public void displayPartMenu(String type) throws DataException {
ArrayList<Part> list = partCtrl.retrieveAvailablePartsByType(type);
System.out.println();
System.out.println("== BattleStations :: Le Part :: " + type + " ==");
for (int i = 0; i < list.size(); i++) {
Part p = list.get(i);
System.out.println((i + 1) + ". " + p.getName() + " (min: L" + p.getLvlReq() + ")");
}
System.out.print("[R]eturn to main | Enter number > ");
}
public void displayBuyMenu(Part p) throws DataException {
System.out.println();
System.out.println("== BattleStations :: Le Part :: Details ==");
System.out.println("Part: " + p.getName());
System.out.println();
System.out.println("Speed: " + p.getSpeed());
System.out.println("HP: " + p.getHP());
System.out.println("Capacity: " + p.getCapacity());
System.out.println("Weight: " + p.getWeight());
System.out.println("Level Required: " + p.getLvlReq());
System.out.println();
System.out.println(
"Gold: "
+ p.getGoldReq()
+ " | Wood: "
+ p.getWoodReq()
+ " | Ore: "
+ p.getOreReq()
+ " | Prock: "
+ p.getPlasmaRockReq());
System.out.println();
System.out.print("[R]eturn to main | [B]uy it > ");
}
/**
* Constructs a new MultipartRequest to handle the specified request, saving any uploaded files to
* the given directory, and limiting the upload size to the specified length. If the content is
* too large, an IOException is thrown. This constructor actually parses the
* <tt>multipart/form-data</tt> and throws an IOException if there's any problem reading or
* parsing the request.
*
* <p>To avoid file collisions, this constructor takes an implementation of the FileRenamePolicy
* interface to allow a pluggable rename policy.
*
* @param request the servlet request.
* @param saveDirectory the directory in which to save any uploaded files.
* @param maxPostSize the maximum size of the POST content.
* @param encoding the encoding of the response, such as ISO-8859-1
* @param policy a pluggable file rename policy
* @exception IOException if the uploaded content is larger than <tt>maxPostSize</tt> or there's a
* problem reading or parsing the request.
*/
public CosMultipartRequest(
HttpServletRequest request,
String saveDirectory,
int maxPostSize,
String encoding,
FileRenamePolicy policy)
throws IOException {
// Sanity check values
if (request == null) throw new IllegalArgumentException("request cannot be null");
if (saveDirectory == null) throw new IllegalArgumentException("saveDirectory cannot be null");
if (maxPostSize <= 0) {
throw new IllegalArgumentException("maxPostSize must be positive");
}
// Save the dir
File dir = new File(saveDirectory);
// Check saveDirectory is truly a directory
if (!dir.isDirectory()) throw new IllegalArgumentException("Not a directory: " + saveDirectory);
// Check saveDirectory is writable
if (!dir.canWrite()) throw new IllegalArgumentException("Not writable: " + saveDirectory);
// Parse the incoming multipart, storing files in the dir provided,
// and populate the meta objects which describe what we found
MultipartParser parser = new MultipartParser(request, maxPostSize, true, true, encoding);
// Some people like to fetch query string parameters from
// MultipartRequest, so here we make that possible. Thanks to
// Ben Johnson, [email protected], for the idea.
if (request.getQueryString() != null) {
// Let HttpUtils create a name->String[] structure
Map<String, String[]> queryParameters =
RequestUtils.parseQueryString(request.getQueryString());
// For our own use, name it a name->Vector structure
for (Entry<String, String[]> entry : queryParameters.entrySet()) {
parameters.put(entry.getKey(), Arrays.asList(entry.getValue()));
}
}
Part part;
while ((part = parser.readNextPart()) != null) {
String name = part.getName();
if (name == null) {
throw new IOException("Malformed input: parameter name missing (known Opera 7 bug)");
}
if (part.isParam()) {
// It's a parameter part, add it to the vector of values
ParamPart paramPart = (ParamPart) part;
String value = paramPart.getStringValue();
List<String> existingValues = parameters.get(name);
if (existingValues == null) {
existingValues = new ArrayList<String>();
parameters.put(name, existingValues);
}
existingValues.add(value);
} else if (part.isFile()) {
// It's a file part
FilePart filePart = (FilePart) part;
String fileName = filePart.getFileName();
if (fileName != null) {
filePart.setRenamePolicy(policy); // null policy is OK
// The part actually contained a file
filePart.writeTo(dir);
files.put(
name,
new UploadedFile(
dir.toString(), filePart.getFileName(), fileName, filePart.getContentType()));
} else {
// The field did not contain a file
files.put(name, new UploadedFile(null, null, null, null));
}
}
}
}
/** Generation of new BioBricks primers for parts * */
public static String[] generatePartPrimers(
RNode node,
Collector coll,
Double meltingTemp,
Integer targetLength,
Integer minPCRLength,
Integer maxPrimerLength) {
// initialize primer parameters
String[] oligos = new String[2];
String partPrimerPrefix = "gaattcgcggccgcttctagag";
String partPrimerSuffix = "tactagtagcggccgctgcag";
String partPrimerPrefixAlt = "gaattcgcggccgcttctag";
String forwardOligoSequence;
String reverseOligoSequence;
Part currentPart = coll.getPart(node.getUUID(), true);
String seq = currentPart.getSeq();
ArrayList<String> type = node.getType();
String fwdHomology;
String revHomology;
// If the part is sufficiently large
if (seq.length() > minPCRLength) {
// Special case primers for coding sequences
if (type.get(0).equals("gene") || type.get(0).equals("reporter")) {
fwdHomology =
seq.substring(
0,
Math.min(
seq.length(),
PrimerDesign.getPrimerHomologyLength(
meltingTemp, targetLength, maxPrimerLength - 20, minPCRLength, seq, true)));
revHomology =
seq.substring(
Math.max(
0,
currentPart.getSeq().length()
- PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 21,
minPCRLength,
PrimerDesign.reverseComplement(seq),
true)));
forwardOligoSequence = partPrimerPrefixAlt + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(revHomology + partPrimerSuffix);
} else {
if (seq.equals("")) {
fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
} else {
fwdHomology =
seq.substring(
0,
Math.min(
seq.length(),
PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 22,
minPCRLength,
seq,
true)));
revHomology =
seq.substring(
Math.max(
0,
currentPart.getSeq().length()
- PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 21,
minPCRLength,
PrimerDesign.reverseComplement(seq),
true)));
}
forwardOligoSequence = partPrimerPrefix + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(revHomology + partPrimerSuffix);
}
// Otherwise make annealing primers or synthesize
} else {
if (type.get(0).equals("gene") || type.get(0).equals("reporter")) {
if (seq.equals("")) {
fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
forwardOligoSequence = partPrimerPrefixAlt + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(partPrimerSuffix) + revHomology;
} else {
fwdHomology = seq;
forwardOligoSequence = partPrimerPrefixAlt + fwdHomology + partPrimerSuffix;
reverseOligoSequence = PrimerDesign.reverseComplement(forwardOligoSequence);
}
} else {
if (seq.equals("")) {
fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
forwardOligoSequence = partPrimerPrefix + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(partPrimerSuffix) + revHomology;
} else {
fwdHomology = seq;
forwardOligoSequence = partPrimerPrefix + fwdHomology + partPrimerSuffix;
reverseOligoSequence = PrimerDesign.reverseComplement(forwardOligoSequence);
}
}
}
oligos[0] = forwardOligoSequence;
oligos[1] = reverseOligoSequence;
return oligos;
}
