import jalview.io.AppletFormatAdapter;
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;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
{ 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
+ */
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _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
- {
- waiting = false;
- for (String file : files)
- {
- 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)
+
+ if (!waitForFileLoad(files))
{
- System.err
- .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
return;
}
- 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 = " ";
+ refStructure);
refStructure = -1;
}
- if (refStructure < -1)
- {
- refStructure = -1;
- }
- StringBuffer command = new StringBuffer();
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns 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++)
{
-
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];
- String[] chainNames = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
- 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;
- }
- }
- }
+ structures[f] = new SuperposeData(alignment.getWidth());
}
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
+ }
String[] selcom = new String[files.length];
int nmatched = 0;
- // generate select statements to select regions to superimpose structures
+ for (boolean b : matched)
+ {
+ if (b)
+ {
+ nmatched++;
+ }
+ }
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
+
+ /*
+ * generate select statements to select regions to superimpose structures
+ */
{
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++)
{
if (matched[r])
{
- if (pdbfnum == 0)
- {
- nmatched++;
- }
- if (lpos != commonrpositions[pdbfnum][r] - 1)
+ int pdbResNo = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNo - 1)
{
// discontinuity
if (lpos != -1)
{
molsel.append(lpos);
molsel.append(chainCd);
- // molsel.append("} {");
molsel.append("|");
}
+ run = false;
}
else
{
}
run = true;
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ lpos = pdbResNo;
}
}
- // add final selection phrase
+ /*
+ * add final selection phrase
+ */
if (lpos != -1)
{
molsel.append(lpos);
}
}
}
+ StringBuilder command = new StringBuilder(256);
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(Integer.toString(1 + refStructure));
// conformation=1 excludes alternate locations for CA (JAL-1757)
command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
- // form the matched pair strings
- String sep = "";
- for (int s = 0; s < 2; s++)
- {
- command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
- }
+ // 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)
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
+ String cmdString = command.toString();
System.out
- .println("Superimpose command(s):\n" + command.toString());
+.println("Superimpose command(s):\n" + cmdString);
- evalStateCommand(command.toString());
+ evalStateCommand(cmdString);
}
}
if (selectioncom.length() > 0)
// ////////////////////////////////
// /StructureListener
+ @Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
jmolpopup.show(x, y);
}
+ /**
+ * Highlight zero, one or more atoms on the structure
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ if (atoms != null)
+ {
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
+ }
+
// jmol/ssm only
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.Comparison;
import jalview.util.MessageManager;
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
// Chimera clause to exclude alternate locations in atom selection
private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
+ private static final String COLOURING_CHIMERA = MessageManager
+ .getString("status.colouring_chimera");
+
private static final boolean debug = false;
private static final String PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
- private StructureManager csm;
-
/*
* Object through which we talk to Chimera
*/
*/
private boolean finishedInit = false;
- private List<String> atomsPicked = new ArrayList<String>();
-
- private List<String> chainNames;
-
- private Map<String, String> chainFile;
-
public String fileLoadingError;
/*
{
super(ssm, pdbentry, sequenceIs, chains, protocol);
viewer = new ChimeraManager(
- csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
/**
}
/**
- * Constructor
- *
- * @param ssm
- * @param theViewer
- */
- public JalviewChimeraBinding(StructureSelectionManager ssm,
- ChimeraManager theViewer)
- {
- super(ssm, null);
- viewer = theViewer;
- csm = viewer.getStructureManager();
- }
-
- /**
* Construct a title string for the viewer window based on the data Jalview
* knows about
*
}
/**
- * prepare the view for a given set of models/chains. chainList contains
- * strings of the form 'pdbfilename:Chaincode'
+ * Tells Chimera to display only the specified chains
*
* @param toshow
- * list of chains to make visible
*/
- public void centerViewer(List<String> toshow)
+ public void showChains(List<String> toshow)
{
+ /*
+ * Construct a chimera command like
+ *
+ * ~display #*;~ribbon #*;ribbon :.A,:.B
+ */
StringBuilder cmd = new StringBuilder(64);
- int mlength, p;
- for (String lbl : toshow)
+ boolean first = true;
+ for (String chain : toshow)
{
- mlength = 0;
- do
+ if (!first)
{
- 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("#" + getModelNum(chainFile.get(lbl)) + "."
- + lbl.substring(mlength + 1) + " or ");
- }
- if (cmd.length() > 0)
- {
- cmd.setLength(cmd.length() - 4);
+ cmd.append(",");
+ }
+ cmd.append(":.").append(chain);
+ first = false;
}
- String cmdstring = cmd.toString();
- evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring, false);
+
+ /*
+ * could append ";focus" to this command to resize the display to fill the
+ * window, but it looks more helpful not to (easier to relate chains to the
+ * whole)
+ */
+ final String command = "~display #*; ~ribbon #*; ribbon "
+ + cmd.toString();
+ sendChimeraCommand(command, false);
}
/**
public void colourByChain()
{
colourBySequence = false;
- evalStateCommand("rainbow chain", false);
- }
-
- public void colourByCharge()
- {
- colourBySequence = false;
- evalStateCommand(
- "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS",
- false);
- }
-
- /**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions.
- */
- public void superposeStructures(AlignmentI alignment)
- {
- superposeStructures(alignment, -1, null);
+ sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
}
/**
- * 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)
+ * Constructs and sends a Chimera command to colour by charge
+ * <ul>
+ * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
+ * <li>Lysine and Arginine (positive charge) blue</li>
+ * <li>Cysteine - yellow</li>
+ * <li>all others - white</li>
+ * </ul>
*/
- public void superposeStructures(AlignmentI alignment, int refStructure)
+ public void colourByCharge()
{
- superposeStructures(alignment, refStructure, null);
+ colourBySequence = false;
+ String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
/**
- * superpose the structures associated with sequences in the alignment
- * according to their corresponding positions. ded)
+ * Construct and send a command to align structures against a reference
+ * structure, based on one or more sequence alignments
*
- * @param refStructure
- * - select which pdb file to use as reference (default is -1 - the
- * first structure in the alignment)
- * @param hiddenCols
- * TODO
+ * @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
*/
- public void superposeStructures(AlignmentI alignment, int refStructure,
- ColumnSelection hiddenCols)
- {
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
- }
-
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
- StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd
+ StringBuilder allComs = new StringBuilder(128);
String[] files = getPdbFile();
- // check to see if we are still waiting for Chimera files
- long starttime = System.currentTimeMillis();
- boolean waiting = true;
- do
- {
- waiting = false;
- for (String file : files)
- {
- 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)
+
+ if (!waitForFileLoad(files))
{
- System.err
- .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures.");
return;
}
+
refreshPdbEntries();
- StringBuffer selectioncom = new StringBuffer();
+ StringBuilder selectioncom = new StringBuilder(256);
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(
- " "))
- {
- selectioncom.append(" ");
- }
- // process this alignment
+
if (refStructure >= files.length)
{
- System.err.println("Invalid reference structure value "
+ System.err.println("Ignoring invalid reference structure value "
+ refStructure);
refStructure = -1;
}
- if (refStructure < -1)
- {
- refStructure = -1;
- }
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns 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++)
{
-
matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
}
- int commonrpositions[][] = new int[files.length][alignment.getWidth()];
- String isel[] = new String[files.length];
- String[] targetC = new String[files.length];
- String[] chainNames = new String[files.length];
- String[] atomSpec = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
- 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_chimera_getting_data"));
- }
- int lastPos = -1;
- final int seqCountForPdbFile = getSequence()[pdbfnum].length;
- for (int s = 0; s < seqCountForPdbFile; s++)
+ structures[f] = new SuperposeData(alignment.getWidth());
+ }
+
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
+ }
+
+ int nmatched = 0;
+ for (boolean b : matched)
+ {
+ if (b)
{
- for (int sp, m = 0; m < mapping.length; m++)
- {
- final SequenceI theSequence = getSequence()[pdbfnum][s];
- if (mapping[m].getSequence() == theSequence
- && (sp = alignment.findIndex(theSequence)) > -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 (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;
- 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];
- atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON;
- // move on to next pdb file
- s = seqCountForPdbFile;
- break;
- }
- }
+ nmatched++;
}
}
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
-
+ /*
+ * Generate select statements to select regions to superimpose structures
+ */
String[] selcom = new String[files.length];
- int nmatched = 0;
- String sep = "";
- // generate select statements to select regions to superimpose structures
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ String chainCd = "." + structures[pdbfnum].chain;
+ int lpos = -1;
+ boolean run = false;
+ StringBuilder molsel = new StringBuilder();
+ for (int r = 0; r < matched.length; r++)
{
- String chainCd = targetC[pdbfnum];
- int lpos = -1;
- boolean run = false;
- StringBuffer molsel = new StringBuffer();
- for (int r = 0; r < matched.length; r++)
+ if (matched[r])
{
- if (matched[r])
+ int pdbResNum = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNum - 1)
{
- if (pdbfnum == 0)
+ /*
+ * discontiguous - append last residue now
+ */
+ if (lpos != -1)
{
- nmatched++;
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ molsel.append(",");
}
- if (lpos != commonrpositions[pdbfnum][r] - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append((run ? "" : ":") + lpos);
- molsel.append(chainCd);
- 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);
+ run = false;
}
- }
- // add final selection phrase
- if (lpos != -1)
- {
- molsel.append((run ? "" : ":") + lpos);
- molsel.append(chainCd);
- // molsel.append("");
- }
- if (molsel.length() > 1)
- {
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("#" + pdbfnum);
- selectioncom.append(selcom[pdbfnum]);
- selectioncom.append(" ");
- if (pdbfnum < files.length - 1)
+ else
{
- selectioncom.append("| ");
+ /*
+ * extending a contiguous run
+ */
+ if (!run)
+ {
+ /*
+ * start the range selection
+ */
+ molsel.append(String.valueOf(lpos));
+ molsel.append("-");
+ }
+ run = true;
}
+ lpos = pdbResNum;
}
- else
+ }
+
+ /*
+ * and terminate final selection
+ */
+ if (lpos != -1)
+ {
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ }
+ if (molsel.length() > 1)
+ {
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("#").append(String.valueOf(pdbfnum))
+ .append(":");
+ selectioncom.append(selcom[pdbfnum]);
+ selectioncom.append(" ");
+ if (pdbfnum < files.length - 1)
{
- selcom[pdbfnum] = null;
+ selectioncom.append("| ");
}
}
+ else
+ {
+ selcom[pdbfnum] = null;
+ }
}
+
StringBuilder command = new StringBuilder(256);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
/*
* Form Chimera match command, from the 'new' structure to the
- * 'reference' structure e.g. (residues 1-91, chain B/A, alphacarbons):
+ * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
*
- * match #1:1-91.B@CA #0:1-91.A@CA
+ * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
*
* @see
* https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
- command.append("match #" + pdbfnum /* +".1" */);
- // TODO: handle sub-models
+ command.append("match ").append(getModelSpec(pdbfnum)).append(":");
command.append(selcom[pdbfnum]);
- command.append("@" + atomSpec[pdbfnum]);
- // JAL-1757 exclude alternative CA locations
+ command.append("@").append(
+ structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
+ // JAL-1757 exclude alternate CA locations
command.append(NO_ALTLOCS);
- command.append(" #" + refStructure /* +".1" */);
+ command.append(" ").append(getModelSpec(refStructure)).append(":");
command.append(selcom[refStructure]);
- command.append("@" + atomSpec[refStructure]);
+ command.append("@").append(
+ structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
command.append(NO_ALTLOCS);
}
if (selectioncom.length() > 0)
System.out.println("Superimpose command(s):\n"
+ command.toString());
}
- allComs.append("~display all; chain @CA|P; ribbon "
- + selectioncom.toString() + ";"+command.toString());
- // selcom.append("; ribbons; ");
+ allComs.append("~display all; chain @CA|P; ribbon ")
+ .append(selectioncom.toString())
+ .append(";" + command.toString());
}
}
if (selectioncom.length() > 0)
- {// finally, mark all regions that were superposed.
