/*
- * 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.
*
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
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)
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++;
}
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();
}
}
}
/**
- * 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)
{
}
/**
- * 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()
{
hiddenSequences = tmp;
}
+ /**
+ * Mark the specified sequence as hidden
+ *
+ * @param sequence
+ */
public void hideSequence(SequenceI sequence)
{
if (hiddenSequences == null)
alignment.deleteSequence(sequence);
}
- public Vector showAll(
+ public List<SequenceI> showAll(
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
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<SequenceI> 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<SequenceI> showSequence(int alignmentIndex,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
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);
{
if (seq.getLength() > 0)
{
- revealedSeqs.addElement(seq);
+ revealedSeqs.add(seq);
asequences.add(alignmentIndex, seq);
}
else
+ " 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)
}
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)
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;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff