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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143 public void addPDBfile() {
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147 scale = findScale();
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149 System.out.println("Scale factor = " + scale);
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152 public void deleteBonds() {
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164 for (int i = 0; i < pdb.chains.size(); i++) {
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165 ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
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169 public void findWidth() {
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170 float[] max = new float[3];
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171 float[] min = new float[3];
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173 max[0] = (float) -1e30;
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174 max[1] = (float) -1e30;
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175 max[2] = (float) -1e30;
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177 min[0] = (float) 1e30;
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178 min[1] = (float) 1e30;
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179 min[2] = (float) 1e30;
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181 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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182 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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183 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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185 for (int i = 0; i < bonds.size(); i++) {
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186 Bond tmp = (Bond) bonds.elementAt(i);
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188 if (tmp.start[0] >= max[0]) {
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189 max[0] = tmp.start[0];
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192 if (tmp.start[1] >= max[1]) {
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193 max[1] = tmp.start[1];
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196 if (tmp.start[2] >= max[2]) {
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197 max[2] = tmp.start[2];
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200 if (tmp.start[0] <= min[0]) {
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201 min[0] = tmp.start[0];
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204 if (tmp.start[1] <= min[1]) {
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205 min[1] = tmp.start[1];
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208 if (tmp.start[2] <= min[2]) {
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209 min[2] = tmp.start[2];
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212 if (tmp.end[0] >= max[0]) {
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213 max[0] = tmp.end[0];
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216 if (tmp.end[1] >= max[1]) {
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217 max[1] = tmp.end[1];
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220 if (tmp.end[2] >= max[2]) {
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221 max[2] = tmp.end[2];
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224 if (tmp.end[0] <= min[0]) {
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225 min[0] = tmp.end[0];
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228 if (tmp.end[1] <= min[1]) {
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229 min[1] = tmp.end[1];
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232 if (tmp.end[2] <= min[2]) {
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233 min[2] = tmp.end[2];
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239 System.out.println("xmax " + max[0] + " min " + min[0]);
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240 System.out.println("ymax " + max[1] + " min " + min[1]);
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241 System.out.println("zmax " + max[2] + " min " + min[2]);
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243 width[0] = (float) Math.abs(max[0] - min[0]);
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244 width[1] = (float) Math.abs(max[1] - min[1]);
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245 width[2] = (float) Math.abs(max[2] - min[2]);
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247 maxwidth = width[0];
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249 if (width[1] > width[0]) {
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250 maxwidth = width[1];
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253 if (width[2] > width[1]) {
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254 maxwidth = width[2];
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257 System.out.println("Maxwidth = " + maxwidth);
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260 public float findScale() {
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265 if (getWidth() != 0) {
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266 width = getWidth();
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267 height = getHeight();
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269 width = prefsize.width;
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270 height = prefsize.height;
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273 if (width < height) {
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279 return (float) (dim / (1.5d * maxwidth));
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282 public void findCentre() {
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289 //Find centre coordinate
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290 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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291 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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292 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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294 bsize += bonds.size();
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296 for (int i = 0; i < bonds.size(); i++) {
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297 xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
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298 ((Bond) bonds.elementAt(i)).end[0];
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300 ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
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301 ((Bond) bonds.elementAt(i)).end[1];
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303 ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
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304 ((Bond) bonds.elementAt(i)).end[2];
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309 centre[0] = xtot / (2 * (float) bsize);
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310 centre[1] = ytot / (2 * (float) bsize);
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311 centre[2] = ztot / (2 * (float) bsize);
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314 public void paint(Graphics g) {
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315 //Only create the image at the beginning -
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316 //this saves much memory usage
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317 if ((img == null) || (prefsize.width != getWidth()) ||
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318 (prefsize.height != getHeight())) {
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319 prefsize.width = getWidth();
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320 prefsize.height = getHeight();
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322 scale = findScale();
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323 img = createImage(prefsize.width, prefsize.height);
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324 ig = img.getGraphics();
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326 redrawneeded = true;
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329 if (redrawneeded == true) {
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330 drawBackground(ig, Color.black);
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332 redrawneeded = false;
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334 ig = img.getGraphics();
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337 g.drawImage(img, 0, 0, this);
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340 public void drawBackground(Graphics g, Color col) {
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342 g.fillRect(0, 0, prefsize.width, prefsize.height);
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345 public void drawScene(Graphics g) {
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346 // Sort the bonds by z coord
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347 Vector bonds = new Vector();
