// ////////////////////////////////
// /StructureListener
- public String getPdbFile()
+ public String[] getPdbFile()
{
- return pdbentry.getFile();
+ return new String[] { pdbentry.getFile() };
}
String lastMessage;
// ////////////////////////////////
// /StructureListener
- public String getPdbFile()
+ public String[] getPdbFile()
{
- return pdbentry.getFile();
+ return new String[] { pdbentry.getFile() };
}
String lastMessage;
import java.awt.*;
import java.awt.event.*;
+import jalview.api.SequenceStructureBinding;
import jalview.datamodel.*;
import jalview.structure.*;
import jalview.io.*;
import jalview.schemes.*;
public class AppletJmol extends EmbmenuFrame implements StructureListener,
- JmolStatusListener, KeyListener, ActionListener, ItemListener
+ JmolStatusListener, KeyListener, ActionListener, ItemListener, SequenceStructureBinding
{
Menu fileMenu = new Menu("File");
embedMenuIfNeeded(renderPanel);
this.add(renderPanel, BorderLayout.CENTER);
viewer = JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter(), "jalviewJmol", ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(), "", this);
+ new SmarterJmolAdapter(), "jalviewJmol", ap.av.applet
+ .getDocumentBase(), ap.av.applet.getCodeBase(), "",
+ this);
jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400);
}
+ /**
+ * create a new binding between structures in an existing jmol viewer instance and
+ * an alignpanel with sequences that have existing PDBFile entries. Note, this does not open a new Jmol window,
+ * or modify the display of the structures in the original jmol window.
+ * @param viewer2
+ * @param alignPanel
+ * @param seqs - sequences to search for associations
+ */
+ public AppletJmol(JmolViewer viewer2, AlignmentPanel alignPanel,
+ SequenceI[] seqs)
+ {
+
+ // TODO Auto-generated constructor stub
+ }
+
public void loadInline(String string)
{
loadedInline = true;
void centerViewer()
{
+ jmolHistory(false);
StringBuffer cmd = new StringBuffer();
+ String lbl;
+ int mlength, p,mnum;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
{
CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
if (item.getState())
- cmd.append(":" + item.getLabel() + " or ");
+ {
+ lbl = item.getLabel();
+ mlength = 0;
+ do
+ {
+ p = mlength;
+ mlength = lbl.indexOf(":", p);
+ } while (p < mlength && mlength < (lbl.length() - 2));
+ mnum = 1+getModelNum(lbl.substring(0, mlength));
+ if (mnum>0)
+ {cmd.append(":" + lbl.substring(mlength + 1) + " /"
+ + mnum + " or ");
+ }
+ }
}
}
viewer
.evalString("select *;restrict " + cmd + ";cartoon;center "
+ cmd);
+ jmolHistory(true);
+ }
+
+ private int getModelNum(String modelFileName)
+ {
+ String[] mfn = getPdbFile();
+ if (mfn == null)
+ {
+ return -1;
+ }
+ for (int i = 0; i < mfn.length; i++)
+ {
+ if (mfn[i].equalsIgnoreCase(modelFileName))
+ return i;
+ }
+ return -1;
}
void closeViewer()
{
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
+ // remove listeners for all structures in viewer
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(this, this.getPdbFile());
+ // and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
- viewer = null;
- // We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getId());
+ viewer = null;
this.setVisible(false);
}
public void actionPerformed(ActionEvent evt)
{
+ jmolHistory(false);
if (evt.getSource() == mappingMenuItem)
{
jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
centerViewer();
allChainsSelected = false;
}
+ jmolHistory(true);
+ }
+ private void jmolHistory(boolean enable)
+ {
+ viewer.setBooleanProperty("history", enable);
}
-
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
String res;
int index;
Color col;
+ jmolHistory(false);
Enumeration en = ResidueProperties.aa3Hash.keys();
StringBuffer command = new StringBuffer("select *;color white;");
}
viewer.evalStringQuiet(command.toString());
+ jmolHistory(true);
}
public void itemStateChanged(ItemEvent evt)
