2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.analysis.AlignSeq;
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23 import jalview.datamodel.*;
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25 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
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27 import java.awt.event.*;
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33 import javax.swing.*;
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36 public class rotCanvas extends JPanel implements KeyListener, MouseListener,
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37 MouseMotionListener {
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38 MCMatrix idmat = new MCMatrix(3, 3);
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39 MCMatrix objmat = new MCMatrix(3, 3);
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40 boolean redrawneeded = true;
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50 float[] centre = new float[3];
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51 float[] width = new float[3];
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56 boolean depthcue = true;
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57 boolean wire = false;
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58 boolean bymolecule = false;
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59 boolean zbuffer = true;
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67 Font font = new Font("Helvetica", Font.PLAIN, 10);
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69 public rotCanvas(PDBfile pdb, Sequence sequence,
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70 jalview.gui.AlignViewport av) throws IOException {
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78 for (int i = 0; i < pdb.chains.size(); i++) {
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79 // Now lets compare the sequences to get
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80 // the start and end points.
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81 java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(),
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83 String newString = "";
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85 while (str.hasMoreTokens()) {
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86 newString += str.nextToken();
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89 // Align the sequence to the pdb
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90 AlignSeq as = new AlignSeq(sequence,
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91 ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
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92 as.calcScoreMatrix();
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93 as.traceAlignment();
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94 as.printAlignment();
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96 if (as.maxscore > max) {
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100 pdbstart = as.seq2start;
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101 pdbend = as.seq2end;
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102 seqstart = as.seq1start - 1;
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103 seqend = as.seq1end - 1;
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106 System.out.println("PDB start/end " + pdbstart + " " + pdbend);
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107 System.out.println("SEQ start/end " + seqstart + " " + seqend);
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110 ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
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111 ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;
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112 ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;
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113 ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;
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114 ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
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115 ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
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116 ((PDBChain) pdb.chains.elementAt(maxchain)).colourBySequence(av,
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120 this.prefsize = new Dimension(getWidth(), getHeight());
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122 //Initialize the matrices to identity
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123 for (int i = 0; i < 3; i++) {
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124 for (int j = 0; j < 3; j++) {
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126 idmat.addElement(i, j, 0);
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127 objmat.addElement(i, j, 0);
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129 idmat.addElement(i, j, 1);
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130 objmat.addElement(i, j, 1);
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135 addMouseMotionListener(this);
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136 addMouseListener(this);
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137 addKeyListener(this);
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140 ToolTipManager.sharedInstance().registerComponent(this);
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141 ToolTipManager.sharedInstance().setInitialDelay(0);
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142 ToolTipManager.sharedInstance().setDismissDelay(10000);
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146 public void addPDBfile() {
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150 scale = findScale();
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152 System.out.println("Scale factor = " + scale);
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155 public void deleteBonds() {
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167 for (int i = 0; i < pdb.chains.size(); i++) {
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168 ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
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172 public void findWidth() {
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173 float[] max = new float[3];
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174 float[] min = new float[3];
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176 max[0] = (float) -1e30;
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177 max[1] = (float) -1e30;
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178 max[2] = (float) -1e30;
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180 min[0] = (float) 1e30;
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181 min[1] = (float) 1e30;
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182 min[2] = (float) 1e30;
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184 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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185 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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186 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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188 for (int i = 0; i < bonds.size(); i++) {
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189 Bond tmp = (Bond) bonds.elementAt(i);
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191 if (tmp.start[0] >= max[0]) {
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192 max[0] = tmp.start[0];
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195 if (tmp.start[1] >= max[1]) {
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196 max[1] = tmp.start[1];
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199 if (tmp.start[2] >= max[2]) {
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200 max[2] = tmp.start[2];
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203 if (tmp.start[0] <= min[0]) {
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204 min[0] = tmp.start[0];
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207 if (tmp.start[1] <= min[1]) {
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208 min[1] = tmp.start[1];
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211 if (tmp.start[2] <= min[2]) {
