2 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
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4 import java.awt.event.*;
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7 import javax.swing.*;
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8 import jalview.analysis.AlignSeq;
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9 import jalview.datamodel.*;
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11 public class rotCanvas extends JPanel implements KeyListener,
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13 MouseMotionListener {
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14 MCMatrix idmat = new MCMatrix(3,3);
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15 MCMatrix objmat = new MCMatrix(3,3);
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17 boolean redrawneeded =true;
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33 float centre[] = new float[3];
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34 float width[] = new float[3];
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42 boolean depthcue = true;
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43 boolean wire = false;
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44 boolean bymolecule = false;
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45 boolean zbuffer = true;
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56 Font font = new Font("Helvetica",Font.PLAIN,10);
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58 public rotCanvas(PDBfile pdb, Sequence sequence, jalview.gui.AlignViewport av) throws IOException {
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62 int pdbstart=0, pdbend=0, seqstart =0, seqend=0;
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65 for (int i=0; i < pdb.chains.size(); i++) {
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66 // Now lets compare the sequences to get
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67 // the start and end points.
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69 java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(), ".");
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70 String newString = "";
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72 while (str.hasMoreTokens()) {
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73 newString += str.nextToken();
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75 // Align the sequence to the pdb
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76 AlignSeq as = new AlignSeq(sequence,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
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77 as.calcScoreMatrix();
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78 as.traceAlignment();
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79 as.printAlignment();
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81 if (as.maxscore > max) {
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85 pdbstart = as.seq2start;
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86 pdbend = as.seq2end;
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87 seqstart = as.seq1start - 1 ;
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88 seqend = as.seq1end -1;
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91 System.out.println("PDB start/end " + pdbstart + " " + pdbend);
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92 System.out.println("SEQ start/end " + seqstart + " " + seqend);
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96 ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
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97 ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbend = pdbend;
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98 ( (PDBChain)pdb.chains.elementAt(maxchain)).seqstart = seqstart;
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99 ( (PDBChain)pdb.chains.elementAt(maxchain)).seqend = seqend;
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100 ( (PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
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101 ( (PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
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102 ( (PDBChain)pdb.chains.elementAt(maxchain)).colourBySequence(av, sequence);
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107 this.prefsize = new Dimension( getWidth(), getHeight());
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109 //Initialize the matrices to identity
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111 for (int i = 0; i < 3; i++) {
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112 for (int j = 0; j < 3 ; j++) {
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114 idmat.addElement(i,j,0);
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115 objmat.addElement(i,j,0);
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117 idmat.addElement(i,j,1);
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118 objmat.addElement(i,j,1);
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123 addMouseMotionListener(this);
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124 addMouseListener(this);
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125 addKeyListener(this);
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128 ToolTipManager.sharedInstance().registerComponent(this);
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132 public void addPDBfile() {
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136 scale = findScale();
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138 System.out.println("Scale factor = " + scale);
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141 public void deleteBonds() {
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153 for (int i=0; i < pdb.chains.size(); i++) {
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154 ((PDBChain)pdb.chains.elementAt(i)).bonds = null;
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158 public void findWidth() {
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159 float max[] = new float[3];
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160 float min[] = new float[3];
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162 max[0] = (float)-1e30;
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163 max[1] = (float)-1e30;
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164 max[2] = (float)-1e30;
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166 min[0] = (float)1e30;
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167 min[1] = (float)1e30;
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168 min[2] = (float)1e30;
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170 for (int ii=0; ii < pdb.chains.size(); ii++) {
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171 if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
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173 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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175 for (int i = 0; i < bonds.size(); i++) {
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176 Bond tmp = (Bond)bonds.elementAt(i);
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178 if (tmp.start[0] >= max[0])
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179 max[0] = tmp.start[0];
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180 if (tmp.start[1] >= max[1])
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181 max[1] = tmp.start[1];
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182 if (tmp.start[2] >= max[2])
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183 max[2] = tmp.start[2];
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184 if (tmp.start[0] <= min[0])
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185 min[0] = tmp.start[0];
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186 if (tmp.start[1] <= min[1])
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187 min[1] = tmp.start[1];
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188 if (tmp.start[2] <= min[2])
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189 min[2] = tmp.start[2];
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191 if (tmp.end[0] >= max[0])
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192 max[0] = tmp.end[0];
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193 if (tmp.end[1] >= max[1])
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194 max[1] = tmp.end[1];
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195 if (tmp.end[2] >= max[2])
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196 max[2] = tmp.end[2];
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197 if (tmp.end[0] <= min[0])
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198 min[0] = tmp.end[0];
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199 if (tmp.end[1] <= min[1])
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200 min[1] = tmp.end[1];
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201 if (tmp.end[2] <= min[2])
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202 min[2] = tmp.end[2];
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207 System.out.println("xmax " + max[0] + " min " + min[0]);
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208 System.out.println("ymax " + max[1] + " min " + min[1]);
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209 System.out.println("zmax " + max[2] + " min " + min[2]);
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211 width[0] = (float)Math.abs(max[0] - min[0]);
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212 width[1] = (float)Math.abs(max[1] - min[1]);
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213 width[2] = (float)Math.abs(max[2] - min[2]);
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215 maxwidth = width[0];
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217 if (width[1] > width[0])
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218 maxwidth = width[1];
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219 if (width[2] > width[1])
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220 maxwidth = width[2];
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222 System.out.println("Maxwidth = " + maxwidth);
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225 public float findScale() {
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226 int dim, width, height;
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228 if ( getWidth() != 0) {
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229 width = getWidth();
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230 height = getHeight();
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233 width = prefsize.width;
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234 height = prefsize.height;
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237 if (width < height) {
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243 return (float)(dim/(1.5d*maxwidth));
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248 public void findCentre() {
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254 //Find centre coordinate
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256 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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257 if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
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259 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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261 bsize += bonds.size();
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263 for (int i = 0; i < bonds.size(); i++) {
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265 xtot = xtot + ((Bond)bonds.elementAt(i)).start[0] +
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266 ((Bond)bonds.elementAt(i)).end[0];
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268 ytot = ytot + ((Bond)bonds.elementAt(i)).start[1] +
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269 ((Bond)bonds.elementAt(i)).end[1];
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271 ztot = ztot + ((Bond)bonds.elementAt(i)).start[2] +
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272 ((Bond)bonds.elementAt(i)).end[2];
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277 centre[0] = xtot / (2 * (float)bsize);
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278 centre[1] = ytot / (2 * (float)bsize);
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279 centre[2] = ztot / (2 * (float)bsize);
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282 public void paint(Graphics g) {
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283 //Only create the image at the beginning -
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284 //this saves much memory usage
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285 if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {
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286 prefsize.width = getWidth();
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287 prefsize.height = getHeight();
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289 scale = findScale();
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290 img = createImage(prefsize.width,prefsize.height);
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291 ig = img.getGraphics();
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293 redrawneeded = true;
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296 if (redrawneeded == true) {
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297 drawBackground(ig,Color.black);
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299 redrawneeded = false;
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301 ig = img.getGraphics();
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304 g.drawImage(img,0,0,this);
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307 public void drawBackground(Graphics g, Color col) {
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309 g.fillRect(0,0,prefsize.width,prefsize.height);
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313 public void drawScene(Graphics g) {
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314 // Sort the bonds by z coord
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316 Vector bonds = new Vector();
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319 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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320 if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
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322 Vector tmp = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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324 for (int i=0; i < tmp.size(); i++) {
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325 bonds.addElement(tmp.elementAt(i));
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331 Zsort.Zsort(bonds);
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334 for (int i = 0; i < bonds.size(); i++) {
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335 Bond tmpBond = (Bond)bonds.elementAt(i);
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337 xstart = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
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338 ystart = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
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340 xend = (int)((tmpBond.end[0] - centre[0])*scale + getWidth()/2);
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341 yend = (int)((tmpBond.end[1] - centre[1])*scale + getHeight()/2);
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343 xmid = (xend+xstart)/2;
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344 ymid = (yend+ystart)/2;
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347 if (depthcue && !bymolecule) {
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349 if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {
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350 g.setColor(tmpBond.startCol.darker().darker());
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351 drawLine(g,xstart,ystart,xmid,ymid);
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353 g.setColor(tmpBond.endCol.darker().darker());