{
}
+ String[] modelFileNames = null;
+
// ////////////////////////////////
// /StructureListener
- public String getPdbFile()
+ public String[] getPdbFile()
{
- return "???";
+ if (modelFileNames == null)
+ {
+ String mset[] = new String[viewer.getModelCount()];
+ for (int i = 0; i < mset.length; i++)
+ {
+ mset[i] = viewer.getModelFileName(i);
+ }
+ modelFileNames = mset;
+ }
+ return modelFileNames;
}
String lastMessage;
+ // jmol/ssm only
public void mouseOverStructure(int atomIndex, String strInfo)
{
int pdbResNum;
-
- int chainSeparator = strInfo.indexOf(":");
+ int mdlSep = strInfo.indexOf("/");
+ int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
if (chainSeparator == -1)
+ {
chainSeparator = strInfo.indexOf(".");
-
+ if (mdlSep > -1 && mdlSep < chainSeparator)
+ {
+ chainSeparator1 = chainSeparator;
+ chainSeparator = mdlSep;
+ }
+ }
pdbResNum = Integer.parseInt(strInfo.substring(
strInfo.indexOf("]") + 1, chainSeparator));
chainId = " ";
}
+ String pdbfilename = pdbentry.getFile();
+ if (mdlSep > -1)
+ {
+ if (chainSeparator1 == -1)
+ {
+ chainSeparator1 = strInfo.indexOf(".", mdlSep);
+ }
+ String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
+ chainSeparator1) : strInfo.substring(mdlSep + 1);
+ try
+ {
+ // recover PDB filename for the model hovered over.
+ pdbfilename = viewer
+ .getModelFileName(new Integer(mdlId).intValue() - 1);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
lastMessage = strInfo;
}
StringBuffer eval = new StringBuffer();
+ // jmol/ssm only
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
- if (!pdbfile.equals(pdbentry.getFile()))
+ int mdlNum = 1+getModelNum(pdbfile);
+ if (mdlNum==0)
+ {
return;
+ }
+ jmolHistory(false);
+ // if (!pdbfile.equals(pdbentry.getFile()))
+ // return;
if (resetLastRes.length() > 0)
{
viewer.evalStringQuiet(resetLastRes.toString());
}
eval.setLength(0);
- eval.append("select " + pdbResNum);
+ eval.append("select " + pdbResNum); // +modelNum
resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
+ resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
- resetLastRes.append(":");
if (!chain.equals(" "))
{
+ eval.append(":");
+ resetLastRes.append(":");
eval.append(chain);
resetLastRes.append(chain);
}
-
+ // if (mdlNum != 0)
+ {
+ eval.append(" /" + (mdlNum));
+ resetLastRes.append("/" + (mdlNum));
+ }
eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
eval.append("spacefill 200;select none");
viewer.evalStringQuiet(eval.toString());
+ jmolHistory(true);
}
if (!colourBySequence)
return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
+ String[] files = getPdbFile();
SequenceRenderer sr = new SequenceRenderer(ap.av);
boolean showFeatures = false;
StringBuffer command = new StringBuffer();
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- for (int sp, m = 0; m < mapping.length; m++)
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ continue;
+
+ int lastPos = -1;
+ for (int s = 0; s < sequence.length; s++)
{
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
+ for (int sp, m = 0; m < mapping.length; m++)
{
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
+ if (mapping[m].getSequence() == sequence[s]
+ && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
{
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ SequenceI asp = ap.av.alignment.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
{
- continue;
+ // no mapping to gaps in sequence
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+ if (pos < 1 || pos == lastPos)
+ continue;
+
+ lastPos = pos;
+
+ Color col = sr.getResidueBoxColour(sequence[s], r);
+
+ if (showFeatures)
+ col = fr.findFeatureColour(col, sequence[s], r);
+ String newSelcom = (mapping[m].getChain() != " " ? ":"
+ + mapping[m].getChain() : "")
+ + "/"
+ + (pdbfnum + 1)
+ + ".1"
+ + ";color["
+ + col.getRed()
+ + ","
+ + col.getGreen()
+ + ","
+ + col.getBlue() + "]";
+ if (command.toString().endsWith(newSelcom))
