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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145 // mainchain.sequence = sequence;
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148 this.prefsize = new Dimension(getWidth(), getHeight());
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150 //Initialize the matrices to identity
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151 for (int i = 0; i < 3; i++) {
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152 for (int j = 0; j < 3; j++) {
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154 idmat.addElement(i, j, 0);
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155 objmat.addElement(i, j, 0);
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157 idmat.addElement(i, j, 1);
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158 objmat.addElement(i, j, 1);
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163 addMouseMotionListener(this);
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164 addMouseListener(this);
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166 addMouseWheelListener(new MouseWheelListener()
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168 public void mouseWheelMoved(MouseWheelEvent e)
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170 if (e.getWheelRotation() > 0)
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172 scale = (float) (scale * 1.1);
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173 redrawneeded = true;
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179 scale = (float) (scale * 0.9);
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180 redrawneeded = true;
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192 scale = findScale();
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195 updateSeqColours();
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196 ToolTipManager.sharedInstance().registerComponent(this);
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197 ToolTipManager.sharedInstance().setInitialDelay(0);
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198 ToolTipManager.sharedInstance().setDismissDelay(10000);
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202 Vector visiblebonds;
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205 // Sort the bonds by z coord
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206 visiblebonds = new Vector();
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208 for (int ii = 0; ii < pdb.chains.size(); ii++)
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210 if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
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212 Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
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214 for (int i = 0; i < tmp.size(); i++)
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216 visiblebonds.addElement(tmp.elementAt(i));
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222 public void deleteBonds() {
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234 for (int i = 0; i < pdb.chains.size(); i++) {
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235 ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
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239 public void findWidth() {
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240 float[] max = new float[3];
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241 float[] min = new float[3];
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243 max[0] = (float) -1e30;
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244 max[1] = (float) -1e30;
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245 max[2] = (float) -1e30;
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247 min[0] = (float) 1e30;
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248 min[1] = (float) 1e30;
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249 min[2] = (float) 1e30;
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251 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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252 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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253 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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255 for (int i = 0; i < bonds.size(); i++) {
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256 Bond tmp = (Bond) bonds.elementAt(i);
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258 if (tmp.start[0] >= max[0]) {
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259 max[0] = tmp.start[0];
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262 if (tmp.start[1] >= max[1]) {
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263 max[1] = tmp.start[1];
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266 if (tmp.start[2] >= max[2]) {
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267 max[2] = tmp.start[2];
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270 if (tmp.start[0] <= min[0]) {
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271 min[0] = tmp.start[0];
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274 if (tmp.start[1] <= min[1]) {
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275 min[1] = tmp.start[1];
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278 if (tmp.start[2] <= min[2]) {
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279 min[2] = tmp.start[2];
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282 if (tmp.end[0] >= max[0]) {
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283 max[0] = tmp.end[0];
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286 if (tmp.end[1] >= max[1]) {
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287 max[1] = tmp.end[1];
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290 if (tmp.end[2] >= max[2]) {
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291 max[2] = tmp.end[2];
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294 if (tmp.end[0] <= min[0]) {
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295 min[0] = tmp.end[0];
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298 if (tmp.end[1] <= min[1]) {
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299 min[1] = tmp.end[1];
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302 if (tmp.end[2] <= min[2]) {
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303 min[2] = tmp.end[2];
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309 System.out.println("xmax " + max[0] + " min " + min[0]);
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310 System.out.println("ymax " + max[1] + " min " + min[1]);
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311 System.out.println("zmax " + max[2] + " min " + min[2]);*/
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313 width[0] = (float) Math.abs(max[0] - min[0]);
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314 width[1] = (float) Math.abs(max[1] - min[1]);
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315 width[2] = (float) Math.abs(max[2] - min[2]);
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317 maxwidth = width[0];
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319 if (width[1] > width[0]) {
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320 maxwidth = width[1];
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323 if (width[2] > width[1]) {
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324 maxwidth = width[2];
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327 // System.out.println("Maxwidth = " + maxwidth);
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330 public float findScale() {
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335 if (getWidth() != 0) {
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336 width = getWidth();
