X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=6b100ea6e3320246a1f9614e579ba26f74b32edd;hb=af7becd656cba3835394e2dc50c2ad8d189a6d46;hp=8ca859f3b438fee0b55aeb9302e3a3a53239390b;hpb=e1e9f9f44944414e474ed500bc9e06f79dae76c7;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 8ca859f..6b100ea 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -28,11 +28,13 @@ import jalview.util.LinkedIdentityHashSet; import jalview.util.MessageManager; import java.util.ArrayList; +import java.util.Arrays; +import java.util.BitSet; import java.util.Collections; import java.util.Enumeration; -import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; @@ -49,7 +51,9 @@ public class Alignment implements AlignmentI { private Alignment dataset; - protected List sequences; + private List sequences; + + private SequenceI hmmConsensus; protected List groups; @@ -144,9 +148,8 @@ public class Alignment implements AlignmentI */ public static AlignmentI createAlignment(CigarArray compactAlignment) { - throw new Error( - MessageManager - .getString("error.alignment_cigararray_not_implemented")); + throw new Error(MessageManager + .getString("error.alignment_cigararray_not_implemented")); // this(compactAlignment.refCigars); } @@ -189,7 +192,6 @@ public class Alignment implements AlignmentI return AlignmentUtils.getSequencesByName(this); } - @Override public SequenceI getSequenceAt(int i) { @@ -200,6 +202,7 @@ public class Alignment implements AlignmentI return sequences.get(i); } } + return null; } @@ -290,6 +293,32 @@ public class Alignment implements AlignmentI } /** + * Inserts a sequence at a point in the alignment. + * + * @param i + * the index of the position the sequence is to be inserted in. + */ + @Override + public void insertSequenceAt(int i, SequenceI snew) + { + synchronized (sequences) + { + if (sequences.size() > i) + { + sequences.add(i, snew); + return; + + } + else + { + sequences.add(snew); + hiddenSequences.adjustHeightSequenceAdded(); + } + return; + } + } + + /** * DOCUMENT ME! * * @return DOCUMENT ME! @@ -476,7 +505,9 @@ public class Alignment implements AlignmentI return; } // remove annotation very quickly - AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length]; + AlignmentAnnotation[] t, + todelete = new AlignmentAnnotation[annotations.length], + tokeep = new AlignmentAnnotation[annotations.length]; int i, p, k; if (gp == null) { @@ -609,7 +640,7 @@ public class Alignment implements AlignmentI sqname = sq.getName(); if (sqname.equals(token) // exact match || (b && // allow imperfect matches - case varies - (sqname.equalsIgnoreCase(token)))) + (sqname.equalsIgnoreCase(token)))) { return getSequenceAt(i); } @@ -690,7 +721,6 @@ public class Alignment implements AlignmentI return -1; } - @Override public int getHeight() { @@ -707,7 +737,7 @@ public class Alignment implements AlignmentI public int getWidth() { int maxLength = -1; - + for (int i = 0; i < sequences.size(); i++) { if (getSequenceAt(i).getLength() > maxLength) @@ -715,9 +745,34 @@ public class Alignment implements AlignmentI maxLength = getSequenceAt(i).getLength(); } } - + return maxLength; } + /* + @Override + public int getWidth() + { + final Wrapper temp = new Wrapper(); + + forEachSequence(new Consumer() + { + @Override + public void accept(SequenceI s) + { + if (s.getLength() > temp.inner) + { + temp.inner = s.getLength(); + } + } + }, 0, sequences.size() - 1); + + return temp.inner; + } + + public static class Wrapper + { + public int inner; + }*/ /** * DOCUMENT ME! @@ -1068,21 +1123,18 @@ public class Alignment implements AlignmentI currentSeq = currentSeq.createDatasetSequence(); } } - if (seqs.contains(currentSeq)) - { - return; - } + 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) @@ -1100,10 +1152,9 @@ public class Alignment implements AlignmentI } if (dbr.getMap().getTo().getDatasetSequence() != null) { - throw new Error( - "Implementation error: Map.getTo() for dbref " + dbr - + " from " + curDs.getName() - + " is not a dataset sequence."); + throw new Error("Implementation error: Map.getTo() for dbref " + + dbr + " from " + curDs.getName() + + " is not a dataset sequence."); } // we recurse to add all forward references to dataset sequences via // DBRefs/etc @@ -1240,8 +1291,8 @@ public class Alignment implements AlignmentI current = getSequenceAt(i); // This should really be a sequence method ends[i * 2] = current.findIndex(current.getStart()); - ends[i * 2 + 1] = current.findIndex(current.getStart() - + current.getLength()); + ends[i * 2 + 1] = current + .findIndex(current.getStart() + current.getLength()); boolean hitres = false; for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++) { @@ -1477,13 +1528,15 @@ public class Alignment implements AlignmentI { // TODO JAL-1270 needs test coverage // currently tested for use in jalview.gui.SequenceFetcher - boolean samegap = toappend.getGapCharacter() == getGapCharacter(); char oldc = toappend.getGapCharacter(); + boolean samegap = oldc == getGapCharacter(); boolean hashidden = toappend.getHiddenSequences() != null && toappend.getHiddenSequences().hiddenSequences != null; // get all sequences including any hidden ones - List sqs = (hashidden) ? toappend.getHiddenSequences() - .getFullAlignment().getSequences() : toappend.getSequences(); + List sqs = (hashidden) + ? toappend.getHiddenSequences().getFullAlignment() + .getSequences() + : toappend.getSequences(); if (sqs != null) { // avoid self append deadlock by @@ -1494,14 +1547,7 @@ public class Alignment implements AlignmentI { if (!samegap) { - char[] oldseq = addedsq.getSequence(); - for (int c = 0; c < oldseq.length; c++) - { - if (oldseq[c] == oldc) - { - oldseq[c] = gapCharacter; - } - } + addedsq.replace(oldc, gapCharacter); } toappendsq.add(addedsq); } @@ -1565,8 +1611,8 @@ public class Alignment implements AlignmentI if (ourval instanceof String) { // append strings - this.setProperty(k, ((String) ourval) + "; " - + ((String) toapprop)); + this.setProperty(k, + ((String) ourval) + "; " + ((String) toapprop)); } else { @@ -1613,7 +1659,10 @@ public class Alignment implements AlignmentI AlignmentAnnotation annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); annot.hasText = false; - annot.setCalcId(new String(calcId)); + if (calcId != null) + { + annot.setCalcId(calcId); + } annot.autoCalculated = autoCalc; if (seqRef != null) { @@ -1628,40 +1677,21 @@ public class Alignment implements AlignmentI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList<>(); AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation(); if (alignmentAnnotation != null) { - for (AlignmentAnnotation a : alignmentAnnotation) - { - if (a.getCalcId() == calcId - || (a.getCalcId() != null && calcId != null && a - .getCalcId().equals(calcId))) - { - aa.add(a); - } - } + return AlignmentAnnotation.findAnnotation( + Arrays.asList(getAlignmentAnnotation()), calcId); } - return aa; + return Arrays.asList(new AlignmentAnnotation[] {}); } @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList<>(); - for (AlignmentAnnotation ann : getAlignmentAnnotation()) - { - 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); - } - } - return aa; + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); } @Override @@ -1920,100 +1950,132 @@ public class Alignment implements AlignmentI } @Override - public int[] getVisibleStartAndEndIndex(List hiddenCols) + public void setHiddenColumns(HiddenColumns cols) { - int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 }; - int startPos = alignmentStartEnd[0]; - int endPos = alignmentStartEnd[1]; - - int[] lowestRange = new int[] { -1, -1 }; - int[] higestRange = new int[] { -1, -1 }; - - for (int[] hiddenCol : hiddenCols) - { - lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; - higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; - } + hiddenCols = cols; + } - if (lowestRange[0] == -1 && lowestRange[1] == -1) - { - startPos = alignmentStartEnd[0]; - } - else - { - startPos = lowestRange[1] + 1; - } + @Override + public SequenceI getHmmConsensus() + { + return hmmConsensus; + } - if (higestRange[0] == -1 && higestRange[1] == -1) - { - endPos = alignmentStartEnd[1]; - } - else - { - endPos = higestRange[0] - 1; - } - return new int[] { startPos, endPos }; + @Override + public void setHmmConsensus(SequenceI hmmConsensus) + { + this.hmmConsensus = hmmConsensus; } @Override - public void setHiddenColumns(HiddenColumns cols) + public void setupJPredAlignment() { - hiddenCols = cols; + SequenceI repseq = getSequenceAt(0); + setSeqrep(repseq); + HiddenColumns cs = new HiddenColumns(); + cs.hideList(repseq.getInsertions()); + setHiddenColumns(cs); } @Override - public Map getHMMConsensusSequences(boolean remove) + public HiddenColumns propagateInsertions(SequenceI profileseq, + AlignmentView input) + { + int profsqpos = 0; + + char gc = getGapCharacter(); + Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc); + HiddenColumns nview = (HiddenColumns) alandhidden[1]; + SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos]; + return propagateInsertions(profileseq, origseq, nview); + } + + /** + * + * @param profileseq + * sequence in al which corresponds to origseq + * @param al + * alignment which is to have gaps inserted into it + * @param origseq + * sequence corresponding to profileseq which defines gap map for + * modifying al + */ + private HiddenColumns propagateInsertions(SequenceI profileseq, + SequenceI origseq, HiddenColumns hc) { - Map seqs = new HashMap<>(); - int position = 0; - for (SequenceI seq : sequences) + // take the set of hidden columns, and the set of gaps in origseq, + // and remove all the hidden gaps from hiddenColumns + + // first get the gaps as a Bitset + // then calculate hidden ^ not(gap) + BitSet gaps = origseq.gapBitset(); + hc.andNot(gaps); + + // for each sequence in the alignment, except the profile sequence, + // insert gaps corresponding to each hidden region but where each hidden + // column region is shifted backwards by the number of preceding visible + // gaps update hidden columns at the same time + HiddenColumns newhidden = new HiddenColumns(); + + int numGapsBefore = 0; + int gapPosition = 0; + Iterator it = hc.iterator(); + while (it.hasNext()) { - if (seq.isHMMConsensusSequence()) + int[] region = it.next(); + + // get region coordinates accounting for gaps + // we can rely on gaps not being *in* hidden regions because we already + // removed those + while (gapPosition < region[0]) { - seqs.put(position, seq); - if (remove) + gapPosition++; + if (gaps.get(gapPosition)) { - sequences.set(position, null); + numGapsBefore++; } - } - position++; - } - boolean endReached = false; - int pos = 0; - while (!endReached) - { - if (sequences.get(pos) == null) - { - sequences.remove(pos); - } - else - { - pos++; - } - if (pos >= sequences.size()) - { - endReached = true; - } - } - return seqs; + int left = region[0] - numGapsBefore; + int right = region[1] - numGapsBefore; + + newhidden.hideColumns(left, right); + padGaps(left, right, profileseq); + } + return newhidden; } - @Override - public List getHMMConsensusSequences() + /** + * Pad gaps in all sequences in alignment except profileseq + * + * @param left + * position of first gap to insert + * @param right + * position of last gap to insert + * @param profileseq + * sequence not to pad + */ + private void padGaps(int left, int right, SequenceI profileseq) { - List seqs = new ArrayList<>(); - for (SequenceI seq : sequences) + char gc = getGapCharacter(); + + // make a string with number of gaps = length of hidden region + StringBuilder sb = new StringBuilder(); + for (int g = 0; g < right - left + 1; g++) + { + sb.append(gc); + } + + // loop over the sequences and pad with gaps where required + for (int s = 0, ns = getHeight(); s < ns; s++) { - if (seq.isHMMConsensusSequence()) + SequenceI sqobj = getSequenceAt(s); + if ((sqobj != profileseq) && (sqobj.getLength() >= left)) { - seqs.add(seq); + String sq = sqobj.getSequenceAsString(); + sqobj.setSequence( + sq.substring(0, left) + sb.toString() + sq.substring(left)); } } - return seqs; } - - - }