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354 drawLine(g,xmid,ymid,xend,yend);
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355 } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {
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356 g.setColor(tmpBond.startCol.darker());
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357 drawLine(g,xstart,ystart,xmid,ymid);
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359 g.setColor(tmpBond.endCol.darker());
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360 drawLine(g,xmid,ymid,xend,yend);
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362 g.setColor(tmpBond.startCol);
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363 drawLine(g,xstart,ystart,xmid,ymid);
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365 g.setColor(tmpBond.endCol);
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366 drawLine(g,xmid,ymid,xend,yend);
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368 } else if (depthcue && bymolecule) {
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369 if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {
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370 g.setColor(Color.green.darker().darker());
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371 drawLine(g,xstart,ystart,xend,yend);
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373 } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {
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374 g.setColor(Color.green.darker());
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375 drawLine(g,xstart,ystart,xend,yend);
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378 g.setColor(Color.green);
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379 drawLine(g,xstart,ystart,xend,yend);
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382 } else if (!depthcue && !bymolecule) {
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383 g.setColor(tmpBond.startCol);
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384 drawLine(g,xstart,ystart,xmid,ymid);
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385 g.setColor(tmpBond.endCol);
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386 drawLine(g,xmid,ymid,xend,yend);
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389 drawLine(g,xstart,ystart,xend,yend);
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394 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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397 if (((float)Math.abs(y2-y1)/(float)Math.abs(x2-x1)) < 0.5) {
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399 g.drawLine(x1,y1,x2,y2);
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400 g.drawLine(x1+1,y1+1,x2+1,y2+1);
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401 g.drawLine(x1,y1-1,x2,y2-1);
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403 g.setColor(g.getColor().brighter());
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404 g.drawLine(x1,y1,x2,y2);
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405 g.drawLine(x1+1,y1,x2+1,y2);
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406 g.drawLine(x1-1,y1,x2-1,y2);
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410 g.drawLine(x1,y1,x2,y2);
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414 public Dimension minimumsize() {
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417 public Dimension preferredsize() {
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421 public void keyTyped(KeyEvent evt) { }
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422 public void keyReleased(KeyEvent evt) { }
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423 public void keyPressed(KeyEvent evt) {
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424 int key = evt.getKeyChar();
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426 if (evt.getKeyCode() == KeyEvent.VK_UP) {
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427 scale = (float)(scale * 1.1);
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428 redrawneeded = true;
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431 } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
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432 scale = (float)(scale * 0.9);
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433 redrawneeded = true;
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436 } else if (key == 'w') {
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439 System.out.println("wireframe " + wire);
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440 redrawneeded = true;
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443 } else if (key == 'd') {
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444 depthcue = !depthcue;
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445 System.out.println("Depth cueing is " + depthcue);
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446 redrawneeded = true;
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449 } else if (key == 'm') {
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450 bymolecule = !bymolecule;
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451 System.out.println("Bymolecule is " + bymolecule);
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452 redrawneeded = true;
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455 } else if (key == 'z') {
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456 zbuffer = !zbuffer;
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457 System.out.println("Z buffering is " + zbuffer);
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458 redrawneeded = true;
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461 } else if (key == 'c') {
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462 bymolecule = false;
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463 pdb.setChainColours();
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464 System.out.println("Colouring by chain");
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465 redrawneeded = true;
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468 } else if (key == 'h') {
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469 bymolecule = false;
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470 pdb.setHydrophobicityColours();
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471 System.out.println("Colouring by hydrophobicity");
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472 redrawneeded = true;
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475 } else if (key == 'q') {
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476 bymolecule = false;
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477 pdb.setChargeColours();
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478 System.out.println("Colouring charges and cysteines");
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479 redrawneeded = true;
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486 public void mousePressed(MouseEvent e)
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496 public void mouseMoved(MouseEvent e)
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498 myAtom fatom = null;
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499 for (int ii = 0; ii < pdb.chains.size(); ii++)
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502 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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503 if (chain.isVisible)
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505 Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
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506 for (int i = 0; i < bonds.size(); i++)
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508 Bond tmpBond = (Bond) bonds.elementAt(i);
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509 int truex = (int) ( (tmpBond.start[0] - centre[0]) * scale +
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511 if (Math.abs(truex - e.getX()) <= 2)
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513 int truey = (int) ( (tmpBond.start[1] - centre[1]) * scale +