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212 min[2] = tmp.start[2];
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215 if (tmp.end[0] >= max[0]) {
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216 max[0] = tmp.end[0];
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219 if (tmp.end[1] >= max[1]) {
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220 max[1] = tmp.end[1];
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223 if (tmp.end[2] >= max[2]) {
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224 max[2] = tmp.end[2];
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227 if (tmp.end[0] <= min[0]) {
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228 min[0] = tmp.end[0];
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231 if (tmp.end[1] <= min[1]) {
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232 min[1] = tmp.end[1];
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235 if (tmp.end[2] <= min[2]) {
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236 min[2] = tmp.end[2];
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242 System.out.println("xmax " + max[0] + " min " + min[0]);
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243 System.out.println("ymax " + max[1] + " min " + min[1]);
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244 System.out.println("zmax " + max[2] + " min " + min[2]);
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246 width[0] = (float) Math.abs(max[0] - min[0]);
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247 width[1] = (float) Math.abs(max[1] - min[1]);
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248 width[2] = (float) Math.abs(max[2] - min[2]);
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250 maxwidth = width[0];
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252 if (width[1] > width[0]) {
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253 maxwidth = width[1];
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256 if (width[2] > width[1]) {
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257 maxwidth = width[2];
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260 System.out.println("Maxwidth = " + maxwidth);
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263 public float findScale() {
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268 if (getWidth() != 0) {
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269 width = getWidth();
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270 height = getHeight();
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272 width = prefsize.width;
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273 height = prefsize.height;
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276 if (width < height) {
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282 return (float) (dim / (1.5d * maxwidth));
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285 public void findCentre() {
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292 //Find centre coordinate
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293 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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294 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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295 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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297 bsize += bonds.size();
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299 for (int i = 0; i < bonds.size(); i++) {
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300 xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
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301 ((Bond) bonds.elementAt(i)).end[0];
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303 ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
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304 ((Bond) bonds.elementAt(i)).end[1];
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306 ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
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307 ((Bond) bonds.elementAt(i)).end[2];
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312 centre[0] = xtot / (2 * (float) bsize);
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313 centre[1] = ytot / (2 * (float) bsize);
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314 centre[2] = ztot / (2 * (float) bsize);
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317 public void paint(Graphics g) {
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318 //Only create the image at the beginning -
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319 //this saves much memory usage
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320 if ((img == null) || (prefsize.width != getWidth()) ||
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321 (prefsize.height != getHeight())) {
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322 prefsize.width = getWidth();
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323 prefsize.height = getHeight();
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325 scale = findScale();
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326 img = createImage(prefsize.width, prefsize.height);
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327 ig = img.getGraphics();
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329 redrawneeded = true;
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332 if (redrawneeded == true) {
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333 drawBackground(ig, Color.black);
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335 redrawneeded = false;
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337 ig = img.getGraphics();
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340 g.drawImage(img, 0, 0, this);
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343 public void drawBackground(Graphics g, Color col) {
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345 g.fillRect(0, 0, prefsize.width, prefsize.height);
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348 public void drawScene(Graphics g) {
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349 // Sort the bonds by z coord
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350 Vector bonds = new Vector();
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352 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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353 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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354 Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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356 for (int i = 0; i < tmp.size(); i++) {
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357 bonds.addElement(tmp.elementAt(i));
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363 Zsort.Zsort(bonds);
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366 for (int i = 0; i < bonds.size(); i++) {
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367 Bond tmpBond = (Bond) bonds.elementAt(i);
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369 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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371 ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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372 (getHeight() / 2));
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374 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
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376 yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
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377 (getHeight() / 2));
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379 xmid = (xend + xstart) / 2;
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380 ymid = (yend + ystart) / 2;
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382 if (depthcue && !bymolecule) {
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383 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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384 g.setColor(tmpBond.startCol.darker().darker());
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385 drawLine(g, xstart, ystart, xmid, ymid);
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387 g.setColor(tmpBond.endCol.darker().darker());
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388 drawLine(g, xmid, ymid, xend, yend);
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389 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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390 g.setColor(tmpBond.startCol.darker());
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391 drawLine(g, xstart, ystart, xmid, ymid);
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393 g.setColor(tmpBond.endCol.darker());
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394 drawLine(g, xmid, ymid, xend, yend);
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396 g.setColor(tmpBond.startCol);
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397 drawLine(g, xstart, ystart, xmid, ymid);
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399 g.setColor(tmpBond.endCol);
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400 drawLine(g, xmid, ymid, xend, yend);
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402 } else if (depthcue && bymolecule) {
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403 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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404 g.setColor(Color.green.darker().darker());
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405 drawLine(g, xstart, ystart, xend, yend);
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406 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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407 g.setColor(Color.green.darker());
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408 drawLine(g, xstart, ystart, xend, yend);
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410 g.setColor(Color.green);
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411 drawLine(g, xstart, ystart, xend, yend);
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413 } else if (!depthcue && !bymolecule) {
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414 g.setColor(tmpBond.startCol);
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415 drawLine(g, xstart, ystart, xmid, ymid);
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416 g.setColor(tmpBond.endCol);
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417 drawLine(g, xmid, ymid, xend, yend);
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419 drawLine(g, xstart, ystart, xend, yend);
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424 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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426 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
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427 g.drawLine(x1, y1, x2, y2);
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428 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
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429 g.drawLine(x1, y1 - 1, x2, y2 - 1);
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431 g.setColor(g.getColor().brighter());
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432 g.drawLine(x1, y1, x2, y2);
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433 g.drawLine(x1 + 1, y1, x2 + 1, y2);
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434 g.drawLine(x1 - 1, y1, x2 - 1, y2);
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437 g.drawLine(x1, y1, x2, y2);
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441 public Dimension minimumsize() {
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445 public Dimension preferredsize() {
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449 public void keyTyped(KeyEvent evt) {
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452 public void keyReleased(KeyEvent evt) {
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455 public void keyPressed(KeyEvent evt) {
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456 int key = evt.getKeyChar();
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458 if (evt.getKeyCode() == KeyEvent.VK_UP) {
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459 scale = (float) (scale * 1.1);
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460 redrawneeded = true;
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462 } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
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463 scale = (float) (scale * 0.9);
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464 redrawneeded = true;
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466 } else if (key == 'w') {
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468 System.out.println("wireframe " + wire);
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469 redrawneeded = true;
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471 } else if (key == 'd') {
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472 depthcue = !depthcue;
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473 System.out.println("Depth cueing is " + depthcue);
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474 redrawneeded = true;
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476 } else if (key == 'm') {
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477 bymolecule = !bymolecule;
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478 System.out.println("Bymolecule is " + bymolecule);
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479 redrawneeded = true;
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481 } else if (key == 'z') {
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482 zbuffer = !zbuffer;
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483 System.out.println("Z buffering is " + zbuffer);
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484 redrawneeded = true;
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486 } else if (key == 'c') {
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487 bymolecule = false;
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488 pdb.setChainColours();
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489 System.out.println("Colouring by chain");
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490 redrawneeded = true;
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492 } else if (key == 'h') {
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493 bymolecule = false;
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494 pdb.setHydrophobicityColours();
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495 System.out.println("Colouring by hydrophobicity");
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496 redrawneeded = true;
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498 } else if (key == 'q') {
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499 bymolecule = false;
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500 pdb.setChargeColours();
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501 System.out.println("Colouring charges and cysteines");
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502 redrawneeded = true;
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509 public void mousePressed(MouseEvent e) {
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517 public void mouseMoved(MouseEvent e) {
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518 myAtom fatom = null;
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520 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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521 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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523 if (chain.isVisible) {
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524 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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526 for (int i = 0; i < bonds.size(); i++) {
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527 Bond tmpBond = (Bond) bonds.elementAt(i);
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528 int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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531 if (Math.abs(truex - e.getX()) <= 2) {
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532 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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533 (getHeight() / 2));
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535 if (Math.abs(truey - e.getY()) <= 2) {
