X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=6c119364fb62b9b77b531696e54f9a54e718960c;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=707eee83868e58ec7c0a99329848dc9761f1248a;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 707eee8..6c11936 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,40 +1,39 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.datamodel;
import java.util.*;
-import jalview.analysis.*;
-
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
/**
* @author JimP
- *
+ *
*/
public class Alignment implements AlignmentI
{
protected Alignment dataset;
- protected Vector sequences;
+ protected List sequences;
- protected Vector groups = new Vector();
+ protected List groups = java.util.Collections
+ .synchronizedList(new ArrayList());
protected char gapCharacter = '-';
@@ -44,6 +43,8 @@ public class Alignment implements AlignmentI
public static final int NUCLEOTIDE = 1;
+ public boolean hasRNAStructure = false;
+
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
@@ -64,18 +65,19 @@ public class Alignment implements AlignmentI
type = PROTEIN;
}
- sequences = new Vector();
+ sequences = java.util.Collections
+ .synchronizedList(new ArrayList());
for (i = 0; i < seqs.length; i++)
{
- sequences.addElement(seqs[i]);
+ sequences.add(seqs[i]);
}
}
/**
* Make an alignment from an array of Sequences.
- *
+ *
* @param sequences
*/
public Alignment(SequenceI[] seqs)
@@ -85,7 +87,7 @@ public class Alignment implements AlignmentI
/**
* Make a new alignment from an array of SeqCigars
- *
+ *
* @param seqs
* SeqCigar[]
*/
@@ -101,7 +103,7 @@ public class Alignment implements AlignmentI
* compactAlignment does not contain hidden regions. JBPNote - must also check
* that compactAlignment resolves to a set of SeqCigars - or construct them
* appropriately.
- *
+ *
* @param compactAlignment
* CigarArray
*/
@@ -113,49 +115,62 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public Vector getSequences()
+ @Override
+ public List getSequences()
+ {
+ return sequences;
+ }
+
+ @Override
+ public List getSequences(
+ Map hiddenReps)
{
+ // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to
+ // work on this.
return sequences;
}
+ @Override
public SequenceI[] getSequencesArray()
{
if (sequences == null)
return null;
- SequenceI[] reply = new SequenceI[sequences.size()];
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- reply[i] = (SequenceI) sequences.elementAt(i);
+ return sequences.toArray(new SequenceI[sequences.size()]);
}
- return reply;
}
/**
* DOCUMENT ME!
- *
+ *
* @param i
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public SequenceI getSequenceAt(int i)
{
- if (i>-1 && i < sequences.size())
+ synchronized (sequences)
{
- return (SequenceI) sequences.elementAt(i);
+ if (i > -1 && i < sequences.size())
+ {
+ return sequences.get(i);
+ }
}
-
return null;
}
/**
* Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ *
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
@@ -180,7 +195,10 @@ public class Alignment implements AlignmentI
}
else
{
- sequences.addElement(snew);
+ synchronized (sequences)
+ {
+ sequences.add(snew);
+ }
}
if (hiddenSequences != null)
hiddenSequences.adjustHeightSequenceAdded();
@@ -188,27 +206,32 @@ public class Alignment implements AlignmentI
/**
* Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ *
* @param snew
*/
+ @Override
public void setSequenceAt(int i, SequenceI snew)
{
SequenceI oldseq = getSequenceAt(i);
- deleteSequence(oldseq);
-
- sequences.setElementAt(snew, i);
+ deleteSequence(i);
+ synchronized (sequences)
+ {
+ sequences.set(i, snew);
+ }
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List getGroups()
{
return groups;
}
+ @Override
public void finalize()
{
if (getDataset() != null)
@@ -235,10 +258,11 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param s
* DOCUMENT ME!
*/
+ @Override
public void deleteSequence(SequenceI s)
{
deleteSequence(findIndex(s));
@@ -246,105 +270,115 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param i
* DOCUMENT ME!
*/
+ @Override
public void deleteSequence(int i)
{
if (i > -1 && i < getHeight())
{
- sequences.removeElementAt(i);
+ synchronized (sequences)
+ {
+ sequences.remove(i);
+ }
hiddenSequences.adjustHeightSequenceDeleted(i);
}
}
- /** */
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ */
+ @Override
public SequenceGroup findGroup(SequenceI s)
{
- for (int i = 0; i < this.groups.size(); i++)
+ synchronized (groups)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (sg.getSequences(null).contains(s))
+ for (int i = 0; i < this.groups.size(); i++)
{
- return sg;
+ SequenceGroup sg = groups.get(i);
+
+ if (sg.getSequences(null).contains(s))
+ {
+ return sg;
+ }
}
}
-
return null;
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
*/
+ @Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
- Vector temp = new Vector();
+ ArrayList temp = new ArrayList();
- int gSize = groups.size();
- for (int i = 0; i < gSize; i++)
+ synchronized (groups)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg == null || sg.getSequences(null) == null)
+ int gSize = groups.size();
+ for (int i = 0; i < gSize; i++)
{
- this.deleteGroup(sg);
- gSize--;
- continue;
- }
+ SequenceGroup sg = groups.get(i);
+ if (sg == null || sg.getSequences(null) == null)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
- if (sg.getSequences(null).contains(s))
- {
- temp.addElement(sg);
+ if (sg.getSequences(null).contains(s))
+ {
+ temp.add(sg);
+ }
}
}
-
SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
- for (int i = 0; i < temp.size(); i++)
- {
- ret[i] = (SequenceGroup) temp.elementAt(i);
- }
-
- return ret;
+ return temp.toArray(ret);
}
/** */
+ @Override
public void addGroup(SequenceGroup sg)
{
- if (!groups.contains(sg))
+ synchronized (groups)
{
- if (hiddenSequences.getSize() > 0)
+ if (!groups.contains(sg))
{
- int i, iSize = sg.getSize();
- for (i = 0; i < iSize; i++)
+ if (hiddenSequences.getSize() > 0)
{
- if (!sequences.contains(sg.getSequenceAt(i)))
+ int i, iSize = sg.getSize();
+ for (i = 0; i < iSize; i++)
{
- sg.deleteSequence(sg.getSequenceAt(i), false);
- iSize--;
- i--;
+ if (!sequences.contains(sg.getSequenceAt(i)))
+ {
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
+ }
}
- }
- if (sg.getSize() < 1)
- {
- return;
+ if (sg.getSize() < 1)
+ {
+ return;
+ }
}
- }
- groups.addElement(sg);
+ groups.add(sg);
+ }
}
}
/**
* remove any annotation that references gp
- *
+ *
* @param gp
* (if null, removes all group associated annotation)
*/
@@ -402,26 +436,35 @@ public class Alignment implements AlignmentI
}
}
+ @Override
public void deleteAllGroups()
{
- if (annotations != null)
+ synchronized (groups)
{
- removeAnnotationForGroup(null);
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ groups.clear();
}
- groups.removeAllElements();
}
/** */
+ @Override
public void deleteGroup(SequenceGroup g)
{
- if (groups.contains(g))
+ synchronized (groups)
{
- removeAnnotationForGroup(g);
- groups.removeElement(g);
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.remove(g);
+ }
}
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
@@ -429,9 +472,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
+ @Override
public SequenceI findName(String token, boolean b)
{
return findName(null, token, b);
@@ -439,10 +483,11 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
* boolean)
*/
+ @Override
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
@@ -483,6 +528,7 @@ public class Alignment implements AlignmentI
return null;
}
+ @Override
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
@@ -509,9 +555,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
@@ -531,10 +578,11 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
+ @Override
public int findIndex(SearchResults results)
{
int i = 0;
@@ -552,9 +600,10 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getHeight()
{
return sequences.size();
@@ -562,9 +611,10 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
int maxLength = -1;
@@ -582,27 +632,30 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param gc
* DOCUMENT ME!
