X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=181d85f259e5cb57aafb926521a6050aa2b8be96;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=dd33b0c76fa6de11a693e6f0b6e19e593129da2c;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java old mode 100755 new mode 100644 index dd33b0c..181d85f --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . */ package MCview; @@ -28,96 +27,160 @@ import java.awt.event.*; import jalview.analysis.*; import jalview.datamodel.*; -public class AppletPDBCanvas - extends Panel implements MouseListener, MouseMotionListener +import jalview.appletgui.*; +import jalview.structure.*; + +public class AppletPDBCanvas extends Panel implements MouseListener, + MouseMotionListener, StructureListener { 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; + + PDBEntry pdbentry; + 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; + + public SequenceI[] 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) + FeatureRenderer fr; + + AlignmentPanel ap; + + StructureSelectionManager ssm; + + public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq, + String[] chains, AlignmentPanel ap, String protocol) + { - this.seqcanvas = seqcanvas; + this.ap = ap; + this.pdbentry = pdbentry; this.sequence = seq; - seqcanvas.setPDBCanvas(this); - addKeyListener(new KeyAdapter() + ssm = StructureSelectionManager.getStructureSelectionManager(ap.av.applet); + + try { + pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol); - public void keyPressed(KeyEvent evt) - { - doKeyPressed(evt); - } - }); - } + if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + pdbentry.setFile("INLINE" + pdb.id); + + } catch (Exception ex) + { + ex.printStackTrace(); + return; + } + + pdbentry.setId(pdb.id); + + ssm.addStructureViewerListener(this); + + colourBySequence(); - 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; ; + + // JUST DEAL WITH ONE SEQUENCE FOR NOW + SequenceI sequence = seq[0]; 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"); + 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 + // TODO: DNa/Pep switch AlignSeq as = new AlignSeq(sequence, - ( (PDBChain) pdb.chains.elementAt(i)).sequence, - "pep"); + ((PDBChain) pdb.chains.elementAt(i)).sequence, + ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA + : AlignSeq.PEP); as.calcScoreMatrix(); as.traceAlignment(); PrintStream ps = new PrintStream(System.out) @@ -144,7 +207,6 @@ public class AppletPDBCanvas pdbend = as.seq2end; seqstart = as.seq1start + sequence.getStart() - 1; seqend = as.seq1end + sequence.getEnd() - 1; - maxAlignseq = as; } mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); @@ -158,12 +220,12 @@ public class AppletPDBCanvas mainchain.seqstart = seqstart; mainchain.seqend = seqend; mainchain.isVisible = true; - mainchain.makeExactMapping(maxAlignseq, sequence); - mainchain.transferRESNUMFeatures(sequence, null); + // mainchain.makeExactMapping(maxAlignseq, sequence); + // mainchain.transferRESNUMFeatures(sequence, null); this.pdb = pdb; this.prefsize = new Dimension(getSize().width, getSize().height); - //Initialize the matrices to identity + // Initialize the matrices to identity for (int i = 0; i < 3; i++) { for (int j = 0; j < 3; j++) @@ -184,6 +246,14 @@ public class AppletPDBCanvas addMouseMotionListener(this); addMouseListener(this); + addKeyListener(new KeyAdapter() + { + public void keyPressed(KeyEvent evt) + { + doKeyPressed(evt); + } + }); + findCentre(); findWidth(); @@ -193,6 +263,7 @@ public class AppletPDBCanvas } Vector visiblebonds; + void setupBonds() { seqColoursReady = false; @@ -201,9 +272,9 @@ public class AppletPDBCanvas for (int ii = 0; ii < pdb.chains.size(); ii++) { - if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible) + if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) { - Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds; + Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds; for (int i = 0; i < tmp.size(); i++) { @@ -211,8 +282,8 @@ public class AppletPDBCanvas } } } - updateSeqColours(); seqColoursReady = true; + colourBySequence(); redrawneeded = true; repaint(); } @@ -222,9 +293,9 @@ public class AppletPDBCanvas float[] max = new float[3]; float[] min = new float[3]; - max[0] = (float) - 1e30; - max[1] = (float) - 1e30; - max[2] = (float) - 1e30; + max[0] = (float) -1e30; + max[1] = (float) -1e30; + max[2] = (float) -1e30; min[0] = (float) 1e30; min[1] = (float) 1e30; @@ -232,9 +303,9 @@ public class AppletPDBCanvas for (int ii = 0; ii < pdb.chains.size(); ii++) { - if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible) + if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) { - Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds; + Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; for (int i = 0; i < bonds.size(); i++) { @@ -359,25 +430,25 @@ public class AppletPDBCanvas int bsize = 0; - //Find centre coordinate + // Find centre coordinate for (int ii = 0; ii < pdb.chains.size(); ii++) { - if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible) + if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) { - Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds; + 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]; + 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]; + 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]; + ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] + + ((Bond) bonds.elementAt(i)).end[2]; } } } @@ -408,10 +479,10 @@ public class AppletPDBCanvas return; } - //Only create the image at the beginning - - //this saves much memory usage - if ( (img == null) || (prefsize.width != getSize().width) || - (prefsize.height != getSize().height)) + // Only create the image at the beginning - + // this saves much memory usage + if ((img == null) || (prefsize.width != getSize().width) + || (prefsize.height != getSize().height)) { try @@ -424,8 +495,7 @@ public class AppletPDBCanvas ig = img.getGraphics(); redrawneeded = true; - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -455,7 +525,7 @@ public class AppletPDBCanvas drawLabels(ig); } - void setColours(jalview.schemes.ColourSchemeI cs) + public void setColours(jalview.schemes.ColourSchemeI cs) { bysequence = false; pdb.setColours(cs); @@ -463,117 +533,83 @@ public class AppletPDBCanvas 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) + void colourBySequence() { - boolean showFeatures = false; + SequenceRenderer sr = new SequenceRenderer(ap.av); - if (seqcanvas.getViewport().getShowSequenceFeatures()) + StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); + + boolean showFeatures = false; + if (ap.av.getShowSequenceFeatures()) { if (fr == null) { - fr = new jalview.appletgui.FeatureRenderer(seqcanvas.getViewport()); + fr = new jalview.appletgui.FeatureRenderer(ap.av); } - fr.transferSettings(seqcanvas.getFeatureRenderer()); + + fr.transferSettings(ap.getFeatureRenderer()); + showFeatures = true; } - for (int i = 0; i < chain.bonds.size(); i++) + PDBChain chain; + if (bysequence && pdb != null) { - 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))) + for (int ii = 0; ii < pdb.chains.size(); ii++) { + chain = (PDBChain) pdb.chains.elementAt(ii); - int index = findTrueIndex(tmp.at1.alignmentMapping); - //sequence.findIndex(tmp.at1.alignmentMapping); - if (index != -1) + for (int i = 0; i < chain.bonds.size(); i++) { - tmp.startCol = seqcanvas.getSequenceRenderer(). - getResidueBoxColour(sequence, index); - - if (showFeatures) + Bond tmp = (Bond) chain.bonds.elementAt(i); + tmp.startCol = Color.lightGray; + tmp.endCol = Color.lightGray; + if (chain != mainchain) { - tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index); + continue; } - } - } - 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); + for (int s = 0; s < sequence.length; s++) + { + for (int m = 0; m < mapping.length; m++) + { + if (mapping[m].getSequence() == sequence[s]) + { + int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1; + if (pos > 0) + { + pos = sequence[s].findIndex(pos); + tmp.startCol = sr.getResidueBoxColour(sequence[s], pos); + if (showFeatures) + { + tmp.startCol = fr.findFeatureColour(tmp.startCol, + sequence[s], pos); + } + } + pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1; + if (pos > 0) + { + pos = sequence[s].findIndex(pos); + tmp.endCol = sr.getResidueBoxColour(sequence[s], pos); + if (showFeatures) + { + tmp.endCol = fr.findFeatureColour(tmp.endCol, + sequence[s], pos); + } + } + + } + } + } } } } } Zsort zsort; + public void drawScene(Graphics g) { if (zbuffer) @@ -591,15 +627,11 @@ public class AppletPDBCanvas { 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)); + xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2)); + ystart = (int) (((centre[1] - tmpBond.start[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)); + xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2)); + yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2)); xmid = (xend + xstart) / 2; ymid = (yend + ystart) / 2; @@ -681,7 +713,7 @@ public class AppletPDBCanvas { if (!wire) { - if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) + 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); @@ -788,7 +820,7 @@ public class AppletPDBCanvas chain = (PDBChain) pdb.chains.elementAt(foundchain); if (chain == mainchain) { - highlightSeqcanvas(fatom.alignmentMapping); + mouseOverStructure(fatom.resNumber, chain.id); } } @@ -797,41 +829,20 @@ public class AppletPDBCanvas toolx = e.getX(); tooly = e.getY(); - appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName; + appletToolTip = chain.id + ":" + fatom.resNumber + " " + + fatom.resName; redrawneeded = true; repaint(); } else { - highlightSeqcanvas( -1); + mouseOverStructure(-1, chain != null ? chain.id : null); 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) { } @@ -854,33 +865,33 @@ public class AppletPDBCanvas MCMatrix objmat = new MCMatrix(3, 3); objmat.setIdentity(); - if ( (evt.getModifiers() & Event.META_MASK) != 0) + if ((evt.getModifiers() & Event.META_MASK) != 0) { - objmat.rotatez( (float) ( (mx - omx))); + objmat.rotatez((float) ((mx - omx))); } else { - objmat.rotatex( (float) ( (my - omy))); - objmat.rotatey( (float) ( (omx - mx))); + objmat.rotatex((float) ((omy - my))); + objmat.rotatey((float) ((omx - mx))); } - //Alter the bonds + // Alter the bonds for (int ii = 0; ii < pdb.chains.size(); ii++) { - Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds; + 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]); + // Translate the bond so the centre is 0,0,0 + tmpBond.translate(-centre[0], -centre[1], -centre[2]); - //Now apply the rotation matrix + // Now apply the rotation matrix tmpBond.start = objmat.vectorMultiply(tmpBond.start); tmpBond.end = objmat.vectorMultiply(tmpBond.end); - //Now translate back again + // Now translate back again tmpBond.translate(centre[0], centre[1], centre[2]); } } @@ -912,7 +923,7 @@ public class AppletPDBCanvas if (chain.isVisible) { - Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds; + Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds; for (int i = 0; i < bonds.size(); i++) { @@ -939,10 +950,8 @@ public class AppletPDBCanvas 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)); + int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2)); + int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2)); g.setColor(Color.red); g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart); @@ -950,10 +959,8 @@ public class AppletPDBCanvas 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)); + int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2)); + int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2)); g.setColor(Color.red); g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart); @@ -961,6 +968,7 @@ public class AppletPDBCanvas } int foundchain = -1; + public Atom findAtom(int x, int y) { Atom fatom = null; @@ -975,19 +983,17 @@ public class AppletPDBCanvas if (chain.isVisible) { - Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds; + 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)); + 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)); + int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2)); if (Math.abs(truey - y) <= 2) { @@ -1000,13 +1006,11 @@ public class AppletPDBCanvas // Still here? Maybe its the last bond - truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) + - (getSize().width / 2)); + 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)); + int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2)); if (Math.abs(truey - y) <= 2) { @@ -1018,7 +1022,7 @@ public class AppletPDBCanvas } - if (fatom != null) //)&& chain.ds != null) + if (fatom != null) // )&& chain.ds != null) { chain = (PDBChain) pdb.chains.elementAt(foundchain); } @@ -1039,8 +1043,7 @@ public class AppletPDBCanvas return; } - if (highlightRes != null - && highlightRes.contains( (ii - 1) + "")) + if (highlightRes != null && highlightRes.contains((ii - 1) + "")) { return; } @@ -1097,4 +1100,103 @@ public class AppletPDBCanvas setupBonds(); } + // //////////////////////////////// + // /StructureListener + public String[] getPdbFile() + { + return new String[] + { pdbentry.getFile() }; + } + + String lastMessage; + + public void mouseOverStructure(int pdbResNum, String chain) + { + if (lastMessage == null || !lastMessage.equals(pdbResNum + chain)) + ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile()); + + lastMessage = pdbResNum + chain; + } + + StringBuffer resetLastRes = new StringBuffer(); + + StringBuffer eval = new StringBuffer(); + + public void highlightAtom(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + if (!seqColoursReady) + { + return; + } + + if (highlightRes != null && highlightRes.contains((atomIndex - 1) + "")) + { + return; + } + + int index = -1; + Bond tmpBond; + for (index = 0; index < mainchain.bonds.size(); index++) + { + tmpBond = (Bond) mainchain.bonds.elementAt(index); + if (tmpBond.at1.atomIndex == atomIndex) + { + if (highlightBond1 != null) + { + highlightBond1.at2.isSelected = false; + } + + if (highlightBond2 != null) + { + highlightBond2.at1.isSelected = false; + } + + highlightBond1 = null; + highlightBond2 = null; + + if (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 Color getColour(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + return Color.white; + // if (!pdbfile.equals(pdbentry.getFile())) + // return null; + + // return new Color(viewer.getAtomArgb(atomIndex)); + } + + public void updateColours(Object source) + { + colourBySequence(); + redrawneeded = true; + repaint(); + } + + @Override + public void releaseReferences(Object svl) + { + // TODO Auto-generated method stub + + } + }