+ {
+ // TODO: visually distinguish regions that were superposed
if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
{
selectioncom.setLength(selectioncom.length() - 1);
{
System.out.println("Select regions:\n" + selectioncom.toString());
}
- allComs.append("; ~display all; chain @CA|P; ribbon "
- + selectioncom.toString() + "; focus");
- // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
- evalStateCommand(allComs.toString(), true /* false */);
+ allComs.append("; ~display all; chain @CA|P; ribbon ")
+ .append(selectioncom.toString()).append("; focus");
+ sendChimeraCommand(allComs.toString(), false);
}
-
+
}
- private void checkLaunched()
+ /**
+ * Helper method to construct model spec in Chimera format:
+ * <ul>
+ * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
+ * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
+ * <ul>
+ * Note for now we only ever choose the first of multiple models. This
+ * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
+ * future if there is a need to select specific sub-models.
+ *
+ * @param pdbfnum
+ * @return
+ */
+ protected String getModelSpec(int pdbfnum)
{
- if (!viewer.isChimeraLaunched())
+ if (pdbfnum < 0 || pdbfnum >= getPdbCount())
{
- viewer.launchChimera(StructureManager.getChimeraPaths());
+ return "";
}
+
+ /*
+ * For now, the test for having sub-models is whether multiple Chimera
+ * models are mapped for the PDB file; the models are returned as a response
+ * to the Chimera command 'list models type molecule', see
+ * ChimeraManager.getModelList().
+ */
+ List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+ boolean hasSubModels = maps != null && maps.size() > 1;
+ return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
+ }
+
+ /**
+ * Launch Chimera, unless an instance linked to this object is already
+ * running. Returns true if chimera is successfully launched, or already
+ * running, else false.
+ *
+ * @return
+ */
+ public boolean launchChimera()
+ {
if (!viewer.isChimeraLaunched())
{
- log("Failed to launch Chimera!");
+ return viewer.launchChimera(StructureManager.getChimeraPaths());
}
+ if (viewer.isChimeraLaunched())
+ {
+ return true;
+ }
+ log("Failed to launch Chimera!");
+ return false;
}
/**
}
/**
- * Send a command to Chimera, launching it first if necessary, and optionally
- * log any responses.
+ * Send a command to Chimera, and optionally log any responses.
*
* @param command
* @param logResponse
*/
- public void evalStateCommand(final String command, boolean logResponse)
+ public void sendChimeraCommand(final String command, boolean logResponse)
{
viewerCommandHistory(false);
- checkLaunched();
if (lastCommand == null || !lastCommand.equals(command))
{
// trim command or it may never find a match in the replyLog!!
lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
- if (debug && logResponse)
+ if (logResponse && debug)
{
log("Response from command ('" + command + "') was:\n" + lastReply);
}
}
/**
+ * Send a Chimera command asynchronously in a new thread. If the progress
+ * message is not null, display this message while the command is executing.
+ *
+ * @param command
+ * @param progressMsg
+ */
+ protected abstract void sendAsynchronousCommand(String command,
+ String progressMsg);
+
+ /**
* colour any structures associated with sequences in the given alignment
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
* if colourBySequence is enabled.
{
for (String command : cpdbbyseq.commands)
{
- executeWhenReady(command);
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
}
protected void executeWhenReady(String command)
{
waitForChimera();
- evalStateCommand(command, false);
+ sendChimeraCommand(command, false);
waitForChimera();
}
{
while (viewer != null && viewer.isBusy())
{
- try {
+ try
+ {
Thread.sleep(15);
} catch (InterruptedException q)
- {}
+ {
+ }
}
}
-
-
// End StructureListener
// //////////////////////////
/**
* 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
+ * prior to matching the viewer's contents to the list of structure files
* Jalview knows about.
*/
public abstract void refreshPdbEntries();
// ////////////////////////////////
// /StructureListener
+ @Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
AlignmentViewPanel alignment);
/**
- * Construct and send a command to highlight an atom.
+ * Construct and send a command to highlight zero, one or more atoms.
*
* <pre>
* Done by generating a command like (to 'highlight' position 44)
- * ~show #0:43.C;show #0:44.C
- * Note this removes the highlight from the previous position.