*/
+ @Override
public void setGapCharacter(char gc)
{
gapCharacter = gc;
-
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence(seq.getSequenceAsString().replace('.', gc)
- .replace('-', gc).replace(' ', gc));
+ for (SequenceI seq : sequences)
+ {
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
+ }
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return gapCharacter;
@@ -610,9 +663,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#isAligned()
*/
+ @Override
public boolean isAligned()
{
return isAligned(false);
@@ -620,9 +674,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#isAligned(boolean)
*/
+ @Override
public boolean isAligned(boolean includeHidden)
{
int width = getWidth();
@@ -646,15 +701,17 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
+ @Override
public boolean deleteAnnotation(AlignmentAnnotation aa)
{
return deleteAnnotation(aa, true);
}
-
+
+ @Override
public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
{
int aSize = 1;
@@ -688,7 +745,8 @@ public class Alignment implements AlignmentI
if (swap)
{
annotations = temp;
- if (unhook) {
+ if (unhook)
+ {
unhookAnnotation(aa);
}
}
@@ -697,7 +755,7 @@ public class Alignment implements AlignmentI
/**
* remove any object references associated with this annotation
- *
+ *
* @param aa
*/
private void unhookAnnotation(AlignmentAnnotation aa)
@@ -715,10 +773,11 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa)
{
addAnnotation(aa, -1);
@@ -726,12 +785,18 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation, int)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa, int pos)
{
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
+ }
+
int aSize = 1;
if (annotations != null)
{
@@ -767,6 +832,7 @@ public class Alignment implements AlignmentI
annotations = temp;
}
+ @Override
public void setAnnotationIndex(AlignmentAnnotation aa, int index)
{
if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -799,16 +865,16 @@ public class Alignment implements AlignmentI
annotations = temp;
}
+ @Override
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * returns all annotation on the alignment
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
{
return annotations;
}
+ @Override
public void setNucleotide(boolean b)
{
if (b)
@@ -821,6 +887,7 @@ public class Alignment implements AlignmentI
}
}
+ @Override
public boolean isNucleotide()
{
if (type == NUCLEOTIDE)
@@ -833,6 +900,14 @@ public class Alignment implements AlignmentI
}
}
+ @Override
+ public boolean hasRNAStructure()
+ {
+ // TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
+
+ @Override
public void setDataset(Alignment data)
{
if (dataset == null && data == null)
@@ -847,7 +922,7 @@ public class Alignment implements AlignmentI
currentSeq = getSequenceAt(i);
if (currentSeq.getDatasetSequence() != null)
{
- seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ seqs[i] = currentSeq.getDatasetSequence();
}
else
{
@@ -877,11 +952,13 @@ public class Alignment implements AlignmentI
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
@@ -928,11 +1005,12 @@ public class Alignment implements AlignmentI
/**
* Justify the sequences to the left or right by deleting and inserting gaps
* before the initial residue or after the terminal residue
- *
+ *
* @param right
* true if alignment padded to right, false to justify to left
* @return true if alignment was changed
*/
+ @Override
public boolean justify(boolean right)
{
boolean modified = false;
@@ -1030,23 +1108,30 @@ public class Alignment implements AlignmentI
return modified;
}
+ @Override
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
}
+ @Override
public CigarArray getCompactAlignment()
{
- SeqCigar alseqs[] = new SeqCigar[sequences.size()];
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+ SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+ int i = 0;
+ for (SequenceI seq : sequences)
+ {
+ alseqs[i++] = new SeqCigar(seq);
+ }
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
}
- CigarArray cal = new CigarArray(alseqs);
- cal.addOperation(CigarArray.M, getWidth());
- return cal;
}
+ @Override
public void setProperty(Object key, Object value)
{
if (alignmentProperties == null)
@@ -1055,6 +1140,7 @@ public class Alignment implements AlignmentI
alignmentProperties.put(key, value);
}
+ @Override
public Object getProperty(Object key)
{
if (alignmentProperties != null)
@@ -1063,6 +1149,7 @@ public class Alignment implements AlignmentI
return null;
}
+ @Override
public Hashtable getProperties()
{
return alignmentProperties;
@@ -1072,11 +1159,12 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
@@ -1095,9 +1183,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
+ @Override
public AlignedCodonFrame getCodonFrame(int index)
{
return codonFrameList[index];
@@ -1105,10 +1194,11 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
+ @Override
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
@@ -1128,9 +1218,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
+ @Override
public AlignedCodonFrame[] getCodonFrames()
{
return codonFrameList;
@@ -1138,10 +1229,11 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
+ @Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
@@ -1168,8 +1260,13 @@ public class Alignment implements AlignmentI
return removed;
}
+ @Override
public void append(AlignmentI toappend)
{
+ if (toappend == this)
+ {
+ System.err.println("Self append may cause a deadlock.");
+ }
// TODO test this method for a future 2.5 release
// currently tested for use in jalview.gui.SequenceFetcher
boolean samegap = toappend.getGapCharacter() == getGapCharacter();
@@ -1177,26 +1274,27 @@ public class Alignment implements AlignmentI
boolean hashidden = toappend.getHiddenSequences() != null
&& toappend.getHiddenSequences().hiddenSequences != null;
// get all sequences including any hidden ones
- Vector sqs = (hashidden) ? toappend.getHiddenSequences()
+ List sqs = (hashidden) ? toappend.getHiddenSequences()
.getFullAlignment().getSequences() : toappend.getSequences();
if (sqs != null)
{
- Enumeration sq = sqs.elements();
- while (sq.hasMoreElements())
+ synchronized (sqs)
{
- SequenceI addedsq = (SequenceI) sq.nextElement();
- if (!samegap)
+ for (SequenceI addedsq : sqs)
{
- char[] oldseq = addedsq.getSequence();
- for (int c = 0; c < oldseq.length; c++)
+ if (!samegap)
{
- if (oldseq[c] == oldc)
+ char[] oldseq = addedsq.getSequence();
+ for (int c = 0; c < oldseq.length; c++)
{
- oldseq[c] = gapCharacter;
+ if (oldseq[c] == oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
}
}
+ addSequence(addedsq);
}
- addSequence(addedsq);
}
}
AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
@@ -1209,13 +1307,12 @@ public class Alignment implements AlignmentI
{
this.addCodonFrame(acod[a]);
}
- Vector sg = toappend.getGroups();
+ List sg = toappend.getGroups();
if (sg != null)
{
- Enumeration el = sg.elements();
- while (el.hasMoreElements())
+ for (SequenceGroup _sg : sg)
{
- addGroup((SequenceGroup) el.nextElement());
+ addGroup(_sg);
}
}
if (toappend.getHiddenSequences() != null)
@@ -1282,4 +1379,99 @@ public class Alignment implements AlignmentI
}
}
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef)
+ {
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
+ {
+ if (annot.autoCalculated == autoCalc
+ && annot.getCalcId().equals(name)
+ && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
+ }
+ AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+ new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+ annot.hasText = false;
+ annot.setCalcId(new String(name));
+ annot.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
+
+ return annot;
+ }
+
+ @Override
+ public Iterable findAnnotation(String calcId)
+ {
+ ArrayList aa = new ArrayList();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a.getCalcId()
+ .equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map map, boolean up)
+ {
+ synchronized (sequences)
+ {
+ if (up)
+ {
+
+ for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i - 1);
+ if (sg.getSequences(null).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i - 1, seq);
+ }
+ }
+ else
+ {
+ for (int i = sequences.size() - 2; i > -1; i--)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i + 1);
+ if (sg.getSequences(map).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i + 1, seq);
+ }
+ }
+
+ }
+ }
+
}