X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=75b18d9f0fcf0d83de9b20c3df37f0ffbcfc2e23;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=23fe0573aa1c86a2fcbf4d7345228b91a3002860;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 23fe057..75b18d9 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,25 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* 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
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
-import jalview.analysis.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
/**
* Data structure to hold and manipulate a multiple sequence alignment
@@ -32,9 +45,10 @@ 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 = '-';
@@ -43,7 +57,7 @@ public class Alignment implements AlignmentI
public static final int PROTEIN = 0;
public static final int NUCLEOTIDE = 1;
-
+
public boolean hasRNAStructure = false;
/** DOCUMENT ME!! */
@@ -53,6 +67,8 @@ public class Alignment implements AlignmentI
public Hashtable alignmentProperties;
+ private Set codonFrameList = new LinkedHashSet();
+
private void initAlignment(SequenceI[] seqs)
{
int i = 0;
@@ -66,13 +82,35 @@ 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 a 'copy' alignment - sequences have new copies of features and
+ * annotations, but share the original dataset sequences.
+ */
+ public Alignment(AlignmentI al)
+ {
+ SequenceI[] seqs = al.getSequencesArray();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = new Sequence(seqs[i]);
}
+ /*
+ * Share the same dataset sequence mappings (if any). TODO: find a better
+ * place for these to live (alignment dataset?).
+ */
+ this.codonFrameList = ((Alignment) al).codonFrameList;
+
+ initAlignment(seqs);
}
/**
@@ -109,37 +147,49 @@ public class Alignment implements AlignmentI
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error("Alignment(CigarArray) not yet implemented");
+ throw new Error(
+ MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
- /**
- * 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.
+ // 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;
+ }
+
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ @Override
+ public Map> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
}
/**
@@ -150,13 +200,16 @@ public class Alignment implements AlignmentI
*
* @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;
}
@@ -165,6 +218,7 @@ public class Alignment implements AlignmentI
*
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
@@ -184,15 +238,19 @@ public class Alignment implements AlignmentI
}
if (sequences == null)
{
- initAlignment(new SequenceI[]
- { snew });
+ initAlignment(new SequenceI[] { snew });
}
else
{
- sequences.addElement(snew);
+ synchronized (sequences)
+ {
+ sequences.add(snew);
+ }
}
if (hiddenSequences != null)
+ {
hiddenSequences.adjustHeightSequenceAdded();
+ }
}
/**
@@ -200,12 +258,14 @@ 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);
+ synchronized (sequences)
+ {
+ deleteSequence(i);
+ sequences.set(i, snew);
+ }
}
/**
@@ -213,15 +273,19 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List getGroups()
{
return groups;
}
+ @Override
public void finalize()
{
if (getDataset() != null)
+ {
getDataset().removeAlignmentRef();
+ }
dataset = null;
sequences = null;
@@ -248,6 +312,7 @@ public class Alignment implements AlignmentI
* @param s
* DOCUMENT ME!
*/
+ @Override
public void deleteSequence(SequenceI s)
{
deleteSequence(findIndex(s));
@@ -259,95 +324,105 @@ public class Alignment implements AlignmentI
* @param i
* DOCUMENT ME!