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349 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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350 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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351 Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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353 for (int i = 0; i < tmp.size(); i++) {
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354 bonds.addElement(tmp.elementAt(i));
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360 Zsort.Zsort(bonds);
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363 for (int i = 0; i < bonds.size(); i++) {
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364 Bond tmpBond = (Bond) bonds.elementAt(i);
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366 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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368 ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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369 (getHeight() / 2));
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371 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
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373 yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
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374 (getHeight() / 2));
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376 xmid = (xend + xstart) / 2;
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377 ymid = (yend + ystart) / 2;
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379 if (depthcue && !bymolecule) {
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380 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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381 g.setColor(tmpBond.startCol.darker().darker());
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382 drawLine(g, xstart, ystart, xmid, ymid);
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384 g.setColor(tmpBond.endCol.darker().darker());
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385 drawLine(g, xmid, ymid, xend, yend);
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386 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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387 g.setColor(tmpBond.startCol.darker());
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388 drawLine(g, xstart, ystart, xmid, ymid);
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390 g.setColor(tmpBond.endCol.darker());
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391 drawLine(g, xmid, ymid, xend, yend);
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393 g.setColor(tmpBond.startCol);
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394 drawLine(g, xstart, ystart, xmid, ymid);
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396 g.setColor(tmpBond.endCol);
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397 drawLine(g, xmid, ymid, xend, yend);
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399 } else if (depthcue && bymolecule) {
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400 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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401 g.setColor(Color.green.darker().darker());
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402 drawLine(g, xstart, ystart, xend, yend);
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403 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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404 g.setColor(Color.green.darker());
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405 drawLine(g, xstart, ystart, xend, yend);
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407 g.setColor(Color.green);
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408 drawLine(g, xstart, ystart, xend, yend);
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410 } else if (!depthcue && !bymolecule) {
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411 g.setColor(tmpBond.startCol);
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412 drawLine(g, xstart, ystart, xmid, ymid);
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413 g.setColor(tmpBond.endCol);
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414 drawLine(g, xmid, ymid, xend, yend);
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416 drawLine(g, xstart, ystart, xend, yend);
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421 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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423 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
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424 g.drawLine(x1, y1, x2, y2);
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425 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
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426 g.drawLine(x1, y1 - 1, x2, y2 - 1);
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428 g.setColor(g.getColor().brighter());
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429 g.drawLine(x1, y1, x2, y2);
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430 g.drawLine(x1 + 1, y1, x2 + 1, y2);
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431 g.drawLine(x1 - 1, y1, x2 - 1, y2);
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434 g.drawLine(x1, y1, x2, y2);
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438 public Dimension minimumsize() {
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442 public Dimension preferredsize() {
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446 public void keyTyped(KeyEvent evt) {
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449 public void keyReleased(KeyEvent evt) {
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452 public void keyPressed(KeyEvent evt) {
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453 int key = evt.getKeyChar();
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455 if (evt.getKeyCode() == KeyEvent.VK_UP) {
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456 scale = (float) (scale * 1.1);
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457 redrawneeded = true;
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459 } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
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460 scale = (float) (scale * 0.9);
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461 redrawneeded = true;
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463 } else if (key == 'w') {
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465 System.out.println("wireframe " + wire);
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466 redrawneeded = true;
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468 } else if (key == 'd') {
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469 depthcue = !depthcue;
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470 System.out.println("Depth cueing is " + depthcue);
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471 redrawneeded = true;
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473 } else if (key == 'm') {
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474 bymolecule = !bymolecule;
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475 System.out.println("Bymolecule is " + bymolecule);
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476 redrawneeded = true;
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478 } else if (key == 'z') {
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479 zbuffer = !zbuffer;
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480 System.out.println("Z buffering is " + zbuffer);
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481 redrawneeded = true;
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483 } else if (key == 'c') {
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484 bymolecule = false;
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485 pdb.setChainColours();
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486 System.out.println("Colouring by chain");
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487 redrawneeded = true;
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489 } else if (key == 'h') {
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490 bymolecule = false;
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491 pdb.setHydrophobicityColours();
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492 System.out.println("Colouring by hydrophobicity");
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493 redrawneeded = true;
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495 } else if (key == 'q') {
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496 bymolecule = false;
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497 pdb.setChargeColours();
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498 System.out.println("Colouring charges and cysteines");
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499 redrawneeded = true;
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506 public void mousePressed(MouseEvent e) {
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514 public void mouseMoved(MouseEvent e) {
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515 myAtom fatom = null;
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517 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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518 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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520 if (chain.isVisible) {
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521 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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523 for (int i = 0; i < bonds.size(); i++) {
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524 Bond tmpBond = (Bond) bonds.elementAt(i);
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525 int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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528 if (Math.abs(truex - e.getX()) <= 2) {
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529 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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530 (getHeight() / 2));
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532 if (Math.abs(truey - e.getY()) <= 2) {
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533 fatom = tmpBond.at1;
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540 if (fatom != null) {
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541 this.setToolTipText(fatom.resName);
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543 this.setToolTipText(null);
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547 public void mouseClicked(MouseEvent e) {
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550 public void mouseEntered(MouseEvent e) {
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553 public void mouseExited(MouseEvent e) {
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556 public void mouseDragged(MouseEvent evt) {
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557 int x = evt.getX();
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558 int y = evt.getY();
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562 MCMatrix objmat = new MCMatrix(3, 3);
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563 objmat.setIdentity();
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565 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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566 objmat.rotatez((float) ((mx - omx)));
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568 objmat.rotatex((float) ((my - omy)));
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569 objmat.rotatey((float) ((omx - mx)));
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573 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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574 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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576 for (int i = 0; i < bonds.size(); i++) {
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577 Bond tmpBond = (Bond) bonds.elementAt(i);
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579 //Translate the bond so the centre is 0,0,0
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580 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
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582 //Now apply the rotation matrix
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583 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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584 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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586 //Now translate back again
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587 tmpBond.translate(centre[0], centre[1], centre[2]);
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596 redrawneeded = true;
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598 paint(this.getGraphics());
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605 public void mouseReleased(MouseEvent evt) {
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606 int x = evt.getX();
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607 int y = evt.getY();
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610 myAtom tmp = findAtom(x, y);
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618 public void drawLabels() {
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619 redrawneeded = true;
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620 paint(this.getGraphics());
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622 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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623 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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625 if (chain.isVisible) {
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626 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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628 for (int i = 0; i < bonds.size(); i++) {
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629 Bond tmpBond = (Bond) bonds.elementAt(i);
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631 if (tmpBond.at1.isSelected) {
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632 labelAtom(img.getGraphics(), tmpBond, 1);
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635 if (tmpBond.at2.isSelected) {
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636 labelAtom(img.getGraphics(), tmpBond, 2);
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642 this.getGraphics().drawImage(img, 0, 0, this);
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647 public void labelAtom(Graphics g, Bond b, int n) {
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651 int xstart = (int) (((b.start[0] - centre[0]) * scale) +
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653 int ystart = (int) (((b.start[1] - centre[1]) * scale) +
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654 (getHeight() / 2));
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656 g.setColor(Color.red);
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657 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
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661 int xstart = (int) (((b.end[0] - centre[0]) * scale) +
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663 int ystart = (int) (((b.end[1] - centre[1]) * scale) +
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664 (getHeight() / 2));
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666 g.setColor(Color.red);
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667 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
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671 public myAtom findAtom(int x, int y) {
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672 myAtom fatom = null;
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674 int foundchain = -1;
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676 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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677 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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679 if (chain.isVisible) {
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680 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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682 for (int i = 0; i < bonds.size(); i++) {
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683 Bond tmpBond = (Bond) bonds.elementAt(i);
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685 int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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688 if (Math.abs(truex - x) <= 2) {
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689 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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690 (getHeight() / 2));
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692 if (Math.abs(truey - y) <= 2) {
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693 System.out.println("Found match");
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694 System.out.println(x + " " + y);
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695 System.out.println(truex + " " + truey);
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696 System.out.println(tmpBond.start[0] + " " +
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698 System.out.println("Atom 1 = " +
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699 tmpBond.at1.resName + " " +
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700 tmpBond.at1.resNumber + " " +
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701 tmpBond.at1.chain);
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702 fatom = tmpBond.at1;
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703 fatom.isSelected = !fatom.isSelected;
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710 if (fatom != null) //)&& chain.ds != null)
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712 chain = (PDBChain) pdb.chains.elementAt(foundchain);
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715 // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
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716 // int pos = chain.ds.findIndex(tmp);
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717 // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);
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724 public void update(Graphics g) {
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