From 5a60f6428df1108a96524aae0c34d615ae48c227 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 21 Dec 2006 13:38:08 +0000 Subject: [PATCH] getSequenceAsString --- src/MCview/AppletPDBCanvas.java | 2006 +++++++++++++------------- src/MCview/PDBCanvas.java | 2030 +++++++++++++-------------- src/jalview/appletgui/AlignFrame.java | 2 +- src/jalview/appletgui/AnnotationLabels.java | 2 +- src/jalview/datamodel/SeqCigar.java | 8 +- 5 files changed, 2024 insertions(+), 2024 deletions(-) diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index 220d5f3..4cba94d 100755 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -1,1003 +1,1003 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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.*; - - - -public class AppletPDBCanvas extends Panel implements 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 bysequence = true; - 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); - jalview.appletgui.SeqCanvas seqcanvas; - public Sequence sequence; - final StringBuffer mappingDetails = new StringBuffer(); - String appletToolTip = null; - int toolx, tooly; - PDBChain mainchain; - Vector highlightRes; - boolean pdbAction = false; - Bond highlightBond1, highlightBond2; - boolean errorLoading = false; - boolean seqColoursReady = false; - jalview.appletgui.FeatureRenderer fr; - - public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq) - { - this.seqcanvas = seqcanvas; - this.sequence = seq; - - seqcanvas.setPDBCanvas(this); - addKeyListener(new KeyAdapter() - { - - public void keyPressed(KeyEvent evt) - { - doKeyPressed(evt); - } - }); - } - - - public void setPDBFile(PDBfile pdb) - { - int max = -10; - int maxchain = -1; - int pdbstart = 0; - int pdbend = 0; - int seqstart = 0; - int seqend = 0; - AlignSeq maxAlignseq = null;; - - for (int i = 0; i < pdb.chains.size(); i++) - { - - mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence()); - mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n"); - - // Now lets compare the sequences to get - // the start and end points. - // Align the sequence to the pdb - AlignSeq as = new AlignSeq(sequence, - ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); - as.calcScoreMatrix(); - as.traceAlignment(); - PrintStream ps = new PrintStream(System.out) - { - public void print(String x) { - mappingDetails.append(x); - } - public void println() - { - mappingDetails.append("\n"); - } - }; - - as.printAlignment(ps); - - if (as.maxscore > max) { - max = as.maxscore; - maxchain = i; - - pdbstart = as.seq2start; - pdbend = as.seq2end; - seqstart = as.seq1start + sequence.getStart()-1; - seqend = as.seq1end + sequence.getEnd()-1; - maxAlignseq = as; - } - - mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); - mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend); - } - - mainchain = (PDBChain) pdb.chains.elementAt(maxchain); - - mainchain.pdbstart = pdbstart; - mainchain.pdbend = pdbend; - mainchain.seqstart = seqstart; - mainchain.seqend = seqend; - mainchain.isVisible = true; - mainchain.makeExactMapping(maxAlignseq, sequence); - - this.pdb = pdb; - this.prefsize = new Dimension(getSize().width, getSize().height); - - //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); - - - findCentre(); - findWidth(); - - setupBonds(); - - scale = findScale(); - } - - - Vector visiblebonds; - void setupBonds() - { - seqColoursReady = false; - // Sort the bonds by z coord - visiblebonds = 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++) - { - visiblebonds.addElement(tmp.elementAt(i)); - } - } - } - updateSeqColours(); - seqColoursReady = true; - redrawneeded = true; - repaint(); - } - - - 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]; - } - } - } - } - - 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 (getSize().width != 0) { - width = getSize().width; - height = getSize().height; - } 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) - { - - if(errorLoading) - { - g.setColor(Color.white); - g.fillRect(0,0,getSize().width, getSize().height); - g.setColor(Color.black); - g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString("Error loading PDB data!!", 50, getSize().height/2); - return; - } - - if( !seqColoursReady ) - { - g.setColor(Color.black); - g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString("Fetching PDB data...", 50, getSize().height/2); - return; - } - - - - //Only create the image at the beginning - - //this saves much memory usage - if ((img == null) || (prefsize.width != getSize().width) || - (prefsize.height != getSize().height)) { - - try{ prefsize.width = getSize().width; - prefsize.height = getSize().height; - - scale = findScale(); - img = createImage(prefsize.width, prefsize.height); - ig = img.getGraphics(); - - redrawneeded = true; - }catch(Exception ex) - { - ex.printStackTrace(); - } - } - - - if (redrawneeded) - { - drawAll(ig, prefsize.width, prefsize.height); - redrawneeded = false; - } - if(appletToolTip!=null) - { - ig.setColor(Color.red); - ig.drawString(appletToolTip, toolx, tooly); - } - - g.drawImage(img, 0, 0, this); - - pdbAction = false; - } - - public void drawAll(Graphics g, int width, int height) - { - ig.setColor(Color.black); - ig.fillRect(0, 0, width, height); - drawScene(ig); - drawLabels(ig); - } - - void setColours(jalview.schemes.ColourSchemeI cs) - { - bysequence = false; - pdb.setColours(cs); - redrawneeded = true; - repaint(); - } - public void updateSeqColours() - { - if (pdbAction) - { - return; - } - - if(bysequence && pdb!=null) - { - for (int ii = 0; ii < pdb.chains.size(); ii++) - { - colourBySequence((PDBChain) pdb.chains.elementAt(ii)); - } - } - - redrawneeded=true; - repaint(); - } - - - int findTrueIndex(int pos) - { - // returns the alignment position for a residue - int j = sequence.getStart(); - int i = 0; - - while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1)) - { - if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) - { - j++; - } - - i++; - } - - if(i>1) - i--; - - if ( (j == sequence.getEnd()) && (j < pos)) - { - return sequence.getEnd() + 1; - } - else - { - return i; - } - } - - - // This method has been taken out of PDBChain to allow - // Applet and Application specific sequence renderers to be used - void colourBySequence(PDBChain chain) - { - boolean showFeatures = false; - - if(seqcanvas.getViewport().getShowSequenceFeatures()) - { - if(fr==null) - { - fr = new jalview.appletgui.FeatureRenderer(seqcanvas.getViewport()); - } - fr.transferSettings( seqcanvas.getFeatureRenderer()); - showFeatures = true; - } - - for (int i = 0; i < chain.bonds.size(); i++) - { - Bond tmp = (Bond) chain.bonds.elementAt(i); - tmp.startCol = Color.lightGray; - tmp.endCol = Color.lightGray; - if(chain!