+ * show #0:44.C
* </pre>
*/
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
- if (cms != null)
+ if (atoms == null)
+ {
+ return;
+ }
+ StringBuilder atomSpecs = new StringBuilder();
+ boolean first = true;
+ for (AtomSpec atom : atoms)
{
- StringBuilder sb = new StringBuilder();
- sb.append(" #" + cms.get(0).getModelNumber());
- sb.append(":" + pdbResNum);
- if (!chain.equals(" "))
+ int pdbResNum = atom.getPdbResNum();
+ String chain = atom.getChain();
+ String pdbfile = atom.getPdbFile();
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
+ if (cms != null && !cms.isEmpty())
{
- sb.append("." + chain);
+ /*
+ * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
+ * concatenate multiple 'show' commands
+ */
+ atomSpecs.append(first ? "" : ";show ");
+ first = false;
+ atomSpecs.append("#" + cms.get(0).getModelNumber());
+ atomSpecs.append(":" + pdbResNum);
+ if (!chain.equals(" "))
+ {
+ atomSpecs.append("." + chain);
+ }
}
- String atomSpec = sb.toString();
+ }
+ String atomSpec = atomSpecs.toString();
- StringBuilder command = new StringBuilder(32);
- if (lastMousedOverAtomSpec != null)
- {
- command.append("~show " + lastMousedOverAtomSpec + ";");
- }
- viewerCommandHistory(false);
+ /*
+ * Avoid repeated commands for the same residue
+ */
+ if (atomSpec.equals(lastMousedOverAtomSpec))
+ {
+ return;
+ }
+
+ StringBuilder command = new StringBuilder(32);
+ viewerCommandHistory(false);
+ if (atomSpec.length() > 0)
+ {
command.append("show ").append(atomSpec);
- String cmd = command.toString();
- if (cmd.length() > 0)
- {
- viewer.stopListening(chimeraListener.getUri());
- viewer.sendChimeraCommand(cmd, false);
- viewer.startListening(chimeraListener.getUri());
- }
- viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
+ viewer.sendChimeraCommand(command.toString(), false);
}
+ viewerCommandHistory(true);
+ this.lastMousedOverAtomSpec = atomSpec;
}
/**
{
continue; // malformed
}
-
+
int hashPos = atomSpec.indexOf("#");
String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
int dotPos = modelSubmodel.indexOf(".");
int modelId = 0;
- try {
+ try
+ {
modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
: modelSubmodel.substring(0, dotPos));
- } catch (NumberFormatException e) {
+ } catch (NumberFormatException e)
+ {
// ignore, default to model 0
}
-
+
String residueChain = atomSpec.substring(colonPos + 1);
dotPos = residueChain.indexOf(".");
int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
: residueChain.substring(0, dotPos));
-
+
String chainId = dotPos == -1 ? "" : residueChain
.substring(dotPos + 1);
-
+
/*
* Work out the pdbfilename from the model number
*/
/ normalise + " ::" + res + ";");
}
- evalStateCommand(command.toString(),false);
+ sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
viewerCommandHistory(true);
}
/**
* Send the Chimera 'background solid <color>" command.
*
- * @see https
+ * @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
{
viewerCommandHistory(false);
double normalise = 255D;
- final String command = "background solid " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
+ final String command = "background solid " + col.getRed() / normalise
+ + "," + col.getGreen() / normalise + "," + col.getBlue()
/ normalise + ";";
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
*/
public boolean openSession(String filepath)
{
- evalStateCommand("open " + filepath, true);
+ sendChimeraCommand("open " + filepath, true);
// todo: test for failure - how?
return true;
}
this.finishedInit = finishedInit;
}
+ /**
+ * Returns a list of chains mapped in this viewer. Note this list is not
+ * currently scoped per structure.
+ *
+ * @return
+ */
public List<String> getChainNames()
{
- return chainNames;
+ List<String> names = new ArrayList<String>();
+ String[][] allNames = getChains();
+ if (allNames != null)
+ {
+ for (String[] chainsForPdb : allNames)
+ {
+ if (chainsForPdb != null)
+ {
+ for (String chain : chainsForPdb)
+ {
+ if (chain != null && !names.contains(chain))
+ {
+ names.add(chain);
+ }
+ }
+ }
+ }
+ }
+ return names;
}
+ /**
+ * Send a 'focus' command to Chimera to recentre the visible display
+ */
+ public void focusView()
+ {
+ sendChimeraCommand("focus", false);
+ }
}
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
import java.util.Random;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import jalview.ws.dbsources.Pdb;
/**
- * GUI elements for handlnig an external chimera display
+ * GUI elements for handling an external chimera display
*
* @author jprocter
*
}
});
viewMenu.add(seqColourBy);
+ viewMenu.add(fitToWindow);
+
final ItemListener handler;
JMenu alpanels = new ViewSelectionMenu(
MessageManager.getString("label.superpose_with"), this,
String[] chains, final AlignmentPanel ap)
{
super();
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
+
+ /*
+ * is the pdb file already loaded?
+ */
+ String pdbId = pdbentry.getId();
String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ .alreadyMappedToFile(pdbId);
if (alreadyMapped != null)
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbentry.getId() }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbentry.getId() }),
- JOptionPane.YES_NO_CANCEL_OPTION);
-
+ int option = chooseAddSequencesToViewer(pdbId);
if (option == JOptionPane.CANCEL_OPTION)
{
return;
}
if (option == JOptionPane.YES_OPTION)
{
- // TODO : Fix multiple seq to one chain issue here.
