X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=25d770d7264402395888d163a15ccd1a22bad918;hb=09cce494f72431183bd3c37e77913170a08c3ac3;hp=a6f2bf4e440035d98d59796921356e9baca65736;hpb=a6875ff6ca7894443c98b1d068f78ea25c5bfc87;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index a6f2bf4..25d770d 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -30,6 +30,7 @@ import jalview.util.MessageManager; import java.util.ArrayList; import java.util.Collections; import java.util.Enumeration; +import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.List; @@ -62,6 +63,8 @@ public class Alignment implements AlignmentI HiddenSequences hiddenSequences; + HiddenColumns hiddenCols; + public Hashtable alignmentProperties; private List codonFrameList; @@ -70,7 +73,8 @@ public class Alignment implements AlignmentI { groups = Collections.synchronizedList(new ArrayList()); hiddenSequences = new HiddenSequences(this); - codonFrameList = new ArrayList(); + hiddenCols = new HiddenColumns(); + codonFrameList = new ArrayList<>(); nucleotide = Comparison.isNucleotide(seqs); @@ -125,7 +129,7 @@ public class Alignment implements AlignmentI public Alignment(SeqCigar[] alseqs) { SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, - gapCharacter, new ColumnSelection(), null); + gapCharacter, new HiddenColumns(), null); initAlignment(seqs); } @@ -185,14 +189,7 @@ public class Alignment implements AlignmentI return AlignmentUtils.getSequencesByName(this); } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override public SequenceI getSequenceAt(int i) { @@ -206,6 +203,28 @@ 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. Note * this currently does not recalculate whether or not the alignment is @@ -320,30 +339,21 @@ 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); @@ -351,6 +361,18 @@ public class Alignment implements AlignmentI } } + @Override + public void deleteHiddenSequence(int i) + { + synchronized (sequences) + { + if (i > -1 && i < getHeight()) + { + sequences.remove(i); + } + } + } + /* * (non-Javadoc) * @@ -384,7 +406,7 @@ public class Alignment implements AlignmentI @Override public SequenceGroup[] findAllGroups(SequenceI s) { - ArrayList temp = new ArrayList(); + ArrayList temp = new ArrayList<>(); synchronized (groups) { @@ -435,7 +457,7 @@ public class Alignment implements AlignmentI return; } } - sg.setContext(this); + sg.setContext(this, true); groups.add(sg); } } @@ -512,7 +534,7 @@ public class Alignment implements AlignmentI } for (SequenceGroup sg : groups) { - sg.setContext(null); + sg.setContext(null, false); } groups.clear(); } @@ -528,7 +550,7 @@ public class Alignment implements AlignmentI { removeAnnotationForGroup(g); groups.remove(g); - g.setContext(null); + g.setContext(null, false); } } } @@ -668,22 +690,19 @@ 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() { @@ -769,6 +788,12 @@ 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. @@ -990,6 +1015,10 @@ 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( @@ -1039,21 +1068,18 @@ 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) @@ -1096,7 +1122,7 @@ 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++) { @@ -1302,6 +1328,12 @@ public class Alignment implements AlignmentI } @Override + public HiddenColumns getHiddenColumns() + { + return hiddenCols; + } + + @Override public CigarArray getCompactAlignment() { synchronized (sequences) @@ -1375,7 +1407,7 @@ public class Alignment implements AlignmentI { return null; } - List cframes = new ArrayList(); + List cframes = new ArrayList<>(); for (AlignedCodonFrame acf : getCodonFrames()) { if (acf.involvesSequence(seq)) @@ -1452,7 +1484,7 @@ 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) @@ -1593,7 +1625,7 @@ public class Alignment implements AlignmentI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList(); + List aa = new ArrayList<>(); AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation(); if (alignmentAnnotation != null) { @@ -1610,20 +1642,18 @@ public class Alignment implements AlignmentI 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); } @@ -1821,7 +1851,7 @@ 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()); @@ -1921,4 +1951,43 @@ public class Alignment implements AlignmentI } return new int[] { startPos, endPos }; } + @Override + public void setHiddenColumns(HiddenColumns cols) + { + hiddenCols = cols; + } + + Map contactmaps = new HashMap(); + @Override + public + ContactListI getContactListFor(AlignmentAnnotation _aa, int column) + { + ContactMatrixI cm = contactmaps.get(_aa.annotationId); + if (cm == null) + { + return null; + } + return cm.getContactList(column); + } + + @Override + public AlignmentAnnotation addContactList(ContactMatrixI cm) + { + Annotation _aa[] = new Annotation[getWidth()]; + Annotation dummy = new Annotation(0.0f); + for (int i = 0; i < _aa.length; _aa[i++] = dummy) + { + ; + } + AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix", + "Contact Matrix", _aa); + aa.graph = AlignmentAnnotation.CUSTOMRENDERER; + aa.graphMin = cm.getMin(); + aa.graphMax = cm.getMax(); + aa.editable = false; + // aa.autoCalculated = true; + contactmaps.put(aa.annotationId, cm); + addAnnotation(aa); + return aa; + } }