From ddc65d82bd02fc77bd836469b4c11afbe4233134 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 10 Nov 2005 10:59:25 +0000 Subject: [PATCH] Rot Canvas replaced with PDBViewer --- src/MCview/rotCanvas.java | 730 --------------------------------------------- 1 file changed, 730 deletions(-) delete mode 100755 src/MCview/rotCanvas.java diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java deleted file mode 100755 index be14db8..0000000 --- a/src/MCview/rotCanvas.java +++ /dev/null @@ -1,730 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package MCview; - -import jalview.analysis.AlignSeq; - -import jalview.datamodel.*; - -// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug -import java.awt.*; -import java.awt.event.*; - -import java.io.*; - -import java.util.*; - -import javax.swing.*; - - -public class rotCanvas extends JPanel implements KeyListener, MouseListener, - MouseMotionListener { - MCMatrix idmat = new MCMatrix(3, 3); - MCMatrix objmat = new MCMatrix(3, 3); - boolean redrawneeded = true; - int omx = 0; - int mx = 0; - int omy = 0; - int my = 0; - public PDBfile pdb; - int bsize; - Image img; - Graphics ig; - Dimension prefsize; - float[] centre = new float[3]; - float[] width = new float[3]; - float maxwidth; - float scale; - String inStr; - String inType; - boolean depthcue = true; - boolean wire = false; - boolean bymolecule = false; - boolean zbuffer = true; - boolean dragging; - int xstart; - int xend; - int ystart; - int yend; - int xmid; - int ymid; - Font font = new Font("Helvetica", Font.PLAIN, 10); - - public rotCanvas(PDBfile pdb, Sequence sequence, - jalview.gui.AlignViewport av) throws IOException { - int max = -10; - int maxchain = -1; - int pdbstart = 0; - int pdbend = 0; - int seqstart = 0; - int seqend = 0; - - for (int i = 0; i < pdb.chains.size(); i++) { - // Now lets compare the sequences to get - // the start and end points. - java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(), - "."); - String newString = ""; - - while (str.hasMoreTokens()) { - newString += str.nextToken(); - } - - // Align the sequence to the pdb - AlignSeq as = new AlignSeq(sequence, - ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); - as.calcScoreMatrix(); - as.traceAlignment(); - as.printAlignment(); - - if (as.maxscore > max) { - max = as.maxscore; - maxchain = i; - - pdbstart = as.seq2start; - pdbend = as.seq2end; - seqstart = as.seq1start - 1; - seqend = as.seq1end - 1; - } - - System.out.println("PDB start/end " + pdbstart + " " + pdbend); - System.out.println("SEQ start/end " + seqstart + " " + seqend); - } - - ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart; - ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend; - ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart; - ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend; - ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true; - ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence; - ((PDBChain) pdb.chains.elementAt(maxchain)).colourBySequence(av, - sequence); - - this.pdb = pdb; - this.prefsize = new Dimension(getWidth(), getHeight()); - - //Initialize the matrices to identity - for (int i = 0; i < 3; i++) { - for (int j = 0; j < 3; j++) { - if (i != j) { - idmat.addElement(i, j, 0); - objmat.addElement(i, j, 0); - } else { - idmat.addElement(i, j, 1); - objmat.addElement(i, j, 1); - } - } - } - - addMouseMotionListener(this); - addMouseListener(this); - addKeyListener(this); - - addPDBfile(); - ToolTipManager.sharedInstance().registerComponent(this); - ToolTipManager.sharedInstance().setInitialDelay(0); - ToolTipManager.sharedInstance().setDismissDelay(10000); - - } - - public void addPDBfile() { - findCentre(); - findWidth(); - - scale = findScale(); - - System.out.println("Scale factor = " + scale); - } - - public void deleteBonds() { - scale = 0; - maxwidth = 0; - - width[0] = 0; - width[1] = 0; - width[2] = 0; - - centre[0] = 0; - centre[1] = 0; - centre[2] = 0; - - for (int i = 0; i < pdb.chains.size(); i++) { - ((PDBChain) pdb.chains.elementAt(i)).bonds = null; - } - } - - public void findWidth() { - float[] max = new