=mainchain) - continue; - - if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && - (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1))) - { - - int index = findTrueIndex(tmp.at1.alignmentMapping); - //sequence.findIndex(tmp.at1.alignmentMapping); - if (index != -1) - { - tmp.startCol = seqcanvas.getSequenceRenderer(). - getResidueBoxColour( sequence, index); - - if(showFeatures) - tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index); - } - } - - int index = findTrueIndex(tmp.at2.alignmentMapping); - //sequence.findIndex( tmp.at2.alignmentMapping ); - if (index != -1) - { - tmp.endCol = seqcanvas.getSequenceRenderer(). - getResidueBoxColour( sequence, index); - - if(showFeatures) - tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index); - } - } - } - - - Zsort zsort; - public void drawScene(Graphics g) - { - if (zbuffer) - { - if(zsort ==null) - zsort = new Zsort(); - - zsort.Zsort(visiblebonds); - } - - - Bond tmpBond=null; - for (int i = 0; i < visiblebonds.size(); i++) - { - tmpBond = (Bond) visiblebonds.elementAt(i); - - - xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + - (getSize().width / 2)); - ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) + - (getSize().height / 2)); - - xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + - (getSize().width / 2)); - yend = (int) (((tmpBond.end[1] - centre[1]) * scale) + - (getSize().height / 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); - } - - if(highlightBond1!=null && highlightBond1==tmpBond) - { - g.setColor(Color.white); - drawLine(g, xmid, ymid, xend, yend); - } - - if(highlightBond2!=null && highlightBond2==tmpBond) - { - g.setColor(Color.white); - drawLine(g, xstart, ystart, xmid, ymid); - } - - } - } - - 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 doKeyPressed(KeyEvent evt) - { - 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(); - } - } - - public void mousePressed(MouseEvent e) { - pdbAction = true; - Atom fatom = findAtom(e.getX(), e.getY()); - if(fatom!=null) - { - fatom.isSelected = !fatom.isSelected; - - redrawneeded = true; - repaint(); - if (foundchain != -1) - { - PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain); - if (chain == mainchain) - { - if (fatom.alignmentMapping != -1) - { - if (highlightRes == null) - highlightRes = new Vector(); - - if (highlightRes.contains(fatom.alignmentMapping+"" + "")) - highlightRes.removeElement(fatom.alignmentMapping + ""); - else - highlightRes.addElement(fatom.alignmentMapping + ""); - } - } - } - - } - mx = e.getX(); - my = e.getY(); - omx = mx; - omy = my; - dragging = false; - } - - public void mouseMoved(MouseEvent e) { - pdbAction = true; - if(highlightBond1!=null) - { - highlightBond1.at2.isSelected = false; - highlightBond2.at1.isSelected = false; - highlightBond1 = null; - highlightBond2 = null; - } - - Atom fatom = findAtom(e.getX(), e.getY()); - - PDBChain chain = null; - if(foundchain!=-1) - { - chain = (PDBChain) pdb.chains.elementAt(foundchain); - if(chain == mainchain) - { - highlightSeqcanvas( fatom.alignmentMapping ); - } - } - - if (fatom != null) { - toolx = e.getX(); - tooly = e.getY(); - - appletToolTip = chain.id+":"+ fatom.resNumber+" "+ fatom.resName; - redrawneeded = true; - repaint(); - } else { - highlightSeqcanvas( -1); - appletToolTip = null; - redrawneeded = true; - repaint(); - } - } - - - void highlightSeqcanvas(int pos) - { - SearchResults searchResults = new SearchResults(); - if(highlightRes!=null) - { - for (int i = 0; i < highlightRes.size(); i++) - { - int a = Integer.parseInt(highlightRes.elementAt( - i).toString())+1; - - searchResults.addResult(sequence, a, a); - } - } - - if(pos!=-1) - { - searchResults.addResult(sequence, pos+1, pos+1); - } - - seqcanvas.highlightSearchResults(searchResults); - } - - - 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; - - dragging = true; - - redrawneeded = true; - - repaint(); - } - - public void mouseReleased(MouseEvent evt) { - dragging = false; - return; - } - - void drawLabels(Graphics g) { - - 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(g, tmpBond, 1); - } - - if (tmpBond.at2.isSelected) - { - - labelAtom(g, tmpBond, 2); - } - } - } - } - } - - public void labelAtom(Graphics g, Bond b, int n) { - g.setFont(font); - - if (n == 1) { - int xstart = (int) (((b.start[0] - centre[0]) * scale) + - (getSize().width / 2)); - int ystart = (int) (((b.start[1] - centre[1]) * scale) + - (getSize().height / 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) + - (getSize().width / 2)); - int ystart = (int) (((b.end[1] - centre[1]) * scale) + - (getSize().height / 2)); - - g.setColor(Color.red); - g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); - } - } - - int foundchain = -1; - public Atom findAtom(int x, int y) { - Atom fatom = null; - - foundchain = -1; - - for (int ii = 0; ii < pdb.chains.size(); ii++) - { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - int truex; - Bond tmpBond=null; - - if (chain.isVisible) - { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) - { - tmpBond = (Bond) bonds.elementAt(i); - - truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + - (getSize().width / 2)); - - if (Math.abs(truex - x) <= 2) - { - int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) + - (getSize().height / 2)); - - if (Math.abs(truey - y) <= 2) - { - fatom = tmpBond.at1; - foundchain = ii; - break; - } - } - } - - // Still here? Maybe its the last bond - - truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) + - (getSize().width / 2)); - - if (Math.abs(truex - x) <= 2) - { - int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) + - (getSize().height / 2)); - - if (Math.abs(truey - y) <= 2) - { - fatom = tmpBond.at2; - foundchain = ii; - break; - } - } - - } - - if (fatom != null) //)&& chain.ds != null) - { - chain = (PDBChain) pdb.chains.elementAt(foundchain); - } - } - - return fatom; - } - - public void update(Graphics g) - { - paint(g); - } - - public void highlightRes(int ii) - { - if(!seqColoursReady) - return; - - if (highlightRes != null - && highlightRes.contains((ii-1) + "")) - { - return; - } - - int index = -1; - Bond tmpBond; - for(index=0; index 0) - { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); - highlightBond1.at2.isSelected = true; - } - - if (index != mainchain.bonds.size()) - { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); - highlightBond2.at1.isSelected = true; - } - - break; - } - } - - redrawneeded = true; - repaint(); - } - - - public void setAllchainsVisible(boolean b) - { - for (int ii = 0; ii < pdb.chains.size(); ii++) - { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - chain.isVisible = b; - } - mainchain.isVisible = true; - findCentre(); - setupBonds(); - } - -} +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2006 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.