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515 if (Math.abs(truey - e.getY()) <= 2)
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516 fatom = tmpBond.at1;
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523 this.setToolTipText(fatom.resName);
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526 this.setToolTipText(null);
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529 public void mouseClicked(MouseEvent e) { }
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530 public void mouseEntered(MouseEvent e) { }
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531 public void mouseExited(MouseEvent e) { }
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533 public void mouseDragged(MouseEvent evt) {
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534 int x = evt.getX();
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535 int y = evt.getY();
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539 MCMatrix objmat = new MCMatrix(3,3);
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540 objmat.setIdentity();
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542 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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543 objmat.rotatez((float)((mx-omx)));
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545 objmat.rotatex((float)((my-omy)));
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546 objmat.rotatey((float)((omx-mx)));
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550 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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551 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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553 for (int i = 0; i < bonds.size(); i++) {
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555 Bond tmpBond = (Bond)bonds.elementAt(i);
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557 //Translate the bond so the centre is 0,0,0
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558 tmpBond.translate(-centre[0],-centre[1],-centre[2]);
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560 //Now apply the rotation matrix
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561 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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562 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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564 //Now translate back again
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565 tmpBond.translate(centre[0],centre[1],centre[2]);
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574 redrawneeded = true;
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576 paint(this.getGraphics());
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582 public void mouseReleased(MouseEvent evt) {
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583 int x = evt.getX();
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584 int y = evt.getY();
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587 myAtom tmp = findAtom(x,y);
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593 public void drawLabels() {
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594 redrawneeded = true;
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595 paint(this.getGraphics());
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597 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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599 PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);
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601 if (chain.isVisible) {
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603 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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605 for (int i = 0; i < bonds.size(); i++) {
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606 Bond tmpBond = (Bond)bonds.elementAt(i);
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608 if (tmpBond.at1.isSelected) {
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609 labelAtom(img.getGraphics(),tmpBond,1);
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612 if (tmpBond.at2.isSelected) {
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613 labelAtom(img.getGraphics(),tmpBond,2);
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620 this.getGraphics().drawImage(img,0,0,this);
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626 public void labelAtom(Graphics g,Bond b, int n) {
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632 int xstart = (int)((b.start[0] - centre[0])*scale + getWidth()/2);
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633 int ystart = (int)((b.start[1] - centre[1])*scale + getHeight()/2);
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635 g.setColor(Color.red);
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636 g.drawString(b.at1.resName + "-" + b.at1.resNumber,xstart,ystart);
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641 int xstart = (int)((b.end[0] - centre[0])*scale + getWidth()/2);
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642 int ystart = (int)((b.end[1] - centre[1])*scale + getHeight()/2);
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644 g.setColor(Color.red);
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645 g.drawString(b.at2.resName + "-" + b.at2.resNumber,xstart,ystart);
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650 public myAtom findAtom(int x, int y) {
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651 myAtom fatom = null;
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653 int foundchain = -1;
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655 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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657 PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);
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659 if (chain.isVisible) {
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661 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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663 for (int i = 0; i < bonds.size(); i++) {
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664 Bond tmpBond = (Bond)bonds.elementAt(i);
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666 int truex = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
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668 if (Math.abs(truex - x) <= 2) {
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670 int truey = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
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672 if (Math.abs(truey - y) <= 2) {
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674 System.out.println("Found match");
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675 System.out.println(x + " " + y);
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676 System.out.println(truex + " " + truey);
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677 System.out.println(tmpBond.start[0] + " " + tmpBond.start[1]);
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678 System.out.println("Atom 1 = " + tmpBond.at1.resName + " " +
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679 tmpBond.at1.resNumber + " " + tmpBond.at1.chain);
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680 fatom = tmpBond.at1;
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681 fatom.isSelected = !fatom.isSelected;
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688 if (fatom != null) //)&& chain.ds != null)
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690 chain = (PDBChain)pdb.chains.elementAt(foundchain);
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692 // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
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693 // int pos = chain.ds.findIndex(tmp);
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694 // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);
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701 public void update(Graphics g) {
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