float[3]; - float[] min = new float[3]; - - max[0] = (float) -1e30; - max[1] = (float) -1e30; - max[2] = (float) -1e30; - - min[0] = (float) 1e30; - min[1] = (float) 1e30; - min[2] = (float) 1e30; - - for (int ii = 0; ii < pdb.chains.size(); ii++) { - if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) { - Bond tmp = (Bond) bonds.elementAt(i); - - if (tmp.start[0] >= max[0]) { - max[0] = tmp.start[0]; - } - - if (tmp.start[1] >= max[1]) { - max[1] = tmp.start[1]; - } - - if (tmp.start[2] >= max[2]) { - max[2] = tmp.start[2]; - } - - if (tmp.start[0] <= min[0]) { - min[0] = tmp.start[0]; - } - - if (tmp.start[1] <= min[1]) { - min[1] = tmp.start[1]; - } - - if (tmp.start[2] <= min[2]) { - min[2] = tmp.start[2]; - } - - if (tmp.end[0] >= max[0]) { - max[0] = tmp.end[0]; - } - - if (tmp.end[1] >= max[1]) { - max[1] = tmp.end[1]; - } - - if (tmp.end[2] >= max[2]) { - max[2] = tmp.end[2]; - } - - if (tmp.end[0] <= min[0]) { - min[0] = tmp.end[0]; - } - - if (tmp.end[1] <= min[1]) { - min[1] = tmp.end[1]; - } - - if (tmp.end[2] <= min[2]) { - min[2] = tmp.end[2]; - } - } - } - } - - System.out.println("xmax " + max[0] + " min " + min[0]); - System.out.println("ymax " + max[1] + " min " + min[1]); - System.out.println("zmax " + max[2] + " min " + min[2]); - - width[0] = (float) Math.abs(max[0] - min[0]); - width[1] = (float) Math.abs(max[1] - min[1]); - width[2] = (float) Math.abs(max[2] - min[2]); - - maxwidth = width[0]; - - if (width[1] > width[0]) { - maxwidth = width[1]; - } - - if (width[2] > width[1]) { - maxwidth = width[2]; - } - - System.out.println("Maxwidth = " + maxwidth); - } - - public float findScale() { - int dim; - int width; - int height; - - if (getWidth() != 0) { - width = getWidth(); - height = getHeight(); - } else { - width = prefsize.width; - height = prefsize.height; - } - - if (width < height) { - dim = width; - } else { - dim = height; - } - - return (float) (dim / (1.5d * maxwidth)); - } - - public void findCentre() { - float xtot = 0; - float ytot = 0; - float ztot = 0; - - int bsize = 0; - - //Find centre coordinate - for (int ii = 0; ii < pdb.chains.size(); ii++) { - if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - bsize += bonds.size(); - - for (int i = 0; i < bonds.size(); i++) { - xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] + - ((Bond) bonds.elementAt(i)).end[0]; - - ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] + - ((Bond) bonds.elementAt(i)).end[1]; - - ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] + - ((Bond) bonds.elementAt(i)).end[2]; - } - } - } - - centre[0] = xtot / (2 * (float) bsize); - centre[1] = ytot / (2 * (float) bsize); - centre[2] = ztot / (2 * (float) bsize); - } - - public void paint(Graphics g) { - //Only create the image at the beginning - - //this saves much memory usage - if ((img == null) || (prefsize.width != getWidth()) || - (prefsize.height != getHeight())) { - prefsize.width = getWidth(); - prefsize.height = getHeight(); - - scale = findScale(); - img = createImage(prefsize.width, prefsize.height); - ig = img.getGraphics(); - - redrawneeded = true; - } - - if (redrawneeded == true) { - drawBackground(ig, Color.black); - drawScene(ig); - redrawneeded = false; - } else { - ig = img.getGraphics(); - } - - g.drawImage(img, 0, 0, this); - } - - public void drawBackground(Graphics g, Color col) { - g.setColor(col); - g.fillRect(0, 0, prefsize.width, prefsize.height); - } - - public void drawScene(Graphics g) { - // Sort the bonds by z coord - Vector bonds = new Vector(); - - for (int ii = 0; ii < pdb.chains.size(); ii++) { - if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) { - Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < tmp.size(); i++) { - bonds.addElement(tmp.elementAt(i)); - } - } - } - - if (zbuffer) { - Zsort.Zsort(bonds); - } - - for (int i = 0; i < bonds.size(); i++) { - Bond tmpBond = (Bond) bonds.elementAt(i); - - xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + - (getWidth() / 2)); - ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) + - (getHeight() / 2)); - - xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + - (getWidth() / 