X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=44bcbe40432599fdc0bfb3b3c6b059de7dd3e881;hb=2d62933ef95beb94c1ec2444bcced4a3a7ec42c0;hp=6fa06d256365dd2210338957aecfc9e7d52b26a1;hpb=defb4c1d5b4edbd8fbd490f25c15ef1f1de6fe37;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 6fa06d2..44bcbe4 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -22,7 +22,6 @@ package jalview.ext.rbvi.chimera; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; -import jalview.api.SequenceRenderer; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; @@ -32,13 +31,11 @@ import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.datamodel.VisibleContigsIterator; import jalview.httpserver.AbstractRequestHandler; import jalview.io.DataSourceType; 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; @@ -251,43 +248,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Tells Chimera to display only the specified chains - * - * @param toshow - */ - public void showChains(List toshow) - { - /* - * Construct a chimera command like - * - * ~display #*;~ribbon #*;ribbon :.A,:.B - */ - StringBuilder cmd = new StringBuilder(64); - boolean first = true; - for (String chain : toshow) - { - int modelNumber = getModelNoForChain(chain); - String showChainCmd = modelNumber == -1 ? "" - : modelNumber + ":." + chain.split(":")[1]; - if (!first) - { - cmd.append(","); - } - cmd.append(showChainCmd); - first = 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); - } - - /** * Close down the Jalview viewer and listener, and (optionally) the associated * Chimera window. */ @@ -502,7 +462,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @see * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html */ - command.append("match ").append(getModelSpec(pdbfnum)).append(":"); + command.append("match ").append(getModelSpec(pdbfnum)) + .append(":"); command.append(selcom[pdbfnum]); command.append("@").append( structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); @@ -579,7 +540,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param pdbfnum * @return */ - protected String getModelSpec(int pdbfnum) + @Override + public String getModelSpec(int pdbfnum) { if (pdbfnum < 0 || pdbfnum >= getPdbCount()) { @@ -594,7 +556,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ List maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); boolean hasSubModels = maps != null && maps.size() > 1; - return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); + String spec = "#" + String.valueOf(pdbfnum); + return hasSubModels ? spec + ".1" : spec; } /** @@ -704,16 +667,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * @param files - * @param sr * @param viewPanel * @return */ @Override protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel) + String[] files, AlignmentViewPanel viewPanel) { - return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, - getSequence(), sr, viewPanel); + return ChimeraCommands.getColourBySequenceCommand(files, viewPanel, + this); } /** @@ -938,7 +900,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return; } - // Chimera expects RBG values in the range 0-1 + // Chimera expects RGB values in the range 0-1 final double normalise = 255D; viewerCommandHistory(false); StringBuilder command = new StringBuilder(128); @@ -951,9 +913,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel ? ResidueProperties.getSingleCharacterCode(resName) : resName.charAt(0); Color col = cs.findColour(res, 0, null, null, 0f); - command.append("color " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() / normalise - + " ::" + resName + ";"); + command.append("color ") + .append(String.valueOf(col.getRed() / normalise)).append(",") + .append(String.valueOf(col.getGreen() / normalise)) + .append(",").append(String.valueOf(col.getBlue() / normalise)) + .append(" ::").append(resName).append(";"); } sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); @@ -1123,8 +1087,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } StructureMappingcommandSet commandSet = ChimeraCommands - .getSetAttributeCommandsForFeatures(getSsm(), files, - getSequence(), avp); + .getSetAttributeCommandsForFeatures(avp, this); String[] commands = commandSet.commands; if (commands.length > 10) { @@ -1324,100 +1287,23 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } @Override - public void showStructures(AlignViewportI av) + public void showStructures(AlignViewportI av, boolean refocus) { StringBuilder cmd = new StringBuilder(128); cmd.append("~display; ~ribbon;"); - if (isShowAlignmentOnly()) - { - String atomSpec = getMappedResidues(av); - cmd.append("ribbon ").append(atomSpec); - } - else + + AtomSpecModel model = getShownResidues(av); + String atomSpec = ChimeraCommands.getAtomSpec(model, this); + + cmd.append("ribbon ").append(atomSpec); + if (!isShowAlignmentOnly()) { cmd.append("chain @CA|P; ribbon"); } - cmd.append("; focus"); - sendChimeraCommand(cmd.toString(), false); - } - - /** - * Builds a Chimera atomSpec of residues mapped from sequences, of the format - * (#model:residues.chain) - * - * 
-   * #0:2-94.A | #1:1-93.C | #2:1-93.A
-   *
- * - * Only residues visible in the alignment are included, that is, hidden columns - * and sequences are excluded. - * - * @param av - * @return - */ - private String getMappedResidues(AlignViewportI av) - { - AlignmentI alignment = av.getAlignment(); - final int width = alignment.getWidth(); - - String[] files = getStructureFiles(); - - StringBuilder atomSpec = new StringBuilder(256); - - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + if (refocus) { - StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); - - /* - * 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++) - { - for (StructureMapping mapping : mappings) - { - final SequenceI theSequence = getSequence()[pdbfnum][s]; - if (mapping.getSequence() == theSequence - && alignment.findIndex(theSequence) > -1) - { - String chainCd = mapping.getChain(); - - // TODO only process sequence ranges within visible columns - VisibleContigsIterator visible = alignment.getHiddenColumns() - .getVisContigsIterator(0, width, true); - while (visible.hasNext()) - { - int[] visibleRegion = visible.next(); - int seqStartPos = theSequence.findPosition(visibleRegion[0]); - int seqEndPos = theSequence.findPosition(visibleRegion[1]); - List residueRanges = mapping - .getPDBResNumRanges(seqStartPos, seqEndPos); - if (!residueRanges.isEmpty()) - { - if (atomSpec.length() > 0) - { - atomSpec.append("| "); - } - atomSpec.append(getModelSpec(pdbfnum)).append(":"); - boolean first = true; - for (int[] range : residueRanges) - { - if (!first) - { - atomSpec.append(","); - } - first = false; - atomSpec.append(range[0]).append("-").append(range[1]); - atomSpec.append(".").append(chainCd); - } - } - } - } - } - } + cmd.append("; focus"); } - - return atomSpec.toString(); + sendChimeraCommand(cmd.toString(), false); } }