+ {
+ command = condenseCommand(command.toString(), pos);
+ continue;
+ }
+ // TODO: deal with case when buffer is too large for Jmol to parse
+ // - execute command and flush
+
+ command.append(";select " + pos);
+ command.append(newSelcom);
}
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
-
- if (command.toString().endsWith(
- ":" + mapping[m].getChain() + ";color[" + col.getRed()
- + "," + col.getGreen() + "," + col.getBlue()
- + "]"))
- {
- command = condenseCommand(command.toString(), pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color[" + col.getRed() + "," + col.getGreen()
- + "," + col.getBlue() + "]");
+ break;
}
- break;
}
}
}
+ jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command.toString()))
{
viewer.evalStringQuiet(command.toString());
}
+ jmolHistory(true);
lastCommand = command.toString();
}
{
}
- public void notifyFileLoaded(String fullPathName, String fileName,
+ public void notifyFileLoaded(String fullPathName, String fileName2,
String modelName, String errorMsg, int modelParts)
{
if (errorMsg != null)
repaint();
return;
}
-
fileLoadingError = null;
-
- if (fileName != null)
+ modelFileNames = null;
+
+ String[] modelfilenames = getPdbFile();
+ ssm = StructureSelectionManager.getStructureSelectionManager();
+ boolean modelsloaded=false;
+ for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
- // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains
- // FILE LOADED OK
- jmolpopup.updateComputedMenus();
- viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdb;
- if (loadedInline)
+ String fileName = modelfilenames[modelnum];
+ if (fileName != null)
{
- pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
- AppletFormatAdapter.PASTE);
- pdbentry.setFile("INLINE" + pdb.id);
- }
- else
- {
- // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs
- // to be tested. See mantis bug
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
+ if (pdbentry.getFile().equals(fileName))
+ {
+ modelsloaded=true;
+ MCview.PDBfile pdb;
+ if (loadedInline)
+ {
+ pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
+ AppletFormatAdapter.PASTE);
+ pdbentry.setFile("INLINE" + pdb.id);
+ }
+ else
+ {
+ // TODO: Jmol can in principle retrieve from CLASSLOADER but this
+ // needs
+ // to be tested. See mantis bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
- AppletFormatAdapter.URL);
+ pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
+ AppletFormatAdapter.URL);
- }
+ }
- pdbentry.setId(pdb.id);
+ pdbentry.setId(pdb.id);
- ssm.addStructureViewerListener(this);
+ Vector chains = new Vector();
+ for (int i = 0; i < pdb.chains.size(); i++)
+ {
+ chains.addElement(new String(pdb.id + ":"
+ + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
+ }
+ setChainMenuItems(chains);
- Vector chains = new Vector();
- for (int i = 0; i < pdb.chains.size(); i++)
- {
- chains.addElement(((MCview.PDBChain) pdb.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
+ colourBySequence(ap);
- colourBySequence(ap);
+ StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+ + pdbentry.getId());
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
+ if (pdbentry.getProperty() != null)
+ {
+ if (pdbentry.getProperty().get("method") != null)
+ {
+ title.append(" Method: ");
+ title.append(pdbentry.getProperty().get("method"));
+ }
+ if (pdbentry.getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdbentry.getProperty().get("chains"));
+ }
+ }
+
+ this.setTitle(title.toString());
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
}
- if (pdbentry.getProperty().get("chains") != null)
+ else
{
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
+ // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
+ // and try to find a home - either on a matching sequence or as a new sequence.
+ String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+ "PDB");
+ // parse pdb file into a chain, etc.
+ // locate best match for pdb in associated views and add mapping to
+ // ssm
+ modelsloaded=true;
}
}
+ }
+ if (modelsloaded) {
+ // FILE LOADED OK
+ jmolpopup.updateComputedMenus();
+ viewer
+ .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
- this.setTitle(title.toString());
-
+ ssm.addStructureViewerListener(this);
}
- else
- return;
}
public void sendConsoleEcho(String strEcho)
public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
{
- if (strData!=null)
+ if (strData != null)
{
- System.err.println("Ignoring additional pick data string "+strData);
+ System.err.println("Ignoring additional pick data string " + strData);
}
int chainSeparator = strInfo.indexOf(":");
-
+ int p=0;
if (chainSeparator == -1)
chainSeparator = strInfo.indexOf(".");
String picked = strInfo.substring(strInfo.indexOf("]") + 1,
chainSeparator);
-
- if (strInfo.indexOf(":") > -1)
- picked += strInfo.substring(strInfo.indexOf(":") + 1, strInfo
+ String mdlString="";
+ if ((p=strInfo.indexOf(":")) > -1)
+ picked += strInfo.substring(p + 1, strInfo
.indexOf("."));
- picked = "(("+picked+".CA" + ")|("+picked+".P"+"))";
+ if ((p=strInfo.indexOf("/"))> -1)
+ {
+ mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
+ }
+ picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
+ jmolHistory(false);
if (!atomsPicked.contains(picked))
{
- viewer.evalString("select " + picked + ";label %n %r:%c");
+ viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
viewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
+ jmolHistory(true);
+
}
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
- if (data!=null)
+ if (data != null)
{
- System.err.println("Ignoring additional hover info: "+data);
+ System.err.println("Ignoring additional hover info: " + data);
}
mouseOverStructure(atomIndex, strInfo);
}
-
public void showUrl(String url)
{
try
public float[][] functionXY(String functionName, int x, int y)
{
- return null ;
+ return null;
}
// /End JmolStatusListener
public void notifyCallback(int type, Object[] data)
{
- try {
- switch (type)
+ try
{
- case JmolConstants.CALLBACK_LOADSTRUCT:
- notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5]).intValue());
-
- break;
- case JmolConstants.CALLBACK_PICK:
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
- // also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
- break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue());
- break;
- case JmolConstants.CALLBACK_ECHO:
- sendConsoleEcho((String)data[1]);
- break;
- case JmolConstants.CALLBACK_MESSAGE:
- sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]);
- break;
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_CLICK:
+ switch (type)
+ {
+ case JmolConstants.CALLBACK_LOADSTRUCT:
+ notifyFileLoaded((String) data[1], (String) data[2],
+ (String) data[3], (String) data[4], ((Integer) data[5])
+ .intValue());
+
+ break;
+ case JmolConstants.CALLBACK_PICK:
+ notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ // also highlight in alignment
+ case JmolConstants.CALLBACK_HOVER:
+ notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ break;
+ case JmolConstants.CALLBACK_SCRIPT:
+ notifyScriptTermination((String) data[2], ((Integer) data[3])
+ .intValue());
+ break;
+ case JmolConstants.CALLBACK_ECHO:
+ sendConsoleEcho((String) data[1]);
+ break;
+ case JmolConstants.CALLBACK_MESSAGE:
+ sendConsoleMessage((data == null) ? ((String) null)
+ : (String) data[1]);
+ break;
+ case JmolConstants.CALLBACK_MEASURE:
+ case JmolConstants.CALLBACK_CLICK:
default:
- System.err.println("Unhandled callback "+type+" "+data);
+ System.err.println("Unhandled callback " + type + " " + data);
break;
- }
- }
- catch (Exception e)
+ }
+ } catch (Exception e)
{
System.err.println("Squashed Jmol callback handler error:");
e.printStackTrace();
case JmolConstants.CALLBACK_ERROR:
return true;
case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
+ case JmolConstants.CALLBACK_ANIMFRAME:
case JmolConstants.CALLBACK_MINIMIZATION:
case JmolConstants.CALLBACK_RESIZE:
case JmolConstants.CALLBACK_SYNC:
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
- System.err.println("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction);
-
+ System.err.println("Ignoring set-callback request to associate "
+ + callbackType + " with function " + callbackFunction);
+
}
}
import java.io.*;
import jalview.jbgui.GStructureViewer;
