import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
-import java.security.AccessControlException;
+import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.StringTokenizer;
import java.util.Vector;
+import javax.swing.SwingUtilities;
+
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
-import org.jmol.constant.EnumCallback;
-import org.jmol.popup.JmolPopup;
+import org.jmol.c.CBK;
+import org.jmol.script.T;
+import org.jmol.viewer.Viewer;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.AppJmol;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
+import jalview.structure.AtomSpec;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
- /*
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
+ private String lastMessage;
boolean allChainsSelected = false;
*/
private boolean associateNewStructs = false;
- Vector atomsPicked = new Vector();
+ Vector<String> atomsPicked = new Vector<>();
- public Vector chainNames;
+ private List<String> chainNames;
- Hashtable chainFile;
-
- StringBuffer eval = new StringBuffer();
-
- public String fileLoadingError;
+ Hashtable<String, String> chainFile;
/*
* the default or current model displayed if the model cannot be identified
*/
int frameNo = 0;
- protected JmolPopup jmolpopup;
+ // protected JmolGenericPopup jmolpopup; // not used - remove?
String lastCommand;
- String lastMessage;
-
boolean loadedInline;
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
-
StringBuffer resetLastRes = new StringBuffer();
- public JmolViewer viewer;
+ public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
}
public JalviewJmolBinding(StructureSelectionManager ssm,
- SequenceI[][] seqs, JmolViewer theViewer)
+ SequenceI[][] seqs, Viewer theViewer)
{
super(ssm, seqs);
*/
public String getViewerTitle()
{
- return getViewerTitle("JMol", true);
+ return getViewerTitle("Jmol", true);
}
/**
* @param chainList
* list of chains to make visible
*/
- public void centerViewer(Vector chainList)
+ public void centerViewer(Vector<String> chainList)
{
- StringBuffer cmd = new StringBuffer();
- String lbl;
+ StringBuilder cmd = new StringBuilder(128);
int mlength, p;
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+ for (String lbl : chainList)
{
mlength = 0;
- lbl = (String) chainList.elementAt(i);
do
{
p = mlength;
} 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) + " /"
- + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
+ + (1 + getModelNum(chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
{
public void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
// remove listeners for all structures in viewer
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
+ viewer.dispose();
lastCommand = null;
viewer = null;
releaseUIResources();
}
+ @Override
public void colourByChain()
{
colourBySequence = false;
evalStateCommand("select *;color chain");
}
+ @Override
public void colourByCharge()
{
colourBySequence = false;
* TODO
*/
public void superposeStructures(AlignmentI alignment, int refStructure,
- ColumnSelection hiddenCols)
+ HiddenColumns hiddenCols)
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[]
+ { refStructure }, new HiddenColumns[] { hiddenCols });
}
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public String superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, HiddenColumns[] _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
+ while (viewer.isScriptExecuting())
{
- waiting = false;
- for (String file : files)
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
{
- try
- {
- // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
- // every possible exception
- StructureMapping[] sm = getSsm().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)
+ }
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */
+ String[] files = getStructureFiles();
+ if (!waitForFileLoad(files))
{
- System.err
- .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
- return;
+ return null;
}
- StringBuffer selectioncom = new StringBuffer();
+
+ StringBuilder selectioncom = new StringBuilder(256);
// 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 ";
+ nSeconds = " 0.005 ";
}
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 = " ";
+ // nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
int refStructure = _refStructure[a];
AlignmentI alignment = _alignment[a];
- ColumnSelection hiddenCols = _hiddenCols[a];
- if (a > 0
- && selectioncom.length() > 0
- && !selectioncom.substring(selectioncom.length() - 1).equals(
- "|"))
+ HiddenColumns hiddenCols = _hiddenCols[a];
+ if (a > 0 && selectioncom.length() > 0 && !selectioncom
+ .substring(selectioncom.length() - 1).equals("|"))
{
selectioncom.append("|");
}
// process this alignment
if (refStructure >= files.length)
{
- System.err.println("Invalid reference structure value "
- + refStructure);
+ System.err.println(
+ "Invalid reference structure value " + refStructure);
refStructure = -1;
}
- if (refStructure < -1)
+
+ /*
+ * 'matched' bit j will be set for visible alignment columns j where
+ * all sequences have a residue with a mapping to the PDB structure
+ */
+ BitSet matched = new BitSet();
+ for (int m = 0; m < alignment.getWidth(); m++)
{
- refStructure = -1;
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
- StringBuffer command = new StringBuffer();
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
-
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ structures[f] = new SuperposeData(alignment.getWidth());
}
- 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];
- String[] chainNames = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
{
- StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
- // RACE CONDITION - getMapping only returns Jmol loaded filenames once
- // Jmol callback has completed.
- if (mapping == null || mapping.length < 1)
- {
- throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data"));
- }
- int lastPos = -1;
- final int sequenceCountForPdbFile = getSequence()[pdbfnum].length;
- for (int s = 0; s < sequenceCountForPdbFile; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == getSequence()[pdbfnum][s]
- && (sp = alignment.findIndex(getSequence()[pdbfnum][s])) > -1)
- {
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
- {
- 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)))
- {
- // no mapping to gaps in sequence
- continue;
- }
- 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;
- // 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();
- }
- chainNames[pdbfnum] = mapping[m].getPdbId()
- + targetC[pdbfnum];
- // move on to next pdb file
- s = getSequence()[pdbfnum].length;
- break;
- }
- }
- }
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
}
- // 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
+ int nmatched = matched.cardinality();
+ if (nmatched < 4)
{
+ return (MessageManager.formatMessage("label.insufficient_residues",
+ nmatched));
+ }
+
+ /*
+ * generate select statements to select regions to superimpose structures
+ */
+ {
+ // TODO extract method to construct selection statements
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- String chainCd = targetC[pdbfnum];
+ String chainCd = ":" + structures[pdbfnum].chain;
int lpos = -1;
boolean run = false;
- StringBuffer molsel = new StringBuffer();
+ StringBuilder molsel = new StringBuilder();
molsel.append("{");
- for (int r = 0; r < matched.length; r++)
+
+ int nextColumnMatch = matched.nextSetBit(0);
+ while (nextColumnMatch != -1)
{
- if (matched[r])
+ int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
+ if (lpos != pdbResNo - 1)
{
- if (pdbfnum == 0)
- {
- nmatched++;
- }
- if (lpos != commonrpositions[pdbfnum][r] - 1)
+ // discontinuity
+ if (lpos != -1)
{
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- // molsel.append("} {");
- molsel.append("|");
- }
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("|");
}
- else
+ run = false;
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
{
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(lpos);
- molsel.append("-");
- }
- run = true;
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ run = true;
}
+ lpos = pdbResNo;
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
- // add final selection phrase
+ /*
+ * add final selection phrase
+ */
if (lpos != -1)
{
molsel.append(lpos);
}
}
}
+ StringBuilder command = new StringBuilder(256);
+ // command.append("set spinFps 10;\n");
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure || selcom[pdbfnum] == null
}
command.append("echo ");
command.append("\"Superposing (");
- command.append(chainNames[pdbfnum]);
+ command.append(structures[pdbfnum].pdbId);
command.append(") against reference (");
- command.append(chainNames[refStructure]);
+ command.append(structures[refStructure].pdbId);
command.append(")\";\ncompare " + nSeconds);
command.append("{");
- command.append(1 + pdbfnum);
+ command.append(Integer.toString(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(Integer.toString(1 + refStructure));
+ // conformation=1 excludes alternate locations for CA (JAL-1757)
+ command.append(
+ ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
+
+ // for (int s = 0; s < 2; s++)
+ // {
+ // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ // }
+ command.append(selcom[pdbfnum]);
+ command.append(selcom[refStructure]);
command.append(" ROTATE TRANSLATE;\n");
}
if (selectioncom.length() > 0)
{
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // TODO is performing selectioncom redundant here? is done later on
+ // 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());
+ String cmdString = command.toString();
+ // System.out.println("Superimpose command(s):\n" + cmdString);
- evalStateCommand(command.toString());
+ evalStateCommand(cmdString);
}
}
if (selectioncom.length() > 0)
{
selectioncom.setLength(selectioncom.length() - 1);
}
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
- // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+";
+ // cartoons; center "+selcom.toString());
}
+
+ return null;
}
public void evalStateCommand(String command)
lastCommand = command;
}
+ Thread colourby = null;
+
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a set of colour commands to the structure viewer
+ *
+ * @param colourBySequenceCommands
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ final StructureMappingcommandSet[] colourBySequenceCommands)
{
- if (!colourBySequence || !isLoadingFinished())
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
+ if (colourby != null)
{
- fr = getFeatureRenderer(alignmentv);
+ colourby.interrupt();
+ colourby = null;
}
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+ colourby = new Thread(new Runnable()
{
- for (String cbyseq : cpdbbyseq.commands)
+ @Override
+ public void run()
{
- executeWhenReady(cbyseq);
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+ {
+ for (String cbyseq : cpdbbyseq.commands)
+ {
+ executeWhenReady(cbyseq);
+ }
+ }
}
- }
+ });
+ colourby.start();
}
/**
* @param files
* @param sr
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
+ @Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
- return JmolCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr,
- alignment);
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, viewPanel);
}
/**
System.out.println("JMOL CREATE IMAGE");
}
+ @Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
return null;
}
+ @Override
public String eval(String strEval)
{
// System.out.println(strEval);
// End StructureListener
// //////////////////////////
+ @Override
public float[][] functionXY(String functionName, int x, int y)
{
return null;
}
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
// TODO Auto-generated method stub
return null;
return null;
}
// TODO: verify atomIndex is selecting correct model.
- return new Color(viewer.getAtomArgb(atomIndex));
+ // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
+ int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
+ return new Color(colour);
}
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
-
- /**
* 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.
private int getModelNum(String modelFileName)
{
- String[] mfn = getPdbFile();
+ String[] mfn = getStructureFiles();
if (mfn == null)
{
return -1;
*/
private int _modelFileNameMap[];
- // ////////////////////////////////
- // /StructureListener
- public synchronized String[] getPdbFile()
+ @Override
+ public synchronized String[] getStructureFiles()
{
+ List<String> mset = new ArrayList<>();
if (viewer == null)
{
return new String[0];
}
+
if (modelFileNames == null)
{
-
- String mset[] = new String[viewer.getModelCount()];
- _modelFileNameMap = new int[mset.length];
- int j = 1;
- String m = viewer.getModelFileName(0);
- if (m != null)
- {
- try
- {
- mset[0] = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet, so keep raw handle
- mset[0] = m;
- // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
- }
- }
- for (int i = 1; i < mset.length; i++)
+ int modelCount = viewer.ms.mc;
+ String filePath = null;
+ for (int i = 0; i < modelCount; ++i)
{
- m = viewer.getModelFileName(i);
- if (m != null)
- {
- try
- {
- mset[j] = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet, so keep raw handle
- mset[j] = m;
- // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
- }
- }
- _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]))))
+ filePath = viewer.ms.getModelFileName(i);
+ if (!mset.contains(filePath))
{
- j++;
+ mset.add(filePath);
}
}
- modelFileNames = new String[j];
- System.arraycopy(mset, 0, modelFileNames, 0, j);
+ modelFileNames = mset.toArray(new String[mset.size()]);
}
+
return modelFileNames;
}
return null;
}
- /**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
// ///////////////////////////////
// JmolStatusListener
public void handlePopupMenu(int x, int y)
{
- jmolpopup.show(x, y);
+ // jmolpopup.show(x, y);
+ // jmolpopup.jpiShow(x, y);
+ }
+
+ /**
+ * Highlight zero, one or more atoms on the structure
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ if (atoms != null)
+ {
+ if (resetLastRes.length() > 0)
+ {
+ viewer.evalStringQuiet(resetLastRes.toString());
+ resetLastRes.setLength(0);
+ }
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
}
// jmol/ssm only
// 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)
}
jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
+ StringBuilder cmd = new StringBuilder(64);
+ cmd.append("select " + pdbResNum); // +modelNum
- resetLastRes.setLength(0);
resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
+ cmd.append(":");
resetLastRes.append(":");
if (!chain.equals(" "))
{
- eval.append(chain);
+ cmd.append(chain);
resetLastRes.append(chain);
}
{
- eval.append(" /" + (mdlNum + 1));
+ cmd.append(" /" + (mdlNum + 1));
resetLastRes.append("/" + (mdlNum + 1));
}
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
+ cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ " and not hetero; spacefill 0;");
- eval.append("spacefill 200;select none");
+ cmd.append("spacefill 200;select none");
- viewer.evalStringQuiet(eval.toString());
+ viewer.evalStringQuiet(cmd.toString());
jmolHistory(true);
}
viewer.openStringInline(string);
}
- public void mouseOverStructure(int atomIndex, String strInfo)
+ protected void mouseOverStructure(int atomIndex, final String strInfo)
{
int pdbResNum;
int alocsep = strInfo.indexOf("^");
// handle insertion codes
if (alocsep != -1)
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, alocsep));
+ pdbResNum = Integer.parseInt(
+ strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
}
else
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
+ pdbResNum = Integer.parseInt(
+ strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator));
}
String chainId;
{
chainSeparator1 = strInfo.indexOf(".", mdlSep);
}
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
+ String mdlId = (chainSeparator1 > -1)
+ ? strInfo.substring(mdlSep + 1, chainSeparator1)
+ : strInfo.substring(mdlSep + 1);
try
{
// recover PDB filename for the model hovered over.
- int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
- .intValue() - 1;
- while (mnumber < _modelFileNameMap[_mp])
+ int mnumber = Integer.valueOf(mdlId).intValue() - 1;
+ if (_modelFileNameMap != null)
{
- _mp--;
+ int _mp = _modelFileNameMap.length - 1;
+
+ while (mnumber < _modelFileNameMap[_mp])
+ {
+ _mp--;
+ }
+ pdbfilename = modelFileNames[_mp];
}
- pdbfilename = modelFileNames[_mp];
- if (pdbfilename == null)
+ else
{
- pdbfilename = new File(viewer.getModelFileName(mnumber))
- .getAbsolutePath();
- }
+ if (mnumber >= 0 && mnumber < modelFileNames.length)
+ {
+ pdbfilename = modelFileNames[mnumber];
+ }
+ if (pdbfilename == null)
+ {
+ pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
+ .getAbsolutePath();
+ }
+ }
} catch (Exception e)
{
}
- ;
}
- if (lastMessage == null || !lastMessage.equals(strInfo))
+
+ /*
+ * highlight position on alignment(s); if some text is returned,
+ * show this as a second line on the structure hover tooltip
+ */
+ String label = getSsm().mouseOverStructure(pdbResNum, chainId,
+ pdbfilename);
+ if (label != null)
{
- getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ // change comma to pipe separator (newline token for Jmol)
+ label = label.replace(',', '|');
+ StringTokenizer toks = new StringTokenizer(strInfo, " ");
+ StringBuilder sb = new StringBuilder();
+ sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
+ .append(chainId).append("/1");
+ sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
+ .append(toks.nextToken());
+ sb.append("|").append(label).append("\"");
+ evalStateCommand(sb.toString());
}
-
- lastMessage = strInfo;
}
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
+ if (strInfo.equals(lastMessage))
+ {
+ return;
+ }
+ lastMessage = strInfo;
if (data != null)
{
System.err.println("Ignoring additional hover info: " + data
* } }
*/
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
+ public void notifyAtomPicked(int atomIndex, String strInfo,
+ String strData)
{
/**
* this implements the toggle label behaviour copied from the original
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
{
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ picked += strInfo.substring(p, strInfo.indexOf("."));
}
if ((p = strInfo.indexOf("/")) > -1)
}
@Override
- public void notifyCallback(EnumCallback type, Object[] data)
+ public void notifyCallback(CBK type, Object[] data)
+ {
+ /*
+ * ensure processed in AWT thread to avoid risk of deadlocks
+ */
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ processCallback(type, data);
+ }
+ });
+ }
+
+ /**
+ * Processes one callback notification from Jmol
+ *
+ * @param type
+ * @param data
+ */
+ protected void processCallback(CBK type, Object[] data)
{
try
{
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
+ // deliberate fall through
case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
sendConsoleEcho((String) data[1]);
break;
case MESSAGE:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
+ sendConsoleMessage(
+ (data == null) ? ((String) null) : (String) data[1]);
break;
case ERROR:
// System.err.println("Ignoring error callback.");
case CLICK:
default:
- System.err.println("Unhandled callback " + type + " "
- + data[1].toString());
+ System.err.println(
+ "Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
}
@Override
- public boolean notifyEnabled(EnumCallback callbackPick)
+ public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
case HOVER:
case ERROR:
return true;
- case RESIZE:
- case SYNC:
- case CLICK:
- case ANIMFRAME:
- case MINIMIZATION:
+ default:
+ return false;
}
- return false;
}
// incremented every time a load notification is successfully handled -
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector();
- chainFile = new Hashtable();
+ chainNames = new ArrayList<>();
+ chainFile = new Hashtable<>();
boolean notifyLoaded = false;
- String[] modelfilenames = getPdbFile();
+ String[] modelfilenames = getStructureFiles();
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
- MCview.PDBfile pdb = null;
- String pdbfile = null, pdbfhash = null;
+ StructureFile pdb = null;
+ String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
{
// 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();
+ pdbfile = viewer.getData(
+ "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
- // search pdbentries and sequences to find correct pdbentry for this
- // model
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
+ addSequence(pe, getSequence()[pe]);
if (fileName == null)
{
if (false)
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, AppletFormatAdapter.PASTE);
- getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
}
else
{
- File fl;
- if (matches = (fl = new File(getPdbEntry(pe).getFile()))
- .equals(new File(fileName)))
+ File fl = new File(getPdbEntry(pe).getFile());
+ matches = fl.equals(new File(fileName));
+ if (matches)
{
foundEntry = true;
// TODO: Jmol can in principle retrieve from CLASSLOADER but
// needs
// to be tested. See mantis bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- String protocol = AppletFormatAdapter.URL;
+ DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
} catch (Exception e)
{
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
if (matches)
{
// add an entry for every chain in the model
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(pdb.id + ":"
- + pdb.chains.elementAt(i).id);
+ String chid = new String(
+ pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
- chainNames.addElement(chid);
+ chainNames.add(chid);
}
notifyLoaded = true;
}
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
- if (jmolpopup != null)
- {
- // potential for deadlock here:
- // 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 *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
- fr.featuresAdded();
+ FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+ ((AppJmol) getViewer()).getAlignmentPanel().av
+ .applyFeaturesStyle(colours);
}
refreshGUI();
loadNotifiesHandled++;
setLoadingFromArchive(false);
}
+ @Override
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return null;
+ }
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
*/
public abstract void sendConsoleMessage(String strStatus);
+ @Override
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
command.append("select *;color white;");
List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
false);
- for (String res : residueSet)
+ for (String resName : residueSet)
{
- Color col = cs.findColour(res.charAt(0));
- command.append("select " + res + ";color[" + col.getRed() + ","
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
+ Color col = cs.findColour(res, 0, null, null, 0f);
+ command.append("select " + resName + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
{
commandOptions = "";
}
- viewer = JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
- + ((Object) this).toString(), documentBase, codeBase,
+ viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
+ (jmolfileio ? new SmarterJmolAdapter() : null),
+ htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+ viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+
+ console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
}
protected abstract JmolAppConsoleInterface createJmolConsole(
- JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+ Container consolePanel, String buttonsToShow);
protected org.jmol.api.JmolAppConsoleInterface console = null;
+ @Override
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
jmolHistory(true);
}
- /**
- *
- * @param pdbfile
- * @return text report of alignment between pdbfile and any associated
- * alignment sequences
- */
- public String printMapping(String pdbfile)
- {
- return getSsm().printMapping(pdbfile);
- }
-
@Override
- public void resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
-
- }
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
+ return null;
}
/**
git://source.jalview.org / jalview.git / blobdiff