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Team:Freiburg software/Code/SequenceView.java
From 2009.igem.org
Revision as of 23:29, 21 October 2009 by JonasOnlyJonas (Talk | contribs)
/*
Copyright: synbiowave
License: GPL
Authors: Jörg Walossek
Version: 0.1
DESCRIPTION:
This class can be used to create different visualizations of a DNA-Sequence
*/
package org.synbiowave.sequence;
import java.util.ArrayList;
import java.util.List;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.RNATools;
import org.biojava.bio.symbol.IllegalSymbolException;
import com.google.wave.api.Annotation;
import com.google.wave.api.Range;
// TODO: Auto-generated Javadoc
/**
* The Class SequenceView.
*/
public class SequenceView {
/** The a color code. */
private static char[][] aColorCode={{'Y','F','A','I','L','M','V'},
{'W'},
{'G'},
{'P'},
{'S','D','E','T'},
{'R','N','K'},
{'H'},
{'Q'},
{'C'}};
/** The a colors. */
private static String[] aColors=
{"green","mediumturquoise","magenta","gold","red","blue","cornflowerblue","gray","saddlebrown"};
/** The n color code. */
private static char[][] nColorCode={{'U','T'},
{'A'},
{'G'},
{'C'}};
/** The n colors. */
private static String[] nColors={"red","green","black","blue"};
/**
* Instantiates a new sequence view.
*/
public SequenceView(){}
/**
* Checks if is sequence.
*
* @param sequence the sequence
*
* @return the string
*/
public static String isSequence(String sequence){
String type="DNA";
try{DNATools.createDNA(sequence);}
catch(IllegalSymbolException e){
type="RNA";
try{RNATools.createRNA(sequence);}
catch(IllegalSymbolException se){
type="PROTEIN";
try{ProteinTools.createProtein(sequence);}
catch(IllegalSymbolException ise){
type="null";}}}
return type;}
/**
* Gets the color.
*
* @param sequence the sequence
* @param type the type
* @param rShift the r shift
*
* @return the color
*/
public static List<Annotation> getColor(String sequence,String type,int rShift){
List<Annotation> cAnnotations=new ArrayList<Annotation>();
return getColor(sequence, type, rShift, cAnnotations);}
/**
* Gets the color.
*
* @param sequence the sequence
* @param type the type
* @param rShift the r shift
* @param cAnnotations the c annotations
*
* @return the color
*/
public static List<Annotation> getColor(String sequence, String type, int rShift,List<Annotation> cAnnotations) {
char[][] colorCode=SequenceView.nColorCode;
String[] colors=SequenceView.nColors;
if(type.contains("PROTEIN")){
colorCode=SequenceView.aColorCode;
colors=SequenceView.aColors;}
boolean na=true;
int position=rShift;
char[] sa=sequence.toUpperCase().toCharArray();
for(char sc:sa){
if(na){
for(int r=0;r<colorCode.length;r++){
for(int c=0;c<colorCode[r].length;c++){
if(colorCode[r][c]==sc){
cAnnotations.add(new Annotation("style/color",colors[r],
new Range(position,position+1)));
na=false;}}}
if(na){cAnnotations.add(new Annotation("style/color","black",new Range(position,position+1)));}
else{na=true;}
position++;}}
return cAnnotations;}
/**
* Gets the scale.
*
* @param length the length
*
* @return the scale
*/
public static ArrayList<String> getScale(int length){
ArrayList<String> sScale=new ArrayList<String>();
StringBuffer scale=new StringBuffer();
StringBuffer numbers=new StringBuffer();
int wait=0;
for(int i=1;i<length+1;i++){
if((i%5)==0){
scale.append('\u23AA');
numbers.append(i);
wait=String.valueOf(i).length()-1;}
else{
scale.append('\'');
if(wait==0){numbers.append(' ');}
else{wait--;}}
if((i%50)==0){
sScale.add(scale.append('\n').append(numbers.append('\n')).toString());
scale=new StringBuffer();
numbers=new StringBuffer();
wait=0;}}
sScale.add(scale.append('\n').append(numbers.append('\n')).toString());
return sScale;}
/**
* Gets the hTML view.
*
* @param sequence the sequence
* @param type the type
*
* @return the hTML view
*/
public static String getHTMLView(String sequence,String type){
StringBuffer scale=new StringBuffer();
StringBuffer numbers=new StringBuffer();
int wait=0;
for(int i=1;i<sequence.length()+1;i++){
if((i%5)==0){
scale.append('|');
numbers.append(i);
wait=String.valueOf(i).length()-1;}
else{
scale.append('\'');
if(wait==0){numbers.append(" ");}
else{wait--;}}}
String htmlView="(br /)"+scale+"(br /)"+numbers+"(br /)";
char[][] colorCode=SequenceView.nColorCode;
String[] colors=SequenceView.nColors;
if(type.contains("PROTEIN")){
colorCode=SequenceView.aColorCode;
colors=SequenceView.aColors;}
char[] sa=sequence.toUpperCase().toCharArray();
for(char sc:sa){
for(int r=0;r<colorCode.length;r++){
for(int c=0;c<colorCode[r].length;c++){
if(colorCode[r][c]==sc){
htmlView+="(span style='color:"+colors[r]+";')"+sc+"(/span)";}}}}
return htmlView+"(br /)(br /)";}
/**
* Gets the hTML view.
*
* @param sequences the sequences
*
* @return the hTML view
*/
public static String getHTMLView(ArrayList<String> sequences){
int maxLength=0;
for(String sequence:sequences){if(sequence.length()>maxLength){maxLength=sequence.length();}}
StringBuffer scale=new StringBuffer();
StringBuffer numbers=new StringBuffer();
int wait=0;
for(int i=1;i<maxLength+1;i++){
if((i%5)==0){
scale.append('|');
numbers.append(i);
wait=String.valueOf(i).length()-1;}
else{
scale.append('\'');
if(wait==0){numbers.append(" ");}
else{wait--;}}}
String htmlView="(br /)"+scale+"(br /)"+numbers+"(br /)";
for(String sequence:sequences){
String type=isSequence(sequence);
char[][] colorCode=SequenceView.nColorCode;
String[] colors=SequenceView.nColors;
if(type.contains("PROTEIN")){
colorCode=SequenceView.aColorCode;
colors=SequenceView.aColors;}
char[] sa=sequence.toUpperCase().toCharArray();
for(char sc:sa){
for(int r=0;r<colorCode.length;r++){
for(int c=0;c<colorCode[r].length;c++){
if(colorCode[r][c]==sc){
htmlView+="(span style='color:"+colors[r]+";')"+sc+"(/span)";}}}}
htmlView+="(br /)";}
return htmlView+"(br /)";}
}
