git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
begin process of allowing for column selection in wrapped mode.
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
47aa94b
..
73ed7a7
100755
(executable)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-83,6
+83,7
@@
public class AppletPDBCanvas
public AppletPDBCanvas(PDBEntry pdbentry,
SequenceI[] seq,
public AppletPDBCanvas(PDBEntry pdbentry,
SequenceI[] seq,
+ String [] chains,
AlignmentPanel ap,
String protocol)
AlignmentPanel ap,
String protocol)
@@
-94,7
+95,7
@@
public class AppletPDBCanvas
ssm = StructureSelectionManager.getStructureSelectionManager();
try{
ssm = StructureSelectionManager.getStructureSelectionManager();
try{
- pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
pdbentry.setFile("INLINE"+pdb.id);
if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
pdbentry.setFile("INLINE"+pdb.id);
@@
-117,7
+118,6
@@
public class AppletPDBCanvas
int pdbend = 0;
int seqstart = 0;
int seqend = 0;
int pdbend = 0;
int seqstart = 0;
int seqend = 0;
- AlignSeq maxAlignseq = null;
//JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
//JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
@@
-164,8
+164,7
@@
public class AppletPDBCanvas
pdbend = as.seq2end;
seqstart = as.seq1start + sequence.getStart() - 1;
seqend = as.seq1end + sequence.getEnd() - 1;
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);
mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
@@
-497,7
+496,7
@@
public class AppletPDBCanvas
// Applet and Application specific sequence renderers to be used
void colourBySequence()
{
// 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());
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
@@
-590,12
+589,12
@@
public class AppletPDBCanvas
xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
(getSize().width / 2));
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));
(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;
(getSize().height / 2));
xmid = (xend + xstart) / 2;
@@
-835,7
+834,7
@@
public class AppletPDBCanvas
}
else
{
}
else
{
- objmat.rotatex( (float) ( (my - omy)));
+ objmat.rotatex( (float) ( (omy - my)));
objmat.rotatey( (float) ( (omx - mx)));
}
objmat.rotatey( (float) ( (omx - mx)));
}
@@
-916,7
+915,7
@@
public class AppletPDBCanvas
{
int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
(getSize().width / 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);
(getSize().height / 2));
g.setColor(Color.red);
@@
-927,7
+926,7
@@
public class AppletPDBCanvas
{
int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
(getSize().width / 2));
{
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);
(getSize().height / 2));
g.setColor(Color.red);
@@
-961,7
+960,7
@@
public class AppletPDBCanvas
if (Math.abs(truex - x) <= 2)
{
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)
(getSize().height / 2));
if (Math.abs(truey - y) <= 2)
@@
-1077,7
+1076,7
@@
public class AppletPDBCanvas
///StructureListener
public String getPdbFile()
{
///StructureListener
public String getPdbFile()
{
- return "???";
+ return pdbentry.getFile();
}
}
@@
-1158,7
+1157,6
@@
public class AppletPDBCanvas
public void updateColours(Object source)
{
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
colourBySequence();
redrawneeded = true;
repaint();
colourBySequence();
redrawneeded = true;
repaint();