/*
- * 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.io.*;
-import java.util.*;
-
+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.StructureFile;
+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;
+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.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-import jalview.appletgui.*;
-import jalview.structure.*;
-
-public class AppletPDBCanvas
- extends Panel implements MouseListener, MouseMotionListener, StructureListener
+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 PDBfile pdb;
+
+ 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;
+
+ public SequenceI[] sequence;
+
final StringBuffer mappingDetails = new StringBuffer();
+
String appletToolTip = null;
+
int toolx, tooly;
+
PDBChain mainchain;
- Vector highlightRes;
+
+ 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,
- 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.getId());
+ }
- }catch(Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
return;
}
- pdbentry.setId(pdb.id);
+ pdbentry.setId(pdb.getId());
ssm.addStructureViewerListener(this);
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++)
+ for (int i = 0; i < pdb.getChains().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 = "
+ + 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,
- ( (PDBChain) pdb.chains.elementAt(i)).sequence,
- "pep");
+ 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");
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 = (PDBChain) pdb.chains.elementAt(maxchain);
+ 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);
+ // 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++)
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
doKeyPressed(evt);
scale = findScale();
}
- Vector visiblebonds;
+ Vector<Bond> visiblebonds;
+
void setupBonds()
{
seqColoursReady = false;
// Sort the bonds by z coord
- visiblebonds = new Vector();
+ visiblebonds = new Vector<Bond>();
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> tmp = pdb.getChains().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;
min[2] = (float) 1e30;
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond tmp : bonds)
{
- Bond tmp = (Bond) bonds.elementAt(i);
-
if (tmp.start[0] >= max[0])
{
max[0] = tmp.start[0];
}
}
- 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]);
+ 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];
int bsize = 0;
- //Find centre coordinate
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ // Find centre coordinate
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
bsize += bonds.size();
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- 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];
+ 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[2] = ztot / (2 * (float) bsize);
}
+ @Override
public void paint(Graphics g)
{
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);
+ g.drawString(
+ MessageManager.getString("label.error_loading_pdb_data"), 50,
+ getSize().height / 2);
return;
}
{
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Fetching PDB data...", 50, getSize().height / 2);
+ 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))
+ // 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()
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
boolean showFeatures = false;
- if (ap.av.getShowSequenceFeatures())
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
PDBChain chain;
if (bysequence && pdb != null)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- chain = (PDBChain) pdb.chains.elementAt(ii);
+ chain = pdb.getChains().elementAt(ii);
for (int i = 0; i < chain.bonds.size(); i++)
{
- Bond tmp = (Bond) chain.bonds.elementAt(i);
+ Bond tmp = chain.bonds.elementAt(i);
tmp.startCol = Color.lightGray;
tmp.endCol = Color.lightGray;
if (chain != mainchain)
{
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)
zsort = new Zsort();
}
- zsort.Zsort(visiblebonds);
+ zsort.sort(visiblebonds);
}
Bond tmpBond = null;
for (int i = 0; i < visiblebonds.size(); i++)
{
- tmpBond = (Bond) visiblebonds.elementAt(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));
+ 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));
+ 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);
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
repaint();
if (foundchain != -1)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ PDBChain chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
if (fatom.alignmentMapping != -1)
{
if (highlightRes == null)
{
- highlightRes = new Vector();
+ highlightRes = new Vector<String>();
}
- if (highlightRes.contains(fatom.alignmentMapping + "" + ""))
+ final String atomString = Integer
+ .toString(fatom.alignmentMapping);
+ if (highlightRes.contains(atomString))
{
- highlightRes.removeElement(fatom.alignmentMapping + "");
+ highlightRes.removeElement(atomString);
}
else
{
- highlightRes.addElement(fatom.alignmentMapping + "");
+ highlightRes.addElement(atomString);
}
}
}
dragging = false;
}
+ @Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
PDBChain chain = null;
if (foundchain != -1)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
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();
}
}
+ @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();
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(((mx - omx)));
}
else
{
- objmat.rotatex( (float) ( (omy - my)));
- objmat.rotatey( (float) ( (omx - mx)));
+ objmat.rotatex(((omy - my)));
+ objmat.rotatey(((omx - mx)));
}
- //Alter the bonds
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ // Alter the bonds
+ for (PDBChain chain : pdb.getChains())
{
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond tmpBond : chain.bonds)
{
- 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]);
}
}
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
void drawLabels(Graphics g)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (PDBChain chain : pdb.getChains())
{
- 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++)
+ for (Bond tmpBond : chain.bonds)
{
- Bond tmpBond = (Bond) bonds.elementAt(i);
-
if (tmpBond.at1.isSelected)
{
labelAtom(g, tmpBond, 1);
if (tmpBond.at2.isSelected)
{
-
labelAtom(g, tmpBond, 2);
}
}
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));
+ 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));
+ 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.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
int truex;
Bond tmpBond = null;
if (chain.isVisible)
{
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
- tmpBond = (Bond) bonds.elementAt(i);
+ tmpBond = 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) ( ( (centre[1] - tmpBond.start[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);
+ chain = pdb.getChains().elementAt(foundchain);
}
}
return fatom;
}
+ @Override
public void update(Graphics g)
{
paint(g);
return;
}
- if (highlightRes != null
- && highlightRes.contains( (ii - 1) + ""))
+ if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
{
return;
}
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
{
- tmpBond = (Bond) mainchain.bonds.elementAt(index);
+ tmpBond = mainchain.bonds.elementAt(index);
if (tmpBond.at1.alignmentMapping == ii - 1)
{
if (highlightBond1 != null)
if (index > 0)
{
- highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+ highlightBond1 = mainchain.bonds.elementAt(index - 1);
highlightBond1.at2.isSelected = true;
}
if (index != mainchain.bonds.size())
{
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+ highlightBond2 = mainchain.bonds.elementAt(index);
highlightBond2.at1.isSelected = true;
}
public void setAllchainsVisible(boolean b)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;
setupBonds();
}
-
- //////////////////////////////////
- ///StructureListener
- public String getPdbFile()
+ // ////////////////////////////////
+ // /StructureListener
+ @Override
+ 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)
+ /**
+ * Highlight the specified atoms in the structure.
+ *
+ * @param atoms
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
if (!seqColoursReady)
{
return;
}
-
- if (highlightRes != null
- && highlightRes.contains( (atomIndex - 1) + ""))
+ for (AtomSpec atom : atoms)
{
- return;
+ 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 = (Bond) mainchain.bonds.elementAt(index);
+ tmpBond = mainchain.bonds.elementAt(index);
if (tmpBond.at1.atomIndex == atomIndex)
{
if (highlightBond1 != null)
if (index > 0)
{
- highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+ highlightBond1 = mainchain.bonds.elementAt(index - 1);
highlightBond1.at2.isSelected = true;
}
if (index != mainchain.bonds.size())
{
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+ highlightBond2 = mainchain.bonds.elementAt(index);
highlightBond2.at1.isSelected = true;
}
break;
}
}
-
- redrawneeded = true;
- 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));
}
+ @Override
public void updateColours(Object source)
{
colourBySequence();
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 / blobdiff