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.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Container;
import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
+import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Vector;
-import javajs.awt.Dimension;
-
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
Vector<String> atomsPicked = new Vector<String>();
- public Vector<String> chainNames;
+ private List<String> chainNames;
Hashtable<String, String> chainFile;
- public String fileLoadingError;
-
/*
* the default or current model displayed if the model cannot be identified
* from the selection message
boolean loadedInline;
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
-
StringBuffer resetLastRes = new StringBuffer();
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 void closeViewer()
{
// remove listeners for all structures in viewer
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
- viewer.dispose();
+ 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 });
+ new int[]
+ { refStructure }, new HiddenColumns[] { hiddenCols });
}
/**
- * Construct and send a command to align structures against a reference
- * structure, based on one or more sequence alignments
- *
- * @param _alignment
- * an array of alignments to process
- * @param _refStructure
- * an array of corresponding reference structures (index into pdb
- * file array); if a negative value is passed, the first PDB file
- * mapped to an alignment sequence is used as the reference for
- * superposition
- * @param _hiddenCols
- * an array of corresponding hidden columns for each alignment
+ * {@inheritDoc}
*/
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ @Override
+ public String superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, HiddenColumns[] _hiddenCols)
{
while (viewer.isScriptExecuting())
{
} catch (InterruptedException i)
{
}
- ;
}
- String[] files = getPdbFile();
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */
+ String[] files = getStructureFiles();
if (!waitForFileLoad(files))
{
- return;
+ return null;
}
StringBuilder selectioncom = new StringBuilder(256);
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 = " ";
{
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;
}
/*
- * 'matched' array will hold 'true' for visible alignment columns where
+ * 'matched' bit j will be set for visible alignment columns j where
* all sequences have a residue with a mapping to the PDB structure
*/
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ BitSet matched = new BitSet();
+ for (int m = 0; m < alignment.getWidth(); m++)
{
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
SuperposeData[] structures = new SuperposeData[files.length];
}
String[] selcom = new String[files.length];
- int nmatched = 0;
- for (boolean b : matched)
- {
- if (b)
- {
- nmatched++;
- }
- }
+ int nmatched = matched.cardinality();
if (nmatched < 4)
{
- // TODO: bail out here because superposition illdefined?
+ 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 = ":" + structures[pdbfnum].chain;
boolean run = false;
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)
{
- int pdbResNo = structures[pdbfnum].pdbResNo[r];
- if (lpos != pdbResNo - 1)
+ // discontinuity
+ if (lpos != -1)
{
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- molsel.append("|");
- }
- run = false;
+ 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 = pdbResNo;
+ run = true;
}
+ lpos = pdbResNo;
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
/*
* add final selection phrase
}
}
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(".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++)
// {
}
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; ");
String cmdString = command.toString();
- System.out.println("Superimpose command(s):\n" + cmdString);
+ // System.out.println("Superimpose command(s):\n" + cmdString);
evalStateCommand(cmdString);
}
{
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)
}
/**
- * 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(AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
{
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
- if (!colourBySequence || !isLoadingFinished())
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
{
for (String cbyseq : cpdbbyseq.commands)
{
/**
* @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);
+ 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;
}
/**
- * 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;
// ////////////////////////////////
// /StructureListener
- @Override
- public synchronized String[] getPdbFile()
+ // @Override
+ public synchronized String[] getPdbFilex()
{
if (viewer == null)
{
}
if (modelFileNames == null)
{
- String mset[] = new String[viewer.ms.mc];
- _modelFileNameMap = new int[mset.length];
+ List<String> mset = new ArrayList<String>();
+ _modelFileNameMap = new int[viewer.ms.mc];
String m = viewer.ms.getModelFileName(0);
if (m != null)
{
- mset[0] = m;
+ String filePath = m;
try
{
- mset[0] = new File(m).getAbsolutePath();
+ 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);
+ System.err.println(
+ "jmolBinding: Using local file string from Jmol: " + m);
}
- if (mset[0].indexOf("/file:") != -1)
+ if (filePath.indexOf("/file:") != -1)
{
// applet path with docroot - discard as format won't match pdbfile
- mset[0] = m;
+ filePath = m;
}
+ mset.add(filePath);
_modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
int j = 1;
- for (int i = 1; i < mset.length; i++)
+ for (int i = 1; i < viewer.ms.mc; i++)
{
m = viewer.ms.getModelFileName(i);
- mset[j] = m;
+ String filePath = m;
if (m != null)
{
try
{
- mset[j] = new File(m).getAbsolutePath();
+ 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);
+ // 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]))))
+
+ /*
+ * add this model unless it is read from a structure file we have
+ * already seen (example: 2MJW is an NMR structure with 10 models)
+ */
+ if (!mset.contains(filePath))
{
+ mset.add(filePath);
+ _modelFileNameMap[j] = i; // record the model index for the filename
j++;
}
}
- modelFileNames = new String[j];
- System.arraycopy(mset, 0, modelFileNames, 0, j);
+ modelFileNames = mset.toArray(new String[mset.size()]);
+ }
+ return modelFileNames;
+ }
+
+ @Override
+ public synchronized String[] getStructureFiles()
+ {
+ List<String> mset = new ArrayList<String>();
+ if (viewer == null)
+ {
+ return new String[0];
+ }
+
+ if (modelFileNames == null)
+ {
+ int modelCount = viewer.ms.mc;
+ String filePath = null;
+ for (int i = 0; i < modelCount; ++i)
+ {
+ filePath = viewer.ms.getModelFileName(i);
+ if (!mset.contains(filePath))
+ {
+ mset.add(filePath);
+ }
+ }
+ 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
// 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;
+ int _mp = _modelFileNameMap.length - 1,
+ mnumber = new Integer(mdlId).intValue() - 1;
while (mnumber < _modelFileNameMap[_mp])
{
_mp--;
* } }
*/
- 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
+ notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
+ (String) data[0]);
+ break;
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 Vector<String>();
+ chainNames = new ArrayList<String>();
chainFile = new Hashtable<String, String>();
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
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);
+ pdbfile, DataSourceType.PASTE);
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
// 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)
{
// 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.addElement(chid);
+ chainNames.add(chid);
}
notifyLoaded = true;
}
// }
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.
setLoadingFromArchive(false);
}
+ @Override
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
}
+ @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 = (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
protected org.jmol.api.JmolAppConsoleInterface console = null;
+ @Override
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
}
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
return null;
git://source.jalview.org / jalview.git / blobdiff