/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on August 13, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.io;
import org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference;
import java.util.*;
/**
* Stores all the content parsed from the #=GF lines
*
*
* @since 3.0.5
* @author Amr AL-Hossary
* @author Marko Vaz
*
*/
public class StockholmFileAnnotation {
public static class StockholmFileAnnotationReference {
private String refMedline;//TODO 8 digits
private CharSequence refTitle;//on several lines
private CharSequence refAuthor;//TODO comma-separated, semicolon terminated list;
/**<b>TODO to be formatted later on.</b><br>
* RL Journal abbreviation year;volume:page-page.<br>
* RL Virus Genes 1997;14:163-165.<br>
* RL J Mol Biol 1994;242:309-320.
*/
private String refLocation;
public String getRefMedline() {
return refMedline;
}
public void setRefMedline(String refMedline) {
this.refMedline = refMedline;
}
public String getRefTitle() {
return refTitle.toString();
}
public void setRefTitle(String refTitle) {
this.refTitle = refTitle;
}
public void addToRefTitle(String refTitle) {
if (this.refTitle== null) {
this.refTitle = new StringBuffer(refTitle);
} else if (this.refTitle instanceof StringBuffer){
((StringBuffer) this.refTitle).append(' ').append(refTitle);
}else {
this.refTitle = new StringBuffer(this.refTitle).append(' ').append(refTitle);
}
}
public String getRefAuthor() {
return refAuthor.toString();
}
public void setRefAuthor(StringBuffer refAuthor) {
this.refAuthor = refAuthor;
}
public void addToRefAuthor(String refAuthor) {
if (this.refAuthor== null) {
this.refAuthor = new StringBuffer(refAuthor);
} else if (this.refAuthor instanceof StringBuffer){
((StringBuffer) this.refAuthor).append(' ').append(refAuthor);
}else {
this.refAuthor = new StringBuffer(this.refAuthor).append(' ').append(refAuthor);
}
}
public String getRefLocation() {
return refLocation;
}
public void setRefLocation(String refLocation) {
this.refLocation = refLocation;
}
}
//TODO revise these 4 fields usage
private final static String TREE_DEFAULT_ID = "DEFAULT_ID";
private static final String PB_PFAM_STRING = "PB";
private static final String PF_PFAM_STRING = "PF";
private static final String RF_RFAM_STRING = "RF";
private StringBuffer format;
private StringBuffer version;
private String accessionNumber;
private StringBuffer identification;
private StringBuffer definition;
private String[] authors;
private String alignmentMethod;
private CharSequence buildMethod;
private StringBuffer searchMethod;
private StringBuffer sourceSeed;
private StringBuffer sourceStructure;
private float[] gatheringThreshs;
private float[] noiseCutoffs;
private float[] trustedCutoffs;
private String typeField;
private String[] previousIDs;
private int numSequences;
private StringBuffer dbComment;
private Set<DatabaseReference> dbReferences;
private StringBuffer refComment;
/**TODO When implementing toString(), the function should loop on the vector */
private Vector<StockholmFileAnnotationReference> references = new Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>();
private StringBuffer keywords;
private CharSequence comment;
private StringBuffer pfamAccession;
private StringBuffer location;
private StringBuffer wikipediaLink;
private StringBuffer clan;
private StringBuffer membership;
private final Map<String, List<String>> embTrees;
private float falseDiscoveryRate;
public StockholmFileAnnotation() {
embTrees = new HashMap<String, List<String>>();
}
public StringBuffer getDbComment() {
return dbComment;
}
public void setDbComment(String dbComment) {
if (this.dbComment != null) {
this.dbComment.append(dbComment);
} else {
this.dbComment = new StringBuffer(dbComment);
}
