X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=83aab4e22e56df58b420f9171a00a0a9d0bcd407;hb=9a729c9cc5344884e81a05b6f2d54c35d1104722;hp=c74be7379ae12f601cf7ec1e3a228481561cfd0b;hpb=483c80a859264f9d743cc7ff801c65b3884d8e88;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c74be73..83aab4e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,37 +1,39 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * Jalview is free software: you can redistribute it and/or
+ * 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
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 = '-';
@@ -41,6 +43,8 @@ public class Alignment implements AlignmentI
public static final int NUCLEOTIDE = 1;
+ public boolean hasRNAStructure = false;
+
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
@@ -61,11 +65,12 @@ 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]);
}
}
@@ -84,7 +89,7 @@ public class Alignment implements AlignmentI
* Make a new alignment from an array of SeqCigars
*
* @param seqs
- * SeqCigar[]
+ * SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs)
{
@@ -100,7 +105,7 @@ public class Alignment implements AlignmentI
* appropriately.
*
* @param compactAlignment
- * CigarArray
+ * CigarArray
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
@@ -113,38 +118,50 @@ public class Alignment implements AlignmentI
*
* @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!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public SequenceI getSequenceAt(int i)
{
- if (i < sequences.size())
+ synchronized (sequences)
{
- return (SequenceI) sequences.elementAt(i);
+ if (i > -1 && i < sequences.size())
+ {
+ return sequences.get(i);
+ }
}
-
return null;
}
@@ -153,6 +170,7 @@ public class Alignment implements AlignmentI
*
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
@@ -177,7 +195,10 @@ public class Alignment implements AlignmentI
}
else
{
- sequences.addElement(snew);
+ synchronized (sequences)
+ {
+ sequences.add(snew);
+ }
}
if (hiddenSequences != null)
hiddenSequences.adjustHeightSequenceAdded();
@@ -188,12 +209,15 @@ public class Alignment implements AlignmentI
*
* @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);
+ }
}
/**
@@ -201,11 +225,13 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List getGroups()
{
return groups;
}
+ @Override
public void finalize()
{
if (getDataset() != null)
@@ -234,8 +260,9 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void deleteSequence(SequenceI s)
{
deleteSequence(findIndex(s));
@@ -245,118 +272,199 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * 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!
+ /*
+ * (non-Javadoc)
*
- * @return DOCUMENT ME!
+ * @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);
+ }
}
}
/**
- * DOCUMENT ME!
+ * remove any annotation that references gp
+ *
+ * @param gp
+ * (if null, removes all group associated annotation)
*/
+ private void removeAnnotationForGroup(SequenceGroup gp)
+ {
+ if (annotations == null || annotations.length == 0)
+ {
+ return;
+ }
+ // remove annotation very quickly
+ AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ int i, p, k;
+ if (gp == null)
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef != null)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ else
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef == gp)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ if (p > 0)
+ {
+ // clear out the group associated annotation.
+ for (i = 0; i < p; i++)
+ {
+ unhookAnnotation(todelete[i]);
+ todelete[i] = null;
+ }
+ t = new AlignmentAnnotation[k];
+ for (i = 0; i < k; i++)
+ {
+ t[i] = tokeep[i];
+ }
+ annotations = t;
+ }
+ }
+
+ @Override
public void deleteAllGroups()
{
- groups.removeAllElements();
+ synchronized (groups)
+ {
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ groups.clear();
+ }
}
/** */
+ @Override
public void deleteGroup(SequenceGroup g)
{
- if (groups.contains(g))
+ synchronized (groups)
{
- groups.removeElement(g);
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.remove(g);
+ }
}
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
@@ -367,6 +475,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
+ @Override
public SequenceI findName(String token, boolean b)
{
return findName(null, token, b);
@@ -376,8 +485,9 @@ public class Alignment implements AlignmentI
* (non-Javadoc)
*
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
- * boolean)
+ * boolean)
*/
+ @Override
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
@@ -418,6 +528,7 @@ public class Alignment implements AlignmentI
return null;
}
+ @Override
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
@@ -447,6 +558,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
@@ -467,8 +579,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
+ @Override
public int findIndex(SearchResults results)
{
int i = 0;
@@ -489,6 +603,7 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public int getHeight()
{
return sequences.size();
@@ -499,6 +614,7 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
int maxLength = -1;
@@ -518,17 +634,19 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param gc
- * DOCUMENT ME!
+ * 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));
+ }
}
}
@@ -537,25 +655,44 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return gapCharacter;
}
- /**
- * DOCUMENT ME!
+ /*
+ * (non-Javadoc)
*
- * @return DOCUMENT ME!
+ * @see jalview.datamodel.AlignmentI#isAligned()
*/
+ @Override
public boolean isAligned()
{
- int width = getWidth();
+ return isAligned(false);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ @Override
+ public boolean isAligned(boolean includeHidden)
+ {
+ int width = getWidth();
+ if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+ {
+ includeHidden = true; // no hidden sequences to check against.
+ }
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() != width)
+ if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
{
- return false;
+ if (getSequenceAt(i).getLength() != width)
+ {
+ return false;
+ }
}
}
@@ -565,10 +702,18 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+ * @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;
if (annotations != null)
@@ -600,20 +745,58 @@ public class Alignment implements AlignmentI
if (swap)
{
annotations = temp;
- if (aa.sequenceRef != null)
- aa.sequenceRef.removeAlignmentAnnotation(aa);
+ if (unhook)
+ {
+ unhookAnnotation(aa);
+ }
}
return swap;
}
/**
- * DOCUMENT ME!
