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 PDBCanvas extends JPanel implements MouseListener, 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 bysequence = true;
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57 boolean depthcue = true;
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58 boolean wire = false;
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59 boolean bymolecule = false;
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60 boolean zbuffer = true;
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68 Font font = new Font("Helvetica", Font.PLAIN, 10);
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69 jalview.gui.SequenceRenderer sr;
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70 jalview.gui.FeatureRenderer fr;
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71 jalview.gui.SeqCanvas seqcanvas;
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73 final StringBuffer mappingDetails = new StringBuffer();
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75 public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)
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77 this.seqcanvas = seqcanvas;
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78 this.sequence = seq;
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79 sr = seqcanvas.getSequenceRenderer();
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80 fr = seqcanvas.getFeatureRenderer();
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82 seqcanvas.setPDBViewer(this);
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85 public void setPDBFile(PDBfile pdb)
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96 for (int i = 0; i < pdb.chains.size(); i++)
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99 mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence());
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100 mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n");
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102 // Now lets compare the sequences to get
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103 // the start and end points.
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104 // Align the sequence to the pdb
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105 AlignSeq as = new AlignSeq(sequence,
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106 ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
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107 as.calcScoreMatrix();
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108 as.traceAlignment();
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109 PrintStream ps = new PrintStream(System.out)
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111 public void print(String x) {
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112 mappingDetails.append(x);
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114 public void println()
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116 mappingDetails.append("\n");
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120 as.printAlignment(ps);
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122 if (as.maxscore > max) {
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126 pdbstart = as.seq2start;
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127 pdbend = as.seq2end;
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128 seqstart = as.seq1start + sequence.getStart()-1;
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129 seqend = as.seq1end + sequence.getEnd()-1;
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132 mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
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133 mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend);
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136 ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
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137 ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;
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138 ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;
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139 ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;
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140 ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
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141 ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
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144 this.prefsize = new Dimension(getWidth(), getHeight());
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146 //Initialize the matrices to identity
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147 for (int i = 0; i < 3; i++) {
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148 for (int j = 0; j < 3; j++) {
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150 idmat.addElement(i, j, 0);
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151 objmat.addElement(i, j, 0);
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153 idmat.addElement(i, j, 1);
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154 objmat.addElement(i, j, 1);
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159 addMouseMotionListener(this);
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160 addMouseListener(this);
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165 scale = findScale();
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168 updateSeqColours();
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169 ToolTipManager.sharedInstance().registerComponent(this);
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170 ToolTipManager.sharedInstance().setInitialDelay(0);
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171 ToolTipManager.sharedInstance().setDismissDelay(10000);
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175 public void deleteBonds() {
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187 for (int i = 0; i < pdb.chains.size(); i++) {
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188 ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
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192 public void findWidth() {
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193 float[] max = new float[3];
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194 float[] min = new float[3];
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196 max[0] = (float) -1e30;
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197 max[1] = (float) -1e30;
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198 max[2] = (float) -1e30;
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200 min[0] = (float) 1e30;
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201 min[1] = (float) 1e30;
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202 min[2] = (float) 1e30;
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204 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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205 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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206 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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208 for (int i = 0; i < bonds.size(); i++) {
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209 Bond tmp = (Bond) bonds.elementAt(i);
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211 if (tmp.start[0] >= max[0]) {
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212 max[0] = tmp.start[0];
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215 if (tmp.start[1] >= max[1]) {
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216 max[1] = tmp.start[1];
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219 if (tmp.start[2] >= max[2]) {
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220 max[2] = tmp.start[2];
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223 if (tmp.start[0] <= min[0]) {
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224 min[0] = tmp.start[0];
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227 if (tmp.start[1] <= min[1]) {
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228 min[1] = tmp.start[1];
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231 if (tmp.start[2] <= min[2]) {
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232 min[2] = tmp.start[2];
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235 if (tmp.end[0] >= max[0]) {
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236 max[0] = tmp.end[0];
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239 if (tmp.end[1] >= max[1]) {
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240 max[1] = tmp.end[1];
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243 if (tmp.end[2] >= max[2]) {
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244 max[2] = tmp.end[2];
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247 if (tmp.end[0] <= min[0]) {
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248 min[0] = tmp.end[0];
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251 if (tmp.end[1] <= min[1]) {
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252 min[1] = tmp.end[1];
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255 if (tmp.end[2] <= min[2]) {
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256 min[2] = tmp.end[2];
