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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35 public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener
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37 public AppletPDBCanvas()
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43 catch (Exception ex)
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45 ex.printStackTrace();
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49 MCMatrix idmat = new MCMatrix(3, 3);
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50 MCMatrix objmat = new MCMatrix(3, 3);
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51 boolean redrawneeded = true;
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61 float[] centre = new float[3];
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62 float[] width = new float[3];
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67 boolean bysequence = true;
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68 boolean depthcue = true;
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69 boolean wire = false;
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70 boolean bymolecule = false;
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71 boolean zbuffer = true;
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79 Font font = new Font("Helvetica", Font.PLAIN, 10);
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80 jalview.appletgui.SequenceRenderer sr;
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81 jalview.appletgui.FeatureRenderer fr;
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82 jalview.appletgui.SeqCanvas seqcanvas;
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84 final StringBuffer mappingDetails = new StringBuffer();
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85 String appletToolTip = null;
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88 public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
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90 this.seqcanvas = seqcanvas;
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91 this.sequence = seq;
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92 sr = seqcanvas.getSequenceRenderer();
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93 fr = seqcanvas.getFeatureRenderer();
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95 seqcanvas.setPDBViewer(this);
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96 addKeyListener(new KeyAdapter()
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99 public void keyPressed(KeyEvent evt)
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107 public void setPDBFile(PDBfile pdb)
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118 for (int i = 0; i < pdb.chains.size(); i++)
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121 mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence());
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122 mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n");
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124 // Now lets compare the sequences to get
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125 // the start and end points.
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126 // Align the sequence to the pdb
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127 AlignSeq as = new AlignSeq(sequence,
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128 ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
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129 as.calcScoreMatrix();
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130 as.traceAlignment();
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131 PrintStream ps = new PrintStream(System.out)
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133 public void print(String x) {
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134 mappingDetails.append(x);
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136 public void println()
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138 mappingDetails.append("\n");
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142 as.printAlignment(ps);
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144 if (as.maxscore > max) {
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148 pdbstart = as.seq2start;
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149 pdbend = as.seq2end;
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150 seqstart = as.seq1start + sequence.getStart()-1;
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151 seqend = as.seq1end + sequence.getEnd()-1;
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154 mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
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155 mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend);
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158 ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
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159 ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;
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160 ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;
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161 ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;
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162 ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
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163 ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
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166 this.prefsize = new Dimension(getSize().width, getSize().height);
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168 //Initialize the matrices to identity
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169 for (int i = 0; i < 3; i++) {
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170 for (int j = 0; j < 3; j++) {
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172 idmat.addElement(i, j, 0);
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173 objmat.addElement(i, j, 0);
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175 idmat.addElement(i, j, 1);
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176 objmat.addElement(i, j, 1);
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181 addMouseMotionListener(this);
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182 addMouseListener(this);
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185 SequenceGroup sg = new SequenceGroup("PDB",
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186 null, true,true,false,
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187 sequence.findIndex(seqstart-1),
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188 sequence.findIndex(seqend-1));
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189 sg.addSequence(sequence, false);
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190 sg.setOutlineColour(Color.black);
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191 seqcanvas.getViewport().getAlignment().addGroup(sg);
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197 scale = findScale();
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199 updateSeqColours();
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202 public void deleteBonds() {
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214 for (int i = 0; i < pdb.chains.size(); i++) {
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215 ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
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219 public void findWidth() {
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220 float[] max = new float[3];
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221 float[] min = new float[3];
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223 max[0] = (float) -1e30;
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224 max[1] = (float) -1e30;
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225 max[2] = (float) -1e30;
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227 min[0] = (float) 1e30;
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228 min[1] = (float) 1e30;
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229 min[2] = (float) 1e30;
