/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
import java.util.List;
/**
* Calculate and display alignment rulers
*
* @author jprocter
*
*/
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)
{
major = isMajor;
column = col;
text = txt;
}
/**
* String representation for inspection when debugging only
*/
@Override
public String toString()
{
return String.format("%s:%d:%s", major ? "major" : "minor", column,
text);
}
}
/**
* Calculates position markers on the alignment ruler
*
* @param av
* @param startx
* left-most column in visible view (0..)
* @param endx
* - right-most column in visible view (0..)
* @return
*/
public List calculateMarks(AlignViewportI av, int startx,
int endx)
{
int scalestartx = (startx / 10) * 10;
SequenceI refSeq = av.getAlignment().getSeqrep();
int refSp = 0, refStartI = 0, refEndI = -1;
if (refSeq != null)
{
// find bounds and set origin appopriately
// locate first visible position for this sequence
int[] refbounds = av.getAlignment().getHiddenColumns()
.locateVisibleBoundsOfSequence(refSeq);
refSp = refbounds[0];
refStartI = refbounds[4];
refEndI = refbounds[5];
scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
}
if (refSeq == null && scalestartx % 10 == 0)
{
scalestartx += 5;
}
List marks = new ArrayList();
// todo: add a 'reference origin column' to set column number relative to
for (int i = scalestartx; i <= endx; i += 5)
{
if (((i - refSp) % 10) == 0)
{
String text;
if (refSeq == null)
{
int iadj = av.getAlignment().getHiddenColumns()
.adjustForHiddenColumns(i - 1) + 1;
text = String.valueOf(iadj);
}
else
{
int iadj = av.getAlignment().getHiddenColumns()
.adjustForHiddenColumns(i - 1);
int refN = refSeq.findPosition(iadj);
// TODO show bounds if position is a gap
// - ie L--R -> "1L|2R" for
// marker
if (iadj < refStartI)
{
text = String.valueOf(iadj - refStartI);
}
else if (iadj > refEndI)
{
text = "+" + String.valueOf(iadj - refEndI);
}
else
{
text = String.valueOf(refN) + refSeq.getCharAt(iadj);
}
}
marks.add(new ScaleMark(true, i - startx - 1, text));
}
else
{
marks.add(new ScaleMark(false, i - startx - 1, null));
}
}
return marks;
}
}