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337 height = getHeight();
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339 width = prefsize.width;
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340 height = prefsize.height;
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343 if (width < height) {
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349 return (float) (dim / (1.5d * maxwidth));
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352 public void findCentre() {
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359 //Find centre coordinate
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360 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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361 if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
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362 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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364 bsize += bonds.size();
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366 for (int i = 0; i < bonds.size(); i++) {
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367 xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
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368 ((Bond) bonds.elementAt(i)).end[0];
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370 ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
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371 ((Bond) bonds.elementAt(i)).end[1];
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373 ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
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374 ((Bond) bonds.elementAt(i)).end[2];
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379 centre[0] = xtot / (2 * (float) bsize);
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380 centre[1] = ytot / (2 * (float) bsize);
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381 centre[2] = ztot / (2 * (float) bsize);
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384 public void paintComponent(Graphics g)
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386 super.paintComponent(g);
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388 if(visiblebonds==null)
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390 g.setColor(Color.black);
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391 g.setFont(new Font("Verdana", Font.BOLD, 14));
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392 g.drawString("Retrieving PDB data....", 20, getHeight()/2);
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397 //Only create the image at the beginning -
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398 //this saves much memory usage
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400 || (prefsize.width != getWidth())
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401 || (prefsize.height != getHeight()))
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404 prefsize.width = getWidth();
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405 prefsize.height = getHeight();
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407 scale = findScale();
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408 img = createImage(prefsize.width, prefsize.height);
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409 ig = img.getGraphics();
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410 Graphics2D ig2 = (Graphics2D) ig;
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412 ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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413 RenderingHints.VALUE_ANTIALIAS_ON);
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415 redrawneeded = true;
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421 drawAll(ig, prefsize.width, prefsize.height);
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422 redrawneeded = false;
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425 g.drawImage(img, 0, 0, this);
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430 public void drawAll(Graphics g, int width, int height)
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432 g.setColor(Color.black);
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433 g.fillRect(0, 0, width, height);
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439 public void updateSeqColours()
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446 // System.out.println("update seq colours");
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447 if(bysequence && pdb!=null)
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449 for (int ii = 0; ii < pdb.chains.size(); ii++)
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451 colourBySequence( (PDBChain) pdb.chains.elementAt(ii) );
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459 int findTrueIndex(int pos)
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461 // returns the alignment position for a residue
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462 int j = sequence.getStart();
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465 while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))
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467 if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
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478 if ( (j == sequence.getEnd()) && (j < pos))
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480 return sequence.getEnd() + 1;
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488 // This method has been taken out of PDBChain to allow
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489 // Applet and Application specific sequence renderers to be used
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490 void colourBySequence(PDBChain chain)
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492 // System.out.println("colour by seq");
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493 for (int i = 0; i < chain.bonds.size(); i++)
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495 Bond tmp = (Bond) chain.bonds.elementAt(i);
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496 tmp.startCol = Color.lightGray;
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497 tmp.endCol = Color.lightGray;
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499 if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
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500 (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
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502 int index = findTrueIndex(tmp.at1.alignmentMapping);
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503 //sequence.findIndex(tmp.at1.alignmentMapping);
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506 tmp.startCol = seqcanvas.getSequenceRenderer().
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507 getResidueBoxColour( sequence, index);
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509 tmp.startCol = seqcanvas.getFeatureRenderer().
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510 findFeatureColour(tmp.startCol, sequence, index);
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514 if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
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515 (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
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518 int index = findTrueIndex(tmp.at2.alignmentMapping);
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519 //sequence.findIndex( tmp.at2.alignmentMapping );
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522 tmp.endCol = seqcanvas.getSequenceRenderer().
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523 getResidueBoxColour( sequence, index);
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524 tmp.endCol = seqcanvas.getFeatureRenderer().
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525 findFeatureColour(tmp.endCol, sequence, index);
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532 public void drawScene(Graphics g)
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538 Zsort.Zsort(visiblebonds);
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542 for (int i = 0; i < visiblebonds.size(); i++)
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544 tmpBond = (Bond) visiblebonds.elementAt(i);
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546 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
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548 ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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549 (getHeight() / 2));
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551 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
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553 yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
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554 (getHeight() / 2));
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556 xmid = (xend + xstart) / 2;
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557 ymid = (yend + ystart) / 2;
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559 if (depthcue && !bymolecule)
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561 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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562 g.setColor(tmpBond.startCol.darker().darker());
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563 drawLine(g, xstart, ystart, xmid, ymid);
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565 g.setColor(tmpBond.endCol.darker().darker());
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566 drawLine(g, xmid, ymid, xend, yend);
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567 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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568 g.setColor(tmpBond.startCol.darker());
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569 drawLine(g, xstart, ystart, xmid, ymid);
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571 g.setColor(tmpBond.endCol.darker());
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572 drawLine(g, xmid, ymid, xend, yend);
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574 g.setColor(tmpBond.startCol);
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575 drawLine(g, xstart, ystart, xmid, ymid);
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577 g.setColor(tmpBond.endCol);
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578 drawLine(g, xmid, ymid, xend, yend);
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580 } else if (depthcue && bymolecule) {
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581 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
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582 g.setColor(Color.green.darker().darker());
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583 drawLine(g, xstart, ystart, xend, yend);
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584 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
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585 g.setColor(Color.green.darker());
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586 drawLine(g, xstart, ystart, xend, yend);
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588 g.setColor(Color.green);
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589 drawLine(g, xstart, ystart, xend, yend);
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591 } else if (!depthcue && !bymolecule) {
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592 g.setColor(tmpBond.startCol);
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593 drawLine(g, xstart, ystart, xmid, ymid);
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594 g.setColor(tmpBond.endCol);
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595 drawLine(g, xmid, ymid, xend, yend);
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597 drawLine(g, xstart, ystart, xend, yend);
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600 if(highlightBond1!=null && highlightBond1==tmpBond)
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602 g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter());
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603 drawLine(g, xmid, ymid, xend, yend);
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606 if(highlightBond2!=null && highlightBond2==tmpBond)
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608 g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());
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609 drawLine(g, xstart, ystart, xmid, ymid);
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617 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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619 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
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620 g.drawLine(x1, y1, x2, y2);
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621 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
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622 g.drawLine(x1, y1 - 1, x2, y2 - 1);
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624 g.setColor(g.getColor().brighter());
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625 g.drawLine(x1, y1, x2, y2);
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626 g.drawLine(x1 + 1, y1, x2 + 1, y2);
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627 g.drawLine(x1 - 1, y1, x2 - 1, y2);
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630 g.drawLine(x1, y1, x2, y2);
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634 public Dimension minimumsize() {
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638 public Dimension preferredsize() {
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642 public void keyPressed(KeyEvent evt)
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644 if (evt.getKeyCode() == KeyEvent.VK_UP)
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646 scale = (float) (scale * 1.1);
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647 redrawneeded = true;
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650 else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
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652 scale = (float) (scale * 0.9);
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653 redrawneeded = true;
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658 public void mousePressed(MouseEvent e)
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661 Atom fatom = findAtom(e.getX(), e.getY());
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664 fatom.isSelected = !fatom.isSelected;
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666 redrawneeded = true;
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668 if (foundchain != -1)
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670 PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
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671 if (chain == mainchain)
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673 if (fatom.alignmentMapping != -1)
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675 if (highlightRes == null)
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676 highlightRes = new Vector();
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678 if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
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679 highlightRes.remove(fatom.alignmentMapping + "");
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681 highlightRes.add(fatom.alignmentMapping + "");
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694 public void mouseMoved(MouseEvent e)
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697 if(highlightBond1!=null)
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699 highlightBond1.at2.isSelected = false;
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700 highlightBond2.at1.isSelected = false;
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701 highlightBond1 = null;
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702 highlightBond2 = null;
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705 Atom fatom = findAtom(e.getX(), e.getY());
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707 PDBChain chain = null;
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710 chain = (PDBChain) pdb.chains.elementAt(foundchain);
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711 if(chain == mainchain)
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713 highlightSeqcanvas( fatom.alignmentMapping );
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719 this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName);
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722 highlightSeqcanvas( -1);
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723 this.setToolTipText(null);
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728 void highlightSeqcanvas(int pos)
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730 int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
