/*
Copyright (c) 2009 The Regents of the University of California.
All rights reserved.
Permission is hereby granted, without written agreement and without
license or royalty fees, to use, copy, modify, and distribute this
software and its documentation for any purpose, provided that the above
copyright notice and the following two paragraphs appear in all copies
of this software.
IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
ENHANCEMENTS, OR MODIFICATIONS..
*/
package org.clothocad.format.bglbricks;
import java.awt.Color;
import java.util.ArrayList;
import org.clothocore.api.data.Annotation;
import org.clothocore.api.data.Feature;
import org.clothocore.api.data.NucSeq;
import org.clothocore.api.data.Part;
import org.clothocore.api.data.Person;
import org.clothocore.api.data.Plasmid;
import org.clothocore.api.data.Vector;
import org.clothocore.api.plugin.ClothoFormat;
/**
* Format Interface is what a ClothoFormat plugin must implement
* @author jcanderson
*/
public class connect implements ClothoFormat {
@Override
public void init() {
}
@Override
public boolean checkPart(Part p) {
String seq = p.getSeq().getSeq();
//If it's a blank Part, that's ok
if(seq.equals("")) {
return true;
}
//Check that it starts with GATCT and ends with G
if(!seq.startsWith("GATCT")) {
return false;
}
if(!seq.endsWith("G")) {
return false;
}
//Check if the sequence contains any forbidden restriction sites
if(seq.indexOf("GAATTC") > 0) {
return false;
}
if(seq.indexOf("GGATCC") > 0) {
return false;
}
if(seq.indexOf("AGATCT") > 0) {
return false;
}
if(seq.indexOf("CTCGAG") > 0) {
return false;
}
return true;
}
@Override
public boolean checkVector(Vector v) {
String seq = v.getSeq().getSeq();
//If it's a blank Vector, that's ok
if(seq.equals("")) {
return true;
}
//If it's a blank genomic Vector, that's ok
if(seq.equals(".")) {
return true;
}
//Check that it starts with GATCC and ends with A
if(!seq.startsWith("GATCC")) {
return false;
}
if(!seq.endsWith("A")) {
return false;
}
//Check if the sequence contains any forbidden restriction sites
if(seq.indexOf("GGATCC") > 0) {
return false;
}
if(seq.indexOf("AGATCT") > 0) {
return false;
}
return true;
}
@Override
public boolean checkComposite(ArrayList<Part> composition, Object additionalRequirements) {
//A BglBrick composite Part should have at least 2 parents
if(composition.size()<2) {
return false;
}
//Both composite parts need to obey BglBricks, but don't need to explicitly be stated to be BglBricks
//For example, they could be the AcuI/BseRI variation on BglBricks
for(Part p: composition) {
if(!checkPart(p)) {
return false;
}
}
return true;
}
@Override
public boolean checkPlasmid(Part p, Vector v, Object additionalRequirements) {
//Confirm that the Part and Vector obey BglBricks
if(!checkPart(p)) {
return false;
}
if(!checkVector(v)) {
return false;
}
return true;
}
@Override
public NucSeq generateCompositeSequence(ArrayList<Part> composition, Object additionalRequirements) {
if(!checkComposite(composition, additionalRequirements)) {
return null;
}
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;
}
@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;
}
@Override
public NucSeq generateSequencingRegion(Plasmid p) {
String seq = generatePlasmidSequence(p).getSeq();
int ecoSite = seq.indexOf("GAATTC");
int bamSite = seq.indexOf("GGATCC");
//If the Plasmid lacks bam or eco, return the Part sequence
if(ecoSite <1) {
return p.getPart().getSeq();
}
if(bamSite <1) {
return p.getPart().getSeq();
}
//Most likely the thing needs to be spun around, else grab eco/bam fragment
String out = "";
if(ecoSite>bamSite) {
out += seq.substring(ecoSite);
out += seq.substring(0,bamSite+6);
} else {
out += seq.substring(ecoSite,bamSite+6);
}
NucSeq outnuc = new NucSeq(out);
outnuc.setTransient();
return outnuc;
}
}