToAbsoluteColumn(i - 1);
refN = refSeq.findPosition(iadj);
// TODO show bounds if position is a gap
// - ie L--R -> "1L|2R" for