- ap.getStructureSelectionManager().setMapping(seq, chains,
- alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.getSeqPanel().seqCanvas.fr != null)
- {
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
-
- // Now this ChimeraViewFrame is mapped to new sequences. We must add
- // them to the existing array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof ChimeraViewFrame)
- {
- final ChimeraViewFrame topView = ((ChimeraViewFrame) frame);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topView.jmb.getPdbCount(); pe++)
- {
- if (topView.jmb.getPdbEntry(pe).getFile()
- .equals(
- alreadyMapped))
- {
- topView.jmb.addSequence(pe, seq);
- topView.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topView.useAlignmentPanelForColourbyseq(ap);
- topView.buildActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
-
+ addSequenceMappingsToStructure(seq, chains, ap, alreadyMapped);
return;
}
}
- // /////////////////////////////////
- // Check if there are other Chimera views involving this alignment
- // and prompt user about adding this molecule to one of them
+
+ /*
+ * Check if there are other Chimera views involving this alignment and give
+ * user the option to add and align this molecule to one of them
+ */
List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame topView : existingViews)
+ for (ChimeraViewFrame view : existingViews)
{
- // TODO: highlight topView in view somehow
+ // TODO: highlight view somehow
/*
* JAL-1742 exclude view with this structure already mapped (don't offer
* to align chain B to chain A of the same structure)
*/
- if (topView.hasPdbId(pdbentry.getId()))
+ if (view.hasPdbId(pdbId))
{
continue;
}
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[]
- { pdbentry.getId(), topView.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
+ int option = chooseAlignStructureToViewer(pdbId, view);
if (option == JOptionPane.CANCEL_OPTION)
{
return;
}
if (option == JOptionPane.YES_OPTION)
{
- topView.useAlignmentPanelForSuperposition(ap);
- topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ view.useAlignmentPanelForSuperposition(ap);
+ view.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
return;
}
}
- // /////////////////////////////////
+
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
openNewChimera(ap, new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq });
}
/**
+ * Presents a dialog with the option to add an align a structure to an
+ * existing Chimera view
+ *
+ * @param pdbId
+ * @param view
+ * @return YES, NO or CANCEL JOptionPane code
+ */
+ protected int chooseAlignStructureToViewer(String pdbId,
+ ChimeraViewFrame view)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new Object[]
+ { pdbId, view.getTitle() }), MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ return option;
+ }
+
+ /**
+ * Presents a dialog with the option to add sequences to a viewer which
+ * already has their structure open
+ *
+ * @param pdbId
+ * @return YES, NO or CANCEL JOptionPane code
+ */
+ protected int chooseAddSequencesToViewer(String pdbId)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new Object[]
+ { pdbId }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
+ return option;
+ }
+
+ /**
+ * Adds mappings for the given sequences to an already opened PDB structure,
+ * and updates any viewers that have the PDB file
+ *
+ * @param seq
+ * @param chains
+ * @param ap
+ * @param pdbFilename
+ */
+ protected void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentPanel ap, String pdbFilename)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ /*
+ * create the mappings
+ */
+ ap.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
+ AppletFormatAdapter.FILE);
+
+ /*
+ * alert the FeatureRenderer to show new (PDB RESNUM) features
+ */
+ if (ap.getSeqPanel().seqCanvas.fr != null)
+ {
+ ap.getSeqPanel().seqCanvas.fr.featuresAdded();
+ ap.paintAlignment(true);
+ }
+
+ /*
+ * add the sequences to any other Chimera viewers for this pdb file
+ */
+ // JBPNOTE: this looks like a binding routine, rather than a gui routine
+ for (JInternalFrame frame : Desktop.instance.getAllFrames())
+ {
+ if (frame instanceof ChimeraViewFrame)
+ {
+ ChimeraViewFrame chimeraView = ((ChimeraViewFrame) frame);
+ for (int pe = 0; pe < chimeraView.jmb.getPdbCount(); pe++)
+ {
+ if (chimeraView.jmb.getPdbEntry(pe).getFile().equals(pdbFilename))
+ {
+ chimeraView.jmb.addSequence(pe, seq);
+ chimeraView.addAlignmentPanel(ap);
+ /*
+ * add it to the set of alignments used for colouring structure by
+ * sequence
+ */
+ chimeraView.useAlignmentPanelForColourbyseq(ap);
+ chimeraView.buildActionMenu();
+ ap.getStructureSelectionManager().sequenceColoursChanged(ap);
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Create a helper to manage progress bar display
*/
protected void createProgressBar()
SequenceI[][] seqs)
{
createProgressBar();
-
String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
}
/**
- * create a new viewer containing several structures superimposed using the
- * given alignPanel.
- *
- * @param ap
- * @param pe
- * @param seqs
- */
- public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
- SequenceI[][] seqs)
- {
- super();
- openNewChimera(ap, pe, seqs);
- }
-
- /**
* Create a new viewer from saved session state data including Chimera session
* file.
*
}
/**
+ * create a new viewer containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param pe
+ * @param seqs
+ * @param ap
+ */
+ public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+ AlignmentPanel ap)
+ {
+ super();
+ openNewChimera(ap, pe, seqs);
+ }
+
+ public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
+ AlignmentPanel alignPanel)
+ {
+ super();
+
+ /*
+ * Convert the map of sequences per pdb entry into the tied arrays expected
+ * by openNewChimera
+ *
+ * TODO pass the Map down to openNewChimera and its callees instead
+ */
+ final Set<PDBEntry> pdbEntries = toView.keySet();
+ PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
+ SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
+ for (int i = 0; i < pdbs.length; i++)
+ {
+ final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
+ seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
+ }
+
+ openNewChimera(alignPanel, pdbs, seqsForPdbs);
+ }
+
+ /**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
*
addingStructures = true;
_started = false;
alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
+ // progressBar = alignFrame; // visual indication happens on caller frame.
