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/* Copyright (c) 2009 Peter Troshin
* Copyright (c) 2013 Alexander Sherstnev
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
//package compbio.data.sequence;
//
//import java.util.List;
//import java.util.ArrayList;
//
//import javax.xml.bind.annotation.XmlAccessType;
//import javax.xml.bind.annotation.XmlAccessorType;
//
//import compbio.util.annotation.Immutable;
//import compbio.data.sequence.Alignment;
///**
// * Multiple sequence alignment and Jpred prediction.
// *
// * Does not give any guarantees on the content of individual FastaSequece
// * records. It does not guarantee neither the uniqueness of the names of
// * sequences nor it guarantees the uniqueness of the sequences.
// *
// * @see FastaSequence
// * @see AlignmentMetadata
// *
// * @author pvtroshin
// *
// * @version 1.0 September 2009
// *
// */
//@XmlAccessorType(XmlAccessType.FIELD)
//public class JpredAlignment extends Alignment{
//
// private JpredAlignment() {
// // This has to has a default constructor for JaxB
// }
//
// /**
// * @param sequences
// * @param program
// * @param gapchar
// */
// public JpredAlignment(List<FastaSequence> sequences, Program program, char gapchar) {
// this.sequences = sequences;
// this.metadata = new AlignmentMetadata(Program.Jpred, gapchar);
// }
//
// /**
// *
// * @param sequences
// * @param metadata
// */
// public JpredAlignment(List<FastaSequence> sequences, AlignmentMetadata metadata) {
// this.sequences = sequences;
// this.metadata = metadata;
// }
//
// private List<FastaSequence> getRealSeqs() {
// List<FastaSequence> realsequences = new ArrayList<FastaSequence>();
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("jnetpred") ||
// s.getId().equals("JNETCONF") ||
// s.getId().equals("JNETSOL25") ||
// s.getId().equals("JNETSOL5") ||
// s.getId().equals("JNETSOL0") ||
// s.getId().equals("JNETHMM") ||
// s.getId().equals("JNETHMM") ||
// s.getId().equals("JNETSOL0") ||
// s.getId().equals("JNETHMM")) {
// // do nothing;
// } else {
// realsequences.add(s);
// }
// }
// return realsequences;
// }
//
//
// public List<FastaSequence> getJpredSequences() {
// List<FastaSequence> realsequences = new ArrayList<FastaSequence>();
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("jnetpred") ||
// s.getId().equals("JNETCONF") ||
// s.getId().equals("JNETSOL25") ||
// s.getId().equals("JNETSOL5") ||
// s.getId().equals("JNETSOL0") ||
// s.getId().equals("JNETHMM") ||
// s.getId().equals("JNETHMM") ||
// s.getId().equals("JNETSOL0") ||
// s.getId().equals("JNETSOL0") ||
// s.getId().equals("QUERY")) {
// realsequences.add(s);
// }
// }
// return realsequences;
// }
// /**
// *
// * @return Jpred prediction
// */
// public String getJpredPrediction() {
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("jnetpred")) {
// return s.getSequence();
// }
// }
// return new String("");
// }
//
// /**
// *
// * @return Jpred JNETSOL25 line
// */
// public String getJpredSOL25() {
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("JNETSOL25")) {
// return s.getSequence();
// }
// }
// return new String("");
// }
//
// /**
// *
// * @return Jpred JNETSOL5 line
// */
// public String getJpredSOL5() {
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("JNETSOL5")) {
// return s.getSequence();
// }
// }
// return new String("");
// }
// /**
// *
// * @return Jpred JNETSOL0 line
// */
// public String getJpredSOL0() {
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("JNETSOL0")) {
// return s.getSequence();
// }
// }
// return new String("");
// }
// /**
// *
// * @return Jpred JNETCONF line
// */
// public String getJpredJNETCONF() {
// for (FastaSequence s : this.sequences) {
// if (s.getId().equals("JNETCONF")) {
// return s.getSequence();
// }
// }
// return new String("");
// }
//
// /**
// *
// * @return list of FastaSequence records
// */
// @Override
// public List<FastaSequence> getSequences() {
// return this.getRealSeqs();
// }
//
// /**
// *
// * @return a number of sequence in the alignment
// */
// @Override
// public int getSize() {
// return this.getRealSeqs().size();
// }
//
// /**
// * Please note that this implementation does not take the order of sequences
// * into account!
// */
// @Override
// public boolean equals(Object obj) {
// if (obj == null) {
// return false;
// }
// if (!(obj instanceof JpredAlignment)) {
// return false;
// }
// JpredAlignment al = (JpredAlignment) obj;
// if (this.getSize() != al.getSize()) {
// return false;
// }
// if (!this.getMetadata().equals(al.getMetadata())) {
// return false;
// }
// int outerCounter = 0;
// int matchCounter = 0;
// for (FastaSequence fs : getSequences()) {
// outerCounter++;
// for (FastaSequence fs1 : al.getSequences()) {
// if (fs.equals(fs1)) {
// matchCounter++;
// continue;
// }
// }
// // Match for at lease one element was not found!
// if (outerCounter != matchCounter) {
// return false;
// }
// }
// return true;
// }
//
//}
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