From: janengelhardt Date: Thu, 30 Jun 2011 10:07:42 +0000 (+0200) Subject: Reorganize the class structure, unfortunately breaks the VARNA-Frame X-Git-Tag: Jalview_2_9~576^2~30 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ed3945c9051ab14090b5012e4a8ef528df734ddb;p=jalview.git Reorganize the class structure, unfortunately breaks the VARNA-Frame Change-Id: Ia3dde7af1beb73e9261e49e81afe3e8594c945bb --- diff --git a/src/jalview/ext/varna/JalviewVarnaBinding.java b/src/jalview/ext/varna/JalviewVarnaBinding.java index 089ee64..a2d020b 100644 --- a/src/jalview/ext/varna/JalviewVarnaBinding.java +++ b/src/jalview/ext/varna/JalviewVarnaBinding.java @@ -48,1505 +48,9 @@ import jalview.schemes.*; import fr.orsay.lri.varna.applications.*; -public abstract class JalviewVarnaBinding implements StructureListener, - JmolStatusListener, SequenceStructureBinding, - JmolSelectionListener, ComponentListener, StructureSelectionManagerProvider +public abstract class JalviewVarnaBinding implements StructureListener, SequenceStructureBinding, + ComponentListener, StructureSelectionManagerProvider { - /** - * set if Jmol state is being restored from some source - instructs binding - * not to apply default display style when structure set is updated for first - * time. - */ - private boolean loadingFromArchive = false; - - /** - * state flag used to check if the Jmol viewer's paint method can be called - */ - private boolean finishedInit = false; - - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } - - boolean allChainsSelected = false; - - /** - * when true, try to search the associated datamodel for sequences that are - * associated with any unknown structures in the Jmol view. - */ - private boolean associateNewStructs = false; - - Vector atomsPicked = new Vector(); - - public Vector chainNames; - - Hashtable chainFile; - - /** - * array of target chains for seuqences - tied to pdbentry and sequence[] - */ - protected String[][] chains; - - boolean colourBySequence = true; - - StringBuffer eval = new StringBuffer(); - - public String fileLoadingError; - - /** - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - int frameNo = 0; - - protected JmolPopup jmolpopup; - - protected VARNAGUI varnagui; - - String lastCommand; - - String lastMessage; - - boolean loadedInline; - - /** - * current set of model filenames loaded in the Jmol instance - */ - String[] modelFileNames = null; - - public PDBEntry[] pdbentry; - - /** - * datasource protocol for access to PDBEntrylatest - */ - String protocol = null; - - StringBuffer resetLastRes = new StringBuffer(); - - /** - * sequences mapped to each pdbentry - */ - public SequenceI[][] sequence; - - public StructureSelectionManager ssm; - - public JmolViewer viewer; - - public JalviewVarnaBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs, - String[][] chains, String protocol) - { - this.ssm = ssm; - this.sequence = sequenceIs; - this.chains = chains; - this.pdbentry = pdbentry; - this.protocol = protocol; - if (chains == null) - { - this.chains = new String[pdbentry.length][]; - } - /* - * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), - * "jalviewJmol", ap.av.applet .getDocumentBase(), - * ap.av.applet.getCodeBase(), "", this); - * - * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); - */ - } - - public JalviewVarnaBinding(StructureSelectionManager ssm, JmolViewer viewer2) - { - this.ssm = ssm; - viewer = viewer2; - viewer.setJmolStatusListener(this); - viewer.addSelectionListener(this); - } - - /** - * construct a title string for the viewer window based on the data jalview - * knows about - * - * @return - */ - public String getViewerTitle() - { - if (sequence == null || pdbentry == null || sequence.length < 1 - || pdbentry.length < 1 || sequence[0].length < 1) - { - return ("Jalview Jmol Window"); - } - // TODO: give a more informative title when multiple structures are - // displayed. - StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":" - + pdbentry[0].getId()); - - if (pdbentry[0].getProperty() != null) - { - if (pdbentry[0].getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbentry[0].getProperty().get("method")); - } - if (pdbentry[0].getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbentry[0].getProperty().get("chains")); - } - } - return title.toString(); - } - - /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' - * - * @param chainList - * list of chains to make visible - */ - public void centerViewer(Vector chainList) - { - StringBuffer cmd = new StringBuffer(); - String lbl; - int mlength, p; - for (int i = 0, iSize = chainList.size(); i < iSize; i++) - { - mlength = 0; - lbl = (String) chainList.elementAt(i); - do - { - 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(":" + lbl.substring(mlength + 1) + " /" - + (1 + getModelNum((String) chainFile.get(lbl))) + " or "); - } - if (cmd.length() > 0) - cmd.setLength(cmd.length() - 4); - evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd); - } - - public void closeViewer() - { - viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); - // remove listeners for all structures in viewer - ssm.removeStructureViewerListener(this, this.getPdbFile()); - // and shut down jmol - viewer.evalStringQuiet("zap"); - viewer.setJmolStatusListener(null); - lastCommand = null; - viewer = null; - releaseUIResources(); - } - - /** - * called by JalviewJmolbinding after closeViewer is called - release any - * resources and references so they can be garbage collected. - */ - protected abstract void releaseUIResources(); - - public void colourByChain() - { - colourBySequence = false; - // TODO: colour by chain should colour each chain distinctly across all - // visible models - // TODO: http://issues.jalview.org/browse/JAL-628 - evalStateCommand("select *;color chain"); - } - - public void colourByCharge() - { - colourBySequence = false; - evalStateCommand("select *;color white;select ASP,GLU;color red;" - + "select LYS,ARG;color blue;select CYS;color yellow"); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. - */ - public void superposeStructures(AlignmentI alignment) - { - superposeStructures(alignment, -1, null); - } - - /** - * 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) - */ - public void superposeStructures(AlignmentI alignment, int refStructure) - { - superposeStructures(alignment, refStructure, null); - } - - /** - * 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) - * @param hiddenCols - * TODO - */ - 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) - { - String[] files = getPdbFile(); - StringBuffer selectioncom = new StringBuffer(); - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - // union of all aligned positions are collected together. - 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 " - + refStructure); - refStructure = -1; - } - if (refStructure < -1) - { - refStructure = -1; - } - StringBuffer command = new StringBuffer(); - - 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++) - { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - continue; - - int lastPos = -1; - for (int s = 0; s < sequence[pdbfnum].length; s++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[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 = sequence[pdbfnum].length; - break; - } - } - } - } - String[] selcom = new String[files.length]; - int nmatched = 0; - // generate select statements to select regions to superimpose structures - { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - molsel.append("{"); - for (int r = 0; r < matched.length; r++) - { - if (matched[r]) - { - if (pdbfnum == 0) - { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) - { - // discontinuity - if (lpos != -1) - { - molsel.append(lpos); - molsel.append(chainCd); - // molsel.append("} {"); - 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); - } - } - // add final selection phrase - if (lpos != -1) - { - molsel.append(lpos); - molsel.append(chainCd); - molsel.append("}"); - } - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("(("); - selectioncom.append(selcom[pdbfnum].substring(1, - selcom[pdbfnum].length() - 1)); - selectioncom.append(" )& "); - selectioncom.append(pdbfnum + 1); - selectioncom.append(".1)"); - if (pdbfnum < files.length - 1) - { - selectioncom.append("|"); - } - } - } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - if (pdbfnum == refStructure) - { - continue; - } - command.append("echo "); - command.append("\"Superposing ("); - command.append(chainNames[pdbfnum]); - command.append(") against reference ("); - command.append(chainNames[refStructure]); - command.append(")\";\ncompare "); - command.append("{"); - command.append(1 + pdbfnum); - command.append(".1} {"); - command.append(1 + refStructure); - command.append(".1} SUBSET {*.CA | *.P} ATOMS "); - - // form the matched pair strings - String sep = ""; - for (int s = 0; s < 2; s++) - { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - } - command.append(" ROTATE TRANSLATE;\n"); - } - System.out.println("Select regions:\n" + selectioncom.toString()); - evalStateCommand("select *; cartoons off; backbone; select (" - + selectioncom.toString() + "); cartoons; "); - // selcom.append("; ribbons; "); - System.out.println("Superimpose command(s):\n" + command.toString()); - - evalStateCommand(command.toString()); - } - if (selectioncom.length() > 0) - {// finally, mark all regions that were superposed. - if (selectioncom.substring(selectioncom.length() - 1).equals("|")) - { - selectioncom.setLength(selectioncom.length() - 1); - } - System.out.println("Select regions:\n" + selectioncom.toString()); - evalStateCommand("select *; cartoons off; backbone; select (" - + selectioncom.toString() + "); cartoons; "); - // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); - } - } - - public void evalStateCommand(String command) - { - jmolHistory(false); - if (lastCommand == null || !lastCommand.equals(command)) - { - viewer.evalStringQuiet(command + "\n"); - } - jmolHistory(true); - lastCommand = command; - } - - /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. - */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) - { - if (!colourBySequence) - return; - if (ssm == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (String cbyseq : VarnaCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment)) { - evalStateCommand(cbyseq); - } - } - public boolean isColourBySequence() - { - return colourBySequence; - } - - public void setColourBySequence(boolean colourBySequence) - { - this.colourBySequence = colourBySequence; - } - - public void createImage(String file, String type, int quality) - { - System.out.println("JMOL CREATE IMAGE"); - } - - public String createImage(String fileName, String type, - Object textOrBytes, int quality) - { - System.out.println("JMOL CREATE IMAGE"); - return null; - } - - public String eval(String strEval) - { - // System.out.println(strEval); - // "# 'eval' is implemented only for the applet."; - return null; - } - - // End StructureListener - // ////////////////////////// - - public float[][] functionXY(String functionName, int x, int y) - { - return null; - } - - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) - { - // TODO Auto-generated method stub - return null; - } - - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (getModelNum(pdbfile) < 0) - return null; - // TODO: verify atomIndex is selecting correct model. - return new Color(viewer.getAtomArgb(atomIndex)); - } - - /** - * 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. - */ - 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 - - * use getPdbFile to get number of unique models. - */ - private int _modelFileNameMap[]; - - // //////////////////////////////// - // /StructureListener - public synchronized String[] getPdbFile() - { - if (viewer == null) - { - return new String[0]; - } - if (modelFileNames == null) - { - - String mset[] = new String[viewer.getModelCount()]; - _modelFileNameMap = new int[mset.length]; - int j = 1; - mset[0] = viewer.getModelFileName(0); - for (int i = 1; i < mset.length; i++) - { - mset[j] = viewer.getModelFileName(i); - _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])))) - { - j++; - } - } - modelFileNames = new String[j]; - System.arraycopy(mset, 0, modelFileNames, 0, j); - } - return modelFileNames; - } - - /** - * map from string to applet - */ - public Map getRegistryInfo() - { - // TODO Auto-generated method stub - return null; - } - - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - // /////////////////////////////// - // JmolStatusListener - - public void handlePopupMenu(int x, int y) - { - jmolpopup.show(x, y); - } - - // jmol/ssm only - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (modelFileNames == null) - { - return; - } - - // look up file model number for this pdbfile - int mdlNum = 0; - String fn; - // may need to adjust for URLencoding here - we don't worry about that yet. - while (mdlNum < modelFileNames.length - && !pdbfile.equals(modelFileNames[mdlNum])) - { - // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn); - mdlNum++; - } - if (mdlNum == modelFileNames.length) - { - return; - } - - jmolHistory(false); - // if (!pdbfile.equals(pdbentry.getFile())) - // return; - if (resetLastRes.length() > 0) - { - viewer.evalStringQuiet(resetLastRes.toString()); - } - - eval.setLength(0); - eval.append("select " + pdbResNum); // +modelNum - - resetLastRes.setLength(0); - resetLastRes.append("select " + pdbResNum); // +modelNum - - eval.append(":"); - resetLastRes.append(":"); - if (!chain.equals(" ")) - { - eval.append(chain); - resetLastRes.append(chain); - } - { - eval.append(" /" + (mdlNum + 1)); - resetLastRes.append("/" + (mdlNum + 1)); - } - eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); - - resetLastRes.append(";wireframe 0;" + resetLastRes.toString() - + " and not hetero; spacefill 0;"); - - eval.append("spacefill 200;select none"); - - viewer.evalStringQuiet(eval.toString()); - jmolHistory(true); - - } - - boolean debug = true; - - private void jmolHistory(boolean enable) - { - viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off")); - } - - public void loadInline(String string) - { - loadedInline = true; - // TODO: re JAL-623 - // viewer.loadInline(strModel, isAppend); - // could do this: - // construct fake fullPathName and fileName so we can identify the file - // later. - // Then, construct pass a reader for the