/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
import jalview.io.AppletFormatAdapter;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
+import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Container;
import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
-import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Map;
import java.util.Vector;
import org.jmol.constant.EnumCallback;
import org.jmol.popup.JmolPopup;
-public abstract class JalviewJmolBinding implements StructureListener,
+public abstract class JalviewJmolBinding extends SequenceStructureBindingModel implements StructureListener,
JmolStatusListener, SequenceStructureBinding,
JmolSelectionListener, ComponentListener,
StructureSelectionManagerProvider
{
/**
- * set if Jmol state is being restored from some source - instructs binding
- * not to apply default display style when structure set is updated for first
- * 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
- */
- private boolean loadingFinished = true;
-
- /**
* state flag used to check if the Jmol viewer's paint method can be called
*/
private boolean finishedInit = false;
+ (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
+ {
cmd.setLength(cmd.length() - 4);
+ }
evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
}
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)
+ long starttime = System.currentTimeMillis();
+ boolean waiting = true;
+ do
+ {
+ waiting = false;
+ for (String file : files)
{
- try {
+ try
+ {
// HACK - in Jalview 2.8 this call may not be threadsafe so we catch
// every possible exception
StructureMapping[] sm = ssm.getMapping(file);
}
}
// we wait around for a reasonable time before we give up
- } while (waiting && System.currentTimeMillis()<(10000+1000*files.length+starttime));
+ } 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.");
+ System.err
+ .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
return;
}
StringBuffer selectioncom = new StringBuffer();
// Jmol callback has completed.
if (mapping == null || mapping.length < 1)
{
- throw new Error("Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data"));
}
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.
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;
}
}
}
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 "+nSeconds);
+ 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.
public void colourBySequence(boolean showFeatures,
jalview.api.AlignmentViewPanel alignmentv)
{
- if (!colourBySequence || !loadingFinished)
+ if (!colourBySequence || !isLoadingFinished())
+ {
return;
+ }
if (ssm == null)
{
return;
for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
.getColourBySequenceCommand(ssm, files, sequence, sr, fr,
alignment))
+ {
for (String cbyseq : cpdbbyseq.commands)
{
evalStateCommand(cbyseq);
}
+ }
}
public boolean isColourBySequence()
String pdbfile)
{
if (getModelNum(pdbfile) < 0)
+ {
return null;
+ }
// TODO: verify atomIndex is selecting correct model.
return new Color(viewer.getAtomArgb(atomIndex));
}
for (int i = 0; i < mfn.length; i++)
{
if (mfn[i].equalsIgnoreCase(modelFileName))
+ {
return i;
+ }
}
return -1;
}
jmolpopup.show(x, y);
}
- // jmol/ssm only
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ /**
+ * Highlight the specified atoms in the structure.
+ *
+ * @param atoms
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
if (modelFileNames == null)
{
return;
}
- // look up file model number for this pdbfile
- int mdlNum = 0;
- String fn;
- // may need to adjust for URLencoding here - we don't worry about that yet.
- while (mdlNum < modelFileNames.length
- && !pdbfile.equals(modelFileNames[mdlNum]))
- {
- // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
- mdlNum++;
- }
- if (mdlNum == modelFileNames.length)
+ for (AtomSpec atom : atoms)
{
- return;
- }
+ String pdbfile = atom.getPdbId();
+ int pdbResNum = atom.getPdbResNum();
+ String chain = atom.getChain();
+
+ // look up file model number for this pdbfile
+ int mdlNum = 0;
+ String fn;
+ // may need to adjust for URLencoding here - we don't worry about that
+ // yet.
+ while (mdlNum < modelFileNames.length
+ && !pdbfile.equals(modelFileNames[mdlNum]))
+ {
+ // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
+ mdlNum++;
+ }
+ if (mdlNum == modelFileNames.length)
+ {
+ return;
+ }
- jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
+ jmolHistory(false);
+ // if (!pdbfile.equals(pdbentry.getFile()))
+ // return;
+ if (resetLastRes.length() > 0)
+ {
+ viewer.evalStringQuiet(resetLastRes.toString());
+ }
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
+ eval.setLength(0);
+ eval.append("select " + pdbResNum); // +modelNum
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum); // +modelNum
+ resetLastRes.setLength(0);
+ resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
- resetLastRes.append(":");
- if (!chain.equals(" "))
- {
- eval.append(chain);
- resetLastRes.append(chain);
- }
- {
- eval.append(" /" + (mdlNum + 1));
- resetLastRes.append("/" + (mdlNum + 1));
- }
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
+ eval.append(":");
+ resetLastRes.append(":");
+ if (!chain.equals(" "))
+ {
+ eval.append(chain);
+ resetLastRes.append(chain);
+ }
+ {
+ eval.append(" /" + (mdlNum + 1));
+ resetLastRes.append("/" + (mdlNum + 1));
+ }
+ eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
+ resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ + " and not hetero; spacefill 0;");
- eval.append("spacefill 200;select none");
+ eval.append("spacefill 200;select none");
- viewer.evalStringQuiet(eval.toString());
- jmolHistory(true);
+ viewer.evalStringQuiet(eval.toString());
+ jmolHistory(true);
+ }
}
String chainId;
if (strInfo.indexOf(":") > -1)
+ {
chainId = strInfo.substring(strInfo.indexOf(":") + 1,
strInfo.indexOf("."));
+ }
else
{
chainId = " ";
;
}
if (lastMessage == null || !lastMessage.equals(strInfo))
+ {
ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ }
lastMessage = strInfo;
}
int chainSeparator = strInfo.indexOf(":");
int p = 0;
if (chainSeparator == -1)
+ {
chainSeparator = strInfo.indexOf(".");
+ }
String picked = strInfo.substring(strInfo.indexOf("]") + 1,
chainSeparator);
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
+ {
picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ }
if ((p = strInfo.indexOf("/")) > -1)
{
for (int i = 0; i < pdb.chains.size(); i++)
{
String chid = new String(pdb.id + ":"
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+ + pdb.chains.elementAt(i).id);
chainFile.put(chid, fileName);
chainNames.addElement(chid);
}
colourBySequence = false;
if (cs == null)
+ {
return;
+ }
- String res;
int index;
Color col;
jmolHistory(false);
// TODO: Switch between nucleotide or aa selection expressions
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
+ StringBuilder command = new StringBuilder(128);
+ command.append("select *;color white;");
+ for (String res : ResidueProperties.aa3Hash.keySet())
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
+ index = ResidueProperties.aa3Hash.get(res).intValue();
if (index > 20)
+ {
continue;
+ }
col = cs.findColour(ResidueProperties.aa[index].charAt(0));
showConsole(false);
}
- public void setLoadingFromArchive(boolean loadingFromArchive)
- {
- this.loadingFromArchive = loadingFromArchive;
- }
-
- /**
- *
- * @return true if Jmol is still restoring state or loading is still going on (see setFinsihedLoadingFromArchive)
- */
- public boolean isLoadingFromArchive()
- {
- return loadingFromArchive && !loadingFinished;
- }
-
- /**
- * 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)
- {
- loadingFinished = finishedLoading;
- }
-
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
{
if (pe < 0 || pe >= pdbentry.length)
{
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
+ throw new Error(MessageManager.formatMessage("error.implementation_error_no_pdbentry_from_index", new String[]{Integer.valueOf(pe).toString()}));
}
final String nullChain = "TheNullChain";
Vector s = new Vector();
git://source.jalview.org / jalview.git / blobdiff