int pdbend = 0;
int seqstart = 0;
int seqend = 0;
- AlignSeq maxAlignseq = null;
//JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
pdbend = as.seq2end;
seqstart = as.seq1start + sequence.getStart() - 1;
seqend = as.seq1end + sequence.getEnd() - 1;
- maxAlignseq = as;
- }
+ }
mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
// Applet and Application specific sequence renderers to be used
void colourBySequence()
{
- SequenceRenderer sr = ap.getSequenceRenderer();
+ SequenceRenderer sr = new SequenceRenderer(ap.av);
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
(getSize().width / 2));
- ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+ ystart = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
(getSize().height / 2));
xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
(getSize().width / 2));
- yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+ yend = (int) ( ( (centre[1] - tmpBond.end[1] ) * scale) +
(getSize().height / 2));
xmid = (xend + xstart) / 2;
{
int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
(getSize().width / 2));
- int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +
+ int ystart = (int) ( ( (centre[1] - b.start[1]) * scale) +
(getSize().height / 2));
g.setColor(Color.red);
{
int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
(getSize().width / 2));
- int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +
+ int ystart = (int) ( ( (centre[1] - b.end[1]) * scale) +
(getSize().height / 2));
g.setColor(Color.red);
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+ int truey = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
(getSize().height / 2));
if (Math.abs(truey - y) <= 2)
///StructureListener
public String getPdbFile()
{
- return "???";
+ return pdbentry.getFile();
}
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
colourBySequence();
redrawneeded = true;
repaint();