/**
* Sets the thickness of the arc used to draw the backbone.
*
* @param width "xxx-small", "xx-small", "x-small", "small", "medium", "large", "x-large",
* "xx-large", "xxx-large".
*/
public void setBackboneThickness(String width) {
try {
backboneThickness = ((Float) BACKBONE_THICKNESSES.get(width)).floatValue();
} catch (NullPointerException e) {
backboneThickness = ((Float) BACKBONE_THICKNESSES.get("medium")).floatValue();
}
}
/**
* Sets the thickness of the arc used to draw features.
*
* @param width "xxx-small", "xx-small", "x-small", "small", "medium", "large", "x-large",
* "xx-large", "xxx-large".
*/
public void setFeatureThickness(String width) {
try {
featureThickness = ((Float) FEATURE_THICKNESSES.get(width)).floatValue();
} catch (NullPointerException e) {
featureThickness = ((Float) FEATURE_THICKNESSES.get("medium")).floatValue();
}
}
private Color getFeatureColor(String type) throws NullPointerException {
Color colorToReturn = (Color) FEATURE_COLORS.get(type);
if (colorScheme == REGULAR) {
colorToReturn = (Color) FEATURE_COLORS.get(type);
} else if (colorScheme == INVERSE) {
colorToReturn = (Color) FEATURE_COLORS_INVERSE.get(type);
}
return colorToReturn;
}
private static Hashtable<String, String> getManifestAttributes(Manifest manifest) {
Hashtable<String, String> h = new Hashtable<String, String>();
try {
Attributes attrs = manifest.getMainAttributes();
Iterator it = attrs.keySet().iterator();
while (it.hasNext()) {
String key = it.next().toString();
h.put(key, attrs.getValue(key));
}
} catch (Exception ignore) {
}
return h;
}
private int getFeatureDecoration(String type, int strand) throws NullPointerException {
int decoration = DECORATION_STANDARD;
if (!(useArrows)) {
decoration = DECORATION_STANDARD;
} else {
if (strand == FORWARD) {
decoration = ((Integer) FEATURE_DECORATIONS_DIRECT.get(type)).intValue();
} else if (strand == NO_DIRECTION) {
decoration = ((Integer) FEATURE_DECORATIONS_DIRECT.get(type)).intValue();
} else {
decoration = ((Integer) FEATURE_DECORATIONS_REVERSE.get(type)).intValue();
}
}
return decoration;
}
/**
* Class constructor; creates a new Installer object, displays a JFrame introducing the program,
* allows the user to select an install directory, and copies files from the jar into the
* directory.
*/
public Installer(String args[]) {
// Inputs are --install-dir INSTALL_DIR
for (int k = 0; k < args.length; k = k + 2) {
switch (args[k]) {
case "--install-dir":
directory = new File(args[k + 1]);
System.out.println(directory);
break;
case "--port":
port = Integer.parseInt(args[k + 1]);
break;
}
}
cp = new Stream();
// Find the installer program so we can get to the files.
installer = getInstallerProgramFile();
String name = installer.getName();
programName = (name.substring(0, name.indexOf("-"))).toUpperCase();
// Get the installation information
thisJava = System.getProperty("java.version");
thisJavaBits = System.getProperty("sun.arch.data.model") + " bits";
// Find the ImageIO Tools and get the version
String javaHome = System.getProperty("java.home");
File extDir = new File(javaHome);
extDir = new File(extDir, "lib");
extDir = new File(extDir, "ext");
File clib = getFile(extDir, "clibwrapper_jiio", ".jar");
File jai = getFile(extDir, "jai_imageio", ".jar");
imageIOTools = (clib != null) && clib.exists() && (jai != null) && jai.exists();
if (imageIOTools) {
Hashtable<String, String> jaiManifest = getManifestAttributes(jai);
imageIOVersion = jaiManifest.get("Implementation-Version");
}
// Get the CTP.jar parameters
Hashtable<String, String> manifest = getJarManifestAttributes("/CTP/libraries/CTP.jar");
programDate = manifest.get("Date");
buildJava = manifest.get("Java-Version");
// Get the util.jar parameters
Hashtable<String, String> utilManifest = getJarManifestAttributes("/CTP/libraries/util.jar");
utilJava = utilManifest.get("Java-Version");
// Get the MIRC.jar parameters (if the plugin is present)
Hashtable<String, String> mircManifest = getJarManifestAttributes("/CTP/libraries/MIRC.jar");
if (mircManifest != null) {
mircJava = mircManifest.get("Java-Version");
mircDate = mircManifest.get("Date");
mircVersion = mircManifest.get("Version");
}
// Set up the installation information for display
if (imageIOVersion.equals("")) {
imageIOVersion = "<b><font color=\"red\">not installed</font></b>";
} else if (imageIOVersion.startsWith("1.0")) {
imageIOVersion = "<b><font color=\"red\">" + imageIOVersion + "</font></b>";
}
if (thisJavaBits.startsWith("64")) {
thisJavaBits = "<b><font color=\"red\">" + thisJavaBits + "</font></b>";
}
boolean javaOK = (thisJava.compareTo(buildJava) >= 0);
javaOK &= (thisJava.compareTo(utilJava) >= 0);
javaOK &= (thisJava.compareTo(mircJava) >= 0);
if (!javaOK) {
thisJava = "<b><font color=\"red\">" + thisJava + "</font></b>";
}
if (directory == null) exit();
// Point to the parent of the directory in which to install the program.
// so the copy process works correctly for directory trees.
//
// If the user has selected a directory named "CTP",
// then assume that this is the directory in which
// to install the program.
//
// If the directory is not CTP, see if it is called "RSNA" and contains
// the Launcher program, in which case we can assume that it is an
// installation that was done with Bill Weadock's all-in-one installer for Windows.
//
// If neither of those cases is true, then this is already the parent of the
// directory in which to install the program
if (directory.getName().equals("CTP")) {
directory = directory.getParentFile();
} else if (directory.getName().equals("RSNA")
&& (new File(directory, "Launcher.jar")).exists()) {
suppressFirstPathElement = true;
}
// Cleanup old releases
cleanup(directory);
// Get a port for the server.
if (port < 0) {
if (checkServer(-port, false)) {
System.err.println(
"CTP appears to be running.\nPlease stop CTP and run the installer again.");
System.exit(0);
}
}
// Now install the files and report the results.
int count =
unpackZipFile(installer, "CTP", directory.getAbsolutePath(), suppressFirstPathElement);
if (count > 0) {
// Create the service installer batch files.
updateWindowsServiceInstaller();
updateLinuxServiceInstaller();
// If this was a new installation, set up the config file and set the port
installConfigFile(port);
// Make any necessary changes in the config file to reflect schema evolution
fixConfigSchema();
System.out.println("Installation complete.");
System.out.println(programName + " has been installed successfully.");
System.out.println(count + " files were installed.");
} else {
System.err.println("Installation failed.");
System.err.println(programName + " could not be fully installed.");
}
if (!programName.equals("ISN") && startRunner(new File(directory, "CTP"))) System.exit(0);
}
public Hashtable processData(
ServletInputStream is, String boundary, String saveInDir, int clength)
throws IllegalArgumentException, IOException {
if (is == null) throw new IllegalArgumentException("InputStream");
if (boundary == null || boundary.trim().length() < 1)
throw new IllegalArgumentException("\"" + boundary + "\" is an illegal boundary indicator");
boundary = "--" + boundary;
StringTokenizer stLine = null, stFields = null;
FileInfo fileInfo = null;
Hashtable dataTable = new Hashtable(5);
String line = null, field = null, paramName = null;
boolean saveFiles = (saveInDir != null && saveInDir.trim().length() > 0);
boolean isFile = false;
if (saveFiles) { // Create the required directory (including parent dirs)
File f = new File(saveInDir);
f.mkdirs();
}
line = getLine(is);
if (line == null || !line.startsWith(boundary))
throw new IOException("Boundary not found; boundary = " + boundary + ", line = " + line);
while (line != null) {
if (line == null || !line.startsWith(boundary)) return dataTable;
line = getLine(is);
if (line == null) return dataTable;
stLine = new StringTokenizer(line, ";\r\n");
if (stLine.countTokens() < 2) throw new IllegalArgumentException("Bad data in second line");
line = stLine.nextToken().toLowerCase();
if (line.indexOf("form-data") < 0)
throw new IllegalArgumentException("Bad data in second line");
stFields = new StringTokenizer(stLine.nextToken(), "=\"");
if (stFields.countTokens() < 2)
throw new IllegalArgumentException("Bad data in second line");
fileInfo = new FileInfo();
stFields.nextToken();
paramName = stFields.nextToken();
isFile = false;
if (stLine.hasMoreTokens()) {
field = stLine.nextToken();
stFields = new StringTokenizer(field, "=\"");
if (stFields.countTokens() > 1) {
if (stFields.nextToken().trim().equalsIgnoreCase("filename")) {