(worker = new Thread(this)).start();
return;
}
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
- /*
- * Pass an empty 'command' to launch Chimera
- */
- jmb.evalStateCommand("", false);
+ jmb.launchChimera();
if (this.chimeraSessionFile != null)
{
jmb.startChimeraListener();
}
+ /**
+ * If the list is not empty, add menu items for 'All' and each individual
+ * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
+ *
+ * @param chainNames
+ */
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
- if (chainNames == null)
+ if (chainNames == null || chainNames.isEmpty())
{
return;
}
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
}
}
- centerViewer();
+ showSelectedChains();
allChainsSelected = false;
}
});
{
if (!allChainsSelected)
{
- centerViewer();
+ showSelectedChains();
}
}
});
}
}
- void centerViewer()
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
}
}
}
- jmb.centerViewer(toshow);
+ jmb.showChains(toshow);
}
/**
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- // TODO: use pe.getId() instead of pe.getFile() ?
- jmb.getSsm().setMapping(jmb.getSequence()[pos], null,
+ jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ jmb.getChains()[pos],
pe.getFile(),
protocol);
} catch (OutOfMemoryError oomerror)
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
String pdbid = processingEntry.getId();
- long hdl = startProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new Object[]
- { pdbid }));
+ long handle = System.currentTimeMillis()
+ + Thread.currentThread().hashCode();
+
+ /*
+ * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
+ */
+ String msg = MessageManager.formatMessage("status.fetching_pdb",
+ new Object[]
+ { pdbid });
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // long hdl = startProgressBar(MessageManager.formatMessage(
+ // "status.fetching_pdb", new Object[]
+ // { pdbid }));
try
{
pdbseq = pdbclient.getSequenceRecords(pdbid);
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- String msg = pdbid + " "
+ msg = pdbid + " "
+ MessageManager.getString("label.state_completed");
- stopProgressBar(msg, hdl);
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // stopProgressBar(msg, hdl);
}
/*
* If PDB data were saved and are not invalid (empty alignment), return the
return tm;
}
+ /**
+ * End the progress bar with the specified handle, leaving a message (if not
+ * null) on the status bar
+ *
+ * @param msg
+ * @param handle
+ */
public void stopProgressBar(String msg, long handle)
{
if (progressBar != null)
{
return;
}
- ;
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
- ;
+
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
-
}
-
}
public void setJalviewColourScheme(ColourSchemeI ucs)
package jalview.gui;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
-
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import javax.swing.JOptionPane;
import javax.swing.table.DefaultTableModel;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
/**
* Provides the behaviors for the Structure chooser Panel
private void launchStructureViewer(StructureSelectionManager ssm,
PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
- SequenceI[] selectedSequences)
+ SequenceI[] sequences)
{
StructureViewer sViewer = new StructureViewer(ssm);
if (pdbEntriesToView.length > 1)
{
- sViewer.viewStructures(alignPanel, pdbEntriesToView,
- alignPanel.av.collateForPDB(pdbEntriesToView));
+ sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView),
+ alignPanel);
}
else
{
- sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+ sViewer.viewStructures(pdbEntriesToView[0], sequences,
alignPanel);
}
}
*/
package jalview.gui;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.StructureViewerModel;
import jalview.structure.StructureSelectionManager;
-import java.awt.Rectangle;
-
/**
* proxy for handling structure viewers.
*
ssm = structureSelectionManager;
}
- public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
- PDBEntry[] pr, SequenceI[][] collateForPDB)
+ /**
+ * View multiple PDB entries, each with associated sequences
+ *
+ * @param pdbs
+ * @param seqsForPdbs
+ * @param ap
+ * @return
+ */
+ public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+ SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
- return viewStructures(getViewerType(), ap, pr, collateForPDB);
+ JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqsForPdbs, ap);
+ if (viewer != null)
+ {
+ return viewer;
+ }
+ return viewStructures(getViewerType(), pdbs, seqsForPdbs, ap);
}
- public JalviewStructureDisplayI viewStructures(ViewerType viewerType,
- AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
+ /**
+ * A strictly temporary method pending JAL-1761 refactoring. Determines if all
+ * the passed PDB entries are the same (this is the case if selected sequences
+ * to view structure for are chains of the same structure). If so, calls the
+ * single-pdb version of viewStructures and returns the viewer, else returns
+ * null.
+ *
+ * @param pdbs
+ * @param seqsForPdbs
+ * @param ap
+ * @return
+ */
+ private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
+ SequenceI[][] seqsForPdbs,
+ AlignmentPanel ap)
+ {
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ if (pdbs == null || pdbs.length == 0)
+ {
+ return null;
+ }
+ int i = 0;
+ String firstFile = pdbs[0].getFile();
+ for (PDBEntry pdb : pdbs)
+ {
+ String pdbFile = pdb.getFile();
+ if (pdbFile == null || !pdbFile.equals(firstFile))
+ {
+ return null;
+ }
+ SequenceI[] pdbseqs = seqsForPdbs[i++];
+ if (pdbseqs != null)
+ {
+ for (SequenceI sq : pdbseqs)
+ {
+ seqs.add(sq);
+ }
+ }
+ }
+ return viewStructures(pdbs[0],
+ seqs.toArray(new SequenceI[seqs.size()]), ap);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+ SequenceI[] seqsForPdb, AlignmentPanel ap)
+ {
+ return viewStructures(getViewerType(), pdb, seqsForPdb, ap);
+ }
+
+ protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+ PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ sview = new AppJmol(ap, pdbs, ap.av.collateForPDB(pdbs));
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+ sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap);
}
else
{
return sview;
}
- public JalviewStructureDisplayI viewStructures(ViewerType viewerType,
- AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB)
+ protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+ PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
{
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(pr, collateForPDB, null, ap);
+ sview = new AppJmol(pdb, seqsForPdb, null, ap);
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(pr, collateForPDB, null, ap);
+ sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
}
else
{
return sview;
}
- public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
- SequenceI[] sequenceIs, Object object, AlignmentPanel ap)
- {
- return viewStructures(getViewerType(), ap, pdb, sequenceIs);
- }
-
/**
* Create a new panel controlling a structure viewer.