string to Jmol. - // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, - // fileName, null, reader, false, null, null, 0); - viewer.openStringInline(string); - } - - public void mouseOverStructure(int atomIndex, String strInfo) - { - int pdbResNum; - int alocsep = strInfo.indexOf("^"); - int mdlSep = strInfo.indexOf("/"); - int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; - - if (chainSeparator == -1) - { - chainSeparator = strInfo.indexOf("."); - if (mdlSep > -1 && mdlSep < chainSeparator) - { - chainSeparator1 = chainSeparator; - chainSeparator = mdlSep; - } - } - // handle insertion codes - if (alocsep != -1) - { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, alocsep)); - - } - else - { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); - } - String chainId; - - if (strInfo.indexOf(":") > -1) - chainId = strInfo.substring(strInfo.indexOf(":") + 1, - strInfo.indexOf(".")); - else - { - chainId = " "; - } - - String pdbfilename = modelFileNames[frameNo]; // default is first or current - // model - if (mdlSep > -1) - { - if (chainSeparator1 == -1) - { - chainSeparator1 = strInfo.indexOf(".", mdlSep); - } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); - try - { - // recover PDB filename for the model hovered over. - pdbfilename = viewer - .getModelFileName(new Integer(mdlId).intValue() - 1); - } catch (Exception e) - { - } - ; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); - - lastMessage = strInfo; - } - - public void notifyAtomHovered(int atomIndex, String strInfo, String data) - { - if (data != null) - { - System.err.println("Ignoring additional hover info: " + data - + " (other info: '" + strInfo + "' pos " + atomIndex + ")"); - } - mouseOverStructure(atomIndex, strInfo); - } - - /* - * { if (history != null && strStatus != null && - * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); - * } } - */ - - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) - { - /** - * this implements the toggle label behaviour copied from the original - * structure viewer, MCView - */ - if (strData != null) - { - System.err.println("Ignoring additional pick data string " + strData); - } - int chainSeparator = strInfo.indexOf(":"); - int p = 0; - if (chainSeparator == -1) - chainSeparator = strInfo.indexOf("."); - - String picked = strInfo.substring(strInfo.indexOf("]") + 1, - chainSeparator); - String mdlString = ""; - if ((p = strInfo.indexOf(":")) > -1) - picked += strInfo.substring(p + 1, strInfo.indexOf(".")); - - if ((p = strInfo.indexOf("/")) > -1) - { - mdlString += strInfo.substring(p, strInfo.indexOf(" #")); - } - picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" - + mdlString + "))"; - jmolHistory(false); - - if (!atomsPicked.contains(picked)) - { - viewer.evalStringQuiet("select " + picked + ";label %n %r:%c"); - atomsPicked.addElement(picked); - } - else - { - viewer.evalString("select " + picked + ";label off"); - atomsPicked.removeElement(picked); - } - jmolHistory(true); - // TODO: in application this happens - // - // if (scriptWindow != null) - // { - // scriptWindow.sendConsoleMessage(strInfo); - // scriptWindow.sendConsoleMessage("\n"); - // } - - } - - public void notifyCallback(int type, Object[] data) - { - try - { - switch (type) - { - case JmolConstants.CALLBACK_LOADSTRUCT: - notifyFileLoaded((String) data[1], (String) data[2], - (String) data[3], (String) data[4], - ((Integer) data[5]).intValue()); - - break; - case JmolConstants.CALLBACK_PICK: - notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: - notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - break; - case JmolConstants.CALLBACK_SCRIPT: - notifyScriptTermination((String) data[2], - ((Integer) data[3]).intValue()); - break; - case JmolConstants.CALLBACK_ECHO: - sendConsoleEcho((String) data[1]); - break; - case JmolConstants.CALLBACK_MESSAGE: - sendConsoleMessage((data == null) ? ((String) null) - : (String) data[1]); - break; - case JmolConstants.CALLBACK_ERROR: - // System.err.println("Ignoring error callback."); - break; - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_RESIZE: - refreshGUI(); - break; - case JmolConstants.CALLBACK_MEASURE: - - case JmolConstants.CALLBACK_CLICK: - default: - System.err.println("Unhandled callback " + type + " " - + data[1].toString()); - break; - } - } catch (Exception e) - { - System.err.println("Squashed Jmol callback handler error:"); - e.printStackTrace(); - } - } - - public boolean notifyEnabled(int callbackPick) - { - switch (callbackPick) - { - case JmolConstants.CALLBACK_ECHO: - case JmolConstants.CALLBACK_LOADSTRUCT: - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_MESSAGE: - case JmolConstants.CALLBACK_PICK: - case JmolConstants.CALLBACK_SCRIPT: - case JmolConstants.CALLBACK_HOVER: - case JmolConstants.CALLBACK_ERROR: - return true; - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: - } - return false; - } - - // incremented every time a load notification is successfully handled - - // lightweight mechanism for other threads to detect when they can start - // referrring to new structures. - private long loadNotifiesHandled = 0; - - public long getLoadNotifiesHandled() - { - return loadNotifiesHandled; - } - - public void notifyFileLoaded(String fullPathName, String fileName2, - String modelName, String errorMsg, int modelParts) - { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - refreshGUI(); - return; - } - // TODO: deal sensibly with models loaded inLine: - // modelName will be null, as will fullPathName. - - // the rest of this routine ignores the arguments, and simply interrogates - // the Jmol view to find out what structures it contains, and adds them to - // the structure selection manager. - fileLoadingError = null; - String[] oldmodels = modelFileNames; - modelFileNames = null; - chainNames = new Vector(); - chainFile = new Hashtable(); - boolean notifyLoaded = false; - String[] modelfilenames = getPdbFile(); - // first check if we've lost any structures - if (oldmodels != null && oldmodels.length > 0) - { - int oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - for (int n = 0; n < modelfilenames.length; n++) - { - if (modelfilenames[n] == oldmodels[i]) - { - oldmodels[i] = null; - break; - } - } - if (oldmodels[i] != null) - { - oldm++; - } - } - if (oldm > 0) - { - String[] oldmfn = new String[oldm]; - oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - if (oldmodels[i] != null) - { - oldmfn[oldm++] = oldmodels[i]; - } - } - // deregister the Jmol instance for these structures - we'll add - // ourselves again at the end for the current structure set. - ssm.removeStructureViewerListener(this, oldmfn); - } - } - refreshPdbEntries(); - for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) - { - String fileName = modelfilenames[modelnum]; - boolean foundEntry = false; - MCview.PDBfile pdb = null; - String pdbfile = null, pdbfhash = null; - // model was probably loaded inline - so check the pdb file hashcode - if (loadedInline) - { - // calculate essential attributes for the pdb data imported inline. - // prolly need to resolve modelnumber properly - for now just use our - // 'best guess' - pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum]) - + ".0", "PDB"); - pdbfhash = "" + pdbfile.hashCode(); - } - if (pdbentry != null) - { - // search pdbentries and sequences to find correct pdbentry for this - // model - for (int pe = 0; pe < pdbentry.length; pe++) - { - boolean matches = false; - if (fileName == null) - { - if (false) - // see JAL-623 - need method of matching pasted data up - { - pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile, - AppletFormatAdapter.PASTE); - pdbentry[modelnum].setFile("INLINE" + pdb.id); - matches = true; - foundEntry = true; - } - } - else - { - if (matches = pdbentry[pe].getFile().equals(fileName)) - { - foundEntry = true; - // TODO: Jmol can in principle retrieve from CLASSLOADER but - // this - // needs - // to be tested. See mantis bug - // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 - String protocol = AppletFormatAdapter.URL; - try - { - File fl = new java.io.File(pdbentry[pe].getFile()); - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) - { - } - ; - pdb = ssm.setMapping(sequence[pe], chains[pe], - pdbentry[pe].getFile(), protocol); - - } - } - if (matches) - { - pdbentry[pe].setId(pdb.id); - // add an entry for every chain in the model - for (int i = 0; i < pdb.chains.size(); i++) - { - String chid = new String(pdb.id + ":" - + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); - chainFile.put(chid, pdbentry[pe].getFile()); - chainNames.addElement(chid); - } - notifyLoaded = true; - } - } - } - if (!foundEntry && associateNewStructs) - { - // this is a foreign pdb file that jalview doesn't know about - add - // it to the dataset and try to find a home - either on a matching - // sequence or as a new sequence. - String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1", - "PDB"); - // parse pdb file into a chain, etc. - // locate best match for pdb in associated views and add mapping to - // ssm - // if properly registered then - notifyLoaded = true; - - } - } - // FILE LOADED OK - // so finally, update the jmol bits and pieces - if (jmolpopup != null) - { - // potential for deadlock here: - // jmolpopup.updateComputedMenus(); - } - if (!isLoadingFromArchive()) - { - viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); - } - // register ourselves as a listener and notify the gui that it needs to - // update itself. - ssm.addStructureViewerListener(this); - if (notifyLoaded) - { - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); - loadNotifiesHandled++; - } - setLoadingFromArchive(false); - } - - public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) - { - notifyAtomPicked(iatom, strMeasure, null); - } - - public abstract void notifyScriptTermination(String strStatus, - int msWalltime); - - /** - * display a message echoed from the jmol viewer - * - * @param strEcho - */ - public abstract void sendConsoleEcho(String strEcho); /* - * { showConsole(true); - * - * history.append("\n" + - * strEcho); } - */ - - // /End JmolStatusListener - // ///////////////////////////// - - /** - * @param strStatus - * status message - usually the response received after a script - * executed - */ - public abstract void sendConsoleMessage(String strStatus); - - public void setCallbackFunction(String callbackType, - String callbackFunction) - { - System.err.println("Ignoring set-callback request to associate " - + callbackType + " with function " + callbackFunction); - - } - - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - - if (cs == null) - return; - - String res; - int index; - Color col; - jmolHistory(false); - // TODO: Switch between nucleotide or aa selection expressions - Enumeration en = ResidueProperties.aa3Hash.keys(); - StringBuffer command = new StringBuffer("select *;color white;"); - while (en.hasMoreElements()) - { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); - if (index > 20) - continue; - - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - - command.append("select " + res + ";color[" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - } - - evalStateCommand(command.toString()); - jmolHistory(true); - } - - public void showHelp() - { - showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp"); - } - - /** - * open the URL somehow - * - * @param target - */ - public abstract void showUrl(String url, String target); - - /** - * called when the binding thinks the UI needs to be refreshed after a Jmol - * state change. this could be because structures were loaded, or because an - * error has occured. - */ - public abstract void refreshGUI(); - - /** - * called to show or hide the associated console window container. - * - * @param show - */ - public abstract void showConsole(boolean show); - - /** - * @param renderPanel - * @param jmolfileio - * - when true will initialise jmol's file IO system (should be false - * in applet context) - * @param htmlName - * @param documentBase - * @param codeBase - * @param commandOptions - */ - public void allocateViewer(Container renderPanel, boolean jmolfileio, - String htmlName, URL documentBase, URL codeBase, - String commandOptions) - { - allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, - codeBase, commandOptions, null, null); - } - - /** - * - * @param renderPanel - * @param jmolfileio - * - when true will initialise jmol's file IO system (should be false - * in applet context) - * @param htmlName - * @param documentBase - * @param codeBase - * @param commandOptions - * @param consolePanel - * - panel to contain Jmol console - * @param buttonsToShow - * - buttons to show on the console, in ordr - */ - public void allocateViewer(Container renderPanel, boolean jmolfileio, - String htmlName, URL documentBase, URL codeBase, - String commandOptions, final Container consolePanel, - String buttonsToShow) - { - if (commandOptions==null) { - commandOptions=""; - } - viewer = JmolViewer.allocateViewer(renderPanel, - (jmolfileio ? new SmarterJmolAdapter() : null), htmlName - + ((Object) this).toString(), documentBase, codeBase, - commandOptions, this); - - console = createJmolConsole(viewer, consolePanel, buttonsToShow); - if (consolePanel != null) - { - consolePanel.addComponentListener(this); - - } - - } - - protected abstract JmolAppConsoleInterface createJmolConsole( - JmolViewer viewer2, Container consolePanel, String buttonsToShow); - - protected org.jmol.api.JmolAppConsoleInterface console = null; - - public void componentResized(ComponentEvent e) - { - - } - - public void componentMoved(ComponentEvent e) - { - - } - - public void componentShown(ComponentEvent e) - { - showConsole(true); - } - - public void componentHidden(ComponentEvent e) - { - showConsole(false); - } - - public void setLoadingFromArchive(boolean loadingFromArchive) - { - this.loadingFromArchive = loadingFromArchive; - } - - public boolean isLoadingFromArchive() - { - return loadingFromArchive; - } - - public void setBackgroundColour(java.awt.Color col) - { - jmolHistory(false); - viewer.evalStringQuiet("background [" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - jmolHistory(true); - } - - /** - * add structures and any known sequence associations - * - * @returns the pdb entries added to the current set. - */ - public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, - SequenceI[][] seq, String[][] chns) - { - int pe = -1; - Vector v = new Vector(); - Vector rtn = new Vector(); - for (int i = 0; i < pdbentry.length; i++) - { - v.addElement(pdbentry[i]); - } - for (int i = 0; i < pdbe.length; i++) - { - int r = v.indexOf(pdbe[i]); - if (r == -1 || r >= pdbentry.length) - { - rtn.addElement(new int[] - { v.size(), i }); - v.addElement(pdbe[i]); - } - else - { - // just make sure the sequence/chain entries are all up to date - addSequenceAndChain(r, seq[i], chns[i]); - } - } - pdbe = new PDBEntry[v.size()]; - v.copyInto(pdbe); - pdbentry = pdbe; - if (rtn.size() > 0) - { - // expand the tied seuqence[] and string[] arrays - SequenceI[][] sqs = new SequenceI[pdbentry.length][]; - String[][] sch = new String[pdbentry.length][]; - System.arraycopy(sequence, 0, sqs, 0, sequence.length); - System.arraycopy(chains, 0, sch, 0, this.chains.length); - sequence = sqs; - chains = sch; - pdbe = new PDBEntry[rtn.size()]; - for (int r = 0; r < pdbe.length; r++) - { - int[] stri = ((int[]) rtn.elementAt(r)); - // record the pdb file as a new addition - pdbe[r] = pdbentry[stri[0]]; - // and add the new sequence/chain entries - addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); - } - } - else - { - pdbe = null; - } - return pdbe; - } - - public void addSequence(int pe, SequenceI[] seq) - { - // add sequences to the pe'th pdbentry's seuqence set. - addSequenceAndChain(pe, seq, null); - } - - private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) - { - if (pe < 0 || pe >= pdbentry.length) - { - throw new Error( - "Implementation error - no corresponding pdbentry (for index " - + pe + ") to add sequences mappings to"); - } - final String nullChain = "TheNullChain"; - Vector s = new Vector(); - Vector c = new Vector(); - if (chains == null) - { - chains = new String[pdbentry.length][]; - } - if (sequence[pe] != null) - { - for (int i = 0; i < sequence[pe].length; i++) - { - s.addElement(sequence[pe][i]); - if (chains[pe] != null) - { - if (i < chains[pe].length) - { - c.addElement(chains[pe][i]); - } - else - { - c.addElement(nullChain); - } - } - else - { - if (tchain != null && tchain.length > 0) - { - c.addElement(nullChain); - } - } - } - } - for (int i = 0; i < seq.length; i++) - { - if (!s.contains(seq[i])) - { - s.addElement(seq[i]); - if (tchain != null && i < tchain.length) - { - c.addElement(tchain[i] == null ? nullChain : tchain[i]); - } - } - } - SequenceI[] tmp = new SequenceI[s.size()]; - s.copyInto(tmp); - sequence[pe] = tmp; - if (c.size() > 0) - { - String[] tch = new String[c.size()]; - c.copyInto(tch); - for (int i = 0; i < tch.length; i++) - { - if (tch[i] == nullChain) - { - tch[i] = null; - } - } - chains[pe] = tch; - } - else - { - chains[pe] = null; - } - } - /** - * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated alignment sequences - */ - public String printMapping(String pdbfile) - { - return ssm.printMapping(pdbfile); - } - } diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index d1772c7..524ac82 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -32,13 +32,21 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.structure.*; import jalview.io.*; import jalview.schemes.*; +import fr.orsay.lri.varna.VARNAPanel; +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; +import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; +import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; +import fr.orsay.lri.varna.models.VARNAConfig; +import fr.orsay.lri.varna.models.rna.RNA; -public class AppVarna extends JInternalFrame // implements Runnable,SequenceStructureBinding, ViewSetProvider + +public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider { AppVarnaBinding vab; - JPanel varnaPanel; + VARNAPanel varnaPanel; String name; @@ -50,12 +58,24 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru //Vector atomsPicked = new Vector(); - public AppVarna(){ + /*public AppVarna(){ vab = new AppVarnaBinding(); initVarna(); - } + }*/ public AppVarna(String seq,String struc,String name){ + ArrayList rnaList = new ArrayList(); + RNA rna1 = new RNA(name); + try { + rna1.setRNA(seq,struc); + } catch (ExceptionUnmatchedClosingParentheses e2) { + e2.printStackTrace(); + } catch (ExceptionFileFormatOrSyntax e3) { + e3.printStackTrace(); + } + rnaList.add(rna1); + + //vab = new AppVarnaBinding(rnaList); vab = new AppVarnaBinding(seq,struc); name=this.name; initVarna(); @@ -65,20 +85,23 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe? //vab.setFinishedInit(false); varnaPanel=vab.get_varnaPanel(); + setBackground(Color.white); + System.out.println("vp: "+vab.get_varnaPanel().getName()); //varnaPanel.setVisible(true); - //getContentPane().setLayout(new BorderLayout()); - //getContentPane().add(varnaPanel, BorderLayout.CENTER); - //setVisible(true); - //jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height); - showPanel(true); + getContentPane().setLayout(new BorderLayout()); + getContentPane().add(varnaPanel, BorderLayout.CENTER); + setVisible(true); + varnaPanel.addVARNAListener(this); + jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height); + //showPanel(true); } public void showPanel(boolean show){ - vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - vab.pack(); - vab.setVisible(show); + //vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + //vab.pack(); + //vab.setVisible(show); - //varnaPanel.setVisible(show); + varnaPanel.setVisible(show); } private boolean _started = false; @@ -97,6 +120,25 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru Cache.log.error("Couldn't open Varna viewer!", ex); } } + +@Override +public void onLayoutChanged() { + // TODO Auto-generated method stub + +} + +@Override +public void onUINewStructure(VARNAConfig v, RNA r) { + //TODO _rnaList.add(v, r,"",true); + // TODO Auto-generated method stub + +} + +@Override +public void onWarningEmitted(String s) { + // TODO Auto-generated method stub + +} } diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index efc1546..54ca3b3 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -33,6 +33,7 @@ import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.ComponentEvent; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.io.File; @@ -72,21 +73,16 @@ import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.Mapping; import fr.orsay.lri.varna.models.rna.RNA; -public class AppVarnaBinding extends JFrame implements DropTargetListener, InterfaceVARNAListener, MouseListener { +public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding implements DropTargetListener, InterfaceVARNAListener, MouseListener { /** * */ //private static final long serialVersionUID = -790155708306987257L; - private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA"; - - private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."; - private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...))))).."; - // private static final String DEFAULT_STRUCTURE1 = "((((....))))"; - // private static final String DEFAULT_STRUCTURE2 = - // "((((..(((....)))..))))"; - + //private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA"; + //private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."; + //private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...))))).."; public VARNAPanel vp; private JPanel _tools = new JPanel(); @@ -120,21 +116,26 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter private BackupHolder _rnaList; - public AppVarnaBinding() { - super("VARNA in Jalview"); + /*public AppVarnaBinding() { + //super("VARNA in Jalview"); //this.set_seq("ATGC"); //this.set_str(".()."); //RNAPanelDemoInit(); //initVarna("ATGCATGATATATATATAT","....((((...))))...."); initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1); - } + }*/ - public AppVarnaBinding(String seq, String struc){ - super("VARNA in Jalview"); + public AppVarnaBinding(String seq,String struc){ + //super("VARNA in Jalview"); initVarna(seq,struc); } + public AppVarnaBinding(ArrayList rnalist){ + //super("VARNA in Jalview"); + initVarnaEdit(rnalist); + } + private void initVarna(String seq, String str){ @@ -179,17 +180,155 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter vp.setPreferredSize(new Dimension(400, 400)); _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true); - setBackground(_backgroundColor); + //TODO setBackground(_backgroundColor); + vp.setBackground(_backgroundColor); + + //TODO getContentPane().setLayout(new BorderLayout()); + //TODO getContentPane().add(vp, BorderLayout.CENTER); + + //setVisible(true); + vp.addVARNAListener(this); + } + + private void initVarnaEdit(ArrayList rnaInList) + { + DefaultListModel dlm = new DefaultListModel(); + + + int marginTools = 40; + + DefaultListSelectionModel m = new DefaultListSelectionModel(); + m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + m.setLeadAnchorNotificationEnabled(false); + + + _sideList = new ReorderableJList(); + _sideList.setModel(dlm); + _sideList.addMouseListener(this); + _sideList.setSelectionModel(m); + _sideList.setPreferredSize(new Dimension(100, 0)); + _sideList.addListSelectionListener( new ListSelectionListener(){ + public void valueChanged(ListSelectionEvent arg0) { + //System.out.println(arg0); + if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting()) + { + FullBackup sel = (FullBackup) _sideList.getSelectedValue(); + Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize()); + vp.showRNAInterpolated(sel.rna,sel.config,map); + _seq.setText(sel.rna.getSeq()); + _str.setText(sel.rna.getStructDBN()); + } + } + }); + + _rnaList = new BackupHolder(dlm,_sideList); + try { + vp = new VARNAPanel("0","."); + for(int i=0;i