*/
+ @Override
public void deleteSequence(int i)
{
if (i > -1 && i < getHeight())
{
- sequences.removeElementAt(i);
- hiddenSequences.adjustHeightSequenceDeleted(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)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
- if (sg.getSequences(null).contains(s))
- {
- temp.addElement(sg);
+ if (sg.getSequences().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;
+ }
}
+ sg.setContext(this);
+ groups.add(sg);
}
-
- groups.addElement(sg);
}
}
@@ -411,26 +486,40 @@ public class Alignment implements AlignmentI
}
}
+ @Override
public void deleteAllGroups()
{
- if (annotations != null)
+ synchronized (groups)
{
- removeAnnotationForGroup(null);
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(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);
+ g.setContext(null);
+ }
}
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
@@ -441,6 +530,7 @@ 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);
@@ -452,6 +542,7 @@ public class Alignment implements AlignmentI
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
* boolean)
*/
+ @Override
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
@@ -492,6 +583,7 @@ public class Alignment implements AlignmentI
return null;
}
+ @Override
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
@@ -521,6 +613,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
@@ -544,6 +637,7 @@ public class Alignment implements AlignmentI
* @see
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
+ @Override
public int findIndex(SearchResults results)
{
int i = 0;
@@ -564,6 +658,7 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public int getHeight()
{
return sequences.size();
@@ -574,6 +669,7 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
int maxLength = -1;
@@ -595,15 +691,17 @@ public class Alignment implements AlignmentI
* @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));
+ }
}
}
@@ -612,6 +710,7 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return gapCharacter;
@@ -622,6 +721,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#isAligned()
*/
+ @Override
public boolean isAligned()
{
return isAligned(false);
@@ -632,6 +732,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#isAligned(boolean)
*/
+ @Override
public boolean isAligned(boolean includeHidden)
{
int width = getWidth();
@@ -653,17 +754,41 @@ public class Alignment implements AlignmentI
return true;
}
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ @Override
+ public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+ {
+ boolean result = false;
+ for (AlignmentAnnotation alan : getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated || includingAutoCalculated)
+ {
+ deleteAnnotation(alan);
+ result = true;
+ }
+ }
+ return result;
+ }
+
/*
* (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;
@@ -691,13 +816,16 @@ public class Alignment implements AlignmentI
continue;
}
if (tIndex < temp.length)
+ {
temp[tIndex++] = annotations[i];
+ }
}
if (swap)
{
annotations = temp;
- if (unhook) {
+ if (unhook)
+ {
unhookAnnotation(aa);
}
}
@@ -728,6 +856,7 @@ public class Alignment implements AlignmentI
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa)
{
addAnnotation(aa, -1);
@@ -739,12 +868,14 @@ public class Alignment implements AlignmentI
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation, int)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa, int pos)
{
- if(aa.getRNAStruc()!= null){
- hasRNAStructure=true;
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
}
-
+
int aSize = 1;
if (annotations != null)
{
@@ -780,6 +911,7 @@ public class Alignment implements AlignmentI
annotations = temp;
}
+ @Override
public void setAnnotationIndex(AlignmentAnnotation aa, int index)
{
if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -821,6 +953,7 @@ public class Alignment implements AlignmentI
return annotations;
}
+ @Override
public void setNucleotide(boolean b)
{
if (b)
@@ -833,6 +966,7 @@ public class Alignment implements AlignmentI
}
}
+ @Override
public boolean isNucleotide()
{
if (type == NUCLEOTIDE)
@@ -844,12 +978,15 @@ public class Alignment implements AlignmentI
return false;
}
}
-
- public boolean hasRNAStructure(){
- //TODO can it happen that structure is removed from alignment?
+
+ @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)
@@ -864,7 +1001,7 @@ public class Alignment implements AlignmentI
currentSeq = getSequenceAt(i);
if (currentSeq.getDatasetSequence() != null)
{
- seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ seqs[i] = currentSeq.getDatasetSequence();
}
else
{
@@ -877,6 +1014,27 @@ public class Alignment implements AlignmentI
else if (dataset == null && data != null)
{
dataset = data;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
+ {
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
+ }
+ else
+ {
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
+ }
+ }
}
dataset.addAlignmentRef();
}
@@ -894,11 +1052,13 @@ public class Alignment implements AlignmentI
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
@@ -950,6 +1110,7 @@ public class Alignment implements AlignmentI
* 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;
@@ -1047,46 +1208,59 @@ 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)
+ {
alignmentProperties = new Hashtable();
+ }
alignmentProperties.put(key, value);
}
+ @Override
public Object getProperty(Object key)
{
if (alignmentProperties != null)
+ {
return alignmentProperties.get(key);
+ }
else
+ {
return null;
+ }
}
+ @Override
public Hashtable getProperties()
{
return alignmentProperties;
}
- AlignedCodonFrame[] codonFrameList = null;
-
/*
* (non-Javadoc)
*
@@ -1094,30 +1268,13 @@ public class Alignment implements AlignmentI
* jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons == null)
- return;
- if (codonFrameList == null)
+ if (codons != null)
{
- codonFrameList = new AlignedCodonFrame[]
- { codons };
- return;
+ codonFrameList.add(codons);
}
- AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
- System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
- t[codonFrameList.length] = codons;
- codonFrameList = t;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
- */
- public AlignedCodonFrame getCodonFrame(int index)
- {
- return codonFrameList[index];
}
/*
@@ -1126,29 +1283,43 @@ public class Alignment implements AlignmentI
* @see
* jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
- public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ @Override
+ public List getCodonFrame(SequenceI seq)
{
- if (seq == null || codonFrameList == null)
+ if (seq == null)
+ {
return null;
- Vector cframes = new Vector();
- for (int f = 0; f < codonFrameList.length; f++)
+ }
+ List cframes = new ArrayList();
+ for (AlignedCodonFrame acf : codonFrameList)
{
- if (codonFrameList[f].involvesSequence(seq))
- cframes.addElement(codonFrameList[f]);
+ if (acf.involvesSequence(seq))
+ {
+ cframes.add(acf);
+ }
}
- if (cframes.size() == 0)
- return null;
- AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
- cframes.copyInto(cfr);
- return cfr;
+ return cframes;
}
- /*
- * (non-Javadoc)
+ /**
+ * Sets the codon frame mappings (replacing any existing mappings).