*
import java.util.List;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
private boolean nucleotide;
/**
+ * Data bean class to simplify parameterisation in superposeStructures
+ */
+ protected class SuperposeData
+ {
+ /**
+ * Constructor with alignment width argument
+ *
+ * @param width
+ */
+ public SuperposeData(int width)
+ {
+ pdbResNo = new int[width];
+ }
+
+ public String filename;
+
+ public String pdbId;
+
+ public String chain = "";
+
+ public boolean isRna;
+
+ /*
+ * The pdb residue number (if any) mapped to each column of the alignment
+ */
+ public int[] pdbResNo;
+ }
+
+ /**
* Constructor
*
* @param ssm
}
}
+ @Override
+ public abstract void highlightAtoms(List<AtomSpec> atoms);
+
+ protected boolean isNucleotide()
+ {
+ return this.nucleotide;
+ }
+
/**
* Returns a readable description of all mappings for the wrapped pdbfile to
* any mapped sequences
return sb.toString();
}
- @Override
- public void highlightAtoms(List<AtomSpec> atoms)
+ /**
+ * Returns the mapped structure position for a given aligned column of a given
+ * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
+ * not mapped to structure.
+ *
+ * @param seq
+ * @param alignedPos
+ * @param mapping
+ * @return
+ */
+ protected int getMappedPosition(SequenceI seq, int alignedPos,
+ StructureMapping mapping)
{
- if (atoms != null)
+ if (alignedPos >= seq.getLength())
{
- for (AtomSpec atom : atoms)
+ return -1;
+ }
+
+ if (Comparison.isGap(seq.getCharAt(alignedPos)))
+ {
+ return -1;
+ }
+ int seqPos = seq.findPosition(alignedPos);
+ int pos = mapping.getPDBResNum(seqPos);
+ return pos;
+ }
+
+ /**
+ * Helper method to identify residues that can participate in a structure
+ * superposition command. For each structure, identify a sequence in the
+ * alignment which is mapped to the structure. Identify non-gapped columns in
+ * the sequence which have a mapping to a residue in the structure. Returns
+ * the index of the first structure that has a mapping to the alignment.
+ *
+ * @param alignment
+ * the sequence alignment which is the basis of structure
+ * superposition
+ * @param matched
+ * an array of booleans, indexed by alignment column, where true
+ * indicates that every structure has a mapped residue present in the
+ * column (so the column can participate in structure alignment)
+ * @param structures
+ * an array of data beans corresponding to pdb file index
+ * @return
+ */
+ protected int findSuperposableResidues(AlignmentI alignment,
+ boolean[] matched, SuperposeData[] structures)
+ {
+ int refStructure = -1;
+ String[] files = getPdbFile();
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+ int lastPos = -1;
+
+ /*
+ * Find the first mapped sequence (if any) for this PDB entry which is in
+ * the alignment
+ */
+ final int seqCountForPdbFile = getSequence()[pdbfnum].length;
+ for (int s = 0; s < seqCountForPdbFile; s++)
{
- highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile());
+ for (StructureMapping mapping : mappings)
+ {
+ final SequenceI theSequence = getSequence()[pdbfnum][s];
+ if (mapping.getSequence() == theSequence
+ && alignment.findIndex(theSequence) > -1)
+ {
+ if (refStructure < 0)
+ {
+ refStructure = pdbfnum;
+ }
+ for (int r = 0; r < matched.length; r++)
+ {
+ if (!matched[r])
+ {
+ continue;
+ }
+ int pos = getMappedPosition(theSequence, r, mapping);
+ if (pos < 1 || pos == lastPos)
+ {
+ matched[r] = false;
+ continue;
+ }
+ lastPos = pos;
+ structures[pdbfnum].pdbResNo[r] = pos;
+ }
+ String chain = mapping.getChain();
+ if (chain != null && chain.trim().length() > 0)
+ {
+ structures[pdbfnum].chain = chain;
+ }
+ structures[pdbfnum].pdbId = mapping.getPdbId();
+ structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ // move on to next pdb file
+ s = seqCountForPdbFile;
+ break;
+ }
+ }
}
}
+ return refStructure;
}
- protected abstract void highlightAtom(int atomIndex, int pdbResNum,
- String chain, String pdbFile);
-
- protected boolean isNucleotide()
+ /**
+ * Returns true if the structure viewer has loaded all of the files of
+ * interest (identified by the file mapping having been set up), or false if
+ * any are still not loaded after a timeout interval.
+ *
+ * @param files
+ */
+ protected boolean waitForFileLoad(String[] files)
{
- return this.nucleotide;
+ /*
+ * give up after 10 secs plus 1 sec per file
+ */
+ long starttime = System.currentTimeMillis();
+ long endTime = 10000 + 1000 * files.length + starttime;
+ String notLoaded = null;
+
+ boolean waiting = true;
+ while (waiting && System.currentTimeMillis() < endTime)
+ {
+ waiting = false;
+ for (String file : files)
+ {
+ notLoaded = file;
+ try
+ {
+ StructureMapping[] sm = getSsm().getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Throwable x)
+ {
+ waiting = true;
+ }
+ }
+ }
+
+ if (waiting)
+ {
+ System.err
+ .println("Timed out waiting for structure viewer to load file "
+ + notLoaded);
+ return false;
+ }
+ return true;
}
}
\ No newline at end of file
import org.junit.Test;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.StructureViewer;
{
final StructureViewer structureViewer = new StructureViewer(af
.getViewport().getStructureSelectionManager());
-
+ structureViewer.setViewerType(ViewerType.JMOL);
JalviewStructureDisplayI jmolViewer = structureViewer
- .viewStructures(ViewerType.JMOL, af.getCurrentView()
- .getAlignPanel(), new PDBEntry[]
- { (PDBEntry) dsq.getPDBId().elementAt(q) },
- new SequenceI[][]
- { new SequenceI[]
- { sq } });
+ .viewStructures(dsq.getPDBId().elementAt(q),
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
/*
* Wait for viewer thread to start
*/
{
final StructureViewer structureViewer = new StructureViewer(af
.getViewport().getStructureSelectionManager());
-
+ structureViewer.setViewerType(ViewerType.CHIMERA);
JalviewStructureDisplayI chimeraViewer = structureViewer
- .viewStructures(ViewerType.CHIMERA, af.getCurrentView()
- .getAlignPanel(), new PDBEntry[]
- { (PDBEntry) dsq.getPDBId().elementAt(q) },
- new SequenceI[][]
- { new SequenceI[]
- { sq } });
+ .viewStructures(dsq.getPDBId().elementAt(q),
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
/*
* Wait for viewer thread to start
*/
--- /dev/null
+package jalview.structures.models;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel.SuperposeData;
+
+/**
+ * Unit tests for non-abstract methods of abstract base class
+ *
+ * @author gmcarstairs
+ *
+ */
+public class AAStructureBindingModelTest
+{
+ private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
+ + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
+ + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
+ + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
+ + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
+ + "ATOM 31 CA LYS A 101 33.323 11.587 43.115 1.00 41.69 C \n";
+
+ private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
+ + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n";
+
+ private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
+ + "ATOM 2 CA SER A 1 29.427 3.330 -6.578 1.00 32.50 C \n"
+ + "ATOM 8 CA PRO A 2 29.975 3.340 -2.797 1.00 17.62 C \n"
+ + "ATOM 16 CA ALYS A 3 26.958 3.024 -0.410 0.50 8.78 C \n"
+ + "ATOM 33 CA ALA A 4 26.790 4.320 3.172 1.00 11.98 C \n"
+ + "ATOM 39 CA AVAL A 5 24.424 3.853 6.106 0.50 13.83 C \n";
+
+ AAStructureBindingModel testee;
+
+ AlignmentI al = null;
+
+ /**
+ * Set up test conditions with three aligned sequences,
+ */
+ @Before
+ public void setUp()
+ {
+ SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
+ SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
+ SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
+ al = new Alignment(new SequenceI[]
+ { seq1, seq2, seq3 });
+ al.setDataset(null);
+
+ PDBEntry[] pdbFiles = new PDBEntry[3];
+ pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb");
+ pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb");
+ pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
+ String[][] chains = new String[3][];
+ SequenceI[][] seqs = new SequenceI[3][];
+ seqs[0] = new SequenceI[]
+ { seq1 };
+ seqs[1] = new SequenceI[]
+ { seq2 };
+ seqs[2] = new SequenceI[]
+ { seq3 };
+ StructureSelectionManager ssm = new StructureSelectionManager();
+
+ ssm.setMapping(new SequenceI[]
+ { seq1 }, null, PDB_1, AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[]
+ { seq2 }, null, PDB_2, AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[]
+ { seq3 }, null, PDB_3, AppletFormatAdapter.PASTE);
+
+ testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+ {
+ @Override
+ public String[] getPdbFile()
+ {
+ /*
+ * fudge 'filenames' to match those generated when PDBFile parses PASTE
+ * data
+ */
+ return new String[]
+ { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
+ }
+ @Override
+ public void updateColours(Object source)
+ {
+ }
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ }
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ }
+ };
+ }
+
+ /**
+ * Verify that the method determines that columns 2, 5 and 6 of the aligment
+ * are alignable in structure
+ */
+ @Test
+ public void testFindSuperposableResidues()
+ {
+ SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ for (int i = 0; i < structs.length; i++)
+ {
+ structs[i] = testee.new SuperposeData(al.getWidth());
+ }
+ /*
+ * initialise array of 'superposable columns' to true (would be false for
+ * hidden columns)
+ */
+ boolean[] matched = new boolean[al.getWidth()];
+ Arrays.fill(matched, true);
+
+ int refStructure = testee
+ .findSuperposableResidues(al, matched, structs);
+
+ assertEquals(0, refStructure);
+
+ /*
+ * only ungapped, structure-mapped columns are superposable
+ */
+ assertFalse(matched[0]); // gap in first sequence
+ assertTrue(matched[1]);
+ assertFalse(matched[2]); // gap in second sequence
+ assertFalse(matched[3]); // gap in third sequence
+ assertTrue(matched[4]);
+ assertTrue(matched[5]);
+ }
+
+ @Test
+ public void testFindSuperposableResidues_hiddenColumn()
+ {
+ SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ for (int i = 0; i < structs.length; i++)
+ {
+ structs[i] = testee.new SuperposeData(al.getWidth());
+ }
+ /*
+ * initialise array of 'superposable columns' to true (would be false for
+ * hidden columns)
+ */
+ boolean[] matched = new boolean[al.getWidth()];
+ Arrays.fill(matched, true);
+ // treat column 5 of the alignment as hidden
+ matched[4] = false;
+
+ int refStructure = testee
+ .findSuperposableResidues(al, matched, structs);
+
+ assertEquals(0, refStructure);
+
+ // only ungapped, structure-mapped columns are not superposable
+ assertFalse(matched[0]);
+ assertTrue(matched[1]);
+ assertFalse(matched[2]);
+ assertFalse(matched[3]);
+ assertFalse(matched[4]); // superposable, but hidden, column
+ assertTrue(matched[5]);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff