/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
* time.
*/
private boolean loadingFromArchive = false;
-
+
/**
* second flag to indicate if the jmol viewer should ignore sequence colouring
* events from the structure manager because the GUI is still setting up
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
+ assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
String[] files = getPdbFile();
+ // check to see if we are still waiting for Jmol files
+ long starttime = System.currentTimeMillis();
+ boolean waiting = true;
+ do
+ {
+ waiting = false;
+ for (String file : files)
+ {
+ try
+ {
+ // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
+ // every possible exception
+ StructureMapping[] sm = ssm.getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Exception x)
+ {
+ waiting = true;
+ } catch (Error q)
+ {
+ waiting = true;
+ }
+ }
+ // we wait around for a reasonable time before we give up
+ } while (waiting
+ && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
+ if (waiting)
+ {
+ System.err
+ .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+ return;
+ }
StringBuffer selectioncom = new StringBuffer();
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+ // In principle - nSeconds specifies the speed of animation for each
+ // superposition - but is seems to behave weirdly, so we don't specify it.
+ String nSeconds = " ";
+ if (files.length > 10)
+ {
+ nSeconds = " 0.00001 ";
+ }
+ else
+ {
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
+ }
+ // see JAL-1345 - should really automatically turn off the animation for
+ // large numbers of structures, but Jmol doesn't seem to allow that.
+ nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
// RACE CONDITION - getMapping only returns Jmol loaded filenames once
// Jmol callback has completed.
if (mapping == null || mapping.length < 1)
- continue;
-
+ {
+ throw new Error(
+ "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
}
}
}
+
+ // TODO: consider bailing if nmatched less than 4 because superposition
+ // not
+ // well defined.
+ // TODO: refactor superposable position search (above) from jmol selection
+ // construction (below)
+
String[] selcom = new String[files.length];
int nmatched = 0;
// generate select statements to select regions to superimpose structures
molsel.append(chainCd);
molsel.append("}");
}
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("((");
- selectioncom.append(selcom[pdbfnum].substring(1,
- selcom[pdbfnum].length() - 1));
- selectioncom.append(" )& ");
- selectioncom.append(pdbfnum + 1);
- selectioncom.append(".1)");
- if (pdbfnum < files.length - 1)
+ if (molsel.length() > 1)
{
- selectioncom.append("|");
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("((");
+ selectioncom.append(selcom[pdbfnum].substring(1,
+ selcom[pdbfnum].length() - 1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum + 1);
+ selectioncom.append(".1)");
+ if (pdbfnum < files.length - 1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ else
+ {
+ selcom[pdbfnum] = null;
}
}
}
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- if (pdbfnum == refStructure)
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
{
continue;
}
command.append(chainNames[pdbfnum]);
command.append(") against reference (");
command.append(chainNames[refStructure]);
- command.append(")\";\ncompare ");
+ command.append(")\";\ncompare " + nSeconds);
command.append("{");
command.append(1 + pdbfnum);
command.append(".1} {");
}
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());
+ if (selectioncom.length() > 0)
+ {
+ 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());
+ }
}
if (selectioncom.length() > 0)
{// finally, mark all regions that were superposed.
{
this.loadingFromArchive = loadingFromArchive;
}
-
+
/**
*
- * @return true if Jmol is still restoring state or loading is still going on (see setFinsihedLoadingFromArchive)
+ * @return true if Jmol is still restoring state or loading is still going on
+ * (see setFinsihedLoadingFromArchive)
*/
public boolean isLoadingFromArchive()
{
}
/**
- * modify flag which controls if sequence colouring events are honoured by the binding.
- * Should be true for normal operation
+ * modify flag which controls if sequence colouring events are honoured by the
+ * binding. Should be true for normal operation
+ *
* @param finishedLoading
*/
public void setFinishedLoadingFromArchive(boolean finishedLoading)
git://source.jalview.org / jalview.git / blobdiff