public Vector chainNames;
- String[] chains;
+ /**
+ * array of target chains for seuqences - tied to pdbentry and sequence[]
+ */
+ protected String[][] chains;
boolean colourBySequence = true;
StringBuffer resetLastRes = new StringBuffer();
- public SequenceI[] sequence;
+ /**
+ * sequences mapped to each pdbentry
+ */
+ public SequenceI[][] sequence;
StructureSelectionManager ssm;
public JmolViewer viewer;
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
- String[] chains, String protocol)
+ public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ String[][] chains, String protocol)
{
- this.sequence = seq;
+ this.sequence = sequenceIs;
this.chains = chains;
this.pdbentry = pdbentry;
this.protocol = protocol;
-
+ if (chains == null)
+ {
+ this.chains = new String[pdbentry.length][];
+ }
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
{
return ("Jalview Jmol Window");
}
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+ StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
+ pdbentry[0].getId());
if (pdbentry[0].getProperty() != null)
*/
public void superposeStructures(AlignmentI alignment)
{
- String[] files = getPdbFile();
+ superposeStructures(alignment, -1, null);
+ }
- StringBuffer command = new StringBuffer();
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ *
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure)
+ {
+ superposeStructures(alignment, refStructure, null);
+ }
+
+ /**
+ * superpose the structures associated with sequences in the alignment
+ * according to their corresponding positions. ded)
+ * @param refStructure
+ * - select which pdb file to use as reference (default is -1 - the
+ * first structure in the alignment)
+ * @param hiddenCols TODO
+ */
+ public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
+ {
+ String[] files = getPdbFile();
+ if (refStructure>=files.length)
+ {
+ System.err.println("Invalid reference structure value "+refStructure);
+ refStructure= -1;
+ }
+ if (refStructure<-1)
+ {
+ refStructure=-1;
+ }
+ StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
+
boolean matched[] = new boolean[alignment.getWidth()];
- String commonpositions[][] = new String[files.length][alignment
- .getWidth()];
+ for (int m = 0; m < matched.length; m++)
+ {
+
+ matched[m] = (hiddenCols!=null) ? hiddenCols.isVisible(m) : true;
+ }
+
+ int commonrpositions[][] = new int[files.length][alignment.getWidth()];
+ String isel[] = new String[files.length];
+ // reference structure - all others are superposed in it
+ String[] targetC = new String[files.length];
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
continue;
int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
{
for (int sp, m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s]
- && (sp = alignment.findIndex(sequence[s])) > -1)
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
{
+ if (refStructure == -1)
+ {
+ refStructure = pdbfnum;
+ }
SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
+ for (int r = 0; r < matched.length; r++)
{
- // no mapping to gaps in sequence
+ if (!matched[r])
+ {
+ continue;
+ }
+ matched[r] = false; // assume this is not a good site
+ if (r >= asp.getLength())
+ {
+ continue;
+ }
+
if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
{
- matched[r] = false; // exclude from common set
+ // no mapping to gaps in sequence
continue;
}
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+ int t = asp.findPosition(r); // sequence position
+ int apos = mapping[m].getAtomNum(t);
+ int pos = mapping[m].getPDBResNum(t);
if (pos < 1 || pos == lastPos)
+ {
+ // can't align unmapped sequence
continue;
-
+ }
+ matched[r] = true; // this is a good ite
lastPos = pos;
-
- commonpositions[m][r] = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/" + (pdbfnum + 1) + ".1";
+ // just record this residue position
+ commonrpositions[pdbfnum][r] = pos;
+ }
+ // create model selection suffix
+ isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+ if (mapping[m].getChain() == null
+ || mapping[m].getChain().trim().length() == 0)
+ {
+ targetC[pdbfnum] = "";
+ }
+ else
+ {
+ targetC[pdbfnum] = ":" + mapping[m].getChain();
}
+ // move on to next pdb file
+ s = sequence[pdbfnum].length;
break;
}
}
}
}
- command.append("select ");
- // form the matched pair selection strings
- String sep = "";
- for (int r = 0; r < matched.length; r++)
+ StringBuffer selcom[] = new StringBuffer[files.length];
+ // generate select statements to select regions to superimpose structures
{
- if (matched[r])
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- command.append(sep);
- command.append("(");
- for (int s = 0; s < commonpositions.length; s++)
+ String chainCd = targetC[pdbfnum];
+ int lpos = -1;
+ boolean run = false;
+ StringBuffer molsel = (selcom[pdbfnum] = new StringBuffer());
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
{
- if (s > 0)
+ if (matched[r])
{
- command.append(" | ");
+
+ if (lpos != commonrpositions[pdbfnum][r] - 1)
+ {
+ // discontinuity
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ // molsel.append("} {");
+ molsel.append("|");
+ }
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
+ {
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
+ }
+ run = true;
+ }
+ lpos = commonrpositions[pdbfnum][r];
+ // molsel.append(lpos);
}
- command.append(commonpositions[s][r]);
}
- command.append(")");
- sep = " | ";
+ // add final selection phrase
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("}");
+ }
+ selectioncom.append("((");
+ selectioncom.append(molsel.subSequence(1, molsel.length()-1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum+1);
+ selectioncom.append(".1)");
+ if (pdbfnum<files.length-1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ }
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ if (pdbfnum == refStructure)
+ {
+ continue;
}
+ command.append("compare ");
+ command.append("{");
+ command.append(1 + pdbfnum);
+ command.append(".1} {");
+ command.append(1 + refStructure);
+ command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+
+ // form the matched pair strings
+ String sep = "";
+ for (int s = 0; s < 2; s++)
+ {
+ command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ }
+ command.append(" ROTATE TRANSLATE;\n");
}
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("+selectioncom.toString()+"); cartoons; ");
+ // selcom.append("; ribbons; ");
+ System.out.println("Superimpose command(s):\n" + command.toString());
+
evalStateCommand(command.toString());
+
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
public void evalStateCommand(String command)
continue;
int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
{
for (int sp, m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s]
- && (sp = alignment.findIndex(sequence[s])) > -1)
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
{
SequenceI asp = alignment.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
lastPos = pos;
- Color col = sr.getResidueBoxColour(sequence[s], r);
+ Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
if (loadedInline)
{
// TODO: replace with getData ?
- pdb = ssm.setMapping(sequence, chains,
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
pdbentry[pe].setFile("INLINE" + pdb.id);
}
{
}
;
- pdb = ssm.setMapping(sequence, chains,
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
pdbentry[pe].getFile(), protocol);
}
*/
public abstract void refreshGUI();
-
/**
* @param renderPanel
- * @param jmolfileio - when true will initialise jmol's file IO system (should be false in applet context)
+ * @param jmolfileio
+ * - when true will initialise jmol's file IO system (should be false
+ * in applet context)
* @param htmlName
* @param documentBase
* @param codeBase
* @param commandOptions
*/
- public void allocateViewer(Component renderPanel, boolean jmolfileio, String htmlName,
- URL documentBase, URL codeBase, String commandOptions)
+ public void allocateViewer(Component renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions)
{
viewer = JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null),
- htmlName + ((Object) this).toString(), documentBase, codeBase,
+ (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
}
git://source.jalview.org / jalview.git / blobdiff