/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/ |
H A D | AtomSetCollectionReader.java | 149 public Map<String, Object> htParams; field in AtomSetCollectionReader 255 this.htParams = htParams; in setupASCR() 464 htParams.get("pdbNoHydrogens")); in setIsPDB() 490 htParams.put("bsFilter", bsFilter); in finish() 564 fillRange = htParams.get("fillRange"); in initialize() 569 o = htParams.get("supercell"); in initialize() 580 int ptFile = (htParams.containsKey("ptFile") ? ((Integer) htParams in initialize() 618 symmetryRange = (htParams.containsKey("symmetryRange") ? ((Float) htParams in initialize() 647 unitCellOffsetFractional = htParams in initialize() 668 domains = htParams.get("domains"); in initialize() [all …]
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H A D | SmarterJmolAdapter.java | 103 bufferedReader, htParams, -1); in staticGetAtomSetCollectionReader() 130 htParams, -1); in getAtomSetCollectionFromReader() 203 if (htParams.containsKey("concatenate")) { in getAtomSetCollectionReaders() 245 htParams.put("vwr", vwr); in getAtomSetCollectionReaders() 252 htParams.put("fullPathName", fullPathName); in getAtomSetCollectionReaders() 254 (types == null ? null : types[i]), reader, htParams, i); in getAtomSetCollectionReaders() 260 r.setup(names[i], htParams, in getAtomSetCollectionReaders() 263 r.setup(names[i], htParams, reader); in getAtomSetCollectionReaders() 323 if (htParams.containsKey("trajectorySteps")) { in getAtomSetCollectionFromSet() 332 (Lst<P3[]>) htParams.get("trajectorySteps"), in getAtomSetCollectionFromSet() [all …]
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H A D | Resolver.java | 107 Map<String, Object> htParams, int ptFile) in getAtomCollectionReader() argument 113 type = (String) htParams.get("filter"); in getAtomCollectionReader() 128 type = (String) htParams.get("defaultType"); in getAtomCollectionReader() 148 htParams.put("ptFile", Integer.valueOf(ptFile)); in getAtomCollectionReader() 150 htParams.put("readerName", readerName); in getAtomCollectionReader() 153 return getReader(readerName, htParams); in getAtomCollectionReader() 162 public static Object getReader(String readerName, Map<String, Object> htParams) { in getReader() argument 204 public static Object DOMResolve(Map<String, Object> htParams) in DOMResolve() argument 206 String rdrName = getXmlType((String) htParams in DOMResolve() 211 htParams.put("readerName", rdrName); in DOMResolve() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/util/ |
H A D | JmolAudio.java | 69 public void playAudio(Viewer vwr, Map<String, Object> htParams) { in playAudio() argument 71 id = (String) htParams.get("id"); in playAudio() 74 htParams.put("id", id = "audio" + ++idCount); in playAudio() 77 params = htParams; in playAudio() 79 fileName = (String) htParams.get("audioFile"); in playAudio() 80 vwr.sm.registerAudio(id, htParams); in playAudio() 86 jmol.playAudio(applet, htParams); in playAudio() 89 if (htParams.containsKey("action")) in playAudio() 90 action((String) htParams.get("action")); in playAudio() 91 else if (htParams.containsKey("loop")) { in playAudio()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/io/ |
H A D | DOMReader.java | 38 private Map<String, Object> htParams; field in DOMReader 42 void set(FileManager fileManager, Viewer vwr, Object DOMNode, Map<String, Object> htParams) { in set() argument 46 this.htParams = htParams; in set() 65 htParams.put("nameSpaceInfo", info); in run() 69 aDOMNode, htParams); in run()
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H A D | FilesReader.java | 33 private Map<String, Object> htParams; field in FilesReader 42 Map<String, Object> htParams, boolean isAppend) { in set() argument 49 this.htParams = htParams; in set() 61 this, fullPathNamesIn, fileTypesIn, htParams, getReadersOnly); in run() 65 atomSetCollection, null, htParams); in run() 101 forceBinary, false, true, htParams); in getBufferedReaderOrBinaryDocument() 109 (BufferedInputStream) t, name, zipDirectory, htParams, 1, true); in getBufferedReaderOrBinaryDocument()
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H A D | FileReader.java | 56 private Map<String, Object> htParams; field in FileReader 73 Map<String, Object> htParams, boolean isAppend) { in FileReader() argument 91 this.htParams = htParams; in FileReader() 105 bytesOrStream, true, false, false, true, htParams); in run() 125 htParams.put("subFileList", subFileList); in run() 128 …zu().getAtomSetCollectionOrBufferedReaderFromZip(vwr, zis, name, zipDirectory, htParams, 1, false); in run() 138 …util.BinaryDocument", vwr, "file")).setStream((BufferedInputStream) t, !htParams.containsKey("isLi… in run() 141 fullPathNameIn, fileTypeIn, readerOrDocument, htParams); in run()
