X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=6c119364fb62b9b77b531696e54f9a54e718960c;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=5a49540a68a562ff589c0d3d0cd4d72f2ec49211;hpb=6357db6c20614a666b7b446aeb3260c5379637eb;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 5a49540..6c11936 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1,32 +1,30 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview 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 + * + * Jalview 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 GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.datamodel; import java.util.*; -import jalview.analysis.*; - /** * Data structure to hold and manipulate a multiple sequence alignment */ /** * @author JimP - * + * */ public class Alignment implements AlignmentI { @@ -44,7 +42,7 @@ public class Alignment implements AlignmentI public static final int PROTEIN = 0; public static final int NUCLEOTIDE = 1; - + public boolean hasRNAStructure = false; /** DOCUMENT ME!! */ @@ -79,7 +77,7 @@ public class Alignment implements AlignmentI /** * Make an alignment from an array of Sequences. - * + * * @param sequences */ public Alignment(SequenceI[] seqs) @@ -89,7 +87,7 @@ public class Alignment implements AlignmentI /** * Make a new alignment from an array of SeqCigars - * + * * @param seqs * SeqCigar[] */ @@ -105,7 +103,7 @@ public class Alignment implements AlignmentI * compactAlignment does not contain hidden regions. JBPNote - must also check * that compactAlignment resolves to a set of SeqCigars - or construct them * appropriately. - * + * * @param compactAlignment * CigarArray */ @@ -117,7 +115,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -125,14 +123,17 @@ public class Alignment implements AlignmentI { return sequences; } + @Override public List getSequences( Map hiddenReps) { - // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to work on this. + // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to + // work on this. return sequences; } + @Override public SequenceI[] getSequencesArray() { if (sequences == null) @@ -145,12 +146,13 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param i * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public SequenceI getSequenceAt(int i) { synchronized (sequences) @@ -165,9 +167,10 @@ public class Alignment implements AlignmentI /** * Adds a sequence to the alignment. Recalculates maxLength and size. - * + * * @param snew */ + @Override public void addSequence(SequenceI snew) { if (dataset != null) @@ -203,9 +206,10 @@ public class Alignment implements AlignmentI /** * Adds a sequence to the alignment. Recalculates maxLength and size. - * + * * @param snew */ + @Override public void setSequenceAt(int i, SequenceI snew) { SequenceI oldseq = getSequenceAt(i); @@ -218,14 +222,16 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public Vector getGroups() + @Override + public List getGroups() { return groups; } + @Override public void finalize() { if (getDataset() != null) @@ -252,10 +258,11 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param s * DOCUMENT ME! */ + @Override public void deleteSequence(SequenceI s) { deleteSequence(findIndex(s)); @@ -263,10 +270,11 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param i * DOCUMENT ME! */ + @Override public void deleteSequence(int i) { if (i > -1 && i < getHeight()) @@ -302,14 +310,13 @@ public class Alignment implements AlignmentI return null; } - /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * (non-Javadoc) + * + * @see + * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI) */ + @Override public SequenceGroup[] findAllGroups(SequenceI s) { ArrayList temp = new ArrayList(); @@ -338,6 +345,7 @@ public class Alignment implements AlignmentI } /** */ + @Override public void addGroup(SequenceGroup sg) { synchronized (groups) @@ -370,7 +378,7 @@ public class Alignment implements AlignmentI /** * remove any annotation that references gp - * + * * @param gp * (if null, removes all group associated annotation) */ @@ -428,6 +436,7 @@ public class Alignment implements AlignmentI } } + @Override public void deleteAllGroups() { synchronized (groups) @@ -441,6 +450,7 @@ public class Alignment implements AlignmentI } /** */ + @Override public void deleteGroup(SequenceGroup g) { synchronized (groups) @@ -454,6 +464,7 @@ public class Alignment implements AlignmentI } /** */ + @Override public SequenceI findName(String name) { return findName(name, false); @@ -461,9 +472,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean) */ + @Override public SequenceI findName(String token, boolean b) { return findName(null, token, b); @@ -471,10 +483,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, * boolean) */ + @Override public SequenceI findName(SequenceI startAfter, String token, boolean b) { @@ -515,6 +528,7 @@ public class Alignment implements AlignmentI return null; } + @Override public SequenceI[] findSequenceMatch(String name) { Vector matches = new Vector(); @@ -541,9 +555,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI) */ + @Override public int findIndex(SequenceI s) { int i = 0; @@ -563,10 +578,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults) */ + @Override public int findIndex(SearchResults results) { int i = 0; @@ -584,9 +600,10 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getHeight() { return sequences.size(); @@ -594,9 +611,10 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getWidth() { int maxLength = -1; @@ -614,10 +632,11 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param gc * DOCUMENT ME! */ + @Override public void setGapCharacter(char gc) { gapCharacter = gc; @@ -633,9 +652,10 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public char getGapCharacter() { return gapCharacter; @@ -643,9 +663,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#isAligned() */ + @Override public boolean isAligned() { return isAligned(false); @@ -653,9 +674,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#isAligned(boolean) */ + @Override public boolean isAligned(boolean includeHidden) { int width = getWidth(); @@ -679,15 +701,17 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel. * AlignmentAnnotation) */ + @Override public boolean deleteAnnotation(AlignmentAnnotation aa) { return deleteAnnotation(aa, true); } - + + @Override public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook) { int aSize = 1; @@ -721,7 +745,8 @@ public class Alignment implements AlignmentI if (swap) { annotations = temp; - if (unhook) { + if (unhook) + { unhookAnnotation(aa); } } @@ -730,7 +755,7 @@ public class Alignment implements AlignmentI /** * remove any object references associated with this annotation - * + * * @param aa */ private void unhookAnnotation(AlignmentAnnotation aa) @@ -748,10 +773,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. * AlignmentAnnotation) */ + @Override public void addAnnotation(AlignmentAnnotation aa) { addAnnotation(aa, -1); @@ -759,16 +785,18 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. * AlignmentAnnotation, int) */ + @Override public void addAnnotation(AlignmentAnnotation aa, int pos) { - if(aa.getRNAStruc()!= null){ - hasRNAStructure=true; + if (aa.getRNAStruc() != null) + { + hasRNAStructure = true; } - + int aSize = 1; if (annotations != null) { @@ -804,6 +832,7 @@ public class Alignment implements AlignmentI annotations = temp; } + @Override public void setAnnotationIndex(AlignmentAnnotation aa, int index) { if (aa == null || annotations == null || annotations.length - 1 < index) @@ -845,6 +874,7 @@ public class Alignment implements AlignmentI return annotations; } + @Override public void setNucleotide(boolean b) { if (b) @@ -857,6 +887,7 @@ public class Alignment implements AlignmentI } } + @Override public boolean isNucleotide() { if (type == NUCLEOTIDE) @@ -868,12 +899,15 @@ public class Alignment implements AlignmentI return false; } } - - public boolean hasRNAStructure(){ - //TODO can it happen that structure is removed from alignment? + + @Override + public boolean hasRNAStructure() + { + // TODO can it happen that structure is removed from alignment? return hasRNAStructure; } + @Override public void setDataset(Alignment data) { if (dataset == null && data == null) @@ -888,7 +922,7 @@ public class Alignment implements AlignmentI currentSeq = getSequenceAt(i); if (currentSeq.getDatasetSequence() != null) { - seqs[i] = (Sequence) currentSeq.getDatasetSequence(); + seqs[i] = currentSeq.getDatasetSequence(); } else { @@ -918,11 +952,13 @@ public class Alignment implements AlignmentI alignmentRefs++; } + @Override public Alignment getDataset() { return dataset; } + @Override public boolean padGaps() { boolean modified = false; @@ -969,11 +1005,12 @@ public class Alignment implements AlignmentI /** * Justify the sequences to the left or right by deleting and inserting gaps * before the initial residue or after the terminal residue - * + * * @param right * true if alignment padded to right, false to justify to left * @return true if alignment was changed */ + @Override public boolean justify(boolean right) { boolean modified = false; @@ -1071,11 +1108,13 @@ public class Alignment implements AlignmentI return modified; } + @Override public HiddenSequences getHiddenSequences() { return hiddenSequences; } + @Override public CigarArray getCompactAlignment() { synchronized (sequences) @@ -1101,6 +1140,7 @@ public class Alignment implements AlignmentI alignmentProperties.put(key, value); } + @Override public Object getProperty(Object key) { if (alignmentProperties != null) @@ -1109,6 +1149,7 @@ public class Alignment implements AlignmentI return null; } + @Override public Hashtable getProperties() { return alignmentProperties; @@ -1118,11 +1159,12 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame * ) */ + @Override public void addCodonFrame(AlignedCodonFrame codons) { if (codons == null) @@ -1141,9 +1183,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#getCodonFrame(int) */ + @Override public AlignedCodonFrame getCodonFrame(int index) { return codonFrameList[index]; @@ -1151,10 +1194,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI) */ + @Override public AlignedCodonFrame[] getCodonFrame(SequenceI seq) { if (seq == null || codonFrameList == null) @@ -1174,9 +1218,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#getCodonFrames() */ + @Override public AlignedCodonFrame[] getCodonFrames() { return codonFrameList; @@ -1184,10 +1229,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel. * AlignedCodonFrame) */ + @Override public boolean removeCodonFrame(AlignedCodonFrame codons) { if (codons == null || codonFrameList == null) @@ -1214,6 +1260,7 @@ public class Alignment implements AlignmentI return removed; } + @Override public void append(AlignmentI toappend) { if (toappend == this) @@ -1263,7 +1310,7 @@ public class Alignment implements AlignmentI List sg = toappend.getGroups(); if (sg != null) { - for (SequenceGroup _sg:sg) + for (SequenceGroup _sg : sg) { addGroup(_sg); } @@ -1333,11 +1380,10 @@ public class Alignment implements AlignmentI } @Override - public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc, - SequenceI seqRef, SequenceGroup groupRef) + public AlignmentAnnotation findOrCreateAnnotation(String name, + boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) { - for (AlignmentAnnotation annot : - getAlignmentAnnotation()) + for (AlignmentAnnotation annot : getAlignmentAnnotation()) { if (annot.autoCalculated == autoCalc && annot.getCalcId().equals(name) @@ -1364,10 +1410,12 @@ public class Alignment implements AlignmentI @Override public Iterable findAnnotation(String calcId) { - ArrayList aa=new ArrayList(); - for (AlignmentAnnotation a:getAlignmentAnnotation()) + ArrayList aa = new ArrayList(); + for (AlignmentAnnotation a : getAlignmentAnnotation()) { - if (a.getCalcId()==calcId || (a.getCalcId()!=null && calcId!=null && a.getCalcId().equals(calcId))) + if (a.getCalcId() == calcId + || (a.getCalcId() != null && calcId != null && a.getCalcId() + .equals(calcId))) { aa.add(a); }