import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.ws.ebi.EBIFetchClient;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
+ lastCommand = null;
colourBySequence = seqColour.isSelected();
colourBySequence(ap.alignFrame.alignPanel);
}
resetLastRes.append(":" + chain);
}
- eval.append(";color gold;wireframe 100");
+ eval.append(";wireframe 100;"+eval.toString()+".CA;");
- Color col = new Color(viewer.getAtomArgb(atomIndex));
+ resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
- resetLastRes.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];wireframe 0");
+ eval.append("spacefill 200;select none");
viewer.evalStringQuiet(eval.toString());
-
}
public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
StringBuffer command = new StringBuffer();
int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ for (int sp,s = 0; s < sequence.length; s++)
{
for (int m = 0; m < mapping.length; m++)
{
- System.out.println(mapping[m].getSequence().getName()+" "+sequence[s].getName()+" "
- +((mapping[m].getSequence() == sequence[s])
- +" "+(ap.av.alignment.findIndex(sequence[s]))));
-
- if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s])>-1)
+ if (mapping[m].getSequence() == sequence[s]
+ && (sp=ap.av.alignment.findIndex(sequence[s]))>-1)
{
- for (int r = 0; r < sequence[s].getLength(); r++)
+ SequenceI asp = ap.av.alignment.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
{
+ // No mapping to gaps in sequence.
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
int pos = mapping[m].getPDBResNum(
- sequence[s].findPosition(r));
+ asp.findPosition(r));
if (pos < 1 || pos==lastPos)
continue;
lastPos = pos;
- Color col = sr.getResidueBoxColour(sequence[s], r);
+ Color col = sr.getResidueBoxColour(asp, r);
if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
+ col = fr.findFeatureColour(col, asp, r);
if (command.toString().endsWith(":" + mapping[m].getChain()+
";color["
if (chainId != null)
picked+=(":"+chainId.substring(1, chainId.length()));
- picked+=".C";
+ picked+=".CA";
+
if (!atomsPicked.contains(picked))
{