\r
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener\r
{\r
- public AppletPDBCanvas()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
\r
MCMatrix idmat = new MCMatrix(3, 3);\r
MCMatrix objmat = new MCMatrix(3, 3);\r
jalview.appletgui.SequenceRenderer sr;\r
jalview.appletgui.FeatureRenderer fr;\r
jalview.appletgui.SeqCanvas seqcanvas;\r
- Sequence sequence;\r
+ public Sequence sequence;\r
final StringBuffer mappingDetails = new StringBuffer();\r
String appletToolTip = null;\r
int toolx, tooly;\r
+ PDBChain mainchain;\r
\r
public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)\r
{\r
sr = seqcanvas.getSequenceRenderer();\r
fr = seqcanvas.getFeatureRenderer();\r
\r
- seqcanvas.setPDBViewer(this);\r
+ seqcanvas.setPDBCanvas(this);\r
addKeyListener(new KeyAdapter()\r
{\r
\r
doKeyPressed(evt);\r
}\r
});\r
-\r
}\r
\r
+ Bond highlightBond1, highlightBond2;\r
+ public void highlightRes(int ii)\r
+ {\r
+ highlightBond1 = null;\r
+ highlightBond2 = null;\r
+\r
+ int index = ii - mainchain.seqstart;\r
+ if(index <0 )\r
+ return;\r
+\r
+ if(index<=mainchain.bonds.size())\r
+ {\r
+ if(index>0)\r
+ {\r
+ highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
+ }\r
+\r
+ if(index!=mainchain.bonds.size())\r
+ highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
+ }\r
+\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+\r
+\r
public void setPDBFile(PDBfile pdb)\r
{\r
this.sr = sr;\r
mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend);\r
}\r
\r
- ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;\r
- ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;\r
- ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;\r
- ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;\r
- ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;\r
- ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;\r
+ mainchain = (PDBChain) pdb.chains.elementAt(maxchain);\r
+\r
+ mainchain.pdbstart = pdbstart;\r
+ mainchain.pdbend = pdbend;\r
+ mainchain.seqstart = seqstart;\r
+ mainchain.seqend = seqend;\r
+ mainchain.isVisible = true;\r
+ mainchain.sequence = sequence;\r
\r
this.pdb = pdb;\r
this.prefsize = new Dimension(getSize().width, getSize().height);\r
//this saves much memory usage\r
if ((img == null) || (prefsize.width != getSize().width) ||\r
(prefsize.height != getSize().height)) {\r
- prefsize.width = getSize().width;\r
- prefsize.height = getSize().height;\r
\r
- scale = findScale();\r
- img = createImage(prefsize.width, prefsize.height);\r
- ig = img.getGraphics();\r
+ try{ prefsize.width = getSize().width;\r
+ prefsize.height = getSize().height;\r
\r
- redrawneeded = true;\r
+ scale = findScale();\r
+ img = createImage(prefsize.width, prefsize.height);\r
+ ig = img.getGraphics();\r
+\r
+ redrawneeded = true;\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println(getSize());\r
+ }\r
}\r
\r
\r
for (int i = 0; i < chain.bonds.size(); i++)\r
{\r
Bond tmp = (Bond) chain.bonds.elementAt(i);\r
-\r
if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
(tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))\r
{\r
+\r
int pos = chain.seqstart +\r
(tmp.at1.resNumber - chain.pdbstart - chain.offset);\r
\r
int index = sequence.findIndex(pos);\r
\r
- tmp.startCol = sr.findSequenceColour(sequence, index);\r
+ if(jalview.util.Comparison.isGap((sequence.getCharAt(index))))\r
+ {\r
+ index--;\r
+ }\r
+\r
+ tmp.startCol = sr.findSequenceColour(sequence, index);\r
\r
// tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
\r
int pos = chain.seqstart +\r
(tmp.at2.resNumber - chain.pdbstart - chain.offset);\r
int index = sequence.findIndex(pos);\r
+ if (jalview.util.Comparison.isGap( (sequence.getCharAt(index))))\r
+ {\r
+ index--;\r
+ }\r
+\r
\r
- tmp.endCol = sr.findSequenceColour( sequence, index);\r
+ tmp.endCol = sr.findSequenceColour(sequence, index);\r
// tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);\r
}\r
else\r
\r
for (int i = 0; i < tmp.size(); i++)\r
{\r
- bonds.addElement(tmp.elementAt(i));\r
+ bonds.addElement(tmp.elementAt(i));\r
}\r
}\r
}\r
for (int i = 0; i < bonds.size(); i++) {\r
Bond tmpBond = (Bond) bonds.elementAt(i);\r
\r
+\r
xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
(getSize().width / 2));\r
ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +\r
xmid = (xend + xstart) / 2;\r
ymid = (yend + ystart) / 2;\r
\r
- if (depthcue && !bymolecule) {\r
+ if (depthcue && !bymolecule)\r
+ {\r
if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {\r
g.setColor(tmpBond.startCol.darker().darker());\r
drawLine(g, xstart, ystart, xmid, ymid);\r
} else {\r
drawLine(g, xstart, ystart, xend, yend);\r
}\r
+\r
+ if(highlightBond1!=null && highlightBond1==tmpBond)\r
+ {\r
+ g.setColor(Color.white);\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+\r
+ if(highlightBond2!=null && highlightBond2==tmpBond)\r
+ {\r
+ g.setColor(Color.white);\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+ }\r
+\r
}\r
}\r
\r
}\r
\r
public void mousePressed(MouseEvent e) {\r
- myAtom fatom = findAtom(e.getX(), e.getY());\r
+ Atom fatom = findAtom(e.getX(), e.getY());\r
if(fatom!=null)\r
{\r
fatom.isSelected = !fatom.isSelected;\r
\r
public void mouseMoved(MouseEvent e) {\r
\r
- myAtom fatom = findAtom(e.getX(), e.getY());\r
+ Atom fatom = findAtom(e.getX(), e.getY());\r
\r
+ PDBChain chain = null;\r
if(foundchain!=-1)\r
{\r
- PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
- int pos = chain.seqstart +\r
- (fatom.resNumber - chain.pdbstart - chain.offset)+1;\r
+ chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
+ if(chain == mainchain)\r
+ {\r
+ int pos = chain.seqstart +\r
+ (fatom.resNumber - chain.pdbstart - chain.offset) + 1;\r
\r
- int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);\r
+ int index = seqcanvas.getViewport().getAlignment().findIndex(\r
+ sequence);\r
\r
- seqcanvas.highlightSearchResults(new int[]{index, pos, pos});\r
+ seqcanvas.highlightSearchResults(new int[]\r
+ {index, pos, pos});\r
+ }\r
}\r
else\r
seqcanvas.highlightSearchResults(null);\r
if (fatom != null) {\r
toolx = e.getX();\r
tooly = e.getY();\r
- appletToolTip = fatom.resNumber+" "+ fatom.resName;\r
+\r
+ appletToolTip = chain.id+":"+ fatom.resNumber+" "+ fatom.resName;\r
redrawneeded = true;\r
repaint();\r
} else {\r
}\r
\r
int foundchain = -1;\r
- public myAtom findAtom(int x, int y) {\r
- myAtom fatom = null;\r
+ public Atom findAtom(int x, int y) {\r
+ Atom fatom = null;\r
\r
foundchain = -1;\r
\r
paint(g);\r
}\r
\r
- private void jbInit()\r
- throws Exception\r
- {\r
- }\r
+ public void setAllchainsVisible(boolean b)\r
+ {\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+ chain.isVisible = b;\r
+ }\r
+ mainchain.isVisible = true;\r
+ findCentre();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff