private AppJmol appJmolWindow;
public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[] seq, String[] chains, String protocol)
+ SequenceI[][] sequenceIs, String[][] chains, String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr=null;
+
+ FeatureRenderer fr = null;
+
@Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
}
fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
+ .getFeatureRenderer());
}
return fr;
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow!=null && strStatus != null
- )
- // && !strStatus.equals("Script completed"))
- // should we squash the script completed string ?
+ if (appJmolWindow.scriptWindow != null && strStatus != null)
+ // && !strStatus.equals("Script completed"))
+ // should we squash the script completed string ?
{
appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
}
@Override
public void showUrl(String url, String target)
{
- try {
+ try
+ {
jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception e) {
+ } catch (Exception e)
+ {
Cache.log.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView()!=ap.av)
+ if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
return;
-
+
colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+ appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
+ msWalltime);
}
public void showUrl(String url)
{
- showUrl(url,"jmol");
+ showUrl(url, "jmol");
}
public void newJmolPopup(boolean translateLocale, String menuName,
jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
asPopup);
}
- public synchronized void addSequence(SequenceI[] seq)
+
+ /**
+ * add structures and any known sequence associations
+ *
+ * @returns the pdb entries added to the current set.
+ */
+ private PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
{
+ int pe = -1;
Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
+ Vector rtn = new Vector();
+ for (int i = 0; i < pdbentry.length; i++)
+ {
+ v.addElement(pdbentry[i]);
+ }
+ for (int i = 0; i < pdbe.length; i++)
+ {
+ int r = v.indexOf(pdbe[i]);
+ if (r == -1 || r >= pdbentry.length)
+ {
+ rtn.addElement(new int[]
+ { v.size(), i });
+ v.addElement(pdbe[i]);
+ }
+ else
+ {
+ // just make sure the sequence/chain entries are all up to date
+ addSequenceAndChain(r, seq[i], chns[i]);
+ }
+ }
+ pdbe = new PDBEntry[v.size()];
+ v.copyInto(pdbe);
+ pdbentry = pdbe;
+ if (rtn.size() > 0)
+ {
+ // expand the tied seuqence[] and string[] arrays
+ SequenceI[][] sqs = new SequenceI[pdbentry.length][];
+ String[][] sch = new String[pdbentry.length][];
+ System.arraycopy(sequence, 0, sqs, 0, sequence.length);
+ System.arraycopy(chains, 0, sch, 0, this.chains.length);
+ sequence = sqs;
+ chains = sch;
+ pdbe = new PDBEntry[rtn.size()];
+ for (int r = 0; r < pdbe.length; r++)
+ {
+ int[] stri = ((int[]) rtn.elementAt(r));
+ // record the pdb file as a new addition
+ pdbe[r] = pdbentry[stri[0]];
+ // and add the new sequence/chain entries
+ addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
+ }
+ }
+ else
+ {
+ pdbe = null;
+ }
+ return pdbe;
+ }
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
+ void addSequence(int pe, SequenceI[] seq)
+ {
+ // add sequences to the pe'th pdbentry's seuqence set.
+ addSequenceAndChain(pe, seq, null);
+ }
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
+ private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ {
+ if (pe < 0 || pe >= pdbentry.length)
+ {
+ throw new Error(
+ "Implementation error - no corresponding pdbentry (for index "
+ + pe + ") to add sequences mappings to");
+ }
+ final String nullChain = "TheNullChain";
+ Vector s = new Vector();
+ Vector c = new Vector();
+ if (chains == null)
+ {
+ chains = new String[pdbentry.length][];
+ }
+ if (sequence[pe] != null)
+ {
+ for (int i = 0; i < sequence[pe].length; i++)
+ {
+ s.addElement(sequence[pe][i]);
+ if (chains[pe] != null)
+ {
+ if (i < chains[pe].length)
+ {
+ c.addElement(chains[pe][i]);
+ }
+ else
+ {
+ c.addElement(nullChain);
+ }
+ }
+ else
+ {
+ if (tchain != null && tchain.length > 0)
+ {
+ c.addElement(nullChain);
+ }
+ }
+ }
+ }
+ for (int i = 0; i < seq.length; i++)
+ {
+ if (!s.contains(seq[i]))
+ {
+ s.addElement(seq[i]);
+ if (tchain != null && i < tchain.length)
+ {
+ c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+ }
+ }
+ }
+ SequenceI[] tmp = new SequenceI[s.size()];
+ s.copyInto(tmp);
+ sequence[pe] = tmp;
+ if (c.size() > 0)
+ {
+ String[] tch = new String[c.size()];
+ c.copyInto(tch);
+ for (int i = 0; i < tch.length; i++)
+ {
+ if (tch[i] == nullChain)
+ {
+ tch[i] = null;
+ }
+ }
+ chains[pe] = tch;
+ }
+ else
+ {
+ chains[pe] = null;
+ }
}
public void selectionChanged(BitSet arg0)
{
// TODO Auto-generated method stub
-
+
}
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
-
+
}
+
+ /**
+ * add another pdb entry into the view, with associated sequences and chains
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ public synchronized void addStructure(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final boolean align)
+ {
+ PDBEntry[] pe = addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ if (pe != null)
+ {
+ StringBuffer cmd = new StringBuffer();
+ cmd.append("load APPEND");
+ for (int p = 0; p < pe.length; p++)
+ {
+ cmd.append(" \"");
+ cmd.append(pe[p].getFile());
+ cmd.append("\"");
+ }
+ cmd.append("\n");
+ final String command = cmd.toString();
+ cmd = null;
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ evalStateCommand(command);
+ if (align)
+ {
+ // may need to wait around until script has finished
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(20);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ superposeStructures(appJmolWindow.ap.av.getAlignment(), -1, null);
+ }
+ }
+ }).start();
+ }
+ }
+
+ /**
+ * add the given sequences to the mapping scope for the given pdb file handle
+ *
+ * @param pdbFile
+ * - pdbFile identifier
+ * @param seq
+ * - set of sequences it can be mapped to
+ */
+ public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+ {
+ for (int pe = 0; pe < pdbentry.length; pe++)
+ {
+ if (pdbentry[pe].getFile().equals(pdbFile))
+ {
+ addSequence(pe, seq);
+ }
+ }
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff