public PDBChain findChain(String id) {
for (int i = 0; i < chains.size(); i++) {
// System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
return (PDBChain) chains.elementAt(i);
}
}
return null;
}
public void parse() {
System.out.println("Parsing");
for (int i = 0; i < lineArray.size(); i++) {
StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
if (str.hasMoreTokens()) {
String inStr = str.nextToken();
if (inStr.indexOf("ATOM") != -1) {
try {
myAtom tmpatom = new myAtom(str);
if (findChain(tmpatom.chain) != null) {
System.out.println("Adding to chain " + tmpatom.chain);
findChain(tmpatom.chain).atoms.addElement(tmpatom);
} else {
System.out.println("Making chain " + tmpatom.chain);
PDBChain tmpchain = new PDBChain(tmpatom.chain);
chains.addElement(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
} catch (NumberFormatException e) {
System.out.println("Caught" + e);
System.out.println("Atom not added");
}
}
}
}
makeResidueList();
makeCaBondList();
// for (int i=0; i < chains.size() ; i++) {
// String pog = ((PDBChain)chains.elementAt(i)).print();
// System.out.println(pog);
// }
}
public RotatableCanvas(Object parent, AlignViewport av, Controller c, Vector points, int npoint) {
this.parent = parent;
this.points = points;
this.npoint = npoint;
this.controller = c;
this.av = av;
controller.addListener(this);
prefsize = getPreferredSize();
orig = new float[npoint][3];
for (int i = 0; i < npoint; i++) {
SequencePoint sp = (SequencePoint) points.elementAt(i);
for (int j = 0; j < 3; j++) {
orig[i][j] = sp.coord[j];
}
}
// Initialize the matrices to identity
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
if (i != j) {
idmat.addElement(i, j, 0);
objmat.addElement(i, j, 0);
rotmat.addElement(i, j, 0);
} else {
idmat.addElement(i, j, 0);
objmat.addElement(i, j, 0);
rotmat.addElement(i, j, 0);
}
}
}
axes = new float[3][3];
initAxes();
findCentre();
findWidth();
scale = findScale();
// System.out.println("Scale factor = " + scale);
addMouseListener(this);
addKeyListener(this);
if (getParent() != null) {
getParent().addKeyListener(this);
}
addMouseMotionListener(this);
// Add rubberband
rubberband = new RubberbandRectangle(this);
rubberband.setActive(true);
rubberband.addListener(this);
}
public void printPoints() {
for (int i = 0; i < npoint; i++) {
SequencePoint sp = (SequencePoint) points.elementAt(i);
Format.print(System.out, "%5d ", i);
for (int j = 0; j < 3; j++) {
Format.print(System.out, "%13.3f ", sp.coord[j]);
}
System.out.println();
}
}
public void drawScene(Graphics g) {
boolean darker = false;
int halfwidth = size().width / 2;
int halfheight = size().height / 2;
for (int i = 0; i < npoint; i++) {
SequencePoint sp = (SequencePoint) points.elementAt(i);
int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) + halfheight;
float z = sp.coord[1] - centre[2];
if (sp.sequence instanceof DrawableSequence) {
if (((DrawableSequence) sp.sequence).color == Color.black) {
g.setColor(Color.white);
} else {
g.setColor(((DrawableSequence) sp.sequence).color);
}
} else {
g.setColor(Color.red);
}
if (av != null) {
if (av.getSelection().contains(((SequencePoint) points.elementAt(i)).sequence)) {
g.setColor(Color.gray);
}
}
if (z < 0) {
g.setColor(g.getColor().darker());
}
g.fillRect(x - 3, y - 3, 6, 6);
g.setColor(Color.red);
}
// //Now the rectangle
// if (rectx2 != -1 && recty2 != -1) {
// g.setColor(Color.white);
//
// g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
// }
}
public AlignSequenceI findPoint(int x, int y) {
int halfwidth = size().width / 2;
int halfheight = size().height / 2;
int found = -1;
for (int i = 0; i < npoint; i++) {
SequencePoint sp = (SequencePoint) points.elementAt(i);
int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) + halfheight;
if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3) {
found = i;
}
}
if (found != -1) {
return ((SequencePoint) points.elementAt(found)).sequence;
} else {
return null;
}
}
public void rectSelect(int x1, int y1, int x2, int y2) {
boolean changedSel = false;
for (int i = 0; i < npoint; i++) {
SequencePoint sp = (SequencePoint) points.elementAt(i);
int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + (float) size().width / 2.0);
int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + (float) size().height / 2.0);
if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {
if (av != null) {
if (!av.getSelection().contains(sp.sequence)) {
changedSel = true;
av.getSelection().addElement(sp.sequence);
}
}
}
}
if (changedSel) {
fireSequenceSelectionEvent(av.getSelection());
}
}
public void mouseDragged(MouseEvent evt) {
mx = evt.getX();
my = evt.getY();
// Check if this is a rectangle drawing drag
if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0) {
// rectx2 = evt.getX();
// recty2 = evt.getY();
} else {
rotmat.setIdentity();
rotmat.rotate((float) (my - omy), 'x');
rotmat.rotate((float) (mx - omx), 'y');
for (int i = 0; i < npoint; i++) {
SequencePoint sp = (SequencePoint) points.elementAt(i);
sp.coord[0] -= centre[0];
sp.coord[1] -= centre[1];
sp.coord[2] -= centre[2];
// Now apply the rotation matrix
sp.coord = rotmat.vectorMultiply(sp.coord);
// Now translate back again
sp.coord[0] += centre[0];
sp.coord[1] += centre[1];
sp.coord[2] += centre[2];
}
for (int i = 0; i < 3; i++) {
axes[i] = rotmat.vectorMultiply(axes[i]);
}
omx = mx;
omy = my;
redrawneeded = true;
paint(this.getGraphics());
}
return;
}
public void findWidth() {
max = new float[3];
min = new float[3];
max[0] = (float) -1e30;
max[1] = (float) -1e30;
max[2] = (float) -1e30;
min[0] = (float) 1e30;
min[1] = (float) 1e30;
min[2] = (float) 1e30;
for (int i = 0; i < 3; i++) {
for (int j = 0; j < npoint; j++) {
SequencePoint sp = (SequencePoint) points.elementAt(j);
if (sp.coord[i] >= max[i]) {
max[i] = sp.coord[i];
}
if (sp.coord[i] <= min[i]) {
min[i] = sp.coord[i];
}
}
}
// System.out.println("xmax " + max[0] + " min " + min[0]);
// System.out.println("ymax " + max[1] + " min " + min[1]);
// System.out.println("zmax " + max[2] + " min " + min[2]);
width[0] = Math.abs(max[0] - min[0]);
width[1] = Math.abs(max[1] - min[1]);
width[2] = Math.abs(max[2] - min[2]);
maxwidth = width[0];
if (width[1] > width[0]) maxwidth = width[1];
if (width[2] > width[1]) maxwidth = width[2];
// System.out.println("Maxwidth = " + maxwidth);
}
public void setChainColours() {
for (int i = 0; i < chains.size(); i++) {
((PDBChain) chains.elementAt(i)).setChainColours();
}
}
public void makeCaBondList() {
for (int i = 0; i < chains.size(); i++) {
((PDBChain) chains.elementAt(i)).makeCaBondList();
}
}
