/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
import java.io.File;
import java.net.URL;
import java.util.*;
+import java.applet.Applet;
import java.awt.*;
import java.awt.event.*;
+import javax.swing.JPanel;
+
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.SequenceStructureBinding;
import org.jmol.popup.*;
import org.jmol.viewer.JmolConstants;
+import org.jmol.viewer.Viewer;
import jalview.schemes.*;
public abstract class JalviewJmolBinding implements StructureListener,
- JmolStatusListener, SequenceStructureBinding
+ JmolStatusListener, SequenceStructureBinding,
+ JmolSelectionListener, ComponentListener
{
/**
* time.
*/
private boolean loadingFromArchive = false;
+
/**
* state flag used to check if the Jmol viewer's paint method can be called
*/
- private boolean finishedInit=false;
-
+ private boolean finishedInit = false;
+
public boolean isFinishedInit()
{
return finishedInit;
public Vector chainNames;
- String[] chains;
+ Hashtable chainFile;
+
+ /**
+ * 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(),
*/
}
+ public JalviewJmolBinding(JmolViewer viewer2)
+ {
+ viewer = viewer2;
+ viewer.setJmolStatusListener(this);
+ viewer.addSelectionListener(this);
+ }
+
/**
- * construct a title string for the viewer window based on the data jalview knows about
- * @return
+ * construct a title string for the viewer window based on the data jalview
+ * knows about
+ *
+ * @return
*/
- public String getViewerTitle() {
- if (sequence==null || pdbentry==null || sequence.length<1 || pdbentry.length<1)
+ public String getViewerTitle()
+ {
+ if (sequence == null || pdbentry == null || sequence.length < 1
+ || pdbentry.length < 1 || sequence[0].length < 1)
{
- return("Jalview Jmol Window");
+ return ("Jalview Jmol Window");
}
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+ // TODO: give a more informative title when multiple structures are
+ // displayed.
+ StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
+ pdbentry[0].getId());
if (pdbentry[0].getProperty() != null)
p = mlength;
mlength = lbl.indexOf(":", p);
} while (p < mlength && mlength < (lbl.length() - 2));
+ // TODO: lookup each pdb id and recover proper model number for it.
cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + getModelNum(lbl.substring(0, mlength)) + " or ");
+ + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
cmd.setLength(cmd.length() - 4);
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
+ evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
}
public void closeViewer()
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
- lastCommand=null;
+ lastCommand = null;
viewer = null;
+ releaseUIResources();
}
+ /**
+ * called by JalviewJmolbinding after closeViewer is called - release any
+ * resources and references so they can be garbage collected.
+ */
+ protected abstract void releaseUIResources();
+
public void colourByChain()
{
colourBySequence = false;
+ // TODO: colour by chain should colour each chain distinctly across all
+ // visible models
+ // TODO: http://issues.jalview.org/browse/JAL-628
evalStateCommand("select *;color chain");
}
*/
public void superposeStructures(AlignmentI alignment)
{
+ superposeStructures(alignment, -1, 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)
+ */
+ 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();
- StringBuffer command = 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++)
+ String[] selcom = new String[files.length];
+ int nmatched = 0;
+ // 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 = new StringBuffer();
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
{
- if (s > 0)
+ if (matched[r])
{
- command.append(" | ");
+ if (pdbfnum == 0)
+ {
+ nmatched++;
+ }
+ 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("}");
+ }
+ 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("|");
+ }
+ }
+ }
+ // 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)
+ {
+ 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) {
+ public void evalStateCommand(String command)
+ {
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
- viewer.evalStringQuiet(command+"\n");
+ viewer.evalStringQuiet(command + "\n");
}
jmolHistory(true);
lastCommand = command;
}
+
/**
* colour any structures associated with sequences in the given alignment
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
{
if (!colourBySequence)
return;
- if (ssm==null)
+ if (ssm == null)
{
return;
}
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);
+ if (showFeatures && fr != null)
+ col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
StringBuffer condenseCommand(String command, int pos)
{
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
+ StringBuffer sb = new StringBuffer(command.substring(0,
+ command.lastIndexOf("select") + 7));
command = command.substring(sb.length());
*/
public abstract FeatureRenderer getFeatureRenderer();
+ /**
+ * instruct the Jalview binding to update the pdbentries vector if necessary
+ * prior to matching the jmol view's contents to the list of structure files
+ * Jalview knows about.
