X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=94df99a3648bb5650de93a44982b24e4e3733089;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=a5775592fe0e9893b21f0ba153bc87f522101871;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index a577559..94df99a 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -27,7 +27,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; 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; @@ -35,6 +35,7 @@ import jalview.structure.AtomSpec; 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; @@ -43,13 +44,13 @@ import java.awt.event.ComponentListener; import java.io.File; import java.net.URL; import java.security.AccessControlException; +import java.util.ArrayList; +import java.util.BitSet; import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.Vector; -import javajs.awt.Dimension; - import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; @@ -73,12 +74,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel Vector atomsPicked = new Vector(); - public Vector chainNames; + private List chainNames; Hashtable chainFile; - public String fileLoadingError; - /* * the default or current model displayed if the model cannot be identified * from the selection message @@ -93,20 +92,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel 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(), @@ -177,6 +171,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel releaseUIResources(); } + @Override public void colourByChain() { colourBySequence = false; @@ -186,6 +181,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel evalStateCommand("select *;color chain"); } + @Override public void colourByCharge() { colourBySequence = false; @@ -234,20 +230,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } /** - * 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, + @Override + public String superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { while (viewer.isScriptExecuting()) @@ -258,12 +244,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } catch (InterruptedException i) { } - ; } + + /* + * get the distinct structure files modelled + * (a file with multiple chains may map to multiple sequences) + */ String[] files = getPdbFile(); if (!waitForFileLoad(files)) { - return; + return null; } StringBuilder selectioncom = new StringBuilder(256); @@ -279,6 +269,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel 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 = " "; @@ -304,14 +295,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } /* - * '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 */ - // TODO could use a BitSet for matched - 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]; @@ -336,17 +329,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } 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)); } /* @@ -361,35 +349,35 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel 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 @@ -421,6 +409,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } } 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 @@ -473,6 +463,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel + selectioncom.toString() + "); cartoons; "); // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); } + + return null; } public void evalStateCommand(String command) @@ -487,35 +479,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } /** - * 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) { @@ -527,16 +499,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel /** * @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); } /** @@ -598,17 +569,6 @@ public abstract class JalviewJmolBinding 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 jmol view's contents to the list of structure files * Jalview knows about. @@ -650,15 +610,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (modelFileNames == null) { - String mset[] = new String[viewer.ms.mc]; - _modelFileNameMap = new int[mset.length]; + List mset = new ArrayList(); + _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 @@ -666,39 +626,43 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel .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); } } - _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; } @@ -713,16 +677,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return null; } - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); + // /////////////////////////////// // JmolStatusListener @@ -1077,7 +1032,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new Vector(); + chainNames = new ArrayList(); chainFile = new Hashtable(); boolean notifyLoaded = false; String[] modelfilenames = getPdbFile(); @@ -1137,13 +1092,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel 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; @@ -1161,12 +1117,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // 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) { @@ -1188,7 +1144,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String chid = new String(pdb.getId() + ":" + pdb.getChains().elementAt(i).id); chainFile.put(chid, fileName); - chainNames.addElement(chid); + chainNames.add(chid); } notifyLoaded = true; } @@ -1236,6 +1192,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel setLoadingFromArchive(false); } + @Override + public List getChainNames() + { + return chainNames; + } + public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) { notifyAtomPicked(iatom, strMeasure, null); @@ -1275,6 +1237,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -1289,10 +1252,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel command.append("select *;color white;"); List 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() + "];"); } @@ -1389,6 +1354,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel protected org.jmol.api.JmolAppConsoleInterface console = null; + @Override public void setBackgroundColour(java.awt.Color col) { jmolHistory(false); @@ -1398,7 +1364,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { // Jalview doesn't honour resize panel requests return null;