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H A D | JmolUtil.java | 158 Map<String, Object> htParams, in getAtomSetCollectionOrBufferedReaderFromZip() argument 167 htParams.put("zipSet", fileName); in getAtomSetCollectionOrBufferedReaderFromZip() 168 String[] subFileList = (String[]) htParams.get("subFileList"); in getAtomSetCollectionOrBufferedReaderFromZip() 177 if (subFileName == null && htParams.containsKey("modelNumber")) { in getAtomSetCollectionOrBufferedReaderFromZip() 178 selectedFile = ((Integer) htParams.get("modelNumber")).intValue(); in getAtomSetCollectionOrBufferedReaderFromZip() 180 htParams.remove("modelNumber"); in getAtomSetCollectionOrBufferedReaderFromZip() 184 String manifest = (String) htParams.get("manifest"); in getAtomSetCollectionOrBufferedReaderFromZip() 220 .getAtomSetCollectionFromReader(fileName, reader, htParams); in getAtomSetCollectionOrBufferedReaderFromZip() 250 htParams.put("subFileName", subFileName); in getAtomSetCollectionOrBufferedReaderFromZip() 265 vwr, bis, fileName + "|" + thisEntry, zipDir2, htParams, in getAtomSetCollectionOrBufferedReaderFromZip() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/ |
H A D | JmolAdapter.java | 130 Object bufferedReader, Map<String, Object> htParams); in getAtomSetCollectionReader() argument 159 Map<String, Object> htParams, boolean getReadersOnly); in getAtomSetCollectionReaders() argument 161 … Object getAtomSetCollectionFromSet(Object readers, Object atomSets, Map<String, Object> htParams); in getAtomSetCollectionFromSet() argument 164 … Object reader, Map<String, Object> htParams) throws Exception; in getAtomSetCollectionFromReader() argument 178 Map<String, Object> htParams) { in getAtomSetCollectionFromReaderType() argument 182 htParams, false)); in getAtomSetCollectionFromReaderType() 196 Map<String, Object> htParams) { in openBufferedReader() argument 197 return getAtomSetCollectionFromReaderType(name, null, bufferedReader, htParams); in openBufferedReader() 205 abstract public Object getAtomSetCollectionFromDOM(Object DOMNode, Map<String, Object> htParams); in getAtomSetCollectionFromDOM() argument
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H A D | JmolDomReaderInterface.java | 10 …public void set(FileManager fileManager, Viewer vwr, Object DOMNode, Map<String, Object> htParams); in set() argument
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H A D | JmolFilesReaderInterface.java | 17 Map<String, Object> htParams, boolean isAppend); in set() argument
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H A D | JmolJDXMOLParser.java | 12 Map<String, Object> htParams); in set() argument
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/ |
H A D | FileManager.java | 102 htParams.put("loadState", vwr.g.getLoadState(htParams)); in setLoadState() 209 setLoadState(htParams); in createAtomSetCollectionFromFile() 214 htParams.put("dbName", name0); in createAtomSetCollectionFromFile() 245 setLoadState(htParams); in createAtomSetCollectionFromFiles() 263 htParams.put("fileTypes", fileTypes); in createAtomSetCollectionFromFiles() 273 setLoadState(htParams); in createAtomSetCollectionFromString() 295 if (!htParams.containsKey("isData")) { in createAtomSeCollectionFromStrings() 309 setLoadState(htParams); in createAtomSeCollectionFromStrings() 318 null, readers, htParams, isAppend); in createAtomSeCollectionFromStrings() 385 reader, htParams, false); in createAtomSetCollectionFromReader() [all …]
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H A D | StatusManager.java | 813 if (htParams == null) in registerAudio() 827 public void playAudio(Map<String, Object> htParams) { in playAudio() argument 829 if (htParams == null) in playAudio() 831 htParams.put("status", "close"); in playAudio() 833 notifyAudioStatus(htParams); in playAudio() 837 String action = (htParams == null ? "close" : (String) htParams in playAudio() 839 String id = (htParams == null ? null : (String) htParams.get("id")); in playAudio() 860 "script")).playAudio(vwr, htParams); in playAudio() 875 String status = (String) htParams.get("status"); in notifyAudioStatus() 877 String script = (String) htParams.get(status); in notifyAudioStatus() [all …]
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H A D | Viewer.java | 2481 if (htParams == null) in setLoadParameters() 2483 htParams.put("vwr", this); in setLoadParameters() 2510 return htParams; in setLoadParameters() 2673 if (htParams == null) in loadModelFromFile() 2767 htParams); in loadModelFromFile() 2904 htParams = setLoadParameters(htParams, isAppend); in openFileFull() 2941 htParams, isAppend); in openFileFull() 3151 htParams = setLoadParameters(htParams, isAppend); in openStringInlineParamsAppend() 3162 htParams, isAppend); in openStringInlineParamsAppend() 3164 htParams); in openStringInlineParamsAppend() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/ |
H A D | MdCrdReader.java | 44 protected void setup(String fullPath, Map<String, Object> htParams, Object readerOrDocument) { in setup() argument 46 setupASCR(fullPath, htParams, readerOrDocument); in setup() 64 int ac = (bsFilter == null ? templateAtomCount : ((Integer) htParams in readCoordinates() 66 boolean isPeriodic = htParams.containsKey("isPeriodic"); in readCoordinates()
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H A D | MdTopReader.java | 125 htParams.put("defaultType", "mdcrd"); in finalizeSubclassReader() 204 htParams.put("isPeriodic", Boolean.TRUE); in getPointers() 207 htParams.put("templateAtomCount", Integer.valueOf(ac)); in getPointers()
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H A D | BinaryDcdReader.java | 54 protected void setup(String fullPath, Map<String, Object> htParams, Object reader) { in setup() argument 57 setupASCR(fullPath, htParams, reader); in setup() 266 int ac = (bsFilter == null ? templateAtomCount : ((Integer) htParams in readCoordinates()
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/dports/science/jmol/jmol-14.32.7/src/jspecview/common/ |
H A D | ScriptToken.java | 165 private static Map<String, ScriptToken> htParams; field in ScriptToken 168 if (htParams == null) { in getParams() 169 htParams = new Hashtable<String, ScriptToken>(); in getParams() 171 htParams.put(item.name(), item); in getParams() 173 return htParams; in getParams()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/jsv/ |
H A D | JDXMOLParser.java | 44 Map<String, Object> htParams) { in set() argument 48 if (htParams != null) { in set() 49 htParams.remove("modelNumber"); in set() 52 if (htParams.containsKey("zipSet")) { in set() 53 peakIndex = (int[]) htParams.get("peakIndex"); in set() 56 htParams.put("peakIndex", peakIndex); in set() 58 if (!htParams.containsKey("subFileName")) in set()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/appletjs/ |
H A D | Jmol.java | 49 private Map<String, Object> htParams; field in Jmol 57 htParams = new Hashtable<String, Object>(); in Jmol() 62 htParams.put(entry.getKey().toLowerCase(), entry.getValue()); in Jmol() 94 Object o = htParams.get(paramName.toLowerCase()); in getJmolParameter()
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/dports/science/jmol/jmol-14.32.7/src/jspecview/appletjs/ |
H A D | JSVApplet.java | 95 private Map<String, Object> htParams; field in JSVApplet 101 htParams = new Hashtable<String, Object>(); in JSVApplet() 103 htParams.put(entry.getKey().toLowerCase(), entry.getValue()); in JSVApplet() 148 Object o = htParams.get(paramName.toLowerCase()); in getParameter()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/script/ |
H A D | ScriptEval.java | 4364 htParams.put("value", m); in cmdLoad() 4683 htParams.put("filter", filter); in cmdLoad() 4712 htParams.put("fileData", o); in cmdLoad() 4824 vwr.sm.playAudio(htParams); in cmdLoad() 4838 htParams.put("eval", this); in cmdLoad() 4923 htParams.put(key, val); in addFilterAttribute() 4936 htParams.put("fileData", strModel); in addLoadData() 4951 htParams.put("outputChannel", out); in loadPNGJVar() 5075 htParams.remove("firstLastStep"); in getLoadModelIndex() 5076 htParams.remove("bsModel"); in getLoadModelIndex() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/simple/ |
H A D | FAHReader.java | 177 && !"xyz".equals(htParams.get("dataType"))) { in readVnnCoords() 232 String fileName = FileManager.stripTypePrefix((String) htParams.get("fullPathName")); in getTopData()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/js/ |
H A D | JmolToJSmolInterface.java | 31 void playAudio(JSmolAppletObject applet, Map<String, Object> htParams); in playAudio() argument
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