+import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.*;
import org.jmol.viewer.JmolConstants;
public class AppJmol extends GStructureViewer implements StructureListener,
- JmolStatusListener, Runnable
+ JmolStatusListener, Runnable, SequenceStructureBinding
{
JmolViewer viewer;
void centerViewer()
{
+ jmolHistory(false);
StringBuffer cmd = new StringBuffer();
+ String lbl;
+ int mlength, p,mnum;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
- cmd.append(":" + item.getText() + " or ");
+ { lbl = item.getText();
+ mlength = 0;
+ do
+ {
+ p = mlength;
+ mlength = lbl.indexOf(":", p);
+ } while (p < mlength && mlength < (lbl.length() - 2));
+ if (pdbentry.getId().equals(lbl.substring(0,mlength)))
+ {
+ mnum = 1+getModelNum(pdbentry.getFile());
+ if (mnum>0)
+ {cmd.append(":" + lbl.substring(mlength + 1) + " /"
+ + mnum + " or ");
+ }
+ }
+ }
}
}
viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
+ cmd);
+ jmolHistory(true);
+ }
+ private int getModelNum(String modelFileName)
+ {
+ String[] mfn = getPdbFile();
+ if (mfn == null)
+ {
+ return -1;
+ }
+ for (int i = 0; i < mfn.length; i++)
+ {
+ if (mfn[i].equalsIgnoreCase(modelFileName))
+ return i;
+ }
+ return -1;
}
void closeViewer()
{
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
+ // remove listeners for all structures in viewer
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(this, getPdbFile());
+ // and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
viewer = null;
-
- // We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getFile());
}
public void run()
{
colourBySequence = false;
seqColour.setSelected(false);
+ jmolHistory(false);
viewer.evalStringQuiet("select *;color chain");
+ jmolHistory(true);
}
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
colourBySequence = false;
seqColour.setSelected(false);
+ jmolHistory(false);
viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
+ "select LYS,ARG;color blue;select CYS;color yellow");
+ jmolHistory(true);
}
public void zappoColour_actionPerformed(ActionEvent actionEvent)
public void setJalviewColourScheme(ColourSchemeI cs)
{
+ jmolHistory(false);
colourBySequence = false;
seqColour.setSelected(false);
}
viewer.evalStringQuiet(command.toString());
+ jmolHistory(true);
}
public void userColour_actionPerformed(ActionEvent actionEvent)
if (col != null)
{
+ jmolHistory(false);
viewer.evalStringQuiet("background [" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
+ jmolHistory(true);
}
}
+ private void jmolHistory(boolean enable)
+ {
+ viewer.setBooleanProperty("history", enable);
+ }
public void jmolHelp_actionPerformed(ActionEvent actionEvent)
{
{
}
}
+ String[] modelFileNames = null;
// ////////////////////////////////
// /StructureListener
- public String getPdbFile()
+ public String[] getPdbFile()
{
- return pdbentry.getFile();
+ if (modelFileNames == null)
+ {
+ String mset[] = new String[viewer.getModelCount()];
+ for (int i = 0; i < mset.length; i++)
+ {
+ try {
+ String mname = viewer.getModelFileName(i);
+ if (mname==null)
+ {
+ System.err.println("Model "+i+" has no filename!");
+ continue;
+ }
+ File fpath = new File(mname);
+ mset[i] = fpath.toString();
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!");
+ }
+ }
+ modelFileNames = mset;
+ }
+ return modelFileNames;
}
Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
+ .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?");
String lastMessage;
public void mouseOverStructure(int atomIndex, String strInfo)
{
+ // copied from AppJmol - will be refactored to binding eventually
+ int pdbResNum;
+ int mdlSep = strInfo.indexOf("/");
+ int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
+
+ if (chainSeparator == -1)
+ {
+ chainSeparator = strInfo.indexOf(".");
+ if (mdlSep > -1 && mdlSep < chainSeparator)
+ {
+ chainSeparator1 = chainSeparator;
+ chainSeparator = mdlSep;
+ }
+ }
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, chainSeparator));
+
+ String chainId;
+
+ if (strInfo.indexOf(":") > -1)
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
+ .indexOf("."));
+ else
+ {
+ chainId = " ";
+ }
+
+ String pdbfilename = pdbentry.getFile();
+ if (mdlSep > -1)
+ {
+ if (chainSeparator1 == -1)
+ {
+ chainSeparator1 = strInfo.indexOf(".", mdlSep);
+ }
+ String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
+ chainSeparator1) : strInfo.substring(mdlSep + 1);
+ try
+ {
+ // recover PDB filename for the model hovered over.
