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Team:Freiburg software/Code/DisplaySequence.java
From 2009.igem.org
org.synbiowave.biojava.DisplaySequence
/*
Copyright: synbiowave
License: GPL
Authors: Paul Staab
Version: 0.1
DESCRIPTION:
This class can be used to create different visualizations of a DNA-Sequence
*/
package org.synbiowave.biojava;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.RNATools;
import org.biojava.bio.symbol.SymbolList;
/**
* <p>Class to create various visualizations of a DNA-Sequence</p>
*/
public class DisplaySequence {
private SymbolList symL;
public DisplaySequence(String[] args) throws Exception
{
}
public DisplaySequence(SymbolList symL) throws Exception
{
//ToDo: Check for DNA and throw error
this.symL = symL;
}
/** Setter for the DNA-Sequence stored in a SymbolList */
public void set_Sequenz(SymbolList symL) throws Exception
{
//ToDo: Check for DNA and throw error
this.symL = symL;
}
/** Getter for the DNA-Sequence stored in a SymbolList */
public SymbolList get_Sequenz() throws Exception
{
return this.symL;
}
/** Displays a Single ReadingFrame (number in 1-6 with 1-3
* being forward and 4-6 being backward readingframes) plus the sequence */
public String displaySingleReadingFrame(int number) throws Exception
{
if (number > 3) return displaySingleReadingFrame(number-3,true);
else return displaySingleReadingFrame(number,false);
}
/** Displays the Sequence and a single readingframe;
* number is the number of the readingframe to display (1-3)
* backwards = false means forward reading frames, true backward ones */
public String displaySingleReadingFrame(int number, boolean backwards) throws Exception
{
return
generateReadingframe(number,backwards) +
this.symL.seqString() + "\n" +
addNumberation(this.symL.length());
}
/** Displays the Sequence and the 3 forward readingframes */
public String displayFwReadingFrames() throws Exception
{
return
generateReadingframe(1,false) +
generateReadingframe(2,false) +
generateReadingframe(3,false) +
this.symL.seqString() + "\n" +
addNumberation(this.symL.length());
}
/** Displays the Sequence and the 3 backward readingframes */
public String displayRevReadingFrames() throws Exception
{
return
generateReadingframe(1,true) +
generateReadingframe(2,true) +
generateReadingframe(3,true) +
DNATools.reverseComplement(this.symL).seqString() + "\n" +
addNumberation(this.symL.length());
}
/** Displays the Sequence and all 6 readingframes */
public String displayAllReadingFrames() throws Exception
{
return
generateReadingframe(1,false) + //"<br>" +
generateReadingframe(2,false) + //"<br>" +
generateReadingframe(3,false) + //"<br>" +
this.symL.seqString() + //"<br>" +
addNumberation(this.symL.length()) + //"<br>" +
DNATools.reverseComplement(this.symL).seqString() + //"<br>" +
generateReadingframe(3,true) + //"<br>" +
generateReadingframe(2,true) + //"<br>" +
generateReadingframe(1,true) ; //"<br>";
}
static private String addNumberation(int end)
{
String returnvalue = "1";
for (int i = 2; i <= end; i++)
{
if (i%10 == 0) returnvalue += Integer.toString(i);
else if (i%10 < Integer.toString(i).length()) ;
else returnvalue += " ";
}
return returnvalue + "\n";
}
/** Generates a basic formatted readingframe */
private String generateReadingframe(int number, boolean backwards) throws Exception
{
SymbolList symL;
String formattedReadingframe = "";
//ToDo: FEHLER AUSGEBEN WENN NUMBER > 3
number --;
if (backwards) symL = DNATools.reverseComplement(this.symL);
else symL = this.symL;
//Translate the DNA into AA
symL = symL.subList(number+1, symL.length() - (symL.length() - number)%3);
symL = DNATools.toRNA(symL);
symL = RNATools.translate(symL);
//Insert beginning spaces
for (int i = 1; i < number + 1; i++)
{
formattedReadingframe += " ";
}
//Insert 2 spaces between each AA
for (int i = 1; i <= symL.length() ; i++)
{
formattedReadingframe += symL.subStr(i, i) + " " ;
}
return formattedReadingframe + "\n";
}
}