+ */
+ public abstract void refreshPdbEntries();
+
private int getModelNum(String modelFileName)
{
String[] mfn = getPdbFile();
return -1;
}
+ /**
+ * map between index of model filename returned from getPdbFile and the first
+ * index of models from this file in the viewer. Note - this is not trimmed -
+ * use getPdbFile to get number of unique models.
+ */
+ private int _modelFileNameMap[];
+
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ public synchronized String[] getPdbFile()
{
+ if (viewer == null)
+ {
+ return new String[0];
+ }
if (modelFileNames == null)
{
+
String mset[] = new String[viewer.getModelCount()];
- for (int i = 0; i < mset.length; i++)
+ _modelFileNameMap = new int[mset.length];
+ int j = 1;
+ mset[0] = viewer.getModelFileName(0);
+ for (int i = 1; i < mset.length; i++)
{
- mset[i] = viewer.getModelFileName(i);
+ mset[j] = viewer.getModelFileName(i);
+ _modelFileNameMap[j] = i; // record the model index for the filename
+ // skip any additional models in the same file (NMR structures)
+ if ((mset[j] == null ? mset[j] != mset[j - 1]
+ : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+ {
+ j++;
+ }
}
- modelFileNames = mset;
+ modelFileNames = new String[j];
+ System.arraycopy(mset, 0, modelFileNames, 0, j);
}
return modelFileNames;
}
- public Hashtable getRegistryInfo()
+ /**
+ * map from string to applet
+ */
+ public Map getRegistryInfo()
{
// TODO Auto-generated method stub
return null;
public void loadInline(String string)
{
loadedInline = true;
+ // TODO: re JAL-623
+ // viewer.loadInline(strModel, isAppend);
+ // could do this:
+ // construct fake fullPathName and fileName so we can identify the file
+ // later.
+ // Then, construct pass a reader for the string to Jmol.
+ // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+ // fileName, null, reader, false, null, null, 0);
viewer.openStringInline(string);
}
String chainId;
if (strInfo.indexOf(":") > -1)
- chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+ strInfo.indexOf("."));
else
{
chainId = " ";
{
if (data != null)
{
- System.err.println("Ignoring additional hover info: " + data+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+ System.err.println("Ignoring additional hover info: " + data
+ + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
jmolHistory(true);
// TODO: in application this happens
//
-//if (scriptWindow != null)
-// {
-// scriptWindow.sendConsoleMessage(strInfo);
-// scriptWindow.sendConsoleMessage("\n");
-// }
-
+ // if (scriptWindow != null)
+ // {
+ // scriptWindow.sendConsoleMessage(strInfo);
+ // scriptWindow.sendConsoleMessage("\n");
+ // }
}
{
case JmolConstants.CALLBACK_LOADSTRUCT:
notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5])
- .intValue());
+ (String) data[3], (String) data[4],
+ ((Integer) data[5]).intValue());
break;
case JmolConstants.CALLBACK_PICK:
(String) data[0]);
break;
case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String) data[2], ((Integer) data[3])
- .intValue());
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
break;
case JmolConstants.CALLBACK_ECHO:
sendConsoleEcho((String) data[1]);
break;
case JmolConstants.CALLBACK_SYNC:
case JmolConstants.CALLBACK_RESIZE:
- updateUI();
+ refreshGUI();
break;
case JmolConstants.CALLBACK_MEASURE:
-
+
case JmolConstants.CALLBACK_CLICK:
-
default:
- System.err.println("Unhandled callback " + type + " " + data[1].toString());
+ System.err.println("Unhandled callback " + type + " "
+ + data[1].toString());
break;
}
} catch (Exception e)
return false;
}
+ // incremented every time a load notification is successfully handled -
+ // lightweight mechanism for other threads to detect when they can start
+ // referrring to new structures.
+ private long loadNotifiesHandled = 0;
+
+ public long getLoadNotifiesHandled()
+ {
+ return loadNotifiesHandled;
+ }
+
public void notifyFileLoaded(String fullPathName, String fileName2,
String modelName, String errorMsg, int modelParts)
{
if (errorMsg != null)
{
fileLoadingError = errorMsg;
- updateUI();
+ refreshGUI();
return;
}
+ // TODO: deal sensibly with models loaded inLine:
+ // modelName will be null, as will fullPathName.
+
+ // the rest of this routine ignores the arguments, and simply interrogates
+ // the Jmol view to find out what structures it contains, and adds them to
+ // the structure selection manager.
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
chainNames = new Vector();
+ chainFile = new Hashtable();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
ssm = StructureSelectionManager.getStructureSelectionManager();
// first check if we've lost any structures
- if (oldmodels!=null && oldmodels.length>0)
+ if (oldmodels != null && oldmodels.length > 0)
{
- int oldm=0;
- for (int i=0;i<oldmodels.length;i++)
+ int oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
{
- for (int n=0;n<modelfilenames.length; n++)
+ for (int n = 0; n < modelfilenames.length; n++)
{
- if (modelfilenames[n]==oldmodels[i])
+ if (modelfilenames[n] == oldmodels[i])
{
- oldmodels[i]=null;
+ oldmodels[i] = null;
break;
}
}
- if (oldmodels[i]!=null)
+ if (oldmodels[i] != null)
{
oldm++;
}
}
- if (oldm>0)
+ if (oldm > 0)
{
String[] oldmfn = new String[oldm];
- oldm=0;
- for (int i=0;i<oldmodels.length; i++)
+ oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
{
- if (oldmodels[i]!=null) {
+ if (oldmodels[i] != null)
+ {
oldmfn[oldm++] = oldmodels[i];
}
}
- // deregister the Jmol instance for these structures - we'll add
- // ourselves again at the end for the current structure set.
+ // deregister the Jmol instance for these structures - we'll add
+ // ourselves again at the end for the current structure set.
ssm.removeStructureViewerListener(this, oldmfn);
}
}
+ refreshPdbEntries();
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
- if (fileName != null)
+ boolean foundEntry = false;
+ MCview.PDBfile pdb = null;
+ String pdbfile = null, pdbfhash = null;
+ // model was probably loaded inline - so check the pdb file hashcode
+ if (loadedInline)
{
- // search pdbentries and sequences to find correct pdbentry and
- // sequence[] pair for this filename
- if (pdbentry != null)
+ // calculate essential attributes for the pdb data imported inline.
+ // prolly need to resolve modelnumber properly - for now just use our
+ // 'best guess'
+ pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ + ".0", "PDB");
+ pdbfhash = "" + pdbfile.hashCode();
+ }
+ if (pdbentry != null)
+ {
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < pdbentry.length; pe++)
{
- boolean foundEntry = false;
- for (int pe = 0; pe < pdbentry.length; pe++)
+ boolean matches = false;
+ if (fileName == null)
{
- if (pdbentry[pe].getFile().equals(fileName))
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
{
+ pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
+ AppletFormatAdapter.PASTE);
+ pdbentry[modelnum].setFile("INLINE" + pdb.id);
+ matches = true;
foundEntry = true;
- MCview.PDBfile pdb;
- if (loadedInline)
- {
- // TODO: replace with getData ?
- pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
- .getFile(), AppletFormatAdapter.PASTE);
- pdbentry[pe].setFile("INLINE" + pdb.id);
- }
- else
+ }
+ }
+ else
+ {
+ if (matches = pdbentry[pe].getFile().equals(fileName))
+ {
+ foundEntry = true;
+ // 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
+ String protocol = AppletFormatAdapter.URL;
+ try
{
- // 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
- String protocol = AppletFormatAdapter.URL;
- try
- {
- File fl = new java.io.File(pdbentry[pe].getFile());
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
+ File fl = new java.io.File(pdbentry[pe].getFile());
+ if (fl.exists())
{
+ protocol = AppletFormatAdapter.FILE;
}
- ;
- pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
- .getFile(), protocol);
-
- }
-
- pdbentry[pe].setId(pdb.id);
-
- for (int i = 0; i < pdb.chains.size(); i++)
+ } catch (Exception e)
+ {
+ } catch (Error e)
{
- chainNames.addElement(new String(pdb.id + ":"
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
}
- notifyLoaded = true;
+ ;
+ pdb = ssm.setMapping(sequence[pe], chains[pe],
+ pdbentry[pe].getFile(), protocol);
+
}
}
- if (!foundEntry && associateNewStructs)
+ if (matches)
{
- // 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
- // if properly registered then
+ pdbentry[pe].setId(pdb.id);
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.chains.size(); i++)
+ {
+ String chid = new String(pdb.id + ":"
+ + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+ chainFile.put(chid, pdbentry[pe].getFile());
+ chainNames.addElement(chid);
+ }
notifyLoaded = true;
}
}
}
+ if (!foundEntry && associateNewStructs)
+ {
+ // 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
+ // if properly registered then
+ notifyLoaded = true;
+
+ }
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
- jmolpopup.updateComputedMenus();
+ if (jmolpopup != null)
+ {
+ // potential for deadlock here:
+ // jmolpopup.updateComputedMenus();
+ }
if (!isLoadingFromArchive())
{
- viewer
- .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
setLoadingFromArchive(false);
// register ourselves as a listener and notify the gui that it needs to
if (notifyLoaded)
{
FeatureRenderer fr = getFeatureRenderer();
- if (fr!=null)
+ if (fr != null)
{
fr.featuresAdded();
}
- updateUI();
+ refreshGUI();
+ loadNotifiesHandled++;
}
}
notifyAtomPicked(iatom, strMeasure, null);
}
- public abstract void notifyScriptTermination(String strStatus, int msWalltime);
+ public abstract void notifyScriptTermination(String strStatus,
+ int msWalltime);
/**
* display a message echoed from the jmol viewer
* state change. this could be because structures were loaded, or because an
* error has occured.
*/
- public abstract void updateUI();
+ public abstract void refreshGUI();
+
+ /**
+ * called to show or hide the associated console window container.
+ *
+ * @param show
+ */
+ public abstract void showConsole(boolean show);
- public void allocateViewer(Component renderPanel, String htmlName,
- URL documentBase, URL codeBase, String commandOptions)
+ /**
+ * @param renderPanel
+ * @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(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions)
+ {
+ allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+ codeBase, commandOptions, null, null);
+ }
+
+ /**
+ *
+ * @param renderPanel
+ * @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
+ * @param consolePanel
+ * - panel to contain Jmol console
+ * @param buttonsToShow
+ * - buttons to show on the console, in ordr
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions, final Container consolePanel,
+ String buttonsToShow)
{
viewer = JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter(), htmlName+((Object) this).toString(), documentBase, codeBase,
+ (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
+
+ console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+ if (consolePanel != null)
+ {
+ consolePanel.addComponentListener(this);
+
+ }
+
+ }
+
+ protected abstract JmolAppConsoleInterface createJmolConsole(
+ JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+
+ protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+ @Override
+ public void componentResized(ComponentEvent e)
+ {
+
+ }
+
+ @Override
+ public void componentMoved(ComponentEvent e)
+ {
+
+ }
+
+ @Override
+ public void componentShown(ComponentEvent e)
+ {
+ showConsole(true);
+ }
+
+ @Override
+ public void componentHidden(ComponentEvent e)
+ {
+ showConsole(false);
}
public void setLoadingFromArchive(boolean loadingFromArchive)
{
return loadingFromArchive;
}
+
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
+ col.getGreen() + "," + col.getBlue() + "];");
jmolHistory(true);
}
+
+ /**
+ * add structures and any known sequence associations
+ *
+ * @returns the pdb entries added to the current set.
+ */
+ public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
+ {
+ int pe = -1;
+ Vector v = new Vector();
+ 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;
+ }
+
+ public void addSequence(int pe, SequenceI[] seq)
+ {
+ // add sequences to the pe'th pdbentry's seuqence set.
+ addSequenceAndChain(pe, seq, null);
+ }
+
+ 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;
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff