X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=2171815ac77c99dede609be1a9d755a81bb666ed;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=501e34550923c97a273c9f1873f372f1beaa6bd3;hpb=ee778ac34b35c8d8fef03f1f3a58efb7d5be650a;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 501e345..2171815 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -30,6 +30,7 @@ import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.httpserver.AbstractRequestHandler; +import jalview.io.DataSourceType; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; @@ -41,6 +42,7 @@ import jalview.util.MessageManager; import java.awt.Color; import java.net.BindException; import java.util.ArrayList; +import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -64,6 +66,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private static final String ALPHACARBON = "CA"; + private List chainNames = new ArrayList(); + + private Hashtable chainFile = new Hashtable(); + /* * Object through which we talk to Chimera */ @@ -87,8 +93,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean loadingFinished = true; - public String fileLoadingError; - /* * Map of ChimeraModel objects keyed by PDB full local file name */ @@ -190,14 +194,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public JalviewChimeraBinding(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 = new ChimeraManager(new StructureManager(true)); } @@ -250,18 +252,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return - */ - public String getViewerTitle(boolean verbose) - { - return getViewerTitle("Chimera", verbose); - } - - /** * Tells Chimera to display only the specified chains * * @param toshow @@ -277,11 +267,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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(":.").append(chain); + cmd.append(showChainCmd); first = false; } @@ -290,7 +283,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * window, but it looks more helpful not to (easier to relate chains to the * whole) */ - final String command = "~display #*; ~ribbon #*; ribbon " + final String command = "~display #*; ~ribbon #*; ribbon :" + cmd.toString(); sendChimeraCommand(command, false); } @@ -321,6 +314,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel releaseUIResources(); } + @Override public void colourByChain() { colourBySequence = false; @@ -336,6 +330,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel *
  • all others - white
    • * */ + @Override public void colourByCharge() { colourBySequence = false; @@ -357,6 +352,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param _hiddenCols * an array of corresponding hidden columns for each alignment */ + @Override public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { @@ -673,34 +669,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String progressMsg); /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) { - if (!colourBySequence || !loadingFinished) - { - 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 command : cpdbbyseq.commands) { @@ -716,6 +693,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param alignment * @return */ + @Override protected StructureMappingcommandSet[] getColourBySequenceCommands( String[] files, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) @@ -751,40 +729,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // ////////////////////////// /** - * 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 viewer's contents to the list of structure files * Jalview knows about. */ public abstract void refreshPdbEntries(); - private int getModelNum(String modelFileName) - { - String[] mfn = getPdbFile(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) - { - if (mfn[i].equalsIgnoreCase(modelFileName)) - { - return i; - } - } - return -1; - } - /** * map between index of model filename returned from getPdbFile and the first * index of models from this file in the viewer. Note - this is not trimmed - @@ -801,35 +751,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { return new String[0]; } - // if (modelFileNames == null) - // { - // Collection chimodels = viewer.getChimeraModels(); - // _modelFileNameMap = new int[chimodels.size()]; - // int j = 0; - // for (ChimeraModel chimodel : chimodels) - // { - // String mdlName = chimodel.getModelName(); - // } - // modelFileNames = new String[j]; - // // System.arraycopy(mset, 0, modelFileNames, 0, j); - // } return chimeraMaps.keySet().toArray( modelFileNames = new String[chimeraMaps.size()]); } /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - /** * Construct and send a command to highlight zero, one or more atoms. We do * this by sending an "rlabel" command to show the residue label at that * position. @@ -981,6 +908,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return loadNotifiesHandled; } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -997,12 +925,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List residueSet = ResidueProperties.getResidues(isNucleotide(), false); - for (String res : residueSet) + for (String resName : residueSet) { - Color col = cs.findColour(res.charAt(0)); + char res = resName.length() == 3 ? ResidueProperties + .getSingleCharacterCode(resName) : resName.charAt(0); + Color col = cs.findColour(res); command.append("color " + col.getRed() / normalise + "," + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + res + ";"); + / normalise + " ::" + resName + ";"); } sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); @@ -1053,6 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * .html * @param col */ + @Override public void setBackgroundColour(Color col) { viewerCommandHistory(false); @@ -1105,35 +1036,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Returns a list of chains mapped in this viewer. Note this list is not - * currently scoped per structure. - * - * @return - */ - public List getChainNames() - { - List names = new ArrayList(); - 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() @@ -1168,4 +1070,31 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sm.highlightStructure(this, seq, positions); } } + + + @Override + public List getChainNames() + { + return chainNames; + } + + public Hashtable getChainFile() + { + return chainFile; + } + + public List getChimeraModelByChain(String chain) + { + return chimeraMaps.get(chainFile.get(chain)); + } + + public int getModelNoForChain(String chain) + { + List foundModels = getChimeraModelByChain(chain); + if (foundModels != null && !foundModels.isEmpty()) + { + return foundModels.get(0).getModelNumber(); + } + return -1; + } }