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732 int size = pos==-1?0:3;
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734 if(highlightRes!=null)
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735 size += highlightRes.size()*3;
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737 int [] array = new int[size];
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739 if(highlightRes!=null)
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741 for (i = 0; i < highlightRes.size(); i++)
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743 int a = Integer.parseInt(highlightRes.elementAt(
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745 array[i * 3] = index;
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746 array[ (i * 3) + 1] = a;
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747 array[ (i * 3) + 2] = a;
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753 array[i * 3] = index;
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754 array[i * 3 + 1] = pos+1;
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755 array[i * 3 + 2] = pos+1;
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758 seqcanvas.highlightSearchResults(array);
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762 public void mouseClicked(MouseEvent e) { }
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764 public void mouseEntered(MouseEvent e) { }
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766 public void mouseExited(MouseEvent e) { }
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768 public void mouseDragged(MouseEvent evt)
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770 int x = evt.getX();
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771 int y = evt.getY();
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776 MCMatrix objmat = new MCMatrix(3, 3);
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777 objmat.setIdentity();
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779 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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780 objmat.rotatez((float) ((mx - omx)));
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782 objmat.rotatex((float) ((my - omy)));
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783 objmat.rotatey((float) ((omx - mx)));
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787 for (int ii = 0; ii < pdb.chains.size(); ii++) {
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788 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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790 for (int i = 0; i < bonds.size(); i++) {
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791 Bond tmpBond = (Bond) bonds.elementAt(i);
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793 //Translate the bond so the centre is 0,0,0
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794 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
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796 //Now apply the rotation matrix
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797 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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798 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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800 //Now translate back again
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801 tmpBond.translate(centre[0], centre[1], centre[2]);
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812 redrawneeded = true;
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817 public void mouseReleased(MouseEvent evt)
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823 void drawLabels(Graphics g) {
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825 for (int ii = 0; ii < pdb.chains.size(); ii++)
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827 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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829 if (chain.isVisible)
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832 for (int i = 0; i < chain.bonds.size(); i++)
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834 Bond tmpBond = (Bond) chain.bonds.elementAt(i);
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836 if (tmpBond.at1.isSelected)
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838 labelAtom(g, tmpBond, 1);
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840 else if (tmpBond.at2.isSelected)
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842 labelAtom(g, tmpBond, 2);
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849 public void labelAtom(Graphics g, Bond b, int n) {
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851 g.setColor(Color.red);
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854 int xstart = (int) (((b.start[0] - centre[0]) * scale) +
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856 int ystart = (int) (((b.start[1] - centre[1]) * scale) +
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857 (getHeight() / 2));
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859 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
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863 int xstart = (int) (((b.end[0] - centre[0]) * scale) +
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865 int ystart = (int) (((b.end[1] - centre[1]) * scale) +
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866 (getHeight() / 2));
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868 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
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872 int foundchain = -1;
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873 public Atom findAtom(int x, int y) {
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878 for (int ii = 0; ii < pdb.chains.size(); ii++)
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880 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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884 if (chain.isVisible)
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886 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
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888 for (int i = 0; i < bonds.size(); i++)
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890 tmpBond = (Bond) bonds.elementAt(i);
\r
892 truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
\r
895 if (Math.abs(truex - x) <= 2)
\r
897 int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
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898 (getHeight() / 2));
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900 if (Math.abs(truey - y) <= 2)
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902 fatom = tmpBond.at1;
\r
909 // Still here? Maybe its the last bond
\r
911 truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
\r
914 if (Math.abs(truex - x) <= 2)
\r
916 int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
\r
917 (getHeight() / 2));
\r
919 if (Math.abs(truey - y) <= 2)
\r
921 fatom = tmpBond.at2;
\r
929 if (fatom != null) //)&& chain.ds != null)
\r
931 chain = (PDBChain) pdb.chains.elementAt(foundchain);
\r
938 Bond highlightBond1, highlightBond2;
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939 String alignMouseOver;
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940 public void highlightRes(int ii)
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943 if (highlightRes != null
\r
944 && highlightRes.contains((ii-1) + ""))
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951 for(index=0; index<mainchain.bonds.size(); index++)
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953 tmpBond = (Bond) mainchain.bonds.elementAt(index);
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954 if (tmpBond.at1.alignmentMapping == ii - 1)
\r
956 if (highlightBond1 != null)
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957 highlightBond1.at2.isSelected = false;
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959 if (highlightBond2 != null)
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960 highlightBond2.at1.isSelected = false;
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962 highlightBond1 = null;
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963 highlightBond2 = null;
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967 highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
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968 highlightBond1.at2.isSelected = true;
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971 if (index != mainchain.bonds.size())
\r
973 highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
\r
974 highlightBond2.at1.isSelected = true;
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981 redrawneeded = true;
\r
985 public void setAllchainsVisible(boolean b)
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987 for (int ii = 0; ii < pdb.chains.size(); ii++)
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989 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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990 chain.isVisible = b;
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992 mainchain.isVisible = true;
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995 redrawneeded = true;
\r