}
public Set<DatabaseReference> getDbReferences() {
return dbReferences;
}
public void setDbReferences(Set<DatabaseReference> dbReferences) {
this.dbReferences = dbReferences;
}
/**
* @param dbReference the string without the initial annotation identifier ( #=GS DR )
*/
public void addDBReference(String dbReferenceRepresentingString) {
if (this.dbReferences == null) {
this.dbReferences = new HashSet<DatabaseReference>();
}
dbReferences.add(new DatabaseReference(dbReferenceRepresentingString));
}
public float getFalseDiscoveryRate() {
return falseDiscoveryRate;
}
public void setFalseDiscoveryRate(float falseDiscoveryRate) {
this.falseDiscoveryRate = falseDiscoveryRate;
}
public StringBuffer getRefComment() {
return refComment;
}
public StringBuffer getKeywords() {
return keywords;
}
public String getComment() {
return comment.toString();
}
public StringBuffer getPfamAccession() {
return pfamAccession;
}
public StringBuffer getLocation() {
return location;
}
public StringBuffer getWikipediaLink() {
return wikipediaLink;
}
public StringBuffer getClan() {
return clan;
}
public StringBuffer getMembership() {
return membership;
}
public Map<String, List<String>> getEmbTrees() {
return embTrees;
}
public void setNumSequences(int numSequences) {
this.numSequences = numSequences;
}
public StringBuffer getIdentification() {
return identification;
}
public void setGFIdentification(String identification) {
if (this.identification != null) {
this.identification.append(identification);
} else {
this.identification = new StringBuffer(identification);
}
}
public StringBuffer getDefinition() {
return definition;
}
public void setGFDefinition(String definition) {
if (this.definition != null) {
this.definition.append(definition);
} else {
this.definition = new StringBuffer(definition);
}
}
public String[] getAuthors() {
return authors;
}
public void setGFAuthors(String authors) {
this.authors = authors.split(",");
}
public String getBuildMethod() {
return buildMethod.toString();
}
public void addGFBuildMethod(String buildMethod) {
if (this.buildMethod == null) {
this.buildMethod = new StringBuffer(buildMethod);
} else if (this.buildMethod instanceof StringBuffer){
((StringBuffer) this.buildMethod).append(System.getProperty("line.seperator")).append(buildMethod);
}else {
this.buildMethod = new StringBuffer(this.buildMethod).append(System.getProperty("line.seperator")).append(buildMethod);
}
}
public StringBuffer getSearchMethod() {
return searchMethod;
}
public void setGFSearchMethod(String searchMethod) {
if (this.searchMethod != null) {
this.searchMethod.append(searchMethod);
} else {
this.searchMethod = new StringBuffer(searchMethod);
}
}
public StringBuffer getSourceSeed() {
return sourceSeed;
}
public void setGFSourceSeed(String sourceSeed) {
if (this.sourceSeed != null) {
this.sourceSeed.append(sourceSeed);
} else {
this.sourceSeed = new StringBuffer(sourceSeed);
}
}
public StringBuffer getSourceStructure() {
return sourceStructure;
}
public void setGFSourceStructure(String sourceStructure) {
if (this.sourceStructure != null) {
this.sourceStructure.append(sourceStructure);
} else {
this.sourceStructure = new StringBuffer(sourceStructure);
}
}
/**Not always 2.<br>
* It may undergo further change.
* @return
*/
public float[] getGatheringThreshs() {
return gatheringThreshs;
}
public void setGFGatheringThreshs(String gatheringThresh) {
this.gatheringThreshs = stringToFloats(gatheringThresh);
}
/**Not always 2.<br>
* It may undergo further change.
* @return
*/
public float[] getNoiseCutoffs() {
return noiseCutoffs;
}
public void setGFNoiseCutoffs(String noiseCutoff) {
this.noiseCutoffs=stringToFloats(noiseCutoff);
}
/**Not always 2.<br>
* It may undergo further change.
