+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package MCview;
-
-import jalview.analysis.AlignSeq;
-import jalview.appletgui.AlignmentPanel;
-import jalview.appletgui.FeatureRenderer;
-import jalview.appletgui.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.InputEvent;import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Image;
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.Panel;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.io.PrintStream;
-import java.util.List;
-import java.util.Vector;
-
-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 StructureFile 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);
-
- public SequenceI[] sequence;
-
- final StringBuffer mappingDetails = new StringBuffer();
-
- String appletToolTip = null;
-
- int toolx, tooly;
-
- PDBChain mainchain;
-
- Vector<String> highlightRes;
-
- boolean pdbAction = false;
-
- Bond highlightBond1, highlightBond2;
-
- boolean errorLoading = false;
-
- boolean seqColoursReady = false;
-
- FeatureRenderer fr;
-
- AlignmentPanel ap;
-
- StructureSelectionManager ssm;
-
- public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, DataSourceType protocol)
-
- {
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
-
- ssm = StructureSelectionManager
- .getStructureSelectionManager(ap.av.applet);
-
- try
- {
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
-
- if (protocol == DataSourceType.PASTE)
- {
- pdbentry.setFile("INLINE" + pdb.getId());
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return;
- }
-
- pdbentry.setId(pdb.getId());
-
- ssm.addStructureViewerListener(this);
-
- colourBySequence();
-
- float max = -10;
- int maxchain = -1;
- int pdbstart = 0;
- int pdbend = 0;
- int seqstart = 0;
- int seqend = 0;
-
- // JUST DEAL WITH ONE SEQUENCE FOR NOW
- SequenceI sequence = seq[0];
-
- for (int i = 0; i < pdb.getChains().size(); i++)
- {
-
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence
- .getSequenceAsString());
- mappingDetails.append("\nNo of residues = "
- + pdb.getChains().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,
- pdb.getChains().elementAt(i).sequence,
- pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA
- : AlignSeq.PEP);
- as.calcScoreMatrix();
- as.traceAlignment();
- PrintStream ps = new PrintStream(System.out)
- {
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- @Override
- 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;
- }
-
- mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
- mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
- }
-
- mainchain = pdb.getChains().elementAt(maxchain);
-
- mainchain.pdbstart = pdbstart;
- mainchain.pdbend = pdbend;
- mainchain.seqstart = seqstart;
- mainchain.seqend = seqend;
- mainchain.isVisible = true;
- // mainchain.makeExactMapping(maxAlignseq, sequence);
- // mainchain.transferRESNUMFeatures(sequence, null);
- 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);
-
- addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent evt)
- {
- doKeyPressed(evt);
- }
- });
-
- findCentre();
- findWidth();
-
- setupBonds();
-
- scale = findScale();
- }
-
- Vector<Bond> visiblebonds;
-
- void setupBonds()
- {
- seqColoursReady = false;
- // Sort the bonds by z coord
- visiblebonds = new Vector<Bond>();
-
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- if (pdb.getChains().elementAt(ii).isVisible)
- {
- Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
-
- for (int i = 0; i < tmp.size(); i++)
- {
- visiblebonds.addElement(tmp.elementAt(i));
- }
- }
- }
- seqColoursReady = true;
- colourBySequence();
- 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.getChains().size(); ii++)
- {
- if (pdb.getChains().elementAt(ii).isVisible)
- {
- Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
-
- for (Bond tmp : bonds)
- {
- 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] = Math.abs(max[0] - min[0]);
- width[1] = Math.abs(max[1] - min[1]);
- width[2] = 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.getChains().size(); ii++)
- {
- if (pdb.getChains().elementAt(ii).isVisible)
- {
- Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
-
- bsize += bonds.size();
-
- for (Bond b : bonds)
- {
- xtot = xtot + b.start[0] + b.end[0];
- ytot = ytot + b.start[1] + b.end[1];
- ztot = ztot + b.start[2] + b.end[2];
- }
- }
- }
-
- centre[0] = xtot / (2 * (float) bsize);
- centre[1] = ytot / (2 * (float) bsize);
- centre[2] = ztot / (2 * (float) bsize);
- }
-
- @Override
- 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(MessageManager.getString("label.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(MessageManager.getString("label.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);
- }
-
- public void setColours(jalview.schemes.ColourSchemeI cs)
- {
- bysequence = false;
- pdb.setColours(cs);
- redrawneeded = true;
- repaint();
- }
-
- // This method has been taken out of PDBChain to allow
- // Applet and Application specific sequence renderers to be used
- void colourBySequence()
- {
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- boolean showFeatures = false;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = new jalview.appletgui.FeatureRenderer(ap.av);
- }
-
- fr.transferSettings(ap.getFeatureRenderer());
-
- showFeatures = true;
- }
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- PDBChain chain;
- if (bysequence && pdb != null)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- chain = pdb.getChains().elementAt(ii);
-
- for (int i = 0; i < chain.bonds.size(); i++)
- {
- Bond tmp = chain.bonds.elementAt(i);
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- if (chain != mainchain)
- {
- continue;
- }
-
- 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.getResidueColour(sequence[s], pos,
- finder);
- }
- pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
- if (pos > 0)
- {
- pos = sequence[s].findIndex(pos);
- tmp.endCol = sr.getResidueColour(sequence[s], pos,
- finder);
- }
- }
- }
- }
- }
- }
- }
- }
-
- Zsort zsort;
-
- public void drawScene(Graphics g)
- {
- if (zbuffer)
- {
- if (zsort == null)
- {
- zsort = new Zsort();
- }
-
- zsort.sort(visiblebonds);
- }
-
- Bond tmpBond = null;
- for (int i = 0; i < visiblebonds.size(); i++)
- {
- tmpBond = visiblebonds.elementAt(i);
-
- 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) (((centre[1] - tmpBond.end[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();
- }
- }
-
- @Override
- 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 = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- if (fatom.alignmentMapping != -1)
- {
- if (highlightRes == null)
- {
- highlightRes = new Vector<String>();
- }
-
- final String atomString = Integer
- .toString(fatom.alignmentMapping);
- if (highlightRes.contains(atomString))
- {
- highlightRes.removeElement(atomString);
- }
- else
- {
- highlightRes.addElement(atomString);
- }
- }
- }
- }
-
- }
- mx = e.getX();
- my = e.getY();
- omx = mx;
- omy = my;
- dragging = false;
- }
-
- @Override
- 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 = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- mouseOverStructure(fatom.resNumber, chain.id);
- }
- }
-
- if (fatom != null)
- {
- toolx = e.getX();
- tooly = e.getY();
-
- appletToolTip = chain.id + ":" + fatom.resNumber + " "
- + fatom.resName;
- redrawneeded = true;
- repaint();
- }
- else
- {
- mouseOverStructure(-1, chain != null ? chain.id : null);
- appletToolTip = null;
- redrawneeded = true;
- repaint();
- }
- }
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- @Override
- 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.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
- {
- objmat.rotatez(((mx - omx)));
- }
- else
- {
- objmat.rotatex(((omy - my)));
- objmat.rotatey(((omx - mx)));
- }
-
- // Alter the bonds
- for (PDBChain chain : pdb.getChains())
- {
- for (Bond tmpBond : chain.bonds)
- {
- // 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();
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- dragging = false;
- return;
- }
-
- void drawLabels(Graphics g)
- {
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond tmpBond : chain.bonds)
- {
- 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) (((centre[1] - b.start[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) (((centre[1] - b.end[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.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- int truex;
- Bond tmpBond = null;
-
- if (chain.isVisible)
- {
- Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
- {
- tmpBond = bonds.elementAt(i);
-
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getSize().width / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) (((centre[1] - tmpBond.start[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 = pdb.getChains().elementAt(foundchain);
- }
- }
-
- return fatom;
- }
-
- @Override
- 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 < mainchain.bonds.size(); index++)
- {
- tmpBond = mainchain.bonds.elementAt(index);
- if (tmpBond.at1.alignmentMapping == ii - 1)
- {
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- }
-
- if (highlightBond2 != null)
- {
- highlightBond2.at1.isSelected = false;
- }
-
- highlightBond1 = null;
- highlightBond2 = null;
-
- if (index > 0)
- {
- highlightBond1 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
-
- redrawneeded = true;
- repaint();
- }
-
- public void setAllchainsVisible(boolean b)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- chain.isVisible = b;
- }
- mainchain.isVisible = true;
- findCentre();
- setupBonds();
- }
-
- // ////////////////////////////////
- // /StructureListener
- @Override
- public String[] getStructureFiles()
- {
- 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();
-
- /**
- * Highlight the specified atoms in the structure.
- *
- * @param atoms
- */
- @Override
- public void highlightAtoms(List<AtomSpec> atoms)
- {
- if (!seqColoursReady)
- {
- return;
- }
- for (AtomSpec atom : atoms)
- {
- int atomIndex = atom.getAtomIndex();
-
- if (highlightRes != null
- && highlightRes.contains((atomIndex - 1) + ""))
- {
- continue;
- }
-
- highlightAtom(atomIndex);
- }
-
- redrawneeded = true;
- repaint();
- }
-
- /**
- * @param atomIndex
- */
- protected void highlightAtom(int atomIndex)
- {
- int index = -1;
- Bond tmpBond;
- for (index = 0; index < mainchain.bonds.size(); index++)
- {
- tmpBond = 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 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
- }
-
- 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));
- }
-
- @Override
- public void updateColours(Object source)
- {
- colourBySequence();
- redrawneeded = true;
- repaint();
- }
-
- @Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean isListeningFor(SequenceI seq)
- {
- if (sequence != null)
- {
- for (SequenceI s : sequence)
- {
- if (s == seq)
- {
- return true;
- }
- }
- }
- return false;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package MCview;
-
-import jalview.schemes.ResidueProperties;
-
-import java.awt.Color;
-
-public class Atom
-{
- public float x;
-
- public float y;
-
- public float z;
-
- public int number;
-
- public String name;
-
- public String resName;
-
- public int resNumber;
-
- public char insCode = ' ';
-
- public String resNumIns = null;
-
- public int type;
-
- Color color = Color.lightGray;
-
- public String chain;
-
- /**
- * this is a temporary value - designed to store the position in sequence that
- * this atom corresponds to after aligning the chain to a SequenceI object. Do
- * not rely on its value being correct when visualizing sequence colourings on
- * the structure - use the StructureSelectionManager's mapping instead.
- */
- public int alignmentMapping = -1;
-
- public int atomIndex;
-
- public float occupancy = 0;
-
- public float tfactor = 0;
-
- // need these if we ever want to export Atom data
- // public boolean tfacset=true,occset=true;
- public boolean isSelected = false;
-
- public Atom(String str)
- {
- atomIndex = Integer.parseInt(str.substring(6, 11).trim());
-
- name = str.substring(12, 15).trim();
-
- resName = str.substring(17, 20);
- // JAL-1828 treat MSE Selenomethionine as MET (etc)
- resName = ResidueProperties.getCanonicalAminoAcid(resName);
-
- chain = str.substring(21, 22);
-
- resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27).trim();
- insCode = str.substring(26, 27).charAt(0);
- this.x = (Float.valueOf(str.substring(30, 38).trim()).floatValue());
- this.y = (Float.valueOf(str.substring(38, 46).trim()).floatValue());
- this.z = (Float.valueOf(str.substring(47, 55).trim()).floatValue());
- // optional entries - see JAL-730
- String tm = str.substring(54, 60).trim();
- if (tm.length() > 0)
- {
- occupancy = (Float.valueOf(tm)).floatValue();
- }
- else
- {
- occupancy = 1f; // default occupancy
- // see note above: occset=false;
- }
- tm = str.substring(60, 66).trim();
- if (tm.length() > 0)
- {
- tfactor = (Float.valueOf(tm).floatValue());
- }
- else
- {
- tfactor = 1f;
- // see note above: tfacset=false;
- }
- }
-
- @Override
- public boolean equals(Object that)
- {
- if (this == that || that == null)
- {
- return true;
- }
- if (that instanceof Atom)
- {
- Atom other = (Atom) that;
- return other.resName.equals(this.resName)
- && other.resNumber == this.resNumber
- && other.resNumIns.equals(this.resNumIns)
- && other.chain.equals(this.chain);
- }
- return false;
- }
-
- public Atom(float x, float y, float z)
- {
- this.x = x;
- this.y = y;
- this.z = z;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package MCview;
-
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.InputEvent;import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.Image;
-import java.awt.RenderingHints;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.io.PrintStream;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JPanel;
-import javax.swing.ToolTipManager;
-
-public class PDBCanvas extends JPanel
- implements MouseListener, MouseMotionListener, StructureListener
-{
- boolean redrawneeded = true;
-
- int omx = 0;
-
- int mx = 0;
-
- int omy = 0;
-
- int my = 0;
-
- public StructureFile 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.gui.SeqCanvas seqcanvas;
-
- public SequenceI[] sequence;
-
- final StringBuffer mappingDetails = new StringBuffer();
-
- PDBChain mainchain;
-
- Vector<String> highlightRes;
-
- boolean pdbAction = false;
-
- boolean seqColoursReady = false;
-
- jalview.renderer.seqfeatures.FeatureRenderer fr;
-
- Color backgroundColour = Color.black;
-
- AlignmentPanel ap;
-
- StructureSelectionManager ssm;
-
- String errorMessage;
-
- void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, DataSourceType protocol)
- {
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
-
- ssm = ap.av.getStructureSelectionManager();
-
- try
- {
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
- ap.alignFrame);
-
- if (protocol.equals(jalview.io.DataSourceType.PASTE))
- {
- pdbentry.setFile("INLINE" + pdb.getId());
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return;
- }
-
- if (pdb == null)
- {
- errorMessage = "Error loading file: " + pdbentry.getId();
- return;
- }
- pdbentry.setId(pdb.getId());
-
- ssm.addStructureViewerListener(this);
-
- colourBySequence();
-
- float max = -10;
- int maxchain = -1;
- int pdbstart = 0;
- int pdbend = 0;
- int seqstart = 0;
- int seqend = 0;
-
- // JUST DEAL WITH ONE SEQUENCE FOR NOW
- SequenceI sequence = seq[0];
-
- for (int i = 0; i < pdb.getChains().size(); i++)
- {
-
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence
- .getSequenceAsString());
- mappingDetails.append("\nNo of residues = "
- + pdb.getChains().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,
- pdb.getChains().elementAt(i).sequence, "pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- PrintStream ps = new PrintStream(System.out)
- {
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- @Override
- 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;
- }
-
- mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
- mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
- }
-
- mainchain = pdb.getChains().elementAt(maxchain);
-
- mainchain.pdbstart = pdbstart;
- mainchain.pdbend = pdbend;
- mainchain.seqstart = seqstart;
- mainchain.seqend = seqend;
- mainchain.isVisible = true;
-
- this.pdb = pdb;
- this.prefsize = new Dimension(getSize().width, getSize().height);
-
- addMouseMotionListener(this);
- addMouseListener(this);
-
- addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent evt)
- {
- keyPressed(evt);
- }
- });
-
- findCentre();
- findWidth();
-
- setupBonds();
-
- scale = findScale();
-
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- }
-
- Vector<Bond> visiblebonds;
-
- void setupBonds()
- {
- seqColoursReady = false;
- // Sort the bonds by z coord
- visiblebonds = new Vector<Bond>();
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond bond : chain.bonds)
- {
- visiblebonds.addElement(bond);
- }
- }
- }
-
- 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 (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond tmp : chain.bonds)
- {
- 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] = Math.abs(max[0] - min[0]);
- width[1] = Math.abs(max[1] - min[1]);
- width[2] = 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 (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- bsize += chain.bonds.size();
-
- for (Bond bond : chain.bonds)
- {
- xtot = xtot + bond.start[0] + bond.end[0];
- ytot = ytot + bond.start[1] + bond.end[1];
- ztot = ztot + bond.start[2] + bond.end[2];
- }
- }
- }
-
- centre[0] = xtot / (2 * (float) bsize);
- centre[1] = ytot / (2 * (float) bsize);
- centre[2] = ztot / (2 * (float) bsize);
- }
-
- @Override
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
-
- if (!seqColoursReady || errorMessage != null)
- {
- g.setColor(Color.black);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(errorMessage == null ? "Retrieving PDB data...."
- : errorMessage, 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;
- }
-
- colourBySequence();
-
- redrawneeded = true;
- repaint();
- }
-
- // This method has been taken out of PDBChain to allow
- // Applet and Application specific sequence renderers to be used
- void colourBySequence()
- {
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- boolean showFeatures = false;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = new FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.alignFrame.getFeatureRenderer());
-
- showFeatures = true;
- }
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- PDBChain chain;
- if (bysequence && pdb != null)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- chain = pdb.getChains().elementAt(ii);
-
- for (int i = 0; i < chain.bonds.size(); i++)
- {
- Bond tmp = chain.bonds.elementAt(i);
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- if (chain != mainchain)
- {
- continue;
- }
-
- 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.getResidueColour(sequence[s], pos,
- finder);
- }
- pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
- if (pos > 0)
- {
- pos = sequence[s].findIndex(pos);
- tmp.endCol = sr.getResidueColour(sequence[s], pos,
- finder);
- }
-
- }
- }
- }
- }
- }
- }
- }
-
- Zsort zsort;
-
- public void drawScene(Graphics g)
- {
- if (zbuffer)
- {
- if (zsort == null)
- {
- zsort = new Zsort();
- }
-
- zsort.sort(visiblebonds);
- }
-
- Bond tmpBond = null;
- for (int i = 0; i < visiblebonds.size(); i++)
- {
- tmpBond = visiblebonds.elementAt(i);
-
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getWidth() / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
- + (getHeight() / 2));
-
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
- + (getWidth() / 2));
- yend = (int) (((centre[1] - tmpBond.end[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();
- }
- }
-
- @Override
- 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 = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- if (fatom.alignmentMapping != -1)
- {
- if (highlightRes == null)
- {
- highlightRes = new Vector<String>();
- }
-
- final String atomString = Integer
- .toString(fatom.alignmentMapping);
- if (highlightRes.contains(atomString))
- {
- highlightRes.remove(atomString);
- }
- else
- {
- highlightRes.add(atomString);
- }
- }
- }
- }
-
- }
- mx = e.getX();
- my = e.getY();
- omx = mx;
- omy = my;
- dragging = false;
- }
-
- @Override
- 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 = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- mouseOverStructure(fatom.resNumber, chain.id);
- }
- }
-
- if (fatom != null)
- {
- this.setToolTipText(
- chain.id + ":" + fatom.resNumber + " " + fatom.resName);
- }
- else
- {
- mouseOverStructure(-1, chain != null ? chain.id : null);
- this.setToolTipText(null);
- }
- }
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- @Override
- 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.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
- {
- objmat.rotatez(((mx - omx)));
- }
- else
- {
- objmat.rotatex(((my - omy)));
- objmat.rotatey(((omx - mx)));
- }
-
- // Alter the bonds
- for (PDBChain chain : pdb.getChains())
- {
- for (Bond tmpBond : chain.bonds)
- {
- // 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();
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- dragging = false;
- return;
- }
-
- void drawLabels(Graphics g)
- {
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond tmpBond : chain.bonds)
- {
- 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) (((centre[1] - b.start[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) (((centre[1] - b.end[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.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- int truex;
- Bond tmpBond = null;
-
- if (chain.isVisible)
- {
- for (Bond bond : chain.bonds)
- {
- tmpBond = bond;
-
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getWidth() / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) (((centre[1] - tmpBond.start[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)
- { // dead code? value of chain is either overwritten or discarded
- chain = pdb.getChains().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 < mainchain.bonds.size(); index++)
- {
- tmpBond = mainchain.bonds.elementAt(index);
- if (tmpBond.at1.alignmentMapping == ii - 1)
- {
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- }
-
- if (highlightBond2 != null)
- {
- highlightBond2.at1.isSelected = false;
- }
-
- highlightBond1 = null;
- highlightBond2 = null;
-
- if (index > 0)
- {
- highlightBond1 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
-
- redrawneeded = true;
- repaint();
- }
-
- public void setAllchainsVisible(boolean b)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- chain.isVisible = b;
- }
- mainchain.isVisible = true;
- findCentre();
- setupBonds();
- }
-
- // ////////////////////////////////
- // /StructureListener
- @Override
- public String[] getStructureFiles()
- {
- 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();
-
- /**
- * Highlight the specified atoms in the structure.
- *
- * @param atoms
- */
- @Override
- public void highlightAtoms(List<AtomSpec> atoms)
- {
- if (!seqColoursReady)
- {
- return;
- }
-
- for (AtomSpec atom : atoms)
- {
- int atomIndex = atom.getAtomIndex();
- if (highlightRes != null
- && highlightRes.contains((atomIndex - 1) + ""))
- {
- continue;
- }
-
- highlightAtom(atomIndex);
- }
-
- redrawneeded = true;
- repaint();
- }
-
- /**
- * Highlight the atom at the specified index.
- *
- * @param atomIndex
- */
- protected void highlightAtom(int atomIndex)
- {
- int index = -1;
- Bond tmpBond;
- for (index = 0; index < mainchain.bonds.size(); index++)
- {
- tmpBond = 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 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
- }
-
- 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));
- }
-
- @Override
- public void updateColours(Object source)
- {
- colourBySequence();
- redrawneeded = true;
- repaint();
- }
-
- @Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean isListeningFor(SequenceI seq)
- {
- if (sequence != null)
- {
- for (SequenceI s : sequence)
- {
- if (s == seq)
- {
- return true;
- }
- }
- }
- return false;
- }
-}
git://source.jalview.org / jalview.git / commitdiff