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536 fatom = tmpBond.at1;
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543 if (fatom != null) {
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544 this.setToolTipText(fatom.resName);
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546 this.setToolTipText(null);
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550 public void mouseClicked(MouseEvent e) {
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553 public void mouseEntered(MouseEvent e) {
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556 public void mouseExited(MouseEvent e) {
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559 public void mouseDragged(MouseEvent evt) {
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560 int x = evt.getX();
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561 int y = evt.getY();
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565 MCMatrix objmat = new MCMatrix(3, 3);
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566 objmat.setIdentity();
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568 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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569 objmat.rotatez((float) ((mx - omx)));
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571 objmat.rotatex((float) ((my - omy)));
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572 objmat.rotatey((float) ((omx - mx)));
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576 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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577 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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579 for (int i = 0; i < bonds.size(); i++) {
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580 Bond tmpBond = (Bond) bonds.elementAt(i);
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582 //Translate the bond so the centre is 0,0,0
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583 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
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585 //Now apply the rotation matrix
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586 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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587 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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589 //Now translate back again
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590 tmpBond.translate(centre[0], centre[1], centre[2]);
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599 redrawneeded = true;
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601 paint(this.getGraphics());
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608 public void mouseReleased(MouseEvent evt) {
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609 //int x = evt.getX();
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610 //int y = evt.getY();
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613 // myAtom tmp = findAtom(x, y);
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621 public void drawLabels() {
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622 redrawneeded = true;
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623 paint(this.getGraphics());
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625 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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626 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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628 if (chain.isVisible) {
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629 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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631 for (int i = 0; i < bonds.size(); i++) {
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632 Bond tmpBond = (Bond) bonds.elementAt(i);
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634 if (tmpBond.at1.isSelected) {
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635 labelAtom(img.getGraphics(), tmpBond, 1);
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638 if (tmpBond.at2.isSelected) {
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639 labelAtom(img.getGraphics(), tmpBond, 2);
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645 this.getGraphics().drawImage(img, 0, 0, this);
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650 public void labelAtom(Graphics g, Bond b, int n) {
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654 int xstart = (int) (((b.start[0] - centre[0]) * scale) +
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656 int ystart = (int) (((b.start[1] - centre[1]) * scale) +
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657 (getHeight() / 2));
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659 g.setColor(Color.red);
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660 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
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664 int xstart = (int) (((b.end[0] - centre[0]) * scale) +
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666 int ystart = (int) (((b.end[1] - centre[1]) * scale) +
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667 (getHeight() / 2));
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669 g.setColor(Color.red);
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670 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
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674 public myAtom findAtom(int x, int y) {
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675 myAtom fatom = null;
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677 int foundchain = -1;
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679 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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680 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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682 if (chain.isVisible) {
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683 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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685 for (int i = 0; i < bonds.size(); i++) {
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686 Bond tmpBond = (Bond) bonds.elementAt(i);
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688 int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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691 if (Math.abs(truex - x) <= 2) {
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692 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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693 (getHeight() / 2));
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695 if (Math.abs(truey - y) <= 2) {
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696 System.out.println("Found match");
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697 System.out.println(x + " " + y);
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698 System.out.println(truex + " " + truey);
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699 System.out.println(tmpBond.start[0] + " " +
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701 System.out.println("Atom 1 = " +
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702 tmpBond.at1.resName + " " +
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703 tmpBond.at1.resNumber + " " +
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704 tmpBond.at1.chain);
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705 fatom = tmpBond.at1;
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706 fatom.isSelected = !fatom.isSelected;
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713 if (fatom != null) //)&& chain.ds != null)
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715 chain = (PDBChain) pdb.chains.elementAt(foundchain);
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718 // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
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719 // int pos = chain.ds.findIndex(tmp);
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720 // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);
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727 public void update(Graphics g) {
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