fileInfo.name = paramName;
String value = stFields.nextToken();
if (value != null && value.trim().length() > 0) {
fileInfo.clientFileName = value;
isFile = true;
} else {
line = getLine(is); // Skip "Content-Type:" line
line = getLine(is); // Skip blank line
line = getLine(is); // Skip blank line
line = getLine(is); // Position to boundary line
continue;
}
}
} else if (field.toLowerCase().indexOf("filename") >= 0) {
line = getLine(is); // Skip "Content-Type:" line
line = getLine(is); // Skip blank line
line = getLine(is); // Skip blank line
line = getLine(is); // Position to boundary line
continue;
}
}
boolean skipBlankLine = true;
if (isFile) {
line = getLine(is);
if (line == null) return dataTable;
if (line.trim().length() < 1) skipBlankLine = false;
else {
stLine = new StringTokenizer(line, ": ");
if (stLine.countTokens() < 2)
throw new IllegalArgumentException("Bad data in third line");
stLine.nextToken(); // Content-Type
fileInfo.fileContentType = stLine.nextToken();
}
}
if (skipBlankLine) {
line = getLine(is);
if (line == null) return dataTable;
}
if (!isFile) {
line = getLine(is);
if (line == null) return dataTable;
dataTable.put(paramName, line);
// If parameter is dir, change saveInDir to dir
if (paramName.equals("dir")) saveInDir = line;
line = getLine(is);
continue;
}
try {
UplInfo uplInfo = new UplInfo(clength);
UploadMonitor.set(fileInfo.clientFileName, uplInfo);
OutputStream os = null;
String path = null;
if (saveFiles)
os = new FileOutputStream(path = getFileName(saveInDir, fileInfo.clientFileName));
else os = new ByteArrayOutputStream(ONE_MB);
boolean readingContent = true;
byte previousLine[] = new byte[2 * ONE_MB];
byte temp[] = null;
byte currentLine[] = new byte[2 * ONE_MB];
int read, read3;
if ((read = is.readLine(previousLine, 0, previousLine.length)) == -1) {
line = null;
break;
}
while (readingContent) {
if ((read3 = is.readLine(currentLine, 0, currentLine.length)) == -1) {
line = null;
uplInfo.aborted = true;
break;
}
if (compareBoundary(boundary, currentLine)) {
os.write(previousLine, 0, read - 2);
line = new String(currentLine, 0, read3);
break;
} else {
os.write(previousLine, 0, read);
uplInfo.currSize += read;
temp = currentLine;
currentLine = previousLine;
previousLine = temp;
read = read3;
} // end else
} // end while
os.flush();
os.close();
if (!saveFiles) {
ByteArrayOutputStream baos = (ByteArrayOutputStream) os;
fileInfo.setFileContents(baos.toByteArray());
} else fileInfo.file = new File(path);
dataTable.put(paramName, fileInfo);
uplInfo.currSize = uplInfo.totalSize;
} // end try
catch (IOException e) {
throw e;
}
}
return dataTable;
}
static UplInfo getInfo(String fName) {
UplInfo info = (UplInfo) uploadTable.get(fName);
return info;
}
static void remove(String fName) {
uploadTable.remove(fName);
}
static void set(String fName, UplInfo info) {
uploadTable.put(fName, info);
}
private void prepareToDraw() {
if (forwardSlot0 != null) {
forwardSlot0.setCgview(p);
forwardSlot0.setFeatureThickness(featureThickness);
}
if (forwardSlot1 != null) {
forwardSlot1.setCgview(p);
forwardSlot1.setFeatureThickness(featureThickness);
}
if (forwardSlot2 != null) {
forwardSlot2.setCgview(p);
forwardSlot2.setFeatureThickness(featureThickness);
}
if (forwardSlot3 != null) {
forwardSlot3.setCgview(p);
forwardSlot3.setFeatureThickness(featureThickness);
}
if (forwardSlot4 != null) {
forwardSlot4.setCgview(p);
forwardSlot4.setFeatureThickness(featureThickness);
}
if (forwardSlot5 != null) {
forwardSlot5.setCgview(p);
forwardSlot5.setFeatureThickness(featureThickness);
}
if (forwardSlot6 != null) {
forwardSlot6.setCgview(p);
forwardSlot6.setFeatureThickness(featureThickness);
}
if (forwardSlot7 != null) {
forwardSlot7.setCgview(p);
forwardSlot7.setFeatureThickness(featureThickness);
}
if (reverseSlot0 != null) {
reverseSlot0.setCgview(p);
reverseSlot0.setFeatureThickness(featureThickness);
}
if (reverseSlot1 != null) {
reverseSlot1.setCgview(p);
reverseSlot1.setFeatureThickness(featureThickness);
}
if (reverseSlot2 != null) {
reverseSlot2.setCgview(p);
reverseSlot2.setFeatureThickness(featureThickness);
}
if (reverseSlot3 != null) {
reverseSlot3.setCgview(p);
reverseSlot3.setFeatureThickness(featureThickness);
}
if (reverseSlot4 != null) {
reverseSlot4.setCgview(p);
reverseSlot4.setFeatureThickness(featureThickness);
}
if (reverseSlot5 != null) {
reverseSlot5.setCgview(p);
reverseSlot5.setFeatureThickness(featureThickness);
}
if (reverseSlot6 != null) {
reverseSlot6.setCgview(p);
reverseSlot6.setFeatureThickness(featureThickness);
}
if (reverseSlot7 != null) {
reverseSlot7.setCgview(p);
reverseSlot7.setFeatureThickness(featureThickness);
}
if (restrictionSlot != null) {
restrictionSlot.setCgview(p);
restrictionSlot.setFeatureThickness(featureThickness);
}
// send settings to p
if (showTitle) {
p.setTitle(title);
}
p.setWidth(imageWidth);
p.setHeight(imageHeight);
p.setLabelsToKeep(MAXLABELS);
p.setDrawTickMarks(drawTickMarks);
p.setTitleFont(titleFont);
p.setLabelFont(labelFont);
p.setFeatureThickness(featureThickness);
p.setBackboneThickness(backboneThickness);
p.setFeatureSlotSpacing(featureSpacing);
p.setLegendFont(legendFont);
p.setTickLength(tickLength);
p.setLabelLineLength(labelLineLength);
p.setLabelPlacementQuality(labelPlacementQuality);
p.setUseColoredLabelBackgrounds(useColoredLabelBackground);
p.setShowBorder(showBorder);
p.setShowShading(showShading);
p.setShadingProportion(shadingProportion);
p.setUseInnerLabels(useInnerLabels);
p.setMoveInnerLabelsToOuter(moveInnerLabelsToOuter);
p.setWarningFont(rulerFont);
p.setRulerFont(rulerFont);
// if not drawing labels, don't show message.
if (!(showLabels)) {
p.setShowWarning(false);
}
// set backboneRadius based on smallest image dimension
int smallestDimension = Math.min(imageWidth, imageHeight);
if (smallestDimension <= 750) {
p.setBackboneRadius(0.50d * (double) smallestDimension / 2.0d);
} else {
p.setBackboneRadius(0.50d * 750.0d / 2.0d);
}
// check coloredLabels
if (!(useColoredLabels)) {
if (colorScheme == REGULAR) {
p.setGlobalLabelColor((Color) MAP_ITEM_COLORS.get("titleFont"));
} else if (colorScheme == INVERSE) {
p.setGlobalLabelColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
}
}
// set map item colors
if (colorScheme == REGULAR) {
p.setLongTickColor((Color) MAP_ITEM_COLORS.get("tick"));
p.setShortTickColor((Color) MAP_ITEM_COLORS.get("partialTick"));
p.setZeroTickColor((Color) MAP_ITEM_COLORS.get("zeroLine"));
p.setRulerFontColor((Color) MAP_ITEM_COLORS.get("rulerFont"));
p.setBackboneColor((Color) MAP_ITEM_COLORS.get("backbone"));
p.setTitleFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
p.setWarningFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
p.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
} else if (colorScheme == INVERSE) {
p.setLongTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("tick"));
p.setShortTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("partialTick"));
p.setZeroTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("zeroLine"));
p.setRulerFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("rulerFont"));
p.setBackboneColor((Color) MAP_ITEM_COLORS_INVERSE.get("backbone"));
p.setTitleFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
p.setWarningFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
p.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
}
// build legend
if ((showLegend) && (DRAW_LEGEND_ITEMS.size() > 0)) {
// create legend
legend = new Legend(p);
legend.setAllowLabelClash(allowLabelClashLegend);
legend.setBackgroundOpacity(0.5f);
legend.setFont(legendFont);
legend.setPosition(legendPosition);
if (colorScheme == REGULAR) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
} else if (colorScheme == INVERSE) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
}
LegendItem legendItem;
Enumeration legendEntries = DRAW_LEGEND_ITEMS.keys();
ArrayList list = new ArrayList();
while (legendEntries.hasMoreElements()) {
list.add(legendEntries.nextElement());
}
Collections.sort(list);
Iterator i = list.iterator();
while (i.hasNext()) {
String key = (String) i.next();
legendItem = new LegendItem(legend);
legendItem.setDrawSwatch(SWATCH_SHOW);
legendItem.setLabel((String) LEGEND_ITEM_NAMES.get(key));
if (colorScheme == REGULAR) {
legendItem.setSwatchColor((Color) FEATURE_COLORS.get(key));
} else if (colorScheme == INVERSE) {
legendItem.setSwatchColor((Color) FEATURE_COLORS_INVERSE.get(key));
}
}
}
// set message
if (showMessage) {
legend = new Legend(p);
legend.setAllowLabelClash(false);
legend.setBackgroundOpacity(0.5f);
legend.setFont(messageFont);
legend.setPosition(LEGEND_LOWER_RIGHT);
LegendItem legendItem;
if (colorScheme == REGULAR) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
legendItem = new LegendItem(legend);
legendItem.setLabel(message);
legendItem.setDrawSwatch(SWATCH_NO_SHOW);
} else if (colorScheme == INVERSE) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
legendItem = new LegendItem(legend);
legendItem.setLabel(message);
legendItem.setDrawSwatch(SWATCH_NO_SHOW);
}
}
}
private void addItemToLegend(String type, int strand) throws NullPointerException {
if ((strand == NO_DIRECTION) || (strand == FORWARD) || (strand == REVERSE)) {
DRAW_LEGEND_ITEMS.put(type, new Boolean(true));
}
}
/**
* Add a feature to this map. Note that the start of the feature should be a smaller number than
* the stop of the feature, regardless of the strand. The only case where start is larger than the
* stop is when the feature runs across the start/stop boundary, for example 6899-10 on a 7000bp
* plasmid.
*
* @param type one of the following: origin_of_replication, promoter, terminator,
* selectable_marker, regulatory_sequence, tag, other_gene, reporter_gene,
* unique_restriction_site, restriction_site.
* @param name the name of the feature, such as EcoRI.
* @param start the start position of the feature. Must be between 1 and the length of the
* plasmid.
* @param stop the end position of the feature. Must be between 1 and the length of the plasmid.
* @param strand the strand of the feature. Can be Plasmid.FORWARD, Plasmid.REVERSE, or
* Plasmid.NO_DIRECTION.
*/
public void addFeature(String type, String name, int start, int stop, int strand) {
// add the feature to the plasmid.
int decoration;
int label;
Color color;
// String slot;
if (start > size) {
start = size;
}
if (start < 1) {
start = 1;
}
if (stop > size) {
stop = size;
}
if (stop < 1) {
stop = 1;
}
try {
color = getFeatureColor(type);
decoration = getFeatureDecoration(type, strand);
label = getLabelType();
addItemToLegend(type, strand);
} catch (NullPointerException e) {
color = new Color(0, 0, 128); // navy
if (colorScheme == REGULAR) {
color = new Color(0, 0, 128); // navy
} else if (colorScheme == INVERSE) {
color = new Color(0, 128, 128); // teal
}
decoration = DECORATION_STANDARD;
label = LABEL;
}
// create a feature and a feature range
// then figure out which feature slot to put the feature in.
Feature feature = new Feature(showShading);
FeatureRange featureRange = new FeatureRange(feature, start, stop);
featureRange.setDecoration(decoration);
featureRange.setColor(color);
featureRange.setOpacity(opacity);
featureRange.setShowLabel(label);
if ((showPositions)
&& ((type.equalsIgnoreCase("restriction_site"))
|| (type.equalsIgnoreCase("unique_restriction_site")))) {
featureRange.setLabel(name + " " + start);
} else {
if (addCategoryInfo) {
try {
featureRange.setLabel(name + (String) FEATURE_CATEGORIES.get(type));
} catch (NullPointerException e) {
featureRange.setLabel(name);
}
} else {
featureRange.setLabel(name);
}
}
if ((type.equalsIgnoreCase("restriction_site"))
|| (type.equalsIgnoreCase("unique_restriction_site"))) {
if (restrictionSlot == null) {
restrictionSlot = new FeatureSlot(DIRECT_STRAND, showShading);
restrictionSlot.setFeatureThickness(1f);
}
feature.setFeatureSlot(restrictionSlot);
} else if ((strand == NO_DIRECTION) || (strand == FORWARD)) {
if (forwardSlot0 == null) {
forwardSlot0 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot0);
} else if (forwardSlot0.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot0);
} else if (forwardSlot1 == null) {
forwardSlot1 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot1);
} else if (forwardSlot1.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot1);
} else if (forwardSlot2 == null) {
forwardSlot2 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot2);
} else if (forwardSlot2.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot2);
} else if (forwardSlot3 == null) {
forwardSlot3 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot3);
} else if (forwardSlot3.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot3);
} else if (forwardSlot4 == null) {
forwardSlot4 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot4);
} else if (forwardSlot4.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot4);
} else if (forwardSlot5 == null) {
forwardSlot5 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot5);
} else if (forwardSlot5.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot5);
} else if (forwardSlot6 == null) {
forwardSlot6 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot6);
} else if (forwardSlot6.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot6);
} else if (forwardSlot7 == null) {
forwardSlot7 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot7);
} else {
feature.setFeatureSlot(forwardSlot7);
}
} else if (strand == REVERSE) {
if (reverseSlot0 == null) {
reverseSlot0 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot0);
} else if (reverseSlot0.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot0);
} else if (reverseSlot1 == null) {
reverseSlot1 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot1);
} else if (reverseSlot1.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot1);
} else if (reverseSlot2 == null) {
reverseSlot2 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot2);
} else if (reverseSlot2.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot2);
} else if (reverseSlot3 == null) {
reverseSlot3 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot3);
} else if (reverseSlot3.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot3);
} else if (reverseSlot4 == null) {
reverseSlot4 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot4);
} else if (reverseSlot4.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot4);
} else if (reverseSlot5 == null) {
reverseSlot5 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot5);
} else if (reverseSlot5.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot5);
} else if (reverseSlot6 == null) {
reverseSlot6 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot6);
} else if (reverseSlot6.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot6);
} else if (reverseSlot7 == null) {
reverseSlot7 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot7);
} else {
feature.setFeatureSlot(reverseSlot7);
}
}
}
/**
* Create a new Plasmid. Note that a constructor accepting a title and length is also available.
*
* @param size the size of the plasmid in base pairs.
*/
public Plasmid(int size) {
this.size = size;
COLORS = new Hashtable();
MAP_ITEM_COLORS = new Hashtable();
MAP_ITEM_COLORS_INVERSE = new Hashtable();
FEATURE_COLORS = new Hashtable();
FEATURE_COLORS_INVERSE = new Hashtable();
FEATURE_DECORATIONS_DIRECT = new Hashtable();
FEATURE_DECORATIONS_REVERSE = new Hashtable();
FEATURE_CATEGORIES = new Hashtable();
FEATURE_THICKNESSES = new Hashtable();
BACKBONE_THICKNESSES = new Hashtable();
DRAW_LEGEND_ITEMS = new Hashtable();
LEGEND_ITEM_NAMES = new Hashtable();
COLORS.put(
"black",
new Color(0, 0, 0)); // tickmark defaults //rulerFontColor default //titleFontColor default
COLORS.put("silver", new Color(192, 192, 192));
COLORS.put(
"gray",
new Color(128, 128, 128)); // backbone default //partial tickmark default //zeroline default
COLORS.put("white", new Color(255, 255, 255)); // background default
COLORS.put("maroon", new Color(128, 0, 0));
COLORS.put("red", new Color(255, 0, 0));
COLORS.put("pink", new Color(255, 153, 204));
COLORS.put("purple", new Color(128, 0, 128));
COLORS.put("fuchsia", new Color(255, 0, 255));
COLORS.put("orange", new Color(255, 153, 0));
COLORS.put("green", new Color(0, 128, 0));
COLORS.put("spring", new Color(204, 255, 204));
COLORS.put("lime", new Color(0, 255, 0));
COLORS.put("olive", new Color(128, 128, 0));
COLORS.put("yellow", new Color(255, 255, 0));
COLORS.put("navy", new Color(0, 0, 128));
COLORS.put("blue", new Color(0, 0, 255));
COLORS.put("azure", new Color(51, 153, 255));
COLORS.put("lightBlue", new Color(102, 204, 255));
COLORS.put("teal", new Color(153, 255, 204));
COLORS.put("aqua", new Color(0, 255, 255));
MAP_ITEM_COLORS.put("tick", COLORS.get("black"));
MAP_ITEM_COLORS.put("rulerFont", COLORS.get("black"));
MAP_ITEM_COLORS.put("titleFont", COLORS.get("black"));
MAP_ITEM_COLORS.put("messageFont", COLORS.get("black"));
MAP_ITEM_COLORS.put("backbone", COLORS.get("gray"));
MAP_ITEM_COLORS.put("partialTick", COLORS.get("gray"));
MAP_ITEM_COLORS.put("zeroLine", COLORS.get("gray"));
MAP_ITEM_COLORS.put("background", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("tick", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("rulerFont", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("titleFont", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("messageFont", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("backbone", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("partialTick", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("zeroLine", COLORS.get("white"));
MAP_ITEM_COLORS_INVERSE.put("background", COLORS.get("black"));
FEATURE_COLORS.put("origin_of_replication", COLORS.get("black"));
FEATURE_COLORS.put("promoter", COLORS.get("green"));
FEATURE_COLORS.put("terminator", COLORS.get("maroon"));
FEATURE_COLORS.put("selectable_marker", COLORS.get("orange"));
FEATURE_COLORS.put("regulatory_sequence", COLORS.get("olive"));
FEATURE_COLORS.put("tag", COLORS.get("silver"));
FEATURE_COLORS.put("other_gene", COLORS.get("fuchsia"));
FEATURE_COLORS.put("reporter_gene", COLORS.get("purple"));
FEATURE_COLORS.put("unique_restriction_site", COLORS.get("blue"));
FEATURE_COLORS.put("restriction_site", COLORS.get("red"));
FEATURE_COLORS.put("open_reading_frame", COLORS.get("pink"));
FEATURE_COLORS_INVERSE.put("origin_of_replication", COLORS.get("white"));
FEATURE_COLORS_INVERSE.put("promoter", COLORS.get("lime"));
FEATURE_COLORS_INVERSE.put("terminator", COLORS.get("yellow"));
FEATURE_COLORS_INVERSE.put("selectable_marker", COLORS.get("orange"));
FEATURE_COLORS_INVERSE.put("regulatory_sequence", COLORS.get("azure"));
FEATURE_COLORS_INVERSE.put("tag", COLORS.get("silver"));
FEATURE_COLORS_INVERSE.put("other_gene", COLORS.get("fuchsia"));
FEATURE_COLORS_INVERSE.put("reporter_gene", COLORS.get("teal"));
FEATURE_COLORS_INVERSE.put("unique_restriction_site", COLORS.get("lightBlue"));
FEATURE_COLORS_INVERSE.put("restriction_site", COLORS.get("pink"));
FEATURE_COLORS_INVERSE.put("open_reading_frame", COLORS.get("red"));
FEATURE_DECORATIONS_DIRECT.put("origin_of_replication", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("promoter", new Integer(DECORATION_CLOCKWISE_ARROW));
FEATURE_DECORATIONS_DIRECT.put("terminator", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("selectable_marker", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("regulatory_sequence", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("tag", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("other_gene", new Integer(DECORATION_CLOCKWISE_ARROW));
FEATURE_DECORATIONS_DIRECT.put("reporter_gene", new Integer(DECORATION_CLOCKWISE_ARROW));
FEATURE_DECORATIONS_DIRECT.put("unique_restriction_site", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("restriction_site", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_DIRECT.put("open_reading_frame", new Integer(DECORATION_CLOCKWISE_ARROW));
FEATURE_DECORATIONS_REVERSE.put("origin_of_replication", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put("promoter", new Integer(DECORATION_COUNTERCLOCKWISE_ARROW));
FEATURE_DECORATIONS_REVERSE.put("terminator", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put("selectable_marker", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put("regulatory_sequence", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put("tag", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put("other_gene", new Integer(DECORATION_COUNTERCLOCKWISE_ARROW));
FEATURE_DECORATIONS_REVERSE.put(
"reporter_gene", new Integer(DECORATION_COUNTERCLOCKWISE_ARROW));
FEATURE_DECORATIONS_REVERSE.put("unique_restriction_site", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put("restriction_site", new Integer(DECORATION_STANDARD));
FEATURE_DECORATIONS_REVERSE.put(
"open_reading_frame", new Integer(DECORATION_COUNTERCLOCKWISE_ARROW));
FEATURE_CATEGORIES.put("origin_of_replication", new String(" origin"));
FEATURE_CATEGORIES.put("promoter", new String(" prom"));
FEATURE_CATEGORIES.put("terminator", new String(" term"));
FEATURE_CATEGORIES.put("selectable_marker", new String(" marker"));
FEATURE_CATEGORIES.put("regulatory_sequence", new String(" reg"));
FEATURE_CATEGORIES.put("tag", new String(" tag"));
FEATURE_CATEGORIES.put("other_gene", new String(" gene"));
FEATURE_CATEGORIES.put("reporter_gene", new String(" gene"));
FEATURE_CATEGORIES.put("unique_restriction_site", new String(""));
FEATURE_CATEGORIES.put("restriction_site", new String(""));
FEATURE_CATEGORIES.put("open_reading_frame", new String(""));
LEGEND_ITEM_NAMES.put("origin_of_replication", "Origin of replication");
LEGEND_ITEM_NAMES.put("promoter", "Promoter");
LEGEND_ITEM_NAMES.put("terminator", "Terminator");
LEGEND_ITEM_NAMES.put("selectable_marker", "Selectable marker");
LEGEND_ITEM_NAMES.put("regulatory_sequence", "Regulatory sequence");
LEGEND_ITEM_NAMES.put("tag", "Tag");
LEGEND_ITEM_NAMES.put("other_gene", "Other gene");
LEGEND_ITEM_NAMES.put("reporter_gene", "Reporter gene");
LEGEND_ITEM_NAMES.put("unique_restriction_site", "Unique restriction site");
LEGEND_ITEM_NAMES.put("restriction_site", "Restriction site");
LEGEND_ITEM_NAMES.put("open_reading_frame", "Open reading frame");
FEATURE_THICKNESSES.put("xxx-small", new Float(4.0f));
FEATURE_THICKNESSES.put("xx-small", new Float(5.0f));
FEATURE_THICKNESSES.put("x-small", new Float(6.0f));
FEATURE_THICKNESSES.put("small", new Float(7.0f));
FEATURE_THICKNESSES.put("medium", new Float(8.0f)); // default for featureThickness
FEATURE_THICKNESSES.put("large", new Float(9.0f));
FEATURE_THICKNESSES.put("x-large", new Float(10.0f));
FEATURE_THICKNESSES.put("xx-large", new Float(11.0f));
FEATURE_THICKNESSES.put("xxx-large", new Float(12.0f));
BACKBONE_THICKNESSES.put("xxx-small", new Float(4.0f));
BACKBONE_THICKNESSES.put("xx-small", new Float(5.0f));
BACKBONE_THICKNESSES.put("x-small", new Float(6.0f));
BACKBONE_THICKNESSES.put("small", new Float(7.0f));
BACKBONE_THICKNESSES.put("medium", new Float(8.0f)); // default for backboneThickness
BACKBONE_THICKNESSES.put("large", new Float(9.0f));
BACKBONE_THICKNESSES.put("x-large", new Float(10.0f));
BACKBONE_THICKNESSES.put("xx-large", new Float(11.0f));
BACKBONE_THICKNESSES.put("xxx-large", new Float(12.0f));
p = new Cgview(size);
}
/** initializes internal hash tables with Jar file resources. */
private byte[] read(String name) {
try {
// extracts just sizes only.
ZipFile zf = new ZipFile(jarFileName);
Enumeration e = zf.entries();
while (e.hasMoreElements()) {
ZipEntry ze = (ZipEntry) e.nextElement();
if (debugOn) {
System.out.println(dumpZipEntry(ze));
}
htSizes.put(ze.getName(), new Integer((int) ze.getSize()));
}
zf.close();
// extract resources and put them into the hashtable.
FileInputStream fis = new FileInputStream(jarFileName);
BufferedInputStream bis = new BufferedInputStream(fis);
ZipInputStream zis = new ZipInputStream(bis);
ZipEntry ze = null;
while ((ze = zis.getNextEntry()) != null) {
if (ze.isDirectory()) {
continue;
}
if (debugOn) {
System.out.println("ze.getName()=" + ze.getName() + "," + "getSize()=" + ze.getSize());
}
int size = (int) ze.getSize();
// -1 means unknown size.
if (size == -1) {
size = ((Integer) htSizes.get(ze.getName())).intValue();
}
byte[] b = new byte[(int) size];
int rb = 0;
int chunk = 0;
while (((int) size - rb) > 0) {
chunk = zis.read(b, rb, (int) size - rb);
if (chunk == -1) {
break;
}
rb += chunk;
}
if (debugOn) {
System.out.println(
ze.getName() + " rb=" + rb + ",size=" + size + ",csize=" + ze.getCompressedSize());
}
if (ze.getName().equals(name)) {
return b;
}
}
} catch (NullPointerException e) {
System.out.println("done.");
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
return null;
}
// =============================================================================