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.SeqCanvas seqcanvas;
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70 public Sequence sequence;
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71 final StringBuffer mappingDetails = new StringBuffer();
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73 Vector highlightRes;
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74 boolean pdbAction = false;
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76 public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)
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78 this.seqcanvas = seqcanvas;
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79 this.sequence = seq;
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80 seqcanvas.setPDBCanvas(this);
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83 public void setPDBFile(PDBfile pdb)
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91 AlignSeq maxAlignseq = null;
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93 for (int i = 0; i < pdb.chains.size(); i++)
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96 mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence());
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97 mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n");
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99 // Now lets compare the sequences to get
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100 // the start and end points.
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101 // Align the sequence to the pdb
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102 AlignSeq as = new AlignSeq(sequence,
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103 ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
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104 as.calcScoreMatrix();
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105 as.traceAlignment();
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106 PrintStream ps = new PrintStream(System.out)
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108 public void print(String x) {
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109 mappingDetails.append(x);
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111 public void println()
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113 mappingDetails.append("\n");
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117 as.printAlignment(ps);
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121 if (as.maxscore > max)
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125 pdbstart = as.seq2start;
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126 pdbend = as.seq2end;
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127 seqstart = as.seq1start + sequence.getStart()-1;
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128 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 mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
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138 mainchain.pdbstart = pdbstart;
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139 mainchain.pdbend = pdbend;
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140 mainchain.seqstart = seqstart;
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141 mainchain.seqend = seqend;
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142 mainchain.isVisible = true;
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143 mainchain.makeExactMapping(maxAlignseq, sequence);
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146 this.prefsize = new Dimension(getWidth(), getHeight());
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148 //Initialize the matrices to identity
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149 for (int i = 0; i < 3; i++) {
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150 for (int j = 0; j < 3; j++) {
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152 idmat.addElement(i, j, 0);
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153 objmat.addElement(i, j, 0);
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155 idmat.addElement(i, j, 1);
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156 objmat.addElement(i, j, 1);
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161 addMouseMotionListener(this);
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162 addMouseListener(this);
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164 addMouseWheelListener(new MouseWheelListener()
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166 public void mouseWheelMoved(MouseWheelEvent e)
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168 if (e.getWheelRotation() > 0)
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170 scale = (float) (scale * 1.1);
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171 redrawneeded = true;
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177 scale = (float) (scale * 0.9);
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178 redrawneeded = true;
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190 scale = findScale();
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192 ToolTipManager.sharedInstance().registerComponent(this);
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193 ToolTipManager.sharedInstance().setInitialDelay(0);
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194 ToolTipManager.sharedInstance().setDismissDelay(10000);
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198 Vector visiblebonds;
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201 // Sort the bonds by z coord
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202 visiblebonds = new Vector();
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204 for (int ii = 0; ii < pdb.chains.size(); ii++)
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206 if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
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208 Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
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210 for (int i = 0; i < tmp.size(); i++)
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212 visiblebonds.addElement(tmp.elementAt(i));
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217 updateSeqColours();
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218 redrawneeded = true;
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223 public void findWidth() {
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224 float[] max = new float[3];
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225 float[] min = new float[3];
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227 max[0] = (float) -1e30;
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228 max[1] = (float) -1e30;
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229 max[2] = (float) -1e30;
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231 min[0] = (float) 1e30;
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232 min[1] = (float) 1e30;
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233 min[2] = (float) 1e30;
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235 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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236 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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237 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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239 for (int i = 0; i < bonds.size(); i++) {
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240 Bond tmp = (Bond) bonds.elementAt(i);
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242 if (tmp.start[0] >= max[0]) {
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243 max[0] = tmp.start[0];
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246 if (tmp.start[1] >= max[1]) {
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247 max[1] = tmp.start[1];
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250 if (tmp.start[2] >= max[2]) {
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251 max[2] = tmp.start[2];
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254 if (tmp.start[0] <= min[0]) {
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255 min[0] = tmp.start[0];
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258 if (tmp.start[1] <= min[1]) {
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259 min[1] = tmp.start[1];
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262 if (tmp.start[2] <= min[2]) {
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263 min[2] = tmp.start[2];
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266 if (tmp.end[0] >= max[0]) {
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267 max[0] = tmp.end[0];
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270 if (tmp.end[1] >= max[1]) {
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271 max[1] = tmp.end[1];
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274 if (tmp.end[2] >= max[2]) {
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275 max[2] = tmp.end[2];
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278 if (tmp.end[0] <= min[0]) {
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279 min[0] = tmp.end[0];
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282 if (tmp.end[1] <= min[1]) {
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283 min[1] = tmp.end[1];
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286 if (tmp.end[2] <= min[2]) {
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287 min[2] = tmp.end[2];
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293 System.out.println("xmax " + max[0] + " min " + min[0]);
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294 System.out.println("ymax " + max[1] + " min " + min[1]);
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295 System.out.println("zmax " + max[2] + " min " + min[2]);*/
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297 width[0] = (float) Math.abs(max[0] - min[0]);
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298 width[1] = (float) Math.abs(max[1] - min[1]);
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299 width[2] = (float) Math.abs(max[2] - min[2]);
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301 maxwidth = width[0];
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303 if (width[1] > width[0]) {
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304 maxwidth = width[1];
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307 if (width[2] > width[1]) {
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308 maxwidth = width[2];
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311 // System.out.println("Maxwidth = " + maxwidth);
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314 public float findScale() {
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319 if (getWidth() != 0) {
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320 width = getWidth();
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321 height = getHeight();
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323 width = prefsize.width;
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324 height = prefsize.height;
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327 if (width < height) {
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333 return (float) (dim / (1.5d * maxwidth));
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336 public void findCentre() {
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343 //Find centre coordinate
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344 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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345 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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346 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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348 bsize += bonds.size();
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350 for (int i = 0; i < bonds.size(); i++) {
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351 xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
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352 ((Bond) bonds.elementAt(i)).end[0];
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354 ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
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355 ((Bond) bonds.elementAt(i)).end[1];
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357 ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
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358 ((Bond) bonds.elementAt(i)).end[2];
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363 centre[0] = xtot / (2 * (float) bsize);
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364 centre[1] = ytot / (2 * (float) bsize);
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365 centre[2] = ztot / (2 * (float) bsize);
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368 public void paintComponent(Graphics g)
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370 super.paintComponent(g);
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372 if(visiblebonds==null)
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374 g.setColor(Color.black);
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375 g.setFont(new Font("Verdana", Font.BOLD, 14));
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376 g.drawString("Retrieving PDB data....", 20, getHeight()/2);
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381 //Only create the image at the beginning -
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382 //this saves much memory usage
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384 || (prefsize.width != getWidth())
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385 || (prefsize.height != getHeight()))
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388 prefsize.width = getWidth();
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389 prefsize.height = getHeight();
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391 scale = findScale();
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392 img = createImage(prefsize.width, prefsize.height);
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393 ig = img.getGraphics();
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394 Graphics2D ig2 = (Graphics2D) ig;
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396 ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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397 RenderingHints.VALUE_ANTIALIAS_ON);
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399 redrawneeded = true;
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405 drawAll(ig, prefsize.width, prefsize.height);
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406 redrawneeded = false;
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409 g.drawImage(img, 0, 0, this);
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414 public void drawAll(Graphics g, int width, int height)
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416 g.setColor(Color.black);
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417 g.fillRect(0, 0, width, height);
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423 public void updateSeqColours()
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430 // System.out.println("update seq colours");
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431 if(bysequence && pdb!=null)
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433 for (int ii = 0; ii < pdb.chains.size(); ii++)
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435 colourBySequence( (PDBChain) pdb.chains.elementAt(ii));
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443 int findTrueIndex(int pos)
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445 // returns the alignment position for a residue
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446 int j = sequence.getStart();
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449 while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))
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451 if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
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462 if ( (j == sequence.getEnd()) && (j < pos))
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464 return sequence.getEnd() + 1;
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472 // This method has been taken out of PDBChain to allow
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473 // Applet and Application specific sequence renderers to be used
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474 void colourBySequence(PDBChain chain)
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476 // System.out.println("colour by seq");
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477 for (int i = 0; i < chain.bonds.size(); i++)
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479 Bond tmp = (Bond) chain.bonds.elementAt(i);
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480 tmp.startCol = Color.lightGray;
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481 tmp.endCol = Color.lightGray;
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483 if(chain!=mainchain)
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486 if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
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487 (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
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489 int index = findTrueIndex(tmp.at1.alignmentMapping);
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490 //sequence.findIndex(tmp.at1.alignmentMapping);
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493 tmp.startCol = seqcanvas.getSequenceRenderer().
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494 getResidueBoxColour( sequence, index);
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496 tmp.startCol = seqcanvas.getFeatureRenderer().
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497 findFeatureColour(tmp.startCol, sequence, index);
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501 if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
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502 (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
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505 int index = findTrueIndex(tmp.at2.alignmentMapping);
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506 //sequence.findIndex( tmp.at2.alignmentMapping );
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509 tmp.endCol = seqcanvas.getSequenceRenderer().
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510 getResidueBoxColour( sequence, index);
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511 tmp.endCol = seqcanvas.getFeatureRenderer().
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512 findFeatureColour(tmp.endCol, sequence, index);
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519 public void drawScene(Graphics g)
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523 Zsort.Zsort(visiblebonds);
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527 for (int i = 0; i < visiblebonds.size(); i++)
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529 tmpBond = (Bond) visiblebonds.elementAt(i);
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531 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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533 ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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534 (getHeight() / 2));
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536 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
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538 yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
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539 (getHeight() / 2));
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541 xmid = (xend + xstart) / 2;
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542 ymid = (yend + ystart) / 2;
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544 if (depthcue && !bymolecule)
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546 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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547 g.setColor(tmpBond.startCol.darker().darker());
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548 drawLine(g, xstart, ystart, xmid, ymid);
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549 g.setColor(tmpBond.endCol.darker().darker());
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550 drawLine(g, xmid, ymid, xend, yend);
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551 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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552 g.setColor(tmpBond.startCol.darker());
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553 drawLine(g, xstart, ystart, xmid, ymid);
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555 g.setColor(tmpBond.endCol.darker());
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556 drawLine(g, xmid, ymid, xend, yend);
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558 g.setColor(tmpBond.startCol);
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559 drawLine(g, xstart, ystart, xmid, ymid);
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561 g.setColor(tmpBond.endCol);
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562 drawLine(g, xmid, ymid, xend, yend);
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564 } else if (depthcue && bymolecule) {
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565 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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566 g.setColor(Color.green.darker().darker());
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567 drawLine(g, xstart, ystart, xend, yend);
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568 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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569 g.setColor(Color.green.darker());
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570 drawLine(g, xstart, ystart, xend, yend);
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572 g.setColor(Color.green);
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573 drawLine(g, xstart, ystart, xend, yend);
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575 } else if (!depthcue && !bymolecule) {
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576 g.setColor(tmpBond.startCol);
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577 drawLine(g, xstart, ystart, xmid, ymid);
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578 g.setColor(tmpBond.endCol);
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579 drawLine(g, xmid, ymid, xend, yend);
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581 drawLine(g, xstart, ystart, xend, yend);
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584 if(highlightBond1!=null && highlightBond1==tmpBond)
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586 g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter());
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587 drawLine(g, xmid, ymid, xend, yend);
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590 if(highlightBond2!=null && highlightBond2==tmpBond)
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592 g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());
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593 drawLine(g, xstart, ystart, xmid, ymid);
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601 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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603 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
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604 g.drawLine(x1, y1, x2, y2);
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605 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
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606 g.drawLine(x1, y1 - 1, x2, y2 - 1);
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608 g.setColor(g.getColor().brighter());
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609 g.drawLine(x1, y1, x2, y2);
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610 g.drawLine(x1 + 1, y1, x2 + 1, y2);
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611 g.drawLine(x1 - 1, y1, x2 - 1, y2);
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614 g.drawLine(x1, y1, x2, y2);
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618 public Dimension minimumsize() {
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622 public Dimension preferredsize() {
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626 public void keyPressed(KeyEvent evt)
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628 if (evt.getKeyCode() == KeyEvent.VK_UP)
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630 scale = (float) (scale * 1.1);
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631 redrawneeded = true;
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634 else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
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636 scale = (float) (scale * 0.9);
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637 redrawneeded = true;
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642 public void mousePressed(MouseEvent e)
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645 Atom fatom = findAtom(e.getX(), e.getY());
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648 fatom.isSelected = !fatom.isSelected;
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650 redrawneeded = true;
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652 if (foundchain != -1)
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654 PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
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655 if (chain == mainchain)
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657 if (fatom.alignmentMapping != -1)
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659 if (highlightRes == null)
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660 highlightRes = new Vector();
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662 if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
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663 highlightRes.remove(fatom.alignmentMapping + "");
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665 highlightRes.add(fatom.alignmentMapping + "");
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678 public void mouseMoved(MouseEvent e)
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681 if(highlightBond1!=null)
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683 highlightBond1.at2.isSelected = false;
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684 highlightBond2.at1.isSelected = false;
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685 highlightBond1 = null;
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686 highlightBond2 = null;
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689 Atom fatom = findAtom(e.getX(), e.getY());
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691 PDBChain chain = null;
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694 chain = (PDBChain) pdb.chains.elementAt(foundchain);
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695 if(chain == mainchain)
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697 highlightSeqcanvas( fatom.alignmentMapping );
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703 this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName);
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706 highlightSeqcanvas( -1);
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707 this.setToolTipText(null);
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712 void highlightSeqcanvas(int pos)
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714 int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
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716 int size = pos==-1?0:3;
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718 if(highlightRes!=null)
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719 size += highlightRes.size()*3;
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721 int [] array = new int[size];
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723 if(highlightRes!=null)
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725 for (i = 0; i < highlightRes.size(); i++)
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727 int a = Integer.parseInt(highlightRes.elementAt(
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729 array[i * 3] = index;
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730 array[ (i * 3) + 1] = a;
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731 array[ (i * 3) + 2] = a;
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737 array[i * 3] = index;
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738 array[i * 3 + 1] = pos+1;
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739 array[i * 3 + 2] = pos+1;
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742 seqcanvas.highlightSearchResults(array);
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746 public void mouseClicked(MouseEvent e) { }
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748 public void mouseEntered(MouseEvent e) { }
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750 public void mouseExited(MouseEvent e) { }
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752 public void mouseDragged(MouseEvent evt)
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754 int x = evt.getX();
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755 int y = evt.getY();
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760 MCMatrix objmat = new MCMatrix(3, 3);
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761 objmat.setIdentity();
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763 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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764 objmat.rotatez((float) ((mx - omx)));
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766 objmat.rotatex((float) ((my - omy)));
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767 objmat.rotatey((float) ((omx - mx)));
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771 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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772 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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774 for (int i = 0; i < bonds.size(); i++) {
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775 Bond tmpBond = (Bond) bonds.elementAt(i);
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777 //Translate the bond so the centre is 0,0,0
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778 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
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780 //Now apply the rotation matrix
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781 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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782 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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784 //Now translate back again
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785 tmpBond.translate(centre[0], centre[1], centre[2]);
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796 redrawneeded = true;
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801 public void mouseReleased(MouseEvent evt)
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807 void drawLabels(Graphics g) {
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809 for (int ii = 0; ii < pdb.chains.size(); ii++)
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811 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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813 if (chain.isVisible)
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815 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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817 for (int i = 0; i < bonds.size(); i++)
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819 Bond tmpBond = (Bond) bonds.elementAt(i);
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821 if (tmpBond.at1.isSelected)
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823 labelAtom(g, tmpBond, 1);
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826 if (tmpBond.at2.isSelected)
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829 labelAtom(g, tmpBond, 2);
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836 public void labelAtom(Graphics g, Bond b, int n) {
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838 g.setColor(Color.red);
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841 int xstart = (int) (((b.start[0] - centre[0]) * scale) +
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843 int ystart = (int) (((b.start[1] - centre[1]) * scale) +
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844 (getHeight() / 2));
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846 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
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850 int xstart = (int) (((b.end[0] - centre[0]) * scale) +
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852 int ystart = (int) (((b.end[1] - centre[1]) * scale) +
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853 (getHeight() / 2));
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855 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
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859 int foundchain = -1;
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860 public Atom findAtom(int x, int y) {
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865 for (int ii = 0; ii < pdb.chains.size(); ii++)
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867 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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871 if (chain.isVisible)
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873 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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875 for (int i = 0; i < bonds.size(); i++)
\r
877 tmpBond = (Bond) bonds.elementAt(i);
\r
879 truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
\r
882 if (Math.abs(truex - x) <= 2)
\r
884 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
\r
885 (getHeight() / 2));
\r
887 if (Math.abs(truey - y) <= 2)
\r
889 fatom = tmpBond.at1;
\r
896 // Still here? Maybe its the last bond
\r
898 truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
\r
901 if (Math.abs(truex - x) <= 2)
\r
903 int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
\r
904 (getHeight() / 2));
\r
906 if (Math.abs(truey - y) <= 2)
\r
908 fatom = tmpBond.at2;
\r
916 if (fatom != null) //)&& chain.ds != null)
\r
918 chain = (PDBChain) pdb.chains.elementAt(foundchain);
\r
925 Bond highlightBond1, highlightBond2;
\r
926 public void highlightRes(int ii)
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929 if (highlightRes != null
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930 && highlightRes.contains((ii-1) + ""))
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937 for(index=0; index<mainchain.bonds.size(); index++)
\r
939 tmpBond = (Bond) mainchain.bonds.elementAt(index);
\r
940 if (tmpBond.at1.alignmentMapping == ii - 1)
\r
942 if (highlightBond1 != null)
\r
943 highlightBond1.at2.isSelected = false;
\r
945 if (highlightBond2 != null)
\r
946 highlightBond2.at1.isSelected = false;
\r
948 highlightBond1 = null;
\r
949 highlightBond2 = null;
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953 highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
\r
954 highlightBond1.at2.isSelected = true;
\r
957 if (index != mainchain.bonds.size())
\r
959 highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
\r
960 highlightBond2.at1.isSelected = true;
\r
967 redrawneeded = true;
\r
971 public void setAllchainsVisible(boolean b)
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973 for (int ii = 0; ii < pdb.chains.size(); ii++)
\r
975 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
\r
976 chain.isVisible = b;
\r
978 mainchain.isVisible = true;
\r