+ pdbfilename = viewer
+ .getModelFileName(new Integer(mdlId).intValue() - 1);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (lastMessage == null || !lastMessage.equals(strInfo))
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+
+ lastMessage = strInfo;
+/*
+ * Old Implementation based on Pattern regex.
Matcher matcher = pattern.matcher(strInfo);
matcher.find();
matcher.group(1);
int pdbResNum = Integer.parseInt(matcher.group(2));
String chainId = matcher.group(3);
-
+
if (chainId != null)
chainId = chainId.substring(1, chainId.length());
else
{
chainId = " ";
}
+ String mdlId = matcher.group(4);
+ String pdbfilename = pdbentry.getFile();
+ if (mdlId!=null && mdlId.length()>0)
+ {
+ try {
+ // recover PDB filename for the model hovered over.
+ pdbfilename = viewer.getModelFileName(new Integer(mdlId).intValue()-1);
+ } catch (Exception e) {};
+ }
if (lastMessage == null || !lastMessage.equals(strInfo))
{
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
}
- lastMessage = strInfo;
+ lastMessage = strInfo; */
}
StringBuffer resetLastRes = new StringBuffer();
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
- // TODO: rna: remove CA dependency in select string
- if (!pdbfile.equals(pdbentry.getFile()))
+ int mdlNum = 1+getModelNum(pdbfile);
+ if (mdlNum==0)
+ {
return;
+ }
+ jmolHistory(false);
+ // if (!pdbfile.equals(pdbentry.getFile()))
+ // return;
if (resetLastRes.length() > 0)
{
viewer.evalStringQuiet(resetLastRes.toString());
}
eval.setLength(0);
- eval.append("select " + pdbResNum);
+ eval.append("select " + pdbResNum); // +modelNum
resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
+ resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
- resetLastRes.append(":");
if (!chain.equals(" "))
{
+ eval.append(":");
+ resetLastRes.append(":");
eval.append(chain);
resetLastRes.append(chain);
}
-
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); // ".*;");
+ // if (mdlNum != 0)
+ {
+ eval.append(" /" + (mdlNum));
+ resetLastRes.append(" /" + (mdlNum));
+ }
+ eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- // + ".*;spacefill 0;");
- + " and not hetero;spacefill 0;");
+ + " and not hetero; spacefill 0;");
eval.append("spacefill 200;select none");
- // System.out.println("jmol:\n"+eval+"\n");
+
viewer.evalStringQuiet(eval.toString());
+ jmolHistory(true);
}
public Color getColour(int atomIndex, int pdbResNum, String chain,
if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
return;
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
+ String[] files = getPdbFile();
+
SequenceRenderer sr = new SequenceRenderer(ap.av);
boolean showFeatures = false;
}
StringBuffer command = new StringBuffer();
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ continue;
+
int lastPos = -1;
for (int sp, s = 0; s < sequence.length; s++)
if (showFeatures)
col = fr.findFeatureColour(col, asp, r);
-
- if (command.toString().endsWith(
- ":" + mapping[m].getChain() + ";color[" + col.getRed()
- + "," + col.getGreen() + "," + col.getBlue()
- + "]"))
+ String newSelcom = (mapping[m].getChain() != " " ? ":"
+ + mapping[m].getChain() : "")
+ + "/"
+ + (pdbfnum + 1)
+ + ".1"
+ + ";color["
+ + col.getRed()
+ + ","
+ + col.getGreen()
+ + ","
+ + col.getBlue() + "]";
+ if (command.toString().endsWith(newSelcom))
{
command = condenseCommand(command, pos);
continue;
}
command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color[" + col.getRed() + "," + col.getGreen()
- + "," + col.getBlue() + "]");
-
+ command.append(newSelcom);
}
break;
}
}
+ }
}
+ jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command.toString()))
{
viewer.evalStringQuiet(command.toString());
}
+ jmolHistory(true);
lastCommand = command.toString();
}
System.out.println("JMOL CREATE IMAGE");
}
- public void notifyFileLoaded(String fullPathName, String fileName,
+ public void notifyFileLoaded(String fullPathName, String fileName2,
String modelName, String errorMsg, int modelParts)
{
if (errorMsg != null)
}
fileLoadingError = null;
+ modelFileNames = null;
+
+ String[] modelfilenames = getPdbFile();
+ ssm = StructureSelectionManager.getStructureSelectionManager();
+ boolean modelsloaded=false;
+ for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
+ {
+ String fileName = modelfilenames[modelnum];
if (fileName != null)
{
- // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains
+ modelsloaded=true;
+ // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
+ if (pdbentry.getFile().equals(fileName))
+ {
+ // TODO: do some checking using the modelPts number of parts against our
+ // own estimate of the number of chains
// FILE LOADED OK
- ssm = StructureSelectionManager.getStructureSelectionManager();
MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
.getFile(), AppletFormatAdapter.FILE);
- ssm.addStructureViewerListener(this);
Vector chains = new Vector();
for (int i = 0; i < pdbFile.chains.size(); i++)
{
chains
- .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
+ .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id));
}
setChainMenuItems(chains);
- jmolpopup.updateComputedMenus();
-
if (!loadingFromArchive)
{
viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
+ .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
colourBySequence(ap);
}
loadingFromArchive = false;
}
- else
- return;
+ else {
+ // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
+ // and try to find a home - either on a matching sequence or as a new sequence.
+ String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+ "PDB");
+ // parse pdb file into a chain, etc.
+ // locate best match for pdb in associated views and add mapping to
+ // ssm
+ modelsloaded=true;
+ }
+ }
+ }
+ if (modelsloaded)
+ {
+ ssm.addStructureViewerListener(this);
+ jmolpopup.updateComputedMenus();
+ }
}
public void sendConsoleEcho(String strEcho)
public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
{
- if (strData!=null)
+ if (strData != null)
{
- Cache.log.info("Non null pick data string: "+strData+" (other info: '"+strInfo+"' pos "+atomIndex+")");
+ Cache.log.info("Non null pick data string: " + strData
+ + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
+ /*
Matcher matcher = pattern.matcher(strInfo);
matcher.find();
String picked = resnum;
+
if (chainId != null)
picked += (":" + chainId.substring(1, chainId.length()));
-
- picked = "(("+picked+".CA" + ")|("+picked+".P"+"))";
-
+*/
+ 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)
+ {
+ mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
+ }
+ picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
+ jmolHistory(false);
if (!atomsPicked.contains(picked))
{
- if (chainId != null)
+ // TODO: re-instate chain ID separator dependent labelling for both applet and application
+// if (chainId != null)
viewer.evalString("select " + picked + ";label %n %r:%c");
- else
- viewer.evalString("select " + picked + ";label %n %r");
+// else
+// viewer.evalString("select " + picked + ";label %n %r");
atomsPicked.addElement(picked);
}
else
viewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
-
+ jmolHistory(true);
if (scriptWindow != null)
{
scriptWindow.sendConsoleMessage(strInfo);
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
- if (data!=null)
+ if (data != null)
{
- Cache.log.info("Non null hover data string: "+data+" (other info: '"+strInfo+"' pos "+atomIndex+")");
+ Cache.log.info("Non null hover data string: " + data
+ + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
@Override
public void showUrl(String url)
{
- try {
+ try
+ {
jalview.util.BrowserLauncher.openURL(url);
} catch (IOException e)
{
- Cache.log.error("Failed to launch Jmol-associated url "+url,e);
+ Cache.log.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
}
@Override
public void notifyCallback(int type, Object[] data)
{
- try {
- switch (type)
+ try
{
- case JmolConstants.CALLBACK_LOADSTRUCT:
- notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5]).intValue());
-
- break;
- case JmolConstants.CALLBACK_PICK:
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
- // also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
- break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue());
- break;
- case JmolConstants.CALLBACK_ECHO:
- sendConsoleEcho((String)data[1]);
- break;
- case JmolConstants.CALLBACK_MESSAGE:
- sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]);
- break;
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_CLICK:
+ switch (type)
+ {
+ case JmolConstants.CALLBACK_LOADSTRUCT:
+ notifyFileLoaded((String) data[1], (String) data[2],
+ (String) data[3], (String) data[4], ((Integer) data[5])
+ .intValue());
+
+ break;
+ case JmolConstants.CALLBACK_PICK:
+ notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ // also highlight in alignment
+ case JmolConstants.CALLBACK_HOVER:
+ notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ break;
+ case JmolConstants.CALLBACK_SCRIPT:
+ notifyScriptTermination((String) data[2], ((Integer) data[3])
+ .intValue());
+ break;
+ case JmolConstants.CALLBACK_ECHO:
+ sendConsoleEcho((String) data[1]);
+ break;
+ case JmolConstants.CALLBACK_MESSAGE:
+ sendConsoleMessage((data == null) ? ((String) null)
+ : (String) data[1]);
+ break;
+ case JmolConstants.CALLBACK_MEASURE:
+ case JmolConstants.CALLBACK_CLICK:
default:
- System.err.println("Unhandled callback "+type+" "+data);
+ System.err.println("Unhandled callback " + type + " " + data);
break;
- }
- }
- catch (Exception e)
+ }
+ } catch (Exception e)
{
- Cache.log.warn("Squashed Jmol callback handler error: ",e);
+ Cache.log.warn("Squashed Jmol callback handler error: ", e);
}
}
case JmolConstants.CALLBACK_ERROR:
return true;
case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
+ case JmolConstants.CALLBACK_ANIMFRAME:
case JmolConstants.CALLBACK_MINIMIZATION:
case JmolConstants.CALLBACK_RESIZE:
case JmolConstants.CALLBACK_SYNC:
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
- Cache.log.debug("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction);
-
+ Cache.log.debug("Ignoring set-callback request to associate "
+ + callbackType + " with function " + callbackFunction);
+
}
}
public interface StructureListener
{
- public String getPdbFile();
+ public String[] getPdbFile();
public void mouseOverStructure(int atomIndex, String strInfo);
for (int i = 0; i < pdb.chains.size(); i++)
{
-
- // TODO: correctly determine sequence type for mixed na/peptide structures
+
+ // TODO: correctly determine sequence type for mixed na/peptide
+ // structures
AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
- .elementAt(i)).sequence, ((PDBChain)pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+ .elementAt(i)).sequence, ((PDBChain) pdb.chains
+ .elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
return pdb;
}
- public void removeStructureViewerListener(Object svl, String pdbfile)
+ public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
-
+ if (pdbfiles==null)
+ {
+ return;
+ }
boolean removeMapping = true;
-
+ String[] handlepdbs;
+ Vector pdbs = new Vector();
+ for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
+ ;
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- if (sl.getPdbFile().equals(pdbfile))
+ handlepdbs = sl.getPdbFile();
+ for (int j = 0; j < handlepdbs.length; j++)
{
- removeMapping = false;
- break;
+ if (pdbs.contains(handlepdbs[j]))
+ {
+ pdbs.removeElement(handlepdbs[j]);
+ }
}
+
}
}
-
- if (removeMapping && mappings != null)
+
+ if (pdbs.size()>0 && mappings != null)
{
Vector tmp = new Vector();
for (int i = 0; i < mappings.length; i++)
{
- if (!mappings[i].pdbfile.equals(pdbfile))
+ if (!pdbs.contains(mappings[i].pdbfile))
{
tmp.addElement(mappings[i]);
}
git://source.jalview.org / jalview.git / commitdiff