X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5232f8e4370609161f49d1d83e1b5e849e64a1f4;hb=45d7b8f24253fa1c49977feedfe8a0f2f7cea85e;hp=b6a5e0f8e0082881f626fa347246c8e78e4123d5;hpb=cfed9d8a9e10be992877d6097260758ee5563630;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index b6a5e0f..5232f8e 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -28,6 +28,7 @@ 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; @@ -46,11 +47,11 @@ import java.util.Vector; * @author JimP * */ -public class Alignment implements AlignmentI +public class Alignment implements AlignmentI, AutoCloseable { private Alignment dataset; - protected List sequences; + private List sequences; protected List groups; @@ -194,11 +195,13 @@ public class Alignment implements AlignmentI { synchronized (sequences) { + if (i > -1 && i < sequences.size()) { return sequences.get(i); } } + return null; } @@ -289,6 +292,32 @@ 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! @@ -300,15 +329,20 @@ public class Alignment implements AlignmentI } @Override - public void finalize() throws Throwable + public void close() { if (getDataset() != null) { - getDataset().removeAlignmentRef(); + try + { + getDataset().removeAlignmentRef(); + } catch (Throwable e) + { + e.printStackTrace(); + } } nullReferences(); - super.finalize(); } /** @@ -583,15 +617,17 @@ public class Alignment implements AlignmentI @Override public SequenceI findName(SequenceI startAfter, String token, boolean b) { - + if (token == null) + return null; int i = 0; SequenceI sq = null; String sqname = null; + int nseq = sequences.size(); if (startAfter != null) { // try to find the sequence in the alignment boolean matched = false; - while (i < sequences.size()) + while (i < nseq) { if (getSequenceAt(i++) == startAfter) { @@ -604,7 +640,7 @@ public class Alignment implements AlignmentI i = 0; } } - while (i < sequences.size()) + while (i < nseq) { sq = getSequenceAt(i); sqname = sq.getName(); @@ -710,15 +746,22 @@ public class Alignment implements AlignmentI for (int i = 0; i < sequences.size(); i++) { - if (getSequenceAt(i).getLength() > maxLength) - { - maxLength = getSequenceAt(i).getLength(); - } + maxLength = Math.max(maxLength, getSequenceAt(i).getLength()); } - return maxLength; } + @Override + public int getVisibleWidth() + { + int w = getWidth(); + if (hiddenCols != null) + { + w -= hiddenCols.getSize(); + } + return w; + } + /** * DOCUMENT ME! * @@ -1179,7 +1222,8 @@ public class Alignment implements AlignmentI int maxLength = -1; SequenceI current; - for (int i = 0; i < sequences.size(); i++) + int nseq = sequences.size(); + for (int i = 0; i < nseq; i++) { current = getSequenceAt(i); for (int j = current.getLength(); j > maxLength; j--) @@ -1196,7 +1240,7 @@ public class Alignment implements AlignmentI maxLength++; int cLength; - for (int i = 0; i < sequences.size(); i++) + for (int i = 0; i < nseq; i++) { current = getSequenceAt(i); cLength = current.getLength(); @@ -1588,71 +1632,71 @@ public class Alignment implements AlignmentI String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) { - if (annotations != null) + AlignmentAnnotation annot = annotations == null ? null + : AlignmentAnnotation.findFirstAnnotation( + Arrays.asList(getAlignmentAnnotation()), name, calcId, + autoCalc, seqRef, groupRef); + + if (annot == null) { - for (AlignmentAnnotation annot : getAlignmentAnnotation()) + + annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f, + AlignmentAnnotation.BAR_GRAPH); + annot.hasText = false; + if (calcId != null) { - if (annot.autoCalculated == autoCalc && (name.equals(annot.label)) - && (calcId == null || annot.getCalcId().equals(calcId)) - && annot.sequenceRef == seqRef - && annot.groupRef == groupRef) - { - return annot; - } + annot.setCalcId(calcId); + } + annot.autoCalculated = autoCalc; + if (seqRef != null) + { + annot.setSequenceRef(seqRef); } + annot.groupRef = groupRef; + addAnnotation(annot); } - AlignmentAnnotation annot = new AlignmentAnnotation(name, name, - new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); - annot.hasText = false; - annot.setCalcId(new String(calcId)); - annot.autoCalculated = autoCalc; - if (seqRef != null) + return annot; + } + + + @Override + public AlignmentAnnotation updateFromOrCopyAnnotation( + AlignmentAnnotation ala) + { + AlignmentAnnotation annot = AlignmentAnnotation.findFirstAnnotation( + Arrays.asList(getAlignmentAnnotation()), ala.label, ala.calcId, + ala.autoCalculated, ala.sequenceRef, ala.groupRef); + if (annot == null) { - annot.setSequenceRef(seqRef); + annot = new AlignmentAnnotation(ala); + addAnnotation(annot); } - annot.groupRef = groupRef; - addAnnotation(annot); - + else + { + annot.updateAlignmentAnnotationFrom(ala); + } + validateAnnotation(annot); return annot; } @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 @@ -1911,9 +1955,12 @@ public class Alignment implements AlignmentI } @Override - public void setHiddenColumns(HiddenColumns cols) + public boolean setHiddenColumns(HiddenColumns cols) { + boolean changed = cols == null ? hiddenCols != null + : !cols.equals(hiddenCols); hiddenCols = cols; + return changed; } @Override @@ -2028,4 +2075,18 @@ public class Alignment implements AlignmentI } } + @Override + public List getHmmSequences() + { + List result = new ArrayList<>(); + for (int i = 0; i < sequences.size(); i++) + { + SequenceI seq = sequences.get(i); + if (seq.hasHMMProfile()) + { + result.add(seq); + } + } + return result; + } }