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262 System.out.println("xmax " + max[0] + " min " + min[0]);
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263 System.out.println("ymax " + max[1] + " min " + min[1]);
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264 System.out.println("zmax " + max[2] + " min " + min[2]);*/
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266 width[0] = (float) Math.abs(max[0] - min[0]);
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267 width[1] = (float) Math.abs(max[1] - min[1]);
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268 width[2] = (float) Math.abs(max[2] - min[2]);
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270 maxwidth = width[0];
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272 if (width[1] > width[0]) {
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273 maxwidth = width[1];
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276 if (width[2] > width[1]) {
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277 maxwidth = width[2];
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280 // System.out.println("Maxwidth = " + maxwidth);
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283 public float findScale() {
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288 if (getWidth() != 0) {
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289 width = getWidth();
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290 height = getHeight();
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292 width = prefsize.width;
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293 height = prefsize.height;
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296 if (width < height) {
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302 return (float) (dim / (1.5d * maxwidth));
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305 public void findCentre() {
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312 //Find centre coordinate
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313 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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314 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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315 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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317 bsize += bonds.size();
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319 for (int i = 0; i < bonds.size(); i++) {
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320 xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
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321 ((Bond) bonds.elementAt(i)).end[0];
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323 ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
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324 ((Bond) bonds.elementAt(i)).end[1];
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326 ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
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327 ((Bond) bonds.elementAt(i)).end[2];
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332 centre[0] = xtot / (2 * (float) bsize);
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333 centre[1] = ytot / (2 * (float) bsize);
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334 centre[2] = ztot / (2 * (float) bsize);
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337 public void paintComponent(Graphics g) {
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339 super.paintComponent(g);
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343 g.setColor(Color.black);
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344 g.setFont(new Font("Verdana", Font.BOLD, 14));
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345 g.drawString("Retrieving PDB data....", 20, getHeight()/2);
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350 //Only create the image at the beginning -
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351 //this saves much memory usage
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352 if ((img == null) || (prefsize.width != getWidth()) ||
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353 (prefsize.height != getHeight())) {
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354 prefsize.width = getWidth();
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355 prefsize.height = getHeight();
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357 scale = findScale();
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358 img = createImage(prefsize.width, prefsize.height);
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359 ig = img.getGraphics();
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360 Graphics2D ig2 = (Graphics2D) ig;
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362 ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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363 RenderingHints.VALUE_ANTIALIAS_ON);
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366 redrawneeded = true;
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372 drawAll(ig, prefsize.width, prefsize.height);
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373 redrawneeded = false;
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376 g.drawImage(img, 0, 0, this);
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379 public void drawAll(Graphics g, int width, int height)
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381 g.setColor(Color.black);
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382 g.fillRect(0, 0, width, height);
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388 public void updateSeqColours()
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390 if(bysequence && pdb!=null)
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392 for (int ii = 0; ii < pdb.chains.size(); ii++)
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394 ( (PDBChain) pdb.chains.elementAt(ii)).colourBySequence(sr, fr);
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403 public void drawScene(Graphics g) {
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404 // Sort the bonds by z coord
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405 Vector bonds = new Vector();
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407 for (int ii = 0; ii < pdb.chains.size(); ii++)
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409 if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
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411 Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
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413 for (int i = 0; i < tmp.size(); i++)
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415 bonds.addElement(tmp.elementAt(i));
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421 Zsort.Zsort(bonds);
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424 for (int i = 0; i < bonds.size(); i++) {
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425 Bond tmpBond = (Bond) bonds.elementAt(i);
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427 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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429 ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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430 (getHeight() / 2));
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432 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
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434 yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
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435 (getHeight() / 2));
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437 xmid = (xend + xstart) / 2;
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438 ymid = (yend + ystart) / 2;
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440 if (depthcue && !bymolecule) {
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441 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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442 g.setColor(tmpBond.startCol.darker().darker());
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443 drawLine(g, xstart, ystart, xmid, ymid);
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445 g.setColor(tmpBond.endCol.darker().darker());
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446 drawLine(g, xmid, ymid, xend, yend);
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447 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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448 g.setColor(tmpBond.startCol.darker());
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449 drawLine(g, xstart, ystart, xmid, ymid);
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451 g.setColor(tmpBond.endCol.darker());
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452 drawLine(g, xmid, ymid, xend, yend);
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454 g.setColor(tmpBond.startCol);
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455 drawLine(g, xstart, ystart, xmid, ymid);
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457 g.setColor(tmpBond.endCol);
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458 drawLine(g, xmid, ymid, xend, yend);
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460 } else if (depthcue && bymolecule) {
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461 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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462 g.setColor(Color.green.darker().darker());
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463 drawLine(g, xstart, ystart, xend, yend);
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464 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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465 g.setColor(Color.green.darker());
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466 drawLine(g, xstart, ystart, xend, yend);
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468 g.setColor(Color.green);
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469 drawLine(g, xstart, ystart, xend, yend);
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471 } else if (!depthcue && !bymolecule) {
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472 g.setColor(tmpBond.startCol);
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473 drawLine(g, xstart, ystart, xmid, ymid);
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474 g.setColor(tmpBond.endCol);
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475 drawLine(g, xmid, ymid, xend, yend);
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477 drawLine(g, xstart, ystart, xend, yend);
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482 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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484 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
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485 g.drawLine(x1, y1, x2, y2);
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486 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
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487 g.drawLine(x1, y1 - 1, x2, y2 - 1);
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489 g.setColor(g.getColor().brighter());
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490 g.drawLine(x1, y1, x2, y2);
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491 g.drawLine(x1 + 1, y1, x2 + 1, y2);
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492 g.drawLine(x1 - 1, y1, x2 - 1, y2);
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495 g.drawLine(x1, y1, x2, y2);
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499 public Dimension minimumsize() {
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503 public Dimension preferredsize() {
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507 public void keyPressed(KeyEvent evt) {
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508 int key = evt.getKeyChar();
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509 if (evt.getKeyCode() == KeyEvent.VK_UP)
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511 scale = (float) (scale * 1.1);
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512 redrawneeded = true;
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515 else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
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517 scale = (float) (scale * 0.9);
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518 redrawneeded = true;
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523 public void mousePressed(MouseEvent e) {
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524 myAtom fatom = findAtom(e.getX(), e.getY());
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527 fatom.isSelected = !fatom.isSelected;
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528 redrawneeded = true;
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538 public void mouseMoved(MouseEvent e) {
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540 myAtom fatom = findAtom(e.getX(), e.getY());
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544 PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
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545 int pos = chain.seqstart +
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546 (fatom.resNumber - chain.pdbstart - chain.offset)+1;
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548 int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
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550 seqcanvas.highlightSearchResults(new int[]{index, pos, pos});
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553 seqcanvas.highlightSearchResults(null);
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555 if (fatom != null) {
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556 this.setToolTipText(fatom.resNumber+" "+ fatom.resName);
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558 this.setToolTipText("");
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562 public void mouseClicked(MouseEvent e) {
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565 public void mouseEntered(MouseEvent e) {
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568 public void mouseExited(MouseEvent e) {
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571 public void mouseDragged(MouseEvent evt) {
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572 int x = evt.getX();
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573 int y = evt.getY();
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577 MCMatrix objmat = new MCMatrix(3, 3);
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578 objmat.setIdentity();
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580 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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581 objmat.rotatez((float) ((mx - omx)));
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583 objmat.rotatex((float) ((my - omy)));
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584 objmat.rotatey((float) ((omx - mx)));
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588 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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589 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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591 for (int i = 0; i < bonds.size(); i++) {
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592 Bond tmpBond = (Bond) bonds.elementAt(i);
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594 //Translate the bond so the centre is 0,0,0
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595 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
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597 //Now apply the rotation matrix
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598 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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599 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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601 //Now translate back again
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602 tmpBond.translate(centre[0], centre[1], centre[2]);
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613 redrawneeded = true;
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618 public void mouseReleased(MouseEvent evt) {
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623 void drawLabels(Graphics g) {
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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(g, tmpBond, 1);
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638 if (tmpBond.at2.isSelected) {
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639 labelAtom(g, tmpBond, 2);
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646 public void labelAtom(Graphics g, Bond b, int n) {
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650 int xstart = (int) (((b.start[0] - centre[0]) * scale) +
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652 int ystart = (int) (((b.start[1] - centre[1]) * scale) +
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653 (getHeight() / 2));
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655 g.setColor(Color.red);
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656 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
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660 int xstart = (int) (((b.end[0] - centre[0]) * scale) +
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662 int ystart = (int) (((b.end[1] - centre[1]) * scale) +
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663 (getHeight() / 2));
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665 g.setColor(Color.red);
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666 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
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670 int foundchain = -1;
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671 public myAtom findAtom(int x, int y) {
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672 myAtom fatom = null;
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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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694 fatom = tmpBond.at1;
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702 if (fatom != null) //)&& chain.ds != null)
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704 chain = (PDBChain) pdb.chains.elementAt(foundchain);
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