2)); - yend = (int) (((tmpBond.end[1] - centre[1]) * scale) + - (getHeight() / 2)); - - xmid = (xend + xstart) / 2; - ymid = (yend + ystart) / 2; - - if (depthcue && !bymolecule) { - if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) { - g.setColor(tmpBond.startCol.darker().darker()); - drawLine(g, xstart, ystart, xmid, ymid); - - g.setColor(tmpBond.endCol.darker().darker()); - drawLine(g, xmid, ymid, xend, yend); - } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) { - g.setColor(tmpBond.startCol.darker()); - drawLine(g, xstart, ystart, xmid, ymid); - - g.setColor(tmpBond.endCol.darker()); - drawLine(g, xmid, ymid, xend, yend); - } else { - g.setColor(tmpBond.startCol); - drawLine(g, xstart, ystart, xmid, ymid); - - g.setColor(tmpBond.endCol); - drawLine(g, xmid, ymid, xend, yend); - } - } else if (depthcue && bymolecule) { - if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) { - g.setColor(Color.green.darker().darker()); - drawLine(g, xstart, ystart, xend, yend); - } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) { - g.setColor(Color.green.darker()); - drawLine(g, xstart, ystart, xend, yend); - } else { - g.setColor(Color.green); - drawLine(g, xstart, ystart, xend, yend); - } - } else if (!depthcue && !bymolecule) { - g.setColor(tmpBond.startCol); - drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol); - drawLine(g, xmid, ymid, xend, yend); - } else { - drawLine(g, xstart, ystart, xend, yend); - } - } - } - - public void drawLine(Graphics g, int x1, int y1, int x2, int y2) { - if (!wire) { - if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) { - g.drawLine(x1, y1, x2, y2); - g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1); - g.drawLine(x1, y1 - 1, x2, y2 - 1); - } else { - g.setColor(g.getColor().brighter()); - g.drawLine(x1, y1, x2, y2); - g.drawLine(x1 + 1, y1, x2 + 1, y2); - g.drawLine(x1 - 1, y1, x2 - 1, y2); - } - } else { - g.drawLine(x1, y1, x2, y2); - } - } - - public Dimension minimumsize() { - return prefsize; - } - - public Dimension preferredsize() { - return prefsize; - } - - public void keyTyped(KeyEvent evt) { - } - - public void keyReleased(KeyEvent evt) { - } - - public void keyPressed(KeyEvent evt) { - int key = evt.getKeyChar(); - - if (evt.getKeyCode() == KeyEvent.VK_UP) { - scale = (float) (scale * 1.1); - redrawneeded = true; - repaint(); - } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) { - scale = (float) (scale * 0.9); - redrawneeded = true; - repaint(); - } else if (key == 'w') { - wire = !wire; - System.out.println("wireframe " + wire); - redrawneeded = true; - repaint(); - } else if (key == 'd') { - depthcue = !depthcue; - System.out.println("Depth cueing is " + depthcue); - redrawneeded = true; - repaint(); - } else if (key == 'm') { - bymolecule = !bymolecule; - System.out.println("Bymolecule is " + bymolecule); - redrawneeded = true; - repaint(); - } else if (key == 'z') { - zbuffer = !zbuffer; - System.out.println("Z buffering is " + zbuffer); - redrawneeded = true; - repaint(); - } else if (key == 'c') { - bymolecule = false; - pdb.setChainColours(); - System.out.println("Colouring by chain"); - redrawneeded = true; - repaint(); - } else if (key == 'h') { - bymolecule = false; - pdb.setHydrophobicityColours(); - System.out.println("Colouring by hydrophobicity"); - redrawneeded = true; - repaint(); - } else if (key == 'q') { - bymolecule = false; - pdb.setChargeColours(); - System.out.println("Colouring charges and cysteines"); - redrawneeded = true; - repaint(); - } - - return; - } - - public void mousePressed(MouseEvent e) { - mx = e.getX(); - my = e.getY(); - omx = mx; - omy = my; - dragging = false; - } - - public void mouseMoved(MouseEvent e) { - myAtom fatom = null; - - for (int ii = 0; ii < pdb.chains.size(); ii++) { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - - if (chain.isVisible) { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) { - Bond tmpBond = (Bond) bonds.elementAt(i); - int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + - (getWidth() / 2)); - - if (Math.abs(truex - e.getX()) <= 2) { - int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) + - (getHeight() / 