* @return
*/
public float[] getTrustedCutoffs() {
return trustedCutoffs;
}
public void setGFTrustedCutoffs(String trustedCutoff) {
this.trustedCutoffs = stringToFloats(trustedCutoff);
}
public float[] stringToFloats(String string) {
String[] coublets= string.split(";");
float[] floats = new float[coublets.length*2];
int counter=0;
for (int i = 0; i < coublets.length; i++) {
String[] subStrings = coublets[i].trim().split("\\s");
float f = Float.parseFloat(subStrings[i]);
floats[counter++]=f;
}
return floats;
}
public String getTypeField() {
return typeField;
}
public void setGFTypeField(String typeField) {
this.typeField = typeField;
}
public String[] getPreviousIDs() {
return previousIDs;
}
public void setGFPreviousIDs(String previousIDs) {
this.previousIDs = previousIDs.split(";");
}
public StringBuffer getFormat() {
return format;
}
public void setFormat(String format) {
if (this.format != null) {
this.format.append(format);
} else {
this.format = new StringBuffer(format);
}
}
public StringBuffer getVersion() {
return version;
}
public void setVersion(String version) {
if (this.version != null) {
this.version.append(version);
} else {
this.version = new StringBuffer(version);
}
}
public String getAccessionNumber() {
return accessionNumber;
}
public void setGFAccessionNumber(String accessionNumber) {
this.accessionNumber = accessionNumber;
}
public boolean isPFam() {
return accessionNumber != null
&& (accessionNumber.startsWith(PF_PFAM_STRING) || accessionNumber.startsWith(PB_PFAM_STRING));
}
public boolean isRFam() {
return accessionNumber == null
|| accessionNumber.startsWith(RF_RFAM_STRING);
}
public int getNumSequences() {
return numSequences;
}
public void setGFNumSequences(String numSequences) {
this.numSequences = Integer.parseInt(numSequences);
}
public void setGFDBComment(String dbComment) {
if (this.dbComment != null) {
this.dbComment.append(dbComment);
} else {
this.dbComment = new StringBuffer(dbComment);
}
}
public void setGFRefComment(String refComment) {
if (this.refComment != null) {
this.refComment.append(refComment);
} else {
this.refComment = new StringBuffer(refComment);
}
}
public void setGFKeywords(String keywords) {
if (this.keywords != null) {
this.keywords.append(keywords);
} else {
this.keywords = new StringBuffer(keywords);
}
}
public void addToGFComment(String comment) {
if (this.comment == null) {
this.comment = new StringBuffer(comment);
} else if (this.comment instanceof StringBuffer){
((StringBuffer) this.comment).append(' ').append(comment);
}else {
this.comment = new StringBuffer(this.comment).append(' ').append(comment);
}
}
public void setGFPfamAccession(String pfamAccession) {
if (this.pfamAccession != null) {
this.pfamAccession.append(pfamAccession);
} else {
this.pfamAccession = new StringBuffer(pfamAccession);
}
}
public void setGFLocation(String location) {
if (this.location != null) {
this.location.append(location);
} else {
this.location = new StringBuffer(location);
}
}
public void setGFWikipediaLink(String wikipediaLink) {
if (this.wikipediaLink != null) {
this.wikipediaLink.append(wikipediaLink);
} else {
this.wikipediaLink = new StringBuffer(wikipediaLink);
}
}
public void setGFClan(String clan) {
if (this.clan != null) {
this.clan.append(clan);
} else {
this.clan = new StringBuffer(clan);
}
}
public void setGFMembership(String membership) {
if (this.membership != null) {
this.membership.append(membership);
} else {
this.membership = new StringBuffer(membership);
}
}
public void addGFNewHampshire(String newHampshire) {
List<String> hampshireTree = embTrees.get(TREE_DEFAULT_ID);
if (hampshireTree == null) {
hampshireTree = new ArrayList<String>();
}
hampshireTree.add(newHampshire);
embTrees.put(TREE_DEFAULT_ID, hampshireTree);
}
public void addGFTreeID(String treeID) {
List<String> hampshireTree = embTrees.remove(TREE_DEFAULT_ID);
embTrees.put(treeID, hampshireTree);
}
public void addGFFalseDiscoveryRate(String falseDiscoveryRate) {
this.falseDiscoveryRate = Float.parseFloat(falseDiscoveryRate);
}
public String getAlignmentMethod() {
return alignmentMethod;
}
public void setAlignmentMethod(String alignmentMethod) {
this.alignmentMethod = alignmentMethod;
}
public Vector<StockholmFileAnnotationReference> getReferences() {
return references;
}
public void setReferences(Vector<StockholmFileAnnotationReference> references) {
this.references = references;
}
}