*/
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;
-import java.awt.Font;
+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.util.List;
import java.util.Vector;
-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.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
-public class AppletPDBCanvas extends Panel implements MouseListener,
- MouseMotionListener, StructureListener
+public class AppletPDBCanvas extends Panel
+ implements MouseListener, MouseMotionListener, StructureListener
{
MCMatrix idmat = new MCMatrix(3, 3);
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, String protocol)
+ String[] chains, AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
- 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
+ + 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
+ 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);
// Sort the bonds by z coord
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<Bond> 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<Bond> bonds = pdb.chains.elementAt(ii).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
for (Bond tmp : bonds)
{
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<Bond> bonds = pdb.chains.elementAt(ii).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
bsize += bonds.size();
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(
- MessageManager.getString("label.error_loading_pdb_data"), 50,
- getSize().height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_pdb_data"),
+ 50, getSize().height / 2);
return;
}
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++)
{
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);
}
-
}
}
}
{
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;
}
}
+ @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)
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();
MCMatrix objmat = new MCMatrix(3, 3);
objmat.setIdentity();
- if ((evt.getModifiers() & Event.META_MASK) != 0)
+ if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
{
objmat.rotatez(((mx - omx)));
}
}
// Alter the bonds
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
for (Bond tmpBond : chain.bonds)
{
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
void drawLabels(Graphics g)
{
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
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);
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<Bond> bonds = pdb.chains.elementAt(ii).bonds;
+ 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));
+ 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)
{
- chain = pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
}
}
return fatom;
}
+ @Override
public void update(Graphics g)
{
paint(g);
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;
// return new Color(viewer.getAtomArgb(atomIndex));
}
+ @Override
public void updateColours(Object source)
{
colourBySequence();
git://source.jalview.org / jalview.git / blobdiff