+ * remove any object references associated with this annotation
*
* @param aa
- * DOCUMENT ME!
*/
+ private void unhookAnnotation(AlignmentAnnotation aa)
+ {
+ if (aa.sequenceRef != null)
+ {
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
+ }
+ if (aa.groupRef != null)
+ {
+ // probably need to do more here in the future (post 2.5.0)
+ aa.groupRef = null;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ @Override
public void addAnnotation(AlignmentAnnotation aa)
{
+ addAnnotation(aa, -1);
+ }
+
+ /*
+ * (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)
{
@@ -621,22 +804,35 @@ public class Alignment implements AlignmentI
}
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
- temp[aSize - 1] = aa;
-
int i = 0;
-
+ if (pos == -1 || pos >= aSize)
+ {
+ temp[aSize - 1] = aa;
+ }
+ else
+ {
+ temp[pos] = aa;
+ }
if (aSize > 1)
{
- for (i = 0; i < (aSize - 1); i++)
+ int p = 0;
+ for (i = 0; i < (aSize - 1); i++, p++)
{
- temp[i] = annotations[i];
+ if (p == pos)
+ {
+ p++;
+ }
+ if (p < temp.length)
+ {
+ temp[p] = annotations[i];
+ }
}
}
annotations = temp;
}
+ @Override
public void setAnnotationIndex(AlignmentAnnotation aa, int index)
{
if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -669,16 +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)
@@ -691,6 +887,7 @@ public class Alignment implements AlignmentI
}
}
+ @Override
public boolean isNucleotide()
{
if (type == NUCLEOTIDE)
@@ -703,6 +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)
@@ -717,7 +922,7 @@ public class Alignment implements AlignmentI
currentSeq = getSequenceAt(i);
if (currentSeq.getDatasetSequence() != null)
{
- seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ seqs[i] = currentSeq.getDatasetSequence();
}
else
{
@@ -747,11 +952,13 @@ public class Alignment implements AlignmentI
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
@@ -795,23 +1002,136 @@ public class Alignment implements AlignmentI
return modified;
}
+ /**
+ * 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;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+ int ends[] = new int[sequences.size() * 2];
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ // This should really be a sequence method
+ ends[i * 2] = current.findIndex(current.getStart());
+ ends[i * 2 + 1] = current.findIndex(current.getStart()
+ + current.getLength());
+ boolean hitres = false;
+ for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
+ {
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ if (!hitres)
+ {
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
+ {
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
+ {
+ maxLength = j - ends[i * 2];
+ }
+ }
+ }
+ }
+ }
+
+ maxLength++;
+ // now edit the flanking gaps to justify to either left or right
+ int cLength, extent, diff;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+
+ cLength = 1 + ends[i * 2 + 1] - ends[i * 2];
+ diff = maxLength - cLength; // number of gaps to indent
+ extent = current.getLength();
+ if (right)
+ {
+ // right justify
+ if (extent > ends[i * 2 + 1])
+ {
+ current.deleteChars(ends[i * 2 + 1] + 1, extent);
+ modified = true;
+ }
+ if (ends[i * 2] > diff)
+ {
+ current.deleteChars(0, ends[i * 2] - diff);
+ modified = true;
+ }
+ else
+ {
+ if (ends[i * 2] < diff)
+ {
+ current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ else
+ {
+ // left justify
+ if (ends[i * 2] > 0)
+ {
+ current.deleteChars(0, ends[i * 2]);
+ modified = true;
+ ends[i * 2 + 1] -= ends[i * 2];
+ extent -= ends[i * 2];
+ }
+ if (extent > maxLength)
+ {
+ current.deleteChars(maxLength + 1, extent);
+ modified = true;
+ }
+ else
+ {
+ if (extent < maxLength)
+ {
+ current.insertCharAt(extent, maxLength - extent, gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ }
+ 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)
@@ -820,6 +1140,7 @@ public class Alignment implements AlignmentI
alignmentProperties.put(key, value);
}
+ @Override
public Object getProperty(Object key)
{
if (alignmentProperties != null)
@@ -828,6 +1149,7 @@ public class Alignment implements AlignmentI
return null;
}
+ @Override
public Hashtable getProperties()
{
return alignmentProperties;
@@ -838,8 +1160,11 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
@@ -861,6 +1186,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
+ @Override
public AlignedCodonFrame getCodonFrame(int index)
{
return codonFrameList[index];
@@ -869,8 +1195,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
+ @Override
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
@@ -893,6 +1221,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
+ @Override
public AlignedCodonFrame[] getCodonFrames()
{
return codonFrameList;
@@ -901,8 +1230,10 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * AlignedCodonFrame)
*/
+ @Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
@@ -929,33 +1260,41 @@ 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();
+ boolean samegap = toappend.getGapCharacter() == getGapCharacter();
char oldc = toappend.getGapCharacter();
- boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+ boolean hashidden = toappend.getHiddenSequences() != null
+ && toappend.getHiddenSequences().hiddenSequences != null;
// get all sequences including any hidden ones
- Vector sqs = (hashidden) ? toappend.getHiddenSequences().getFullAlignment().getSequences() : toappend.getSequences();
+ 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 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)
+ if (toappend.getHiddenSequences() != null)
{
HiddenSequences hs = toappend.getHiddenSequences();
- if (hiddenSequences==null)
+ if (hiddenSequences == null)
{
hiddenSequences = new HiddenSequences(this);
}
- if (hs.hiddenSequences!=null)
+ if (hs.hiddenSequences != null)
{
- for (int s=0;s 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);
+ }
+ }
+
+ }
+ }
+
}