*; + + + +public class AppletPDBCanvas extends Panel implements 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 bysequence = true; + 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); + jalview.appletgui.SeqCanvas seqcanvas; + public Sequence sequence; + final StringBuffer mappingDetails = new StringBuffer(); + String appletToolTip = null; + int toolx, tooly; + PDBChain mainchain; + Vector highlightRes; + boolean pdbAction = false; + Bond highlightBond1, highlightBond2; + boolean errorLoading = false; + boolean seqColoursReady = false; + jalview.appletgui.FeatureRenderer fr; + + public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq) + { + this.seqcanvas = seqcanvas; + this.sequence = seq; + + seqcanvas.setPDBCanvas(this); + addKeyListener(new KeyAdapter() + { + + public void keyPressed(KeyEvent evt) + { + doKeyPressed(evt); + } + }); + } + + + public void setPDBFile(PDBfile pdb) + { + int max = -10; + int maxchain = -1; + int pdbstart = 0; + int pdbend = 0; + int seqstart = 0; + int seqend = 0; + AlignSeq maxAlignseq = null;; + + for (int i = 0; i < pdb.chains.size(); i++) + { + + mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequenceAsString()); + mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n"); + + // Now lets compare the sequences to get + // the start and end points. + // Align the sequence to the pdb + AlignSeq as = new AlignSeq(sequence, + ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); + as.calcScoreMatrix(); + as.traceAlignment(); + PrintStream ps = new PrintStream(System.out) + { + public void print(String x) { + mappingDetails.append(x); + } + public void println() + { + mappingDetails.append("\n"); + } + }; + + as.printAlignment(ps); + + if (as.maxscore > max) { + max = as.maxscore; + maxchain = i; + + pdbstart = as.seq2start; + pdbend = as.seq2end; + seqstart = as.seq1start + sequence.getStart()-1; + seqend = as.seq1end + sequence.getEnd()-1; + maxAlignseq = as; + } + + mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); + mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend); + } + + mainchain = (PDBChain) pdb.chains.elementAt(maxchain); + + mainchain.pdbstart = pdbstart; + mainchain.pdbend = pdbend; + mainchain.seqstart = seqstart; + mainchain.seqend = seqend; + mainchain.isVisible = true; + mainchain.makeExactMapping(maxAlignseq, sequence); + + this.pdb = pdb; + this.prefsize = new Dimension(getSize().width, getSize().height); + + //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); + + + findCentre(); + findWidth(); + + setupBonds(); + + scale = findScale(); + } + + + Vector visiblebonds; + void setupBonds() + { + seqColoursReady = false; + // Sort the bonds by z coord + visiblebonds = 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++) + { + visiblebonds.addElement(tmp.elementAt(i)); + } + } + } + updateSeqColours(); + seqColoursReady = true; + redrawneeded = true; + repaint(); + } + + + 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]; + } + } + } + } + + 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 (getSize().width != 0) { + width = getSize().width; + height = getSize().height; + } 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) + { + + if(errorLoading) + { + g.setColor(Color.white); + g.fillRect(0,0,getSize().width, getSize().height); + g.setColor(Color.black); + g.setFont(new Font("Verdana", Font.BOLD, 14)); + g.drawString("Error loading PDB data!!", 50, getSize().height/2); + return; + } + + if( !seqColoursReady ) + { + g.setColor(Color.black); + g.setFont(new Font("Verdana", Font.BOLD, 14)); + g.drawString("Fetching PDB data...", 50, getSize().height/2); + return; + } + + + + //Only create the image at the beginning - + //this saves much memory usage + if ((img == null) || (prefsize.width != getSize().width) || + (prefsize.height != getSize().height)) { + + try{ prefsize.width = getSize().width; + prefsize.height = getSize().height; + + scale = findScale(); + img = createImage(prefsize.width, prefsize.height); + ig = img.getGraphics(); + + redrawneeded = true; + }catch(Exception ex) + { + ex.printStackTrace(); + } + } + + + if (redrawneeded) + { + drawAll(ig, prefsize.width, prefsize.height); + redrawneeded = false; + } + if(appletToolTip!=null) + { + ig.setColor(Color.red); + ig.drawString(appletToolTip, toolx, tooly); + } + + g.drawImage(img, 0, 0, this); + + pdbAction = false; + } + + public void drawAll(Graphics g, int width, int height) + { + ig.setColor(Color.black); + ig.fillRect(0, 0, width, height); + drawScene(ig); + drawLabels(ig); + } + + void setColours(jalview.schemes.ColourSchemeI cs) + { + bysequence = false; + pdb.setColours(cs); + redrawneeded = true; + repaint(); + } + public void updateSeqColours() + { + if (pdbAction) + { + return; + } + + if(bysequence && pdb!=null) + { + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + colourBySequence((PDBChain) pdb.chains.elementAt(ii)); + } + } + + redrawneeded=true; + repaint(); + } + + + int findTrueIndex(int pos) + { + // returns the alignment position for a residue + int j = sequence.getStart(); + int i = 0; + + while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1)) + { + if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) + { + j++; + } + + i++; + } + + if(i>1) + i--; + + if ( (j == sequence.getEnd()) && (j < pos)) + { + return sequence.getEnd() + 1; + } + else + { + return i; + } + } + + + // This method has been taken out of PDBChain to allow + // Applet and Application specific sequence renderers to be used + void colourBySequence(PDBChain chain) + { + boolean showFeatures = false; + + if(seqcanvas.getViewport().getShowSequenceFeatures()) + { + if(fr==null) + { + fr = new jalview.appletgui.FeatureRenderer(seqcanvas.getViewport()); + } + fr.transferSettings( seqcanvas.getFeatureRenderer()); + showFeatures = true; + } + + for (int i = 0; i < chain.bonds.size(); i++) + { + Bond tmp = (Bond) chain.bonds.elementAt(i); + tmp.startCol = Color.lightGray; + tmp.endCol = Color.lightGray; + if(chain!=mainchain) + continue; + + if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && + (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1))) + { + + int index = findTrueIndex(tmp.at1.alignmentMapping); + //sequence.findIndex(tmp.at1.alignmentMapping); + if (index != -1) + { + tmp.startCol = seqcanvas.getSequenceRenderer(). + getResidueBoxColour( sequence, index); + + if(showFeatures) + tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index); + } + } + + int index = findTrueIndex(tmp.at2.alignmentMapping); + //sequence.findIndex( tmp.at2.alignmentMapping ); + if (index != -1) + { + tmp.endCol = seqcanvas.getSequenceRenderer(). + getResidueBoxColour( sequence, index); + + if(showFeatures) + tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index); + } + } + } + + + Zsort zsort; + public void drawScene(Graphics g) + { + if (zbuffer) + { + if(zsort ==null) + zsort = new Zsort(); + + zsort.Zsort(visiblebonds); + } + + + Bond tmpBond=null; + for (int i = 0; i < visiblebonds.size(); i++) + { + tmpBond = (Bond) visiblebonds.elementAt(i); + + + xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + + (getSize().width / 2)); + ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) + + (getSize().height / 2)); + + xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + + (getSize().width / 2)); + yend = (int) (((tmpBond.end[1] - centre[1]) * scale) + + (getSize().height / 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); + } + + if(highlightBond1!=null && highlightBond1==tmpBond) + { + g.setColor(Color.white); + drawLine(g, xmid, ymid, xend, yend); + } + + if(highlightBond2!=null && highlightBond2==tmpBond) + { + g.setColor(Color.white); + drawLine(g, xstart, ystart, xmid, ymid); + } + + } + } + + 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 doKeyPressed(KeyEvent evt) + { + 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(); + } + } + + public void mousePressed(MouseEvent e) { + pdbAction = true; + Atom fatom = findAtom(e.getX(), e.getY()); + if(fatom!=null) + { + fatom.isSelected = !fatom.isSelected; + + redrawneeded = true; + repaint(); + if (foundchain != -1) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain); + if (chain == mainchain) + { + if (fatom.alignmentMapping != -1) + { + if (highlightRes == null) + highlightRes = new Vector(); + + if (highlightRes.contains(fatom.alignmentMapping+"" + "")) + highlightRes.removeElement(fatom.alignmentMapping + ""); + else + highlightRes.addElement(fatom.alignmentMapping + ""); + } + } + } + + } + mx = e.getX(); + my = e.getY(); + omx = mx; + omy = my; + dragging = false; + } + + public void mouseMoved(MouseEvent e) { + pdbAction = true; + if(highlightBond1!=null) + { + highlightBond1.at2.isSelected = false; + highlightBond2.at1.isSelected = false; + highlightBond1 = null; + highlightBond2 = null; + } + + Atom fatom = findAtom(e.getX(), e.getY()); + + PDBChain chain = null; + if(foundchain!=-1) + { + chain = (PDBChain) pdb.chains.elementAt(foundchain); + if(chain == mainchain) + { + highlightSeqcanvas( fatom.alignmentMapping ); + } + } + + if (fatom != null) { + toolx = e.getX(); + tooly = e.getY(); + + appletToolTip = chain.id+":"+ fatom.resNumber+" "+ fatom.resName; + redrawneeded = true; + repaint(); + } else { + highlightSeqcanvas( -1); + appletToolTip = null; + redrawneeded = true; + repaint(); + } + } + + + void highlightSeqcanvas(int pos) + { + SearchResults searchResults = new SearchResults(); + if(highlightRes!=null) + { + for (int i = 0; i < highlightRes.size(); i++) + { + int a = Integer.parseInt(highlightRes.elementAt( + i).toString())+1; + + searchResults.addResult(sequence, a, a); + } + } + + if(pos!=-1) + { + searchResults.addResult(sequence, pos+1, pos+1); + } + + seqcanvas.highlightSearchResults(searchResults); + } + + + 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; + + dragging = true; + + redrawneeded = true; + + repaint(); + } + + public void mouseReleased(MouseEvent evt) { + dragging = false; + return; + } + + void drawLabels(Graphics g) { + + 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(g, tmpBond, 1); + } + + if (tmpBond.at2.isSelected) + { + + labelAtom(g, tmpBond, 2); + } + } + } + } + } + + public void labelAtom(Graphics g, Bond b, int n) { + g.setFont(font); + + if (n == 1) { + int xstart = (int) (((b.start[0] - centre[0]) * scale) + + (getSize().width / 2)); + int ystart = (int) (((b.start[1] - centre[1]) * scale) + + (getSize().height / 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) + + (getSize().width / 2)); + int ystart = (int) (((b.end[1] - centre[1]) * scale) + + (getSize().height / 2)); + + g.setColor(Color.red); + g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); + } + } + + int foundchain = -1; + public Atom findAtom(int x, int y) { + Atom fatom = null; + + foundchain = -1; + + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); + int truex; + Bond tmpBond=null; + + if (chain.isVisible) + { + Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; + + for (int i = 0; i < bonds.size(); i++) + { + tmpBond = (Bond) bonds.elementAt(i); + + truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + + (getSize().width / 2)); + + if (Math.abs(truex - x) <= 2) + { + int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) + + (getSize().height / 2)); + + if (Math.abs(truey - y) <= 2) + { + fatom = tmpBond.at1; + foundchain = ii; + break; + } + } + } + + // Still here? Maybe its the last bond + + truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) + + (getSize().width / 2)); + + if (Math.abs(truex - x) <= 2) + { + int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) + + (getSize().height / 2)); + + if (Math.abs(truey - y) <= 2) + { + fatom = tmpBond.at2; + foundchain = ii; + break; + } + } + + } + + if (fatom != null) //)&& chain.ds != null) + { + chain = (PDBChain) pdb.chains.elementAt(foundchain); + } + } + + return fatom; + } + + public void update(Graphics g) + { + paint(g); + } + + public void highlightRes(int ii) + { + if(!seqColoursReady) + return; + + if (highlightRes != null + && highlightRes.contains((ii-1) + "")) + { + return; + } + + int index = -1; + Bond tmpBond; + for(index=0; index 0) + { + highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1.at2.isSelected = true; + } + + if (index != mainchain.bonds.size()) + { + highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2.at1.isSelected = true; + } + + break; + } + } + + redrawneeded = true; + repaint(); + } + + + public void setAllchainsVisible(boolean b) + { + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); + chain.isVisible = b; + } + mainchain.isVisible = true; + findCentre(); + setupBonds(); + } + +} diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 9805c35..163326c 100755 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -1,1015 +1,1015 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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 PDBCanvas extends JPanel implements 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 bysequence = true; - 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); - jalview.gui.SeqCanvas seqcanvas; - public Sequence sequence; - final StringBuffer mappingDetails = new StringBuffer(); - PDBChain mainchain; - Vector highlightRes; - boolean pdbAction = false; - boolean seqColoursReady = false; - jalview.gui.FeatureRenderer fr; - Color backgroundColour = Color.black; - - public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq) - { - this.seqcanvas = seqcanvas; - this.sequence = seq; - seqcanvas.setPDBCanvas(this); - } - - public void setPDBFile(PDBfile pdb) - { - int max = -10; - int maxchain = -1; - int pdbstart = 0; - int pdbend = 0; - int seqstart = 0; - int seqend = 0; - AlignSeq maxAlignseq = null; - - for (int i = 0; i < pdb.chains.size(); i++) - { - - mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence()); - mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n"); - - // Now lets compare the sequences to get - // the start and end points. - // Align the sequence to the pdb - AlignSeq as = new AlignSeq(sequence, - ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); - as.calcScoreMatrix(); - as.traceAlignment(); - PrintStream ps = new PrintStream(System.out) - { - public void print(String x) { - mappingDetails.append(x); - } - public void println() - { - mappingDetails.append("\n"); - } - }; - - as.printAlignment(ps); - - - - if (as.maxscore > max) - { - max = as.maxscore; - maxchain = i; - pdbstart = as.seq2start; - pdbend = as.seq2end; - seqstart = as.seq1start + sequence.getStart()-1; - seqend = as.seq1end + sequence.getEnd()-1; - maxAlignseq = as; - } - - mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); - mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend); - } - - mainchain = (PDBChain) pdb.chains.elementAt(maxchain); - - mainchain.pdbstart = pdbstart; - mainchain.pdbend = pdbend; - mainchain.seqstart = seqstart; - mainchain.seqend = seqend; - mainchain.isVisible = true; - mainchain.makeExactMapping(maxAlignseq, 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); - - addMouseWheelListener(new MouseWheelListener() - { - public void mouseWheelMoved(MouseWheelEvent e) - { - if (e.getWheelRotation() > 0) - { - scale = (float) (scale * 1.1); - redrawneeded = true; - repaint(); - } - - else - { - scale = (float) (scale * 0.9); - redrawneeded = true; - repaint(); - } - } - }); - - - findCentre(); - findWidth(); - - setupBonds(); - - scale = findScale(); - - ToolTipManager.sharedInstance().registerComponent(this); - ToolTipManager.sharedInstance().setInitialDelay(0); - ToolTipManager.sharedInstance().setDismissDelay(10000); - } - - - Vector visiblebonds; - void setupBonds() - { - seqColoursReady = false; - // Sort the bonds by z coord - visiblebonds = 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++) - { - visiblebonds.addElement(tmp.elementAt(i)); - } - } - } - - updateSeqColours(); - seqColoursReady = true; - redrawneeded = true; - repaint(); - } - - - 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 paintComponent(Graphics g) - { - super.paintComponent(g); - - if(!seqColoursReady) - { - g.setColor(Color.black); - g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString("Retrieving PDB data....", 20, getHeight()/2); - return; - } - - - //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(); - Graphics2D ig2 = (Graphics2D) ig; - - ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - - redrawneeded = true; - } - - - if (redrawneeded) - { - drawAll(ig, prefsize.width, prefsize.height); - redrawneeded = false; - } - - g.drawImage(img, 0, 0, this); - - pdbAction = false; - } - - public void drawAll(Graphics g, int width, int height) - { - g.setColor(backgroundColour); - g.fillRect(0, 0, width, height); - drawScene(g); - drawLabels(g); - } - - - public void updateSeqColours() - { - if(pdbAction) - { - return; - } - - // System.out.println("update seq colours"); - if(bysequence && pdb!=null) - { - for (int ii = 0; ii < pdb.chains.size(); ii++) - { - colourBySequence( (PDBChain) pdb.chains.elementAt(ii)); - } - } - - redrawneeded=true; - repaint(); - } - - int findTrueIndex(int pos) - { - // returns the alignment position for a residue - int j = sequence.getStart(); - int i = 0; - - while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1)) - { - if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) - { - j++; - } - - i++; - } - - if(i>1) - i--; - - if ( (j == sequence.getEnd()) && (j < pos)) - { - return sequence.getEnd() + 1; - } - else - { - return i; - } - } - - // This method has been taken out of PDBChain to allow - // Applet and Application specific sequence renderers to be used - void colourBySequence(PDBChain chain) - { - // System.out.println("colour by seq"); - boolean showFeatures = false; - if(seqcanvas.getViewport().getShowSequenceFeatures()) - { - showFeatures = true; - if (fr == null) - fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport()); - - fr.transferSettings( seqcanvas.getFeatureRenderer() ); - } - - Bond tmp; - for (int i = 0; i < chain.bonds.size(); i++) - { - tmp = (Bond) chain.bonds.elementAt(i); - - if(chain!=mainchain) - continue; - - if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && - (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1))) - { - int index = findTrueIndex(tmp.at1.alignmentMapping); - //sequence.findIndex(tmp.at1.alignmentMapping); - if (index != -1) - { - tmp.startCol = seqcanvas.getSequenceRenderer(). - getResidueBoxColour( sequence, index); - - if(showFeatures) - tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index); - - if(tmp.startCol==null) - tmp.startCol = Color.white; - } - } - - if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && - (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1))) - { - - int index = findTrueIndex(tmp.at2.alignmentMapping); - //sequence.findIndex( tmp.at2.alignmentMapping ); - if (index != -1) - { - tmp.endCol = seqcanvas.getSequenceRenderer(). - getResidueBoxColour( sequence, index); - - if(showFeatures) - tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index); - - if(tmp.endCol==null) - tmp.endCol = Color.white; - } - } - } - } - - - Zsort zsort; - public void drawScene(Graphics g) - { - if (zbuffer) - { - if (zsort == null) - zsort = new Zsort(); - - zsort.Zsort(visiblebonds); - } - - Bond tmpBond = null; - for (int i = 0; i < visiblebonds.size(); i++) - { - tmpBond = (Bond) visiblebonds.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); - } - - if (highlightBond1 != null && highlightBond1 == tmpBond) - { - g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter()); - drawLine(g, xmid, ymid, xend, yend); - } - - if (highlightBond2 != null && highlightBond2 == tmpBond) - { - g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter()); - drawLine(g, xstart, ystart, xmid, ymid); - } - - } - - - } - - 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 keyPressed(KeyEvent evt) - { - 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(); - } - } - - public void mousePressed(MouseEvent e) - { - pdbAction = true; - Atom fatom = findAtom(e.getX(), e.getY()); - if(fatom!=null) - { - fatom.isSelected = !fatom.isSelected; - - redrawneeded = true; - repaint(); - if (foundchain != -1) - { - PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain); - if (chain == mainchain) - { - if (fatom.alignmentMapping != -1) - { - if (highlightRes == null) - highlightRes = new Vector(); - - if (highlightRes.contains(fatom.alignmentMapping+"")) - highlightRes.remove(fatom.alignmentMapping + ""); - else - highlightRes.add(fatom.alignmentMapping + ""); - } - } - } - - } - mx = e.getX(); - my = e.getY(); - omx = mx; - omy = my; - dragging = false; - } - - public void mouseMoved(MouseEvent e) - { - pdbAction = true; - if(highlightBond1!=null) - { - highlightBond1.at2.isSelected = false; - highlightBond2.at1.isSelected = false; - highlightBond1 = null; - highlightBond2 = null; - } - - Atom fatom = findAtom(e.getX(), e.getY()); - - PDBChain chain = null; - if(foundchain!=-1) - { - chain = (PDBChain) pdb.chains.elementAt(foundchain); - if(chain == mainchain) - { - highlightSeqcanvas( fatom.alignmentMapping ); - } - } - - if (fatom != null) - { - this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName); - } else - { - highlightSeqcanvas( -1); - this.setToolTipText(null); - } - } - - - void highlightSeqcanvas(int pos) - { - SearchResults searchResults = new SearchResults(); - if(highlightRes!=null) - { - for (int i = 0; i < highlightRes.size(); i++) - { - int a = Integer.parseInt(highlightRes.elementAt( - i).toString())+1; - - searchResults.addResult(sequence, a, a); - } - } - - if(pos!=-1) - { - searchResults.addResult(sequence, pos+1, pos+1); - } - - seqcanvas.highlightSearchResults(searchResults); - } - - - 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; - - dragging = true; - - redrawneeded = true; - - repaint(); - } - - public void mouseReleased(MouseEvent evt) - { - dragging = false; - return; - } - - void drawLabels(Graphics g) { - - 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(g, tmpBond, 1); - } - - if (tmpBond.at2.isSelected) - { - - labelAtom(g, tmpBond, 2); - } - } - } - } - } - - public void labelAtom(Graphics g, Bond b, int n) { - g.setFont(font); - g.setColor(Color.red); - 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.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.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); - } - } - - int foundchain = -1; - public Atom findAtom(int x, int y) { - Atom fatom = null; - - foundchain = -1; - - for (int ii = 0; ii < pdb.chains.size(); ii++) - { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - int truex; - Bond tmpBond=null; - - if (chain.isVisible) - { - Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; - - for (int i = 0; i < bonds.size(); i++) - { - tmpBond = (Bond) bonds.elementAt(i); - - 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) - { - fatom = tmpBond.at1; - foundchain = ii; - break; - } - } - } - - // Still here? Maybe its the last bond - - truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) + - (getWidth() / 2)); - - if (Math.abs(truex - x) <= 2) - { - int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) + - (getHeight() / 2)); - - if (Math.abs(truey - y) <= 2) - { - fatom = tmpBond.at2; - foundchain = ii; - break; - } - } - - } - - if (fatom != null) //)&& chain.ds != null) - { - chain = (PDBChain) pdb.chains.elementAt(foundchain); - } - } - - return fatom; - } - - Bond highlightBond1, highlightBond2; - public void highlightRes(int ii) - { - if( !seqColoursReady ) - return; - - if (highlightRes != null - && highlightRes.contains((ii-1) + "")) - { - return; - } - - int index = -1; - Bond tmpBond; - for(index=0; index 0) - { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); - highlightBond1.at2.isSelected = true; - } - - if (index != mainchain.bonds.size()) - { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); - highlightBond2.at1.isSelected = true; - } - - break; - } - } - - redrawneeded = true; - repaint(); - } - - public void setAllchainsVisible(boolean b) - { - for (int ii = 0; ii < pdb.chains.size(); ii++) - { - PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); - chain.isVisible = b; - } - mainchain.isVisible = true; - findCentre(); - setupBonds(); - } -} +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2006 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 PDBCanvas extends JPanel implements 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 bysequence = true; + 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); + jalview.gui.SeqCanvas seqcanvas; + public Sequence sequence; + final StringBuffer mappingDetails = new StringBuffer(); + PDBChain mainchain; + Vector highlightRes; + boolean pdbAction = false; + boolean seqColoursReady = false; + jalview.gui.FeatureRenderer fr; + Color backgroundColour = Color.black; + + public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq) + { + this.seqcanvas = seqcanvas; + this.sequence = seq; + seqcanvas.setPDBCanvas(this); + } + + public void setPDBFile(PDBfile pdb) + { + int max = -10; + int maxchain = -1; + int pdbstart = 0; + int pdbend = 0; + int seqstart = 0; + int seqend = 0; + AlignSeq maxAlignseq = null; + + for (int i = 0; i < pdb.chains.size(); i++) + { + + mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequenceAsString()); + mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n"); + + // Now lets compare the sequences to get + // the start and end points. + // Align the sequence to the pdb + AlignSeq as = new AlignSeq(sequence, + ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); + as.calcScoreMatrix(); + as.traceAlignment(); + PrintStream ps = new PrintStream(System.out) + { + public void print(String x) { + mappingDetails.append(x); + } + public void println() + { + mappingDetails.append("\n"); + } + }; + + as.printAlignment(ps); + + + + if (as.maxscore > max) + { + max = as.maxscore; + maxchain = i; + pdbstart = as.seq2start; + pdbend = as.seq2end; + seqstart = as.seq1start + sequence.getStart()-1; + seqend = as.seq1end + sequence.getEnd()-1; + maxAlignseq = as; + } + + mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); + mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend); + } + + mainchain = (PDBChain) pdb.chains.elementAt(maxchain); + + mainchain.pdbstart = pdbstart; + mainchain.pdbend = pdbend; + mainchain.seqstart = seqstart; + mainchain.seqend = seqend; + mainchain.isVisible = true; + mainchain.makeExactMapping(maxAlignseq, 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); + + addMouseWheelListener(new MouseWheelListener() + { + public void mouseWheelMoved(MouseWheelEvent e) + { + if (e.getWheelRotation() > 0) + { + scale = (float) (scale * 1.1); + redrawneeded = true; + repaint(); + } + + else + { + scale = (float) (scale * 0.9); + redrawneeded = true; + repaint(); + } + } + }); + + + findCentre(); + findWidth(); + + setupBonds(); + + scale = findScale(); + + ToolTipManager.sharedInstance().registerComponent(this); + ToolTipManager.sharedInstance().setInitialDelay(0); + ToolTipManager.sharedInstance().setDismissDelay(10000); + } + + + Vector visiblebonds; + void setupBonds() + { + seqColoursReady = false; + // Sort the bonds by z coord + visiblebonds = 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++) + { + visiblebonds.addElement(tmp.elementAt(i)); + } + } + } + + updateSeqColours(); + seqColoursReady = true; + redrawneeded = true; + repaint(); + } + + + 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 paintComponent(Graphics g) + { + super.paintComponent(g); + + if(!seqColoursReady) + { + g.setColor(Color.black); + g.setFont(new Font("Verdana", Font.BOLD, 14)); + g.drawString("Retrieving PDB data....", 20, getHeight()/2); + return; + } + + + //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(); + Graphics2D ig2 = (Graphics2D) ig; + + ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + + redrawneeded = true; + } + + + if (redrawneeded) + { + drawAll(ig, prefsize.width, prefsize.height); + redrawneeded = false; + } + + g.drawImage(img, 0, 0, this); + + pdbAction = false; + } + + public void drawAll(Graphics g, int width, int height) + { + g.setColor(backgroundColour); + g.fillRect(0, 0, width, height); + drawScene(g); + drawLabels(g); + } + + + public void updateSeqColours() + { + if(pdbAction) + { + return; + } + + // System.out.println("update seq colours"); + if(bysequence && pdb!=null) + { + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + colourBySequence( (PDBChain) pdb.chains.elementAt(ii)); + } + } + + redrawneeded=true; + repaint(); + } + + int findTrueIndex(int pos) + { + // returns the alignment position for a residue + int j = sequence.getStart(); + int i = 0; + + while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1)) + { + if (!jalview.util.Comparison.isGap(sequence.getCharAt(i))) + { + j++; + } + + i++; + } + + if(i>1) + i--; + + if ( (j == sequence.getEnd()) && (j < pos)) + { + return sequence.getEnd() + 1; + } + else + { + return i; + } + } + + // This method has been taken out of PDBChain to allow + // Applet and Application specific sequence renderers to be used + void colourBySequence(PDBChain chain) + { + // System.out.println("colour by seq"); + boolean showFeatures = false; + if(seqcanvas.getViewport().getShowSequenceFeatures()) + { + showFeatures = true; + if (fr == null) + fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport()); + + fr.transferSettings( seqcanvas.getFeatureRenderer() ); + } + + Bond tmp; + for (int i = 0; i < chain.bonds.size(); i++) + { + tmp = (Bond) chain.bonds.elementAt(i); + + if(chain!=mainchain) + continue; + + if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && + (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1))) + { + int index = findTrueIndex(tmp.at1.alignmentMapping); + //sequence.findIndex(tmp.at1.alignmentMapping); + if (index != -1) + { + tmp.startCol = seqcanvas.getSequenceRenderer(). + getResidueBoxColour( sequence, index); + + if(showFeatures) + tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index); + + if(tmp.startCol==null) + tmp.startCol = Color.white; + } + } + + if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && + (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1))) + { + + int index = findTrueIndex(tmp.at2.alignmentMapping); + //sequence.findIndex( tmp.at2.alignmentMapping ); + if (index != -1) + { + tmp.endCol = seqcanvas.getSequenceRenderer(). + getResidueBoxColour( sequence, index); + + if(showFeatures) + tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index); + + if(tmp.endCol==null) + tmp.endCol = Color.white; + } + } + } + } + + + Zsort zsort; + public void drawScene(Graphics g) + { + if (zbuffer) + { + if (zsort == null) + zsort = new Zsort(); + + zsort.Zsort(visiblebonds); + } + + Bond tmpBond = null; + for (int i = 0; i < visiblebonds.size(); i++) + { + tmpBond = (Bond) visiblebonds.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); + } + + if (highlightBond1 != null && highlightBond1 == tmpBond) + { + g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter()); + drawLine(g, xmid, ymid, xend, yend); + } + + if (highlightBond2 != null && highlightBond2 == tmpBond) + { + g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter()); + drawLine(g, xstart, ystart, xmid, ymid); + } + + } + + + } + + 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 keyPressed(KeyEvent evt) + { + 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(); + } + } + + public void mousePressed(MouseEvent e) + { + pdbAction = true; + Atom fatom = findAtom(e.getX(), e.getY()); + if(fatom!=null) + { + fatom.isSelected = !fatom.isSelected; + + redrawneeded = true; + repaint(); + if (foundchain != -1) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain); + if (chain == mainchain) + { + if (fatom.alignmentMapping != -1) + { + if (highlightRes == null) + highlightRes = new Vector(); + + if (highlightRes.contains(fatom.alignmentMapping+"")) + highlightRes.remove(fatom.alignmentMapping + ""); + else + highlightRes.add(fatom.alignmentMapping + ""); + } + } + } + + } + mx = e.getX(); + my = e.getY(); + omx = mx; + omy = my; + dragging = false; + } + + public void mouseMoved(MouseEvent e) + { + pdbAction = true; + if(highlightBond1!=null) + { + highlightBond1.at2.isSelected = false; + highlightBond2.at1.isSelected = false; + highlightBond1 = null; + highlightBond2 = null; + } + + Atom fatom = findAtom(e.getX(), e.getY()); + + PDBChain chain = null; + if(foundchain!=-1) + { + chain = (PDBChain) pdb.chains.elementAt(foundchain); + if(chain == mainchain) + { + highlightSeqcanvas( fatom.alignmentMapping ); + } + } + + if (fatom != null) + { + this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName); + } else + { + highlightSeqcanvas( -1); + this.setToolTipText(null); + } + } + + + void highlightSeqcanvas(int pos) + { + SearchResults searchResults = new SearchResults(); + if(highlightRes!=null) + { + for (int i = 0; i < highlightRes.size(); i++) + { + int a = Integer.parseInt(highlightRes.elementAt( + i).toString())+1; + + searchResults.addResult(sequence, a, a); + } + } + + if(pos!=-1) + { + searchResults.addResult(sequence, pos+1, pos+1); + } + + seqcanvas.highlightSearchResults(searchResults); + } + + + 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; + + dragging = true; + + redrawneeded = true; + + repaint(); + } + + public void mouseReleased(MouseEvent evt) + { + dragging = false; + return; + } + + void drawLabels(Graphics g) { + + 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(g, tmpBond, 1); + } + + if (tmpBond.at2.isSelected) + { + + labelAtom(g, tmpBond, 2); + } + } + } + } + } + + public void labelAtom(Graphics g, Bond b, int n) { + g.setFont(font); + g.setColor(Color.red); + 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.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.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); + } + } + + int foundchain = -1; + public Atom findAtom(int x, int y) { + Atom fatom = null; + + foundchain = -1; + + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); + int truex; + Bond tmpBond=null; + + if (chain.isVisible) + { + Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; + + for (int i = 0; i < bonds.size(); i++) + { + tmpBond = (Bond) bonds.elementAt(i); + + 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) + { + fatom = tmpBond.at1; + foundchain = ii; + break; + } + } + } + + // Still here? Maybe its the last bond + + truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) + + (getWidth() / 2)); + + if (Math.abs(truex - x) <= 2) + { + int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) + + (getHeight() / 2)); + + if (Math.abs(truey - y) <= 2) + { + fatom = tmpBond.at2; + foundchain = ii; + break; + } + } + + } + + if (fatom != null) //)&& chain.ds != null) + { + chain = (PDBChain) pdb.chains.elementAt(foundchain); + } + } + + return fatom; + } + + Bond highlightBond1, highlightBond2; + public void highlightRes(int ii) + { + if( !seqColoursReady ) + return; + + if (highlightRes != null + && highlightRes.contains((ii-1) + "")) + { + return; + } + + int index = -1; + Bond tmpBond; + for(index=0; index 0) + { + highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1.at2.isSelected = true; + } + + if (index != mainchain.bonds.size()) + { + highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2.at1.isSelected = true; + } + + break; + } + } + + redrawneeded = true; + repaint(); + } + + public void setAllchainsVisible(boolean b) + { + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(ii); + chain.isVisible = b; + } + mainchain.isVisible = true; + findCentre(); + setupBonds(); + } +} diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index bfd4f45..479b37f 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -996,7 +996,7 @@ public void itemStateChanged(ItemEvent evt) copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes + "\t" + - seq.getSequence(sg.getStartRes(), + seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1) + "\n"); } diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index ae6ef37..e8cbd2e 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -176,7 +176,7 @@ public class AnnotationLabels jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd() + "\t" + - sq.getSequence() + "\n"); + sq.getSequenceAsString() + "\n"); if (av.hasHiddenColumns) { jalview.appletgui.AlignFrame.copiedHiddenColumns=new Vector(); diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java index 07abd53..760123b 100644 --- a/src/jalview/datamodel/SeqCigar.java +++ b/src/jalview/datamodel/SeqCigar.java @@ -479,8 +479,8 @@ public class SeqCigar if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence())) { System.err.println("Couldn't reconstruct sequence.\n" + - gen_sgapped_s.getSequence() + "\n" + - s_gapped.getSequence()); + gen_sgapped_s.getSequenceAsString() + "\n" + + s_gapped.getSequenceAsString()); return false; } return true; @@ -552,7 +552,7 @@ public class SeqCigar + "\nCigar String:" + sub_se_gp.getCigarstring() + "\n" ); SequenceI ssgp = sub_se_gp.getSeq('-'); - System.out.println("\t " + ssgp.getSequence()); + System.out.println("\t " + ssgp.getSequenceAsString()); for (int r = 0; r < 10; r++) { sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48); @@ -594,7 +594,7 @@ public class SeqCigar System.out.println("" + al.getSequenceAt(i).getName() + "\t" + al.getSequenceAt(i).getStart() + "\t" + al.getSequenceAt(i).getEnd() + "\t" + - al.getSequenceAt(i).getSequence()); + al.getSequenceAt(i).getSequenceAsString()); } } // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh")) -- 1.7.10.2