2)); - - if (Math.abs(truey - e.getY()) <= 2) { - fatom = tmpBond.at1; - } - } - } - } - } - - if (fatom != null) { - this.setToolTipText(fatom.resName); - } else { - this.setToolTipText(null); - } - } - - public void mouseClicked(MouseEvent e) { - } - - public void mouseEntered(MouseEvent e) { - } - - public void mouseExited(MouseEvent e) { - } - - public void mouseDragged(MouseEvent evt) { - int x = evt.getX(); - int y = evt.getY(); - mx = x; - my = y; - - MCMatrix objmat = new MCMatrix(3, 3); - objmat.setIdentity(); - - if ((evt.getModifiers() & Event.META_MASK) != 0) { - objmat.rotatez((float) ((mx - omx))); - } else { - objmat.rotatex((float) ((my - omy))); - objmat.rotatey((float) ((omx - mx))); - } - - //Alter the bonds - for (int ii = 0; ii < pdb.chains.size(); ii++) { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) { - Bond tmpBond = (Bond) bonds.elementAt(i); - - //Translate the bond so the centre is 0,0,0 - tmpBond.translate(-centre[0], -centre[1], -centre[2]); - - //Now apply the rotation matrix - tmpBond.start = objmat.vectorMultiply(tmpBond.start); - tmpBond.end = objmat.vectorMultiply(tmpBond.end); - - //Now translate back again - tmpBond.translate(centre[0], centre[1], centre[2]); - } - } - - objmat = null; - - omx = mx; - omy = my; - - redrawneeded = true; - - paint(this.getGraphics()); - - dragging = true; - - return; - } - - public void mouseReleased(MouseEvent evt) { - //int x = evt.getX(); - //int y = evt.getY(); - - //if (!dragging) { - // myAtom tmp = findAtom(x, y); - //} - - drawLabels(); - - return; - } - - public void drawLabels() { - redrawneeded = true; - paint(this.getGraphics()); - - for (int ii = 0; ii < pdb.chains.size(); ii++) { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - - if (chain.isVisible) { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) { - Bond tmpBond = (Bond) bonds.elementAt(i); - - if (tmpBond.at1.isSelected) { - labelAtom(img.getGraphics(), tmpBond, 1); - } - - if (tmpBond.at2.isSelected) { - labelAtom(img.getGraphics(), tmpBond, 2); - } - } - } - } - - this.getGraphics().drawImage(img, 0, 0, this); - - dragging = false; - } - - public void labelAtom(Graphics g, Bond b, int n) { - g.setFont(font); - - if (n == 1) { - int xstart = (int) (((b.start[0] - centre[0]) * scale) + - (getWidth() / 2)); - int ystart = (int) (((b.start[1] - centre[1]) * scale) + - (getHeight() / 2)); - - g.setColor(Color.red); - g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart); - } - - if (n == 2) { - int xstart = (int) (((b.end[0] - centre[0]) * scale) + - (getWidth() / 2)); - int ystart = (int) (((b.end[1] - centre[1]) * scale) + - (getHeight() / 2)); - - g.setColor(Color.red); - g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); - } - } - - public myAtom findAtom(int x, int y) { - myAtom fatom = null; - - int foundchain = -1; - - for (int ii = 0; ii < pdb.chains.size(); ii++) { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - - if (chain.isVisible) { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) { - Bond tmpBond = (Bond) bonds.elementAt(i); - - int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + - (getWidth() / 2)); - - if (Math.abs(truex - x) <= 2) { - int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) + - (getHeight() / 2)); - - if (Math.abs(truey - y) <= 2) { - System.out.println("Found match"); - System.out.println(x + " " + y); - System.out.println(truex + " " + truey); - System.out.println(tmpBond.start[0] + " " + - tmpBond.start[1]); - System.out.println("Atom 1 = " + - tmpBond.at1.resName + " " + - tmpBond.at1.resNumber + " " + - tmpBond.at1.chain); - fatom = tmpBond.at1; - fatom.isSelected = !fatom.isSelected; - foundchain = ii; - } - } - } - } - - if (fatom != null) //)&& chain.ds != null) - { - chain = (PDBChain) pdb.chains.elementAt(foundchain); - - // SMJS TODO - // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset; - // int pos = chain.ds.findIndex(tmp); - // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos); - } - } - - return fatom; - } - - public void update(Graphics g) { - paint(g); - } -} -- 1.7.10.2