X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=9e2cf72b416d1d5a69f3945305d55ce1b12ee7ae;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=aefb5ccce6154327489029ceb9afa03f805cd78d;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java index aefb5cc..9e2cf72 100755 --- a/src/jalview/datamodel/HiddenSequences.java +++ b/src/jalview/datamodel/HiddenSequences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,7 +20,9 @@ */ package jalview.datamodel; -import java.util.*; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; public class HiddenSequences { @@ -31,11 +33,21 @@ public class HiddenSequences AlignmentI alignment; + /** + * Constructor given a reference to an alignment (with no hidden sequences) + * + * @param al + */ public HiddenSequences(AlignmentI al) { alignment = al; } + /** + * Answers the number of hidden sequences + * + * @return + */ public int getSize() { if (hiddenSequences == null) @@ -43,9 +55,9 @@ public class HiddenSequences return 0; } int count = 0; - for (int i = 0; i < hiddenSequences.length; i++) + for (SequenceI seq : hiddenSequences) { - if (hiddenSequences[i] != null) + if (seq != null) { count++; } @@ -54,15 +66,23 @@ public class HiddenSequences return count; } + /** + * Answers the length of the longest hidden sequence + * + * @return + */ public int getWidth() { + if (hiddenSequences == null) + { + return 0; + } int width = 0; - for (int i = 0; i < hiddenSequences.length; i++) + for (SequenceI seq : hiddenSequences) { - if (hiddenSequences[i] != null - && hiddenSequences[i].getLength() > width) + if (seq != null && seq.getLength() > width) { - width = hiddenSequences[i].getLength(); + width = seq.getLength(); } } @@ -70,7 +90,7 @@ public class HiddenSequences } /** - * Call this method if sequences are removed from the main alignment + * Call this method after a sequence is removed from the main alignment */ public void adjustHeightSequenceDeleted(int seqIndex) { @@ -106,8 +126,7 @@ public class HiddenSequences } /** - * Call this method if sequences are added to or removed from the main - * alignment + * Call this method after a sequence is added to the main alignment */ public void adjustHeightSequenceAdded() { @@ -123,6 +142,11 @@ public class HiddenSequences hiddenSequences = tmp; } + /** + * Mark the specified sequence as hidden + * + * @param sequence + */ public void hideSequence(SequenceI sequence) { if (hiddenSequences == null) @@ -143,34 +167,45 @@ public class HiddenSequences alignment.deleteSequence(sequence); } - public Vector showAll( + public List showAll( Map hiddenRepSequences) { - Vector revealedSeqs = new Vector(); + List revealedSeqs = new ArrayList(); for (int i = 0; i < hiddenSequences.length; i++) { if (hiddenSequences[i] != null) { - Vector tmp = showSequence(i, hiddenRepSequences); - for (int t = 0; t < tmp.size(); t++) + List tmp = showSequence(i, hiddenRepSequences); + for (SequenceI seq : tmp) { - revealedSeqs.addElement(tmp.elementAt(t)); + revealedSeqs.add(seq); } } } return revealedSeqs; } - public Vector showSequence(int alignmentIndex, + /** + * Reveals (unhides) consecutive hidden sequences just above the given + * alignment index. The revealed sequences are selected (including their + * visible representative sequence if there was one and 'reveal' is being + * performed on it). + * + * @param alignmentIndex + * @param hiddenRepSequences + * a map of representative sequences to the sequences they represent + * @return + */ + public List showSequence(int alignmentIndex, Map hiddenRepSequences) { - Vector revealedSeqs = new Vector(); + List revealedSeqs = new ArrayList(); SequenceI repSequence = alignment.getSequenceAt(alignmentIndex); if (repSequence != null && hiddenRepSequences != null && hiddenRepSequences.containsKey(repSequence)) { hiddenRepSequences.remove(repSequence); - revealedSeqs.addElement(repSequence); + revealedSeqs.add(repSequence); } int start = adjustForHiddenSeqs(alignmentIndex - 1); @@ -192,7 +227,7 @@ public class HiddenSequences { if (seq.getLength() > 0) { - revealedSeqs.addElement(seq); + revealedSeqs.add(seq); asequences.add(alignmentIndex, seq); } else @@ -201,20 +236,22 @@ public class HiddenSequences + " has been deleted whilst hidden"); } } - } } - return revealedSeqs; } public SequenceI getHiddenSequence(int alignmentIndex) { - return hiddenSequences[alignmentIndex]; + return hiddenSequences == null ? null : hiddenSequences[alignmentIndex]; } public int findIndexWithoutHiddenSeqs(int alignmentIndex) { + if (hiddenSequences == null) + { + return alignmentIndex; + } int index = 0; int hiddenSeqs = 0; if (hiddenSequences.length <= alignmentIndex) @@ -230,13 +267,16 @@ public class HiddenSequences } index++; } - ; return (alignmentIndex - hiddenSeqs); } public int adjustForHiddenSeqs(int alignmentIndex) { + if (hiddenSequences == null) + { + return alignmentIndex; + } int index = 0; int hSize = hiddenSequences.length; while (index <= alignmentIndex && index < hSize) @@ -252,35 +292,59 @@ public class HiddenSequences return alignmentIndex; } + /** + * makes a copy of the alignment with hidden sequences included. Using the + * copy for anything other than simple output is not recommended. Note - this + * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR! + * + * @return + */ public AlignmentI getFullAlignment() { - int isize = hiddenSequences.length; - SequenceI[] seq = new Sequence[isize]; - - int index = 0; - for (int i = 0; i < hiddenSequences.length; i++) + SequenceI[] seq; + if (hiddenSequences == null) { - if (hiddenSequences[i] != null) - { - seq[i] = hiddenSequences[i]; - } - else + seq = alignment.getSequencesArray(); + } + else + { + int isize = hiddenSequences.length; + seq = new Sequence[isize]; + + int index = 0; + for (int i = 0; i < hiddenSequences.length; i++) { - seq[i] = alignment.getSequenceAt(index); - index++; + if (hiddenSequences[i] != null) + { + seq[i] = hiddenSequences[i]; + } + else + { + seq[i] = alignment.getSequenceAt(index); + index++; + } } } - - return new Alignment(seq); + Alignment fAlignmt = new Alignment(seq); + fAlignmt.annotations = alignment.getAlignmentAnnotation(); + fAlignmt.alignmentProperties = alignment.getProperties(); + fAlignmt.groups = alignment.getGroups(); + fAlignmt.hasRNAStructure = alignment.hasRNAStructure(); + fAlignmt.setSeqrep(alignment.getSeqrep()); + + return fAlignmt; } public boolean isHidden(SequenceI seq) { - for (int i = 0; i < hiddenSequences.length; i++) + if (hiddenSequences != null) { - if (hiddenSequences[i] != null && hiddenSequences[i] == seq) + for (int i = 0; i < hiddenSequences.length; i++) { - return true; + if (hiddenSequences[i] != null && hiddenSequences[i] == seq) + { + return true; + } } }