Object createAtomSeCollectionFromStrings(
String[] arrayModels, SB loadScript, Map<String, Object> htParams, boolean isAppend) {
if (!htParams.containsKey("isData")) {
String oldSep = "\"" + viewer.getDataSeparator() + "\"";
String tag = "\"" + (isAppend ? "append" : "model") + " inline\"";
SB sb = new SB();
sb.append("set dataSeparator \"~~~next file~~~\";\ndata ").append(tag);
for (int i = 0; i < arrayModels.length; i++) {
if (i > 0) sb.append("~~~next file~~~");
sb.append(arrayModels[i]);
}
sb.append("end ").append(tag).append(";set dataSeparator ").append(oldSep);
loadScript.appendSB(sb);
}
setLoadState(htParams);
Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");
String[] fullPathNames = new String[arrayModels.length];
DataReader[] readers = new DataReader[arrayModels.length];
for (int i = 0; i < arrayModels.length; i++) {
fullPathNames[i] = "string[" + i + "]";
readers[i] = newDataReader(arrayModels[i]);
}
JmolFilesReaderInterface filesReader =
newFilesReader(fullPathNames, fullPathNames, null, readers, htParams, isAppend);
filesReader.run();
return filesReader.getAtomSetCollection();
}
Object createAtomSetCollectionFromString(
String strModel, Map<String, Object> htParams, boolean isAppend) {
setLoadState(htParams);
boolean isAddH = (strModel.indexOf(JC.ADD_HYDROGEN_TITLE) >= 0);
String[] fnames = (isAddH ? getFileInfo() : null);
FileReader fileReader =
new FileReader(
this,
viewer,
"string",
"string",
"string",
null,
JmolBinary.getBR(strModel),
htParams,
isAppend);
fileReader.run();
if (fnames != null) setFileInfo(fnames);
if (!isAppend && !(fileReader.getAtomSetCollection() instanceof String)) {
viewer.zap(false, true, false);
setFileInfo(
new String[] {strModel == JC.MODELKIT_ZAP_STRING ? JC.MODELKIT_ZAP_TITLE : "string"});
}
return fileReader.getAtomSetCollection();
}
/*
* note -- createAtomSetCollectionFromXXX methods
* were "openXXX" before refactoring 11/29/2008 -- BH
*
* The problem was that while they did open the file, they
* (mostly) also closed them, and this was confusing.
*
* The term "clientFile" was replaced by "atomSetCollection"
* here because that's what it is --- an AtomSetCollection,
* not a file. The file is closed at this point. What is
* returned is the atomSetCollection object.
*
* One could say this is just semantics, but there were
* subtle bugs here, where readers were not always being
* closed explicitly. In the process of identifying Out of
* Memory Errors, I felt it was necessary to clarify all this.
*
* Apologies to those who feel the original clientFile notation
* was more generalizable or understandable.
*
*/
Object createAtomSetCollectionFromFile(
String name, Map<String, Object> htParams, boolean isAppend) {
if (htParams.get("atomDataOnly") == null) {
setLoadState(htParams);
}
name = viewer.resolveDatabaseFormat(name);
int pt = name.indexOf("::");
String nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
String fileType = (pt >= 0 ? name.substring(0, pt) : null);
Logger.info(
"\nFileManager.getAtomSetCollectionFromFile("
+ nameAsGiven
+ ")"
+ (name.equals(nameAsGiven) ? "" : " //" + name));
String[] names = classifyName(nameAsGiven, true);
if (names.length == 1) return names[0];
String fullPathName = names[0];
String fileName = names[1];
htParams.put(
"fullPathName",
(fileType == null ? "" : fileType + "::") + fullPathName.replace('\\', '/'));
if (viewer.getBoolean(T.messagestylechime) && viewer.getBoolean(T.debugscript))
viewer.scriptStatus("Requesting " + fullPathName);
FileReader fileReader =
new FileReader(
this, viewer, fileName, fullPathName, nameAsGiven, fileType, null, htParams, isAppend);
fileReader.run();
return fileReader.getAtomSetCollection();
}
Object createAtomSetCollectionFromFiles(
String[] fileNames, Map<String, Object> htParams, boolean isAppend) {
setLoadState(htParams);
String[] fullPathNames = new String[fileNames.length];
String[] namesAsGiven = new String[fileNames.length];
String[] fileTypes = new String[fileNames.length];
for (int i = 0; i < fileNames.length; i++) {
int pt = fileNames[i].indexOf("::");
String nameAsGiven = (pt >= 0 ? fileNames[i].substring(pt + 2) : fileNames[i]);
String fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
String[] names = classifyName(nameAsGiven, true);
if (names.length == 1) return names[0];
fullPathNames[i] = names[0];
fileNames[i] = names[0].replace('\\', '/');
fileTypes[i] = fileType;
namesAsGiven[i] = nameAsGiven;
}
htParams.put("fullPathNames", fullPathNames);
htParams.put("fileTypes", fileTypes);
JmolFilesReaderInterface filesReader =
newFilesReader(fullPathNames, namesAsGiven, fileTypes, null, htParams, isAppend);
filesReader.run();
return filesReader.getAtomSetCollection();
}