+ *
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ */
+ @Override
+ public void setCodonFrames(Set acfs)
+ {
+ this.codonFrameList = acfs;
+ }
+
+ /**
+ * Returns the set of codon frame mappings. Any changes to the returned set
+ * will affect the alignment.
*
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
- public AlignedCodonFrame[] getCodonFrames()
+ @Override
+ public Set getCodonFrames()
{
return codonFrameList;
}
@@ -1159,34 +1330,23 @@ public class Alignment implements AlignmentI
* @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
+ @Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
- return false;
- boolean removed = false;
- int i = 0, iSize = codonFrameList.length;
- while (i < iSize)
{
- if (codonFrameList[i] == codons)
- {
- removed = true;
- if (i + 1 < iSize)
- {
- System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
- - i - 1);
- }
- iSize--;
- }
- else
- {
- i++;
- }
+ return false;
}
- return removed;
+ return codonFrameList.remove(codons);
}
+ @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();
@@ -1194,26 +1354,27 @@ 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();
@@ -1221,15 +1382,13 @@ public class Alignment implements AlignmentI
{
addAnnotation(alan[a]);
}
- AlignedCodonFrame[] acod = toappend.getCodonFrames();
- for (int a = 0; acod != null && a < acod.length; a++)
- {
- this.addCodonFrame(acod[a]);
- }
+
+ this.codonFrameList.addAll(toappend.getCodonFrames());
+
List sg = toappend.getGroups();
if (sg != null)
{
- for (SequenceGroup _sg:sg)
+ for (SequenceGroup _sg : sg)
{
addGroup(_sg);
}
@@ -1299,23 +1458,28 @@ public class Alignment implements AlignmentI
}
@Override
- public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
- SequenceI seqRef, SequenceGroup groupRef)
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
{
- for (AlignmentAnnotation annot :
- getAlignmentAnnotation())
+ assert (name != null);
+ if (annotations != null)
{
- if (annot.autoCalculated == autoCalc
- && annot.getCalcId().equals(name)
- && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
{
- return annot;
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && 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.setCalcId(new String(calcId));
annot.autoCalculated = autoCalc;
if (seqRef != null)
{
@@ -1330,10 +1494,12 @@ public class Alignment implements AlignmentI
@Override
public Iterable findAnnotation(String calcId)
{
- ArrayList aa=new ArrayList();
- for (AlignmentAnnotation a:getAlignmentAnnotation())
+ ArrayList aa = new ArrayList();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
{
- if (a.getCalcId()==calcId || (a.getCalcId()!=null && calcId!=null && a.getCalcId().equals(calcId)))
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a.getCalcId()
+ .equals(calcId)))
{
aa.add(a);
}
@@ -1341,4 +1507,245 @@ public class Alignment implements AlignmentI
return aa;
}
+ /**
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
+ */
+ @Override
+ public Iterable findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList aa = new ArrayList();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ 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);
+ }
+ }
+
+ }
+ }
+
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
+ }
+ }
+
+ private SequenceI seqrep = null;
+
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
+
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
+
+ /**
+ * Align this alignment like the given (mapped) one.
+ */
+ @Override
+ public int alignAs(AlignmentI al)
+ {
+ /*
+ * Currently retains unmapped gaps (in introns), regaps mapped regions
+