X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f5e6fc7f10bfc4ccfbe6b5f930df8c234e6556aa;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=90bdcae2ee318ae29b290bbb5ea1e5a145b2389a;hpb=8677e6e34e291edc58c1da2fc9c958473754143f;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 90bdcae..f5e6fc7 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -54,11 +54,7 @@ public class Alignment implements AlignmentI protected char gapCharacter = '-'; - protected int type = NUCLEOTIDE; - - public static final int PROTEIN = 0; - - public static final int NUCLEOTIDE = 1; + private boolean nucleotide = true; public boolean hasRNAStructure = false; @@ -66,6 +62,8 @@ public class Alignment implements AlignmentI HiddenSequences hiddenSequences; + HiddenColumns hiddenCols; + public Hashtable alignmentProperties; private List codonFrameList; @@ -74,16 +72,10 @@ public class Alignment implements AlignmentI { groups = Collections.synchronizedList(new ArrayList()); hiddenSequences = new HiddenSequences(this); - codonFrameList = new ArrayList(); + hiddenCols = new HiddenColumns(); + codonFrameList = new ArrayList<>(); - if (Comparison.isNucleotide(seqs)) - { - type = NUCLEOTIDE; - } - else - { - type = PROTEIN; - } + nucleotide = Comparison.isNucleotide(seqs); sequences = Collections.synchronizedList(new ArrayList()); @@ -136,7 +128,7 @@ public class Alignment implements AlignmentI public Alignment(SeqCigar[] alseqs) { SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, - gapCharacter, new ColumnSelection(), null); + gapCharacter, new HiddenColumns(), null); initAlignment(seqs); } @@ -196,14 +188,7 @@ public class Alignment implements AlignmentI return AlignmentUtils.getSequencesByName(this); } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override public SequenceI getSequenceAt(int i) { @@ -217,8 +202,32 @@ public class Alignment implements AlignmentI return null; } + @Override + public SequenceI getSequenceAtAbsoluteIndex(int i) + { + SequenceI seq = null; + if (getHiddenSequences().getSize() > 0) + { + seq = getHiddenSequences().getHiddenSequence(i); + if (seq == null) + { + // didn't find the sequence in the hidden sequences, get it from the + // alignment + int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i); + seq = getSequenceAt(index); + } + } + else + { + seq = getSequenceAt(i); + } + return seq; + } + /** - * Adds a sequence to the alignment. Recalculates maxLength and size. + * Adds a sequence to the alignment. Recalculates maxLength and size. Note + * this currently does not recalculate whether or not the alignment is + * nucleotide, so mixed alignments may have undefined behaviour. * * @param snew */ @@ -329,30 +338,21 @@ public class Alignment implements AlignmentI } } - /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - */ @Override public void deleteSequence(SequenceI s) { - deleteSequence(findIndex(s)); + synchronized (sequences) + { + deleteSequence(findIndex(s)); + } } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - */ @Override public void deleteSequence(int i) { - if (i > -1 && i < getHeight()) + synchronized (sequences) { - synchronized (sequences) + if (i > -1 && i < getHeight()) { sequences.remove(i); hiddenSequences.adjustHeightSequenceDeleted(i); @@ -360,6 +360,18 @@ public class Alignment implements AlignmentI } } + @Override + public void deleteHiddenSequence(int i) + { + synchronized (sequences) + { + if (i > -1 && i < getHeight()) + { + sequences.remove(i); + } + } + } + /* * (non-Javadoc) * @@ -393,7 +405,7 @@ public class Alignment implements AlignmentI @Override public SequenceGroup[] findAllGroups(SequenceI s) { - ArrayList temp = new ArrayList(); + ArrayList temp = new ArrayList<>(); synchronized (groups) { @@ -444,7 +456,7 @@ public class Alignment implements AlignmentI return; } } - sg.setContext(this); + sg.setContext(this, true); groups.add(sg); } } @@ -521,7 +533,7 @@ public class Alignment implements AlignmentI } for (SequenceGroup sg : groups) { - sg.setContext(null); + sg.setContext(null, false); } groups.clear(); } @@ -537,7 +549,7 @@ public class Alignment implements AlignmentI { removeAnnotationForGroup(g); groups.remove(g); - g.setContext(null); + g.setContext(null, false); } } } @@ -677,22 +689,19 @@ public class Alignment implements AlignmentI return -1; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override public int getHeight() { return sequences.size(); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override + public int getAbsoluteHeight() + { + return sequences.size() + getHiddenSequences().getSize(); + } + @Override public int getWidth() { @@ -778,6 +787,12 @@ public class Alignment implements AlignmentI return true; } + @Override + public boolean isHidden(int alignmentIndex) + { + return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null); + } + /** * Delete all annotations, including auto-calculated if the flag is set true. * Returns true if at least one annotation was deleted, else false. @@ -978,29 +993,9 @@ public class Alignment implements AlignmentI } @Override - public void setNucleotide(boolean b) - { - if (b) - { - type = NUCLEOTIDE; - } - else - { - type = PROTEIN; - } - } - - @Override public boolean isNucleotide() { - if (type == NUCLEOTIDE) - { - return true; - } - else - { - return false; - } + return nucleotide; } @Override @@ -1019,6 +1014,10 @@ public class Alignment implements AlignmentI } else if (dataset == null && data != null) { + if (data == this) + { + throw new IllegalArgumentException("Circular dataset reference"); + } if (!(data instanceof Alignment)) { throw new Error( @@ -1068,21 +1067,18 @@ public class Alignment implements AlignmentI currentSeq = currentSeq.createDatasetSequence(); } } - if (seqs.contains(currentSeq)) - { - return; - } - List toProcess = new ArrayList(); + + List toProcess = new ArrayList<>(); toProcess.add(currentSeq); while (toProcess.size() > 0) { // use a queue ? SequenceI curDs = toProcess.remove(0); - if (seqs.contains(curDs)) + + if (!seqs.add(curDs)) { continue; } - seqs.add(curDs); // iterate over database references, making sure we add forward referenced // sequences if (curDs.getDBRefs() != null) @@ -1125,7 +1121,7 @@ public class Alignment implements AlignmentI return; } // try to avoid using SequenceI.equals at this stage, it will be expensive - Set seqs = new LinkedIdentityHashSet(); + Set seqs = new LinkedIdentityHashSet<>(); for (int i = 0; i < getHeight(); i++) { @@ -1331,6 +1327,12 @@ public class Alignment implements AlignmentI } @Override + public HiddenColumns getHiddenColumns() + { + return hiddenCols; + } + + @Override public CigarArray getCompactAlignment() { synchronized (sequences) @@ -1404,7 +1406,7 @@ public class Alignment implements AlignmentI { return null; } - List cframes = new ArrayList(); + List cframes = new ArrayList<>(); for (AlignedCodonFrame acf : getCodonFrames()) { if (acf.involvesSequence(seq)) @@ -1481,7 +1483,7 @@ public class Alignment implements AlignmentI if (sqs != null) { // avoid self append deadlock by - List toappendsq = new ArrayList(); + List toappendsq = new ArrayList<>(); synchronized (sqs) { for (SequenceI addedsq : sqs) @@ -1591,7 +1593,6 @@ public class Alignment implements AlignmentI String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) { - assert (name != null); if (annotations != null) { for (AlignmentAnnotation annot : getAlignmentAnnotation()) @@ -1623,33 +1624,35 @@ public class Alignment implements AlignmentI @Override public Iterable findAnnotation(String calcId) { - ArrayList aa = new ArrayList(); - for (AlignmentAnnotation a : getAlignmentAnnotation()) + List aa = new ArrayList<>(); + AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation(); + if (alignmentAnnotation != null) { - if (a.getCalcId() == calcId - || (a.getCalcId() != null && calcId != null && a.getCalcId() - .equals(calcId))) + for (AlignmentAnnotation a : alignmentAnnotation) { - aa.add(a); + if (a.getCalcId() == calcId + || (a.getCalcId() != null && calcId != null && a + .getCalcId().equals(calcId))) + { + aa.add(a); + } } } return aa; } - /** - * Returns an iterable collection of any annotations that match on given - * sequence ref, calcId and label (ignoring null values). - */ @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList(); + ArrayList aa = new ArrayList<>(); for (AlignmentAnnotation ann : getAlignmentAnnotation()) { - if (ann.getCalcId() != null && ann.getCalcId().equals(calcId) - && ann.sequenceRef != null && ann.sequenceRef == seq - && ann.label != null && ann.label.equals(label)) + if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId() + .equals(calcId))) + && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq)) + && (label == null || (ann.label != null && ann.label + .equals(label)))) { aa.add(ann); } @@ -1847,7 +1850,7 @@ public class Alignment implements AlignmentI @Override public Set getSequenceNames() { - Set names = new HashSet(); + Set names = new HashSet<>(); for (SequenceI seq : getSequences()) { names.add(seq.getName()); @@ -1947,4 +1950,10 @@ public class Alignment implements AlignmentI } return new int[] { startPos, endPos }; } + + @Override + public void setHiddenColumns(HiddenColumns cols) + { + hiddenCols = cols; + } }