*/
package jalview.ext.jmol;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
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.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
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 org.jmol.adapter.smarter.SmarterJmolAdapter;
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
+ private String lastMessage;
+
boolean allChainsSelected = false;
/*
*/
private boolean associateNewStructs = false;
- Vector<String> atomsPicked = new Vector<String>();
+ Vector<String> atomsPicked = new Vector<>();
private List<String> chainNames;
String lastCommand;
- String lastMessage;
-
boolean loadedInline;
StringBuffer resetLastRes = new StringBuffer();
public void closeViewer()
{
// remove listeners for all structures in viewer
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
viewer.dispose();
lastCommand = null;
viewer = null;
* TODO
*/
public void superposeStructures(AlignmentI alignment, int refStructure,
- ColumnSelection hiddenCols)
+ HiddenColumns hiddenCols)
{
superposeStructures(new AlignmentI[] { alignment },
- new int[] { refStructure },
- new ColumnSelection[] { hiddenCols });
+ new int[]
+ { refStructure }, new HiddenColumns[] { hiddenCols });
}
/**
*/
@Override
public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ int[] _refStructure, HiddenColumns[] _hiddenCols)
{
while (viewer.isScriptExecuting())
{
* get the distinct structure files modelled
* (a file with multiple chains may map to multiple sequences)
*/
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (!waitForFileLoad(files))
{
return null;
{
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;
}
int nmatched = matched.cardinality();
if (nmatched < 4)
{
- return (MessageManager.formatMessage(
-"label.insufficient_residues",
+ return (MessageManager.formatMessage("label.insufficient_residues",
nmatched));
}
command.append(".1} {");
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 ");
+ command.append(
+ ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
// for (int s = 0; s < 2; s++)
// {
// 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;
lastCommand = command;
}
+ Thread colourby = null;
/**
* Sends a set of colour commands to the structure viewer
*
*/
@Override
protected void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands)
+ final StructureMappingcommandSet[] colourBySequenceCommands)
{
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+ if (colourby != null)
+ {
+ colourby.interrupt();
+ colourby = null;
+ }
+ 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 viewport
+ * @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, viewport);
+ getSequence(), sr, viewPanel);
}
/**
}
@Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
// TODO Auto-generated method stub
return null;
private int getModelNum(String modelFileName)
{
- String[] mfn = getPdbFile();
+ String[] mfn = getStructureFiles();
if (mfn == null)
{
return -1;
*/
private int _modelFileNameMap[];
- // ////////////////////////////////
- // /StructureListener
@Override
- public synchronized String[] getPdbFile()
+ public synchronized String[] getStructureFiles()
{
+ List<String> mset = new ArrayList<>();
if (viewer == null)
{
return new String[0];
}
+
if (modelFileNames == null)
{
- List<String> mset = new ArrayList<String>();
- _modelFileNameMap = new int[viewer.ms.mc];
- String m = viewer.ms.getModelFileName(0);
- if (m != null)
- {
- String filePath = m;
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet
- System.err
- .println("jmolBinding: Using local file string from Jmol: "
- + m);
- }
- if (filePath.indexOf("/file:") != -1)
- {
- // applet path with docroot - discard as format won't match pdbfile
- filePath = m;
- }
- mset.add(filePath);
- _modelFileNameMap[0] = 0; // filename index for first model is always 0.
- }
- int j = 1;
- for (int i = 1; i < viewer.ms.mc; i++)
+ int modelCount = viewer.ms.mc;
+ String filePath = null;
+ for (int i = 0; i < modelCount; ++i)
{
- m = viewer.ms.getModelFileName(i);
- String filePath = m;
- if (m != null)
- {
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet, so keep raw handle
- // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
- }
- }
-
- /*
- * add this model unless it is read from a structure file we have
- * already seen (example: 2MJW is an NMR structure with 10 models)
- */
+ filePath = viewer.ms.getModelFileName(i);
if (!mset.contains(filePath))
{
mset.add(filePath);
- _modelFileNameMap[j] = i; // record the model index for the filename
- j++;
}
}
modelFileNames = mset.toArray(new String[mset.size()]);
}
+
return modelFileNames;
}
return null;
}
-
-
// ///////////////////////////////
// JmolStatusListener
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.ms.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
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)
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new ArrayList<String>();
- chainFile = new Hashtable<String, String>();
+ 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)
{
// 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");
+ pdbfile = viewer.getData(
+ "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
// model
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE);
+ pdbfile, DataSourceType.PASTE,
+ getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
// add an entry for every chain in the model
for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(pdb.getId() + ":"
- + pdb.getChains().elementAt(i).id);
+ String chid = new String(
+ pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
chainNames.add(chid);
}
// }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet("model *; 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.
return chainNames;
}
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return null;
+ }
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
false);
for (String resName : residueSet)
{
- char res = resName.length() == 3 ? ResidueProperties
- .getSingleCharacterCode(resName) : resName.charAt(0);
+ 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 = (Viewer) JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
- + ((Object) this).toString(), documentBase, codeBase,
+ (jmolfileio ? new SmarterJmolAdapter() : null),
+ htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
viewer.setJmolStatusListener(this); // extends JmolCallbackListener
git://source.jalview.org / jalview.git / blobdiff