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231 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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232 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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233 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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235 for (int i = 0; i < bonds.size(); i++) {
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236 Bond tmp = (Bond) bonds.elementAt(i);
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238 if (tmp.start[0] >= max[0]) {
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239 max[0] = tmp.start[0];
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242 if (tmp.start[1] >= max[1]) {
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243 max[1] = tmp.start[1];
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246 if (tmp.start[2] >= max[2]) {
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247 max[2] = tmp.start[2];
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250 if (tmp.start[0] <= min[0]) {
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251 min[0] = tmp.start[0];
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254 if (tmp.start[1] <= min[1]) {
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255 min[1] = tmp.start[1];
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258 if (tmp.start[2] <= min[2]) {
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259 min[2] = tmp.start[2];
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262 if (tmp.end[0] >= max[0]) {
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263 max[0] = tmp.end[0];
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266 if (tmp.end[1] >= max[1]) {
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267 max[1] = tmp.end[1];
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270 if (tmp.end[2] >= max[2]) {
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271 max[2] = tmp.end[2];
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274 if (tmp.end[0] <= min[0]) {
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275 min[0] = tmp.end[0];
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278 if (tmp.end[1] <= min[1]) {
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279 min[1] = tmp.end[1];
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282 if (tmp.end[2] <= min[2]) {
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283 min[2] = tmp.end[2];
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289 width[0] = (float) Math.abs(max[0] - min[0]);
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290 width[1] = (float) Math.abs(max[1] - min[1]);
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291 width[2] = (float) Math.abs(max[2] - min[2]);
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293 maxwidth = width[0];
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295 if (width[1] > width[0]) {
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296 maxwidth = width[1];
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299 if (width[2] > width[1]) {
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300 maxwidth = width[2];
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303 // System.out.println("Maxwidth = " + maxwidth);
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306 public float findScale() {
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311 if (getSize().width != 0) {
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312 width = getSize().width;
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313 height = getSize().height;
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315 width = prefsize.width;
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316 height = prefsize.height;
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319 if (width < height) {
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325 return (float) (dim / (1.5d * maxwidth));
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328 public void findCentre() {
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335 //Find centre coordinate
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336 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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337 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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338 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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340 bsize += bonds.size();
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342 for (int i = 0; i < bonds.size(); i++) {
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343 xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
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344 ((Bond) bonds.elementAt(i)).end[0];
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346 ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
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347 ((Bond) bonds.elementAt(i)).end[1];
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349 ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
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350 ((Bond) bonds.elementAt(i)).end[2];
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355 centre[0] = xtot / (2 * (float) bsize);
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356 centre[1] = ytot / (2 * (float) bsize);
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357 centre[2] = ztot / (2 * (float) bsize);
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360 public void paint(Graphics g)
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365 g.setColor(Color.black);
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366 g.setFont(new Font("Verdana", Font.BOLD, 14));
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367 g.drawString("Error Parsing Pasted PDB data!!", 50, getSize().height/2);
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372 //Only create the image at the beginning -
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373 //this saves much memory usage
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374 if ((img == null) || (prefsize.width != getSize().width) ||
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375 (prefsize.height != getSize().height)) {
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376 prefsize.width = getSize().width;
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377 prefsize.height = getSize().height;
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379 scale = findScale();
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380 img = createImage(prefsize.width, prefsize.height);
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381 ig = img.getGraphics();
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383 redrawneeded = true;
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389 drawAll(ig, prefsize.width, prefsize.height);
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390 redrawneeded = false;
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392 if(appletToolTip!=null)
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394 ig.setColor(Color.red);
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395 ig.drawString(appletToolTip, toolx, tooly);
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398 g.drawImage(img, 0, 0, this);
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403 public void drawAll(Graphics g, int width, int height)
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405 g.setColor(Color.black);
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406 g.fillRect(0, 0, width, height);
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412 public void updateSeqColours()
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414 if(bysequence && pdb!=null)
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416 for (int ii = 0; ii < pdb.chains.size(); ii++)
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418 colourBySequence((PDBChain) pdb.chains.elementAt(ii));
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426 // This method has been taken out of PDBChain to allow
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427 // Applet and Application specific sequence renderers to be used
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428 void colourBySequence(PDBChain chain)
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430 for (int i = 0; i < chain.bonds.size(); i++)
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432 Bond tmp = (Bond) chain.bonds.elementAt(i);
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434 if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
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435 (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
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437 int pos = chain.seqstart +
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438 (tmp.at1.resNumber - chain.pdbstart - chain.offset);
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440 int index = sequence.findIndex(pos);
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442 tmp.startCol = sr.findSequenceColour(sequence, index);
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444 // tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
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449 tmp.startCol = Color.gray;
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452 if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
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453 (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
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455 int pos = chain.seqstart +
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456 (tmp.at2.resNumber - chain.pdbstart - chain.offset);
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457 int index = sequence.findIndex(pos);
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459 tmp.endCol = sr.findSequenceColour( sequence, index);
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460 // tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
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464 tmp.endCol = Color.gray;
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470 public void drawScene(Graphics g) {
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471 // Sort the bonds by z coord
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472 Vector bonds = new Vector();
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474 for (int ii = 0; ii < pdb.chains.size(); ii++)
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476 if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
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478 Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
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480 for (int i = 0; i < tmp.size(); i++)
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482 bonds.addElement(tmp.elementAt(i));
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488 Zsort.Zsort(bonds);
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491 for (int i = 0; i < bonds.size(); i++) {
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492 Bond tmpBond = (Bond) bonds.elementAt(i);
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494 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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495 (getSize().width / 2));
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496 ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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497 (getSize().height / 2));
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499 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
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500 (getSize().width / 2));
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501 yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
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502 (getSize().height / 2));
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504 xmid = (xend + xstart) / 2;
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505 ymid = (yend + ystart) / 2;
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507 if (depthcue && !bymolecule) {
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508 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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509 g.setColor(tmpBond.startCol.darker().darker());
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510 drawLine(g, xstart, ystart, xmid, ymid);
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512 g.setColor(tmpBond.endCol.darker().darker());
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513 drawLine(g, xmid, ymid, xend, yend);
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514 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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515 g.setColor(tmpBond.startCol.darker());
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516 drawLine(g, xstart, ystart, xmid, ymid);
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518 g.setColor(tmpBond.endCol.darker());
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519 drawLine(g, xmid, ymid, xend, yend);
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521 g.setColor(tmpBond.startCol);
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522 drawLine(g, xstart, ystart, xmid, ymid);
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524 g.setColor(tmpBond.endCol);
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525 drawLine(g, xmid, ymid, xend, yend);
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527 } else if (depthcue && bymolecule) {
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528 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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529 g.setColor(Color.green.darker().darker());
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530 drawLine(g, xstart, ystart, xend, yend);
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531 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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532 g.setColor(Color.green.darker());
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533 drawLine(g, xstart, ystart, xend, yend);
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535 g.setColor(Color.green);
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536 drawLine(g, xstart, ystart, xend, yend);
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538 } else if (!depthcue && !bymolecule) {
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539 g.setColor(tmpBond.startCol);
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540 drawLine(g, xstart, ystart, xmid, ymid);
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541 g.setColor(tmpBond.endCol);
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542 drawLine(g, xmid, ymid, xend, yend);
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544 drawLine(g, xstart, ystart, xend, yend);
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549 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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551 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
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552 g.drawLine(x1, y1, x2, y2);
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553 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
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554 g.drawLine(x1, y1 - 1, x2, y2 - 1);
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556 g.setColor(g.getColor().brighter());
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557 g.drawLine(x1, y1, x2, y2);
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558 g.drawLine(x1 + 1, y1, x2 + 1, y2);
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559 g.drawLine(x1 - 1, y1, x2 - 1, y2);
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562 g.drawLine(x1, y1, x2, y2);
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566 public Dimension minimumsize() {
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570 public Dimension preferredsize() {
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574 public void doKeyPressed(KeyEvent evt)
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576 if (evt.getKeyCode() == KeyEvent.VK_UP)
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578 scale = (float) (scale * 1.1);
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579 redrawneeded = true;
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582 else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
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584 scale = (float) (scale * 0.9);
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585 redrawneeded = true;
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590 public void mousePressed(MouseEvent e) {
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591 myAtom fatom = findAtom(e.getX(), e.getY());
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594 fatom.isSelected = !fatom.isSelected;
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595 redrawneeded = true;
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605 public void mouseMoved(MouseEvent e) {
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607 myAtom fatom = findAtom(e.getX(), e.getY());
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611 PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
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612 int pos = chain.seqstart +
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613 (fatom.resNumber - chain.pdbstart - chain.offset)+1;
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615 int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
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617 seqcanvas.highlightSearchResults(new int[]{index, pos, pos});
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620 seqcanvas.highlightSearchResults(null);
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622 if (fatom != null) {
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625 appletToolTip = fatom.resNumber+" "+ fatom.resName;
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626 redrawneeded = true;
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629 appletToolTip = null;
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630 redrawneeded = true;
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635 public void mouseClicked(MouseEvent e) {
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638 public void mouseEntered(MouseEvent e) {
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641 public void mouseExited(MouseEvent e) {
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644 public void mouseDragged(MouseEvent evt) {
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645 int x = evt.getX();
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646 int y = evt.getY();
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650 MCMatrix objmat = new MCMatrix(3, 3);
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651 objmat.setIdentity();
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653 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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654 objmat.rotatez((float) ((mx - omx)));
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656 objmat.rotatex((float) ((my - omy)));
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657 objmat.rotatey((float) ((omx - mx)));
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661 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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662 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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664 for (int i = 0; i < bonds.size(); i++) {
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665 Bond tmpBond = (Bond) bonds.elementAt(i);
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667 //Translate the bond so the centre is 0,0,0
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668 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
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670 //Now apply the rotation matrix
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671 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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672 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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674 //Now translate back again
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675 tmpBond.translate(centre[0], centre[1], centre[2]);
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686 redrawneeded = true;
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691 public void mouseReleased(MouseEvent evt) {
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696 void drawLabels(Graphics g) {
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698 for (int ii = 0; ii < pdb.chains.size(); ii++)
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700 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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702 if (chain.isVisible)
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704 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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706 for (int i = 0; i < bonds.size(); i++)
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708 Bond tmpBond = (Bond) bonds.elementAt(i);
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710 if (tmpBond.at1.isSelected)
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712 labelAtom(g, tmpBond, 1);
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715 if (tmpBond.at2.isSelected)
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718 labelAtom(g, tmpBond, 2);
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725 public void labelAtom(Graphics g, Bond b, int n) {
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729 int xstart = (int) (((b.start[0] - centre[0]) * scale) +
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730 (getSize().width / 2));
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731 int ystart = (int) (((b.start[1] - centre[1]) * scale) +
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732 (getSize().height / 2));
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734 g.setColor(Color.red);
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735 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
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739 int xstart = (int) (((b.end[0] - centre[0]) * scale) +
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740 (getSize().width / 2));
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741 int ystart = (int) (((b.end[1] - centre[1]) * scale) +
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742 (getSize().height / 2));
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744 g.setColor(Color.red);
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745 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
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749 int foundchain = -1;
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750 public myAtom findAtom(int x, int y) {
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751 myAtom fatom = null;
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755 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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756 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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758 if (chain.isVisible) {
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759 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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761 for (int i = 0; i < bonds.size(); i++) {
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762 Bond tmpBond = (Bond) bonds.elementAt(i);
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764 int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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765 (getSize().width / 2));
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767 if (Math.abs(truex - x) <= 2) {
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768 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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769 (getSize().height / 2));
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771 if (Math.abs(truey - y) <= 2)
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773 fatom = tmpBond.at1;
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781 if (fatom != null) //)&& chain.ds != null)
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783 chain = (PDBChain) pdb.chains.elementAt(foundchain);
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790 public void update(Graphics g)
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795 private void jbInit()
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