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;
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBChain mainchain;
- Vector highlightRes;
+ Vector<String> highlightRes;
boolean pdbAction = false;
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, String protocol)
+ String[] chains, AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
{
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
- pdbentry.setFile("INLINE" + pdb.id);
+ pdbentry.setFile("INLINE" + pdb.getId());
}
} catch (Exception ex)
return;
}
- pdbentry.setId(pdb.id);
+ pdbentry.setId(pdb.getId());
ssm.addStructureViewerListener(this);
colourBySequence();
- int max = -10;
+ float max = -10;
int maxchain = -1;
int pdbstart = 0;
int pdbend = 0;
// 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 = "
- + pdb.chains.elementAt(i).sequence
- .getSequenceAsString());
+ mappingDetails
+ .append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + pdb.chains.elementAt(i).residues.size()
- + "\n\n");
+ + 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.chains.elementAt(i).sequence,
- pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
- : AlignSeq.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");
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
- mainchain = pdb.chains.elementAt(maxchain);
+ mainchain = pdb.getChains().elementAt(maxchain);
mainchain.pdbstart = pdbstart;
mainchain.pdbend = pdbend;
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 (pdb.chains.elementAt(ii).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector tmp = pdb.chains.elementAt(ii).bonds;
+ Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
for (int i = 0; i < tmp.size(); i++)
{
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 (pdb.chains.elementAt(ii).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector bonds = 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];
int bsize = 0;
// Find centre coordinate
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if (pdb.chains.elementAt(ii).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector bonds = 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)
{
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
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 = 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 (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
- if (showFeatures)
- {
- tmp.startCol = fr.findFeatureColour(tmp.startCol,
- sequence[s], pos);
- }
+ 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.getResidueBoxColour(sequence[s], pos);
- if (showFeatures)
- {
- tmp.endCol = fr.findFeatureColour(tmp.endCol,
- sequence[s], pos);
- }
+ tmp.endCol = sr
+ .getResidueColour(sequence[s], pos, finder);
}
-
}
}
}
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));
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
repaint();
if (foundchain != -1)
{
- PDBChain chain = 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 = pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
}
}
+ @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();
}
// Alter the bonds
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (PDBChain chain : pdb.getChains())
{
- Vector bonds = 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]);
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 = pdb.chains.elementAt(ii);
-
if (chain.isVisible)
{
- Vector bonds = 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);
}
}
foundchain = -1;
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
int truex;
Bond tmpBond = null;
if (chain.isVisible)
{
- Vector bonds = 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));
if (fatom != null) // )&& chain.ds != null)
{
- chain = pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
}
}
return fatom;
}
+ @Override
public void update(Graphics g)
{
paint(g);
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 = pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ @Override
+ public String[] getStructureFiles()
{
- return new String[]
- { pdbentry.getFile() };
+ return new String[] { pdbentry.getFile() };
}
String lastMessage;
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;
}
// return new Color(viewer.getAtomArgb(atomIndex));
}
+ @Override
public void updateColours(Object source)
{
colourBySequence();
}
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ if (sequence != null)
+ {
+ for (SequenceI s : sequence)
+ {
+ if (s == seq)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
}