Team:Freiburg software/Code/Sequence.java
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(New page: <nowiki> /* Copyright: synbiowave License: GPL Authors: Jörg Walossek Version: 0.1 DESCRIPTION: This class can be used to create di...)
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(New page: <nowiki> /* Copyright: synbiowave License: GPL Authors: Jörg Walossek Version: 0.1 DESCRIPTION: This class can be used to create di...)
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Revision as of 23:26, 21 October 2009
/* 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.database; import java.util.ArrayList; import javax.jdo.annotations.IdGeneratorStrategy; import javax.jdo.annotations.IdentityType; import javax.jdo.annotations.PersistenceCapable; import javax.jdo.annotations.Persistent; import javax.jdo.annotations.PrimaryKey; import com.google.appengine.api.datastore.Text; import com.google.wave.api.Annotation; import com.google.wave.api.Range; // TODO: Auto-generated Javadoc /** * The Class Sequence. */ @PersistenceCapable(identityType = IdentityType.APPLICATION) public class Sequence { /** The id. */ @PrimaryKey @Persistent(valueStrategy = IdGeneratorStrategy.IDENTITY) private Long id; /** The author. */ @Persistent private String author; /** The timestamp. */ @Persistent private Long timestamp; /** The wave id. */ @Persistent private ArrayList<String> waveID; /** The wavelet id. */ @Persistent private ArrayList<String> waveletID; /** The blip id. */ @Persistent private ArrayList<String> blipID; /** The name. */ @Persistent private String name; /** The sequence. */ @Persistent(defaultFetchGroup="true") private Text sequence; /** The type. */ @Persistent private String type; /** The annotations. */ @Persistent private ArrayList<String> annotations; /** The plain. */ @Persistent(defaultFetchGroup="true") private Text plain; /** * Instantiates a new sequence. */ public Sequence(){} /** * Instantiates a new sequence. * * @param author the author * @param timestamp the timestamp * @param waveID the wave id * @param waveletID the wavelet id * @param blipID the blip id * @param sequence the sequence * @param type the type */ public Sequence(String author,Long timestamp,String waveID,String waveletID,String blipID,String sequence,String type) { this.author=author; this.timestamp=timestamp; this.waveID=new ArrayList<String>(); this.waveID.add(waveID); this.waveletID=new ArrayList<String>(); this.waveletID.add(waveletID); this.blipID=new ArrayList<String>(); this.blipID.add(blipID); this.name=null; this.sequence=new Text(sequence); this.type=type; this.annotations=new ArrayList<String>(); this.plain=null;} /** * Gets the id. * * @return the id */ public Long getId(){return id;} /** * Gets the author. * * @return the author */ public String getAuthor(){return author;} /** * Gets the timestamp. * * @return the timestamp */ public Long getTimestamp(){return timestamp;} /** * Gets the wave id. * * @return the wave id */ public ArrayList<String> getWaveID(){return waveID;} /** * Gets the wavelet id. * * @return the wavelet id */ public ArrayList<String> getWaveletID(){return waveletID;} /** * Gets the blip id. * * @return the blip id */ public ArrayList<String> getBlipID(){return blipID;} /** * Gets the name. * * @return the name */ public String getName(){return name;} /** * Gets the sequence. * * @return the sequence */ public String getSequence(){return sequence.getValue();} /** * Gets the type. * * @return the type */ public String getType(){return type;} /** * Gets the annotations. * * @return the annotations */ public ArrayList<Annotation> getAnnotations(){ ArrayList<Annotation> annotations=new ArrayList<Annotation>(); for(String stringAnnotation:this.annotations){ String[] annotationParts=stringAnnotation.split("§"); annotations.add(new Annotation(annotationParts[0],annotationParts[1], new Range(Integer.parseInt(annotationParts[2]),Integer.parseInt(annotationParts[3]))));} return annotations;} /** * Gets the plain. * * @return the plain */ public String getPlain(){return plain.getValue();} /** * Sets the name. * * @param name the new name */ public void setName(String name){this.name=name;} /** * Sets the sequence. * * @param sequence the new sequence */ public void setSequence(String sequence){this.sequence=new Text(sequence);} /** * Sets the type. * * @param type the new type */ public void setType(String type){this.type=type;} /** * Adds the annotation. * * @param annotation the annotation */ public void addAnnotation(Annotation annotation){ String stringAnnotation= annotation.getName()+"§"+annotation.getValue()+"§"+annotation.getRange().getStart() +"§"+annotation.getRange().getEnd(); this.annotations.add(stringAnnotation);} /** * Sets the annotations. * * @param annotations the new annotations */ public void setAnnotations(ArrayList<Annotation> annotations){ String stringAnnotation; for(Annotation annotation:annotations){ stringAnnotation= annotation.getName()+"§"+annotation.getValue()+"§"+annotation.getRange().getStart() +"§"+annotation.getRange().getEnd(); this.annotations.add(stringAnnotation);}} /** * Sets the plain. * * @param plain the new plain */ public void setPlain(String plain){this.plain=new Text(plain);} }