@Override
public NucSeq generateCompositeSequence(
ArrayList<Part> composition, Object additionalRequirements) {
StringBuffer sb = new StringBuffer();
for (Part p : composition) {
sb.append(p.getSeq().getSeq());
}
NucSeq outnuc = new NucSeq(sb.toString());
outnuc.setTransient();
int offset = 0;
for (Part p : composition) {
String parseq = p.getSeq().getSeq();
for (Annotation ann : p.getSeq().getAnnotations()) {
Feature afeature = ann.getFeature();
String name = ann.getName();
Color forColor = ann.getForwardColor();
Color revColor = ann.getReverseColor();
int Start = offset + ann.getStart();
int End = offset + ann.getEnd();
Person user = ann.getAuthor();
boolean plusstrandtrue = ann.isForwardStrand();
String symbol = ann.getSymbol();
Annotation newann;
if (afeature == null) {
newann =
new Annotation(
name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
} else {
newann =
new Annotation(
afeature, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
}
System.out.println("Generated annotation: " + newann.getName());
}
offset += parseq.length();
}
return outnuc;
}
private void saveButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_saveButtonActionPerformed
String desc = _sv.getSequenceView().getOutputTextArea().getText();
if (desc == null) {
desc = "";
}
String name = nameTextField.getText();
String seq = null;
System.out.println("saving: " + name);
if (intervalRadioButton.isSelected()) {
try {
if (dataTextPane.getText() != null) {
seq =
dataTextPane
.getText()
.substring(
Integer.parseInt(fromTextField.getText()),
Integer.parseInt(toTextField.getText()));
}
} catch (NumberFormatException e) {
System.out.println("tried to use invalid sequence interval to generate Clotho object");
return;
}
} else {
seq = dataTextPane.getText();
}
Format form = null;
Collection coll = null;
if (objectTypeComboBox.getSelectedIndex() != 1 && objectTypeComboBox.getSelectedIndex() != 0) {
if (formatComboBox.getSelectedIndex() == -1) {
statusLabel.setText("Warning: format not set");
return;
}
form = Collector.getFormat(((ObjLink) formatComboBox.getSelectedItem()).uuid);
}
if (collectionComboBox.getSelectedIndex() != -1) {
coll = Collector.getCollection(((ObjLink) collectionComboBox.getSelectedItem()).uuid);
} else {
statusLabel.setText("Warning: collection not selected");
return;
}
if (objectTypeComboBox.getSelectedIndex() == -1) {
statusLabel.setText("Warning: object Type not set");
return;
}
Boolean saved = false;
ObjBase newObject = null;
if (coll != null) {
if (objectTypeComboBox.getSelectedIndex() == 0) {
// feature
if (seq.toUpperCase().indexOf("ATG") != -1) {
newObject = Feature.generateFeature(name, seq, Collector.getCurrentUser(), true);
} else {
newObject = Feature.generateFeature(name, seq, Collector.getCurrentUser(), false);
}
} else if (objectTypeComboBox.getSelectedIndex() == 1) {
newObject = new Oligo(name, desc, Collector.getCurrentUser(), seq);
} else if (form != null && objectTypeComboBox.getSelectedIndex() == 2) {
// part
newObject = Part.generateBasic(name, desc, seq, form, Collector.getCurrentUser());
} else if (form != null && objectTypeComboBox.getSelectedIndex() == 3) {
Vector.generateVector(name, desc, seq, form, Collector.getCurrentUser());
} else {
statusLabel.setText("error saving new Clotho object, check selected fields");
return;
}
} else {
statusLabel.setText("Not all fields are filled");
return;
}
if (newObject != null) {
statusLabel.setText("saving: " + newObject.getName());
}
saved = newObject.saveDefault();
coll.addObject(newObject);
coll.saveDefault();
Collector.add(newObject);
if (saved) {
statusLabel.setText("Successful save!");
NucSeq.refreshFeatureTable();
this.dispose();
}
} // GEN-LAST:event_saveButtonActionPerformed
@Override
public NucSeq generatePlasmidSequence(Plasmid p) {
String out = "";
out += p.getPart().getSeq().getSeq();
out += p.getVector().getSeq().getSeq();
NucSeq outnuc = new NucSeq(out);
outnuc.setTransient();
for (Annotation ann : p.getPart().getSeq().getAnnotations()) {
Feature afeature = ann.getFeature();
String name = ann.getName();
Color forColor = ann.getForwardColor();
Color revColor = ann.getReverseColor();
int Start = ann.getStart();
int End = ann.getEnd();
Person user = ann.getAuthor();
boolean plusstrandtrue = ann.isForwardStrand();
String symbol = ann.getSymbol();
Annotation newann;
if (afeature == null) {
newann =
new Annotation(
name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
} else {
newann =
new Annotation(
afeature, outnuc, forColor, revColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
}
System.out.println("Generated annotation: " + newann.getName());
}
String parseq = p.getPart().getSeq().getSeq();
int offset = parseq.length();
for (Annotation ann : p.getVector().getSeq().getAnnotations()) {
Feature afeature = ann.getFeature();
String name = ann.getName();
Color forColor = ann.getForwardColor();
Color revColor = ann.getReverseColor();
int Start = offset + ann.getStart();
int End = offset + ann.getEnd();
Person user = ann.getAuthor();
boolean plusstrandtrue = ann.isForwardStrand();
String symbol = ann.getSymbol();
Annotation newann;
if (afeature == null) {
newann =
new Annotation(
name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
} else {
newann =
new Annotation(
afeature, outnuc, forColor, revColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
}
System.out.println("Generated annotation: " + newann.getName());
}
return outnuc;
}