/*
- * 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, J Engelhardt, LM Lui, 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 <http://www.gnu.org/licenses/>.
*/
package MCview;
import jalview.appletgui.*;
import jalview.structure.*;
-public class AppletPDBCanvas
- extends Panel implements MouseListener, MouseMotionListener, StructureListener
+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);
- public SequenceI [] 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;
+
FeatureRenderer fr;
+
AlignmentPanel ap;
+
StructureSelectionManager ssm;
- public AppletPDBCanvas(PDBEntry pdbentry,
- SequenceI[] seq,
- String [] chains,
- AlignmentPanel ap,
- String protocol)
+ public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, AlignmentPanel ap, String protocol)
{
this.ap = ap;
this.pdbentry = pdbentry;
this.sequence = seq;
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(ap.av.applet);
- try{
+ try
+ {
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
- if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- pdbentry.setFile("INLINE"+pdb.id);
+ if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ pdbentry.setFile("INLINE" + pdb.id);
- }catch(Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
return;
int seqstart = 0;
int seqend = 0;
- //JUST DEAL WITH ONE SEQUENCE FOR NOW
+ // 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)
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.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++)
}
Vector visiblebonds;
+
void setupBonds()
{
seqColoursReady = false;
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++)
{
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;
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++)
{
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];
}
}
}
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
ig = img.getGraphics();
redrawneeded = true;
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
repaint();
}
-
-
// This method has been taken out of PDBChain to allow
// Applet and Application specific sequence renderers to be used
void colourBySequence()
{
if (mapping[m].getSequence() == sequence[s])
{
- int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;
+ int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
if (showFeatures)
{
tmp.startCol = fr.findFeatureColour(tmp.startCol,
- sequence[s],
- pos);
+ sequence[s], pos);
}
}
- pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;
+ pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
if (showFeatures)
{
tmp.endCol = fr.findFeatureColour(tmp.endCol,
- sequence[s],
- pos);
+ sequence[s], pos);
}
}
}
Zsort zsort;
+
public void drawScene(Graphics g)
{
if (zbuffer)
{
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;
{
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);
toolx = e.getX();
tooly = e.getY();
- appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;
+ appletToolTip = chain.id + ":" + fatom.resNumber + " "
+ + fatom.resName;
redrawneeded = true;
repaint();
}
else
{
- mouseOverStructure(-1, chain!=null?chain.id:null);
+ mouseOverStructure(-1, chain != null ? chain.id : null);
appletToolTip = null;
redrawneeded = true;
repaint();
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]);
}
}
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++)
{
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);
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);
}
int foundchain = -1;
+
public Atom findAtom(int x, int y)
{
Atom fatom = null;
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)
{
// 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)
{
}
- if (fatom != null) //)&& chain.ds != null)
+ if (fatom != null) // )&& chain.ds != null)
{
chain = (PDBChain) pdb.chains.elementAt(foundchain);
}
return;
}
- if (highlightRes != null
- && highlightRes.contains( (ii - 1) + ""))
+ if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
{
return;
}
setupBonds();
}
-
- //////////////////////////////////
- ///StructureListener
- public String getPdbFile()
+ // ////////////////////////////////
+ // /StructureListener
+ public String[] getPdbFile()
{
- return pdbentry.getFile();
+ 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());
+ if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+ ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
- lastMessage = pdbResNum+chain;
+ lastMessage = pdbResNum + chain;
}
StringBuffer resetLastRes = new StringBuffer();
+
StringBuffer eval = new StringBuffer();
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
{
if (!seqColoursReady)
{
return;
}
- if (highlightRes != null
- && highlightRes.contains( (atomIndex - 1) + ""))
+ if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
{
return;
}
repaint();
}
-
- public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ public Color getColour(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
{
return Color.white;
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return null;
+ // if (!pdbfile.equals(pdbentry.getFile()))
+ // return null;
- //return new Color(viewer.getAtomArgb(atomIndex));
+ // return new Color(viewer.getAtomArgb(atomIndex));
}
public void updateColours(Object source)
repaint();
}
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff