001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.core.sequence.storage; 022 023import org.biojava.nbio.core.sequence.Strand; 024import org.biojava.nbio.core.sequence.template.Compound; 025import org.biojava.nbio.core.sequence.template.CompoundSet; 026 027import java.util.List; 028 029/** 030 * This is a common method that can be used across multiple storage/proxy implementations to 031 * handle Negative strand and other interesting elements of sequence data. 032 * @author Scooter Willis <willishf at gmail dot com> 033 */ 034public class SequenceAsStringHelper<C extends Compound> { 035 036 /** 037 * 038 * @param parsedCompounds 039 * @param compoundSet 040 * @param bioBegin 041 * @param bioEnd 042 * @param strand 043 * @return 044 */ 045 public String getSequenceAsString(List<C> parsedCompounds, CompoundSet<C> compoundSet, Integer bioBegin, Integer bioEnd, Strand strand) { 046 // TODO Optimise/cache. 047 if(parsedCompounds.size() == 0) 048 return ""; 049 StringBuilder builder = new StringBuilder(); 050 if (strand.equals(Strand.NEGATIVE)) { 051 //we expect bioBegin to be bigger but could have circular case 052 if (bioBegin <= bioEnd) { 053 for (int index = bioEnd - 1; index >= bioBegin - 1; index--) { 054 C compound = parsedCompounds.get(index); 055 builder.append(compoundSet.getStringForCompound(compound)); 056 } 057 }else{ 058 //go to 0 and the up 059 for (int index = bioBegin - 1; index >= 0; index--) { 060 C compound = parsedCompounds.get(index); 061 builder.append(compoundSet.getStringForCompound(compound)); 062 } 063 064 for (int index = parsedCompounds.size() - 1; index >= bioEnd - 1; index--) { 065 C compound = parsedCompounds.get(index); 066 builder.append(compoundSet.getStringForCompound(compound)); 067 } 068 } 069 } else { 070 if (bioBegin <= bioEnd) { 071 for (int index = bioBegin - 1; index <= bioEnd - 1 ; index++) { 072 C compound = parsedCompounds.get(index); 073 builder.append(compoundSet.getStringForCompound(compound)); 074 } 075 }else{ 076 //go to 0 and the up 077 for (int index = bioBegin - 1; index <= parsedCompounds.size() - 1; index++) { 078 C compound = parsedCompounds.get(index); 079 builder.append(compoundSet.getStringForCompound(compound)); 080 } 081 082 for (int index = 0; index <= bioEnd - 1; index++) { 083 C compound = parsedCompounds.get(index); 084 builder.append(compoundSet.getStringForCompound(compound)); 085 } 086 } 087 088 089 } 090 091 return builder.toString(); 092 } 093}