/*
- * 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.analysis;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
+import jalview.util.Comparison;
+import jalview.util.Format;
+import jalview.util.MapList;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
/**
*
}
/**
- * DOCUMENT ME!
+ * Returns the given sequence with all of the given gap characters removed.
*
- * @param gapChar
- * DOCUMENT ME!
+ * @param gapChars
+ * a string of characters to be treated as gaps
* @param seq
- * DOCUMENT ME!
+ * the input sequence
*
- * @return DOCUMENT ME!
+ * @return
*/
- public static String extractGaps(String gapChar, String seq)
+ public static String extractGaps(String gapChars, String seq)
{
- StringTokenizer str = new StringTokenizer(seq, gapChar);
- StringBuffer newString = new StringBuffer();
+ if (gapChars == null || seq == null)
+ {
+ return null;
+ }
+ StringTokenizer str = new StringTokenizer(seq, gapChars);
+ StringBuilder newString = new StringBuilder(seq.length());
while (str.hasMoreTokens())
{
if (allowmismatch || c1 == c2)
{
- lastmatch = true;
- // extend mapping interval.
+ // extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
{
as1.add(Integer.valueOf(alignpos));
as2.add(Integer.valueOf(pdbpos));
}
+ lastmatch = true;
lp1 = alignpos;
lp2 = pdbpos;
}
else
{
+ // extend mapping interval
+ if (lastmatch)
+ {
+ as1.add(Integer.valueOf(lp1));
+ as2.add(Integer.valueOf(lp2));
+ }
lastmatch = false;
}
}
// construct range pairs
+
int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
.size() + (lastmatch ? 1 : 0)];
int i = 0;
* @param ochains
* @param al
* @param dnaOrProtein
- * @param removeOldAnnots when true, old annotation is cleared before new annotation transferred
+ * @param removeOldAnnots
+ * when true, old annotation is cleared before new annotation
+ * transferred
+ * @return List<List<SequenceI> originals, List<SequenceI> replacement,
+ * List<AlignSeq> alignment between each>
*/
- public static void replaceMatchingSeqsWith(List<SequenceI> seqs, List<AlignmentAnnotation> annotations, List<SequenceI> ochains,
+ public static List<List<? extends Object>> replaceMatchingSeqsWith(
+ List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
+ List<SequenceI> ochains,
AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
{
+ List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
+ List<AlignSeq> aligs = new ArrayList<AlignSeq>();
if (al != null && al.getHeight() > 0)
{
ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
if ((q = ochains.indexOf(sp)) > -1)
{
seqs.set(p, sq = matches.get(q));
+ orig.add(sp);
+ repl.add(sq);
sq.setName(sp.getName());
sq.setDescription(sp.getDescription());
Mapping sp2sq;
sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+ aligs.add(aligns.get(q));
int inspos = -1;
for (int ap = 0; ap < annotations.size();)
{
if (removeOldAnnots) {
annotations.remove(ap);
} else {
- AlignmentAnnotation alan = annotations.get(ap);
+ AlignmentAnnotation alan = annotations.remove(ap);
alan.liftOver(sq, sp2sq);
alan.setSequenceRef(sq);
+ sq.addAlignmentAnnotation(alan);
}
}
else
ap++;
}
}
- if (sq.getAnnotation() != null)
+ if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
{
- annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+ Arrays.asList(sq.getAnnotation()));
}
}
}
}
+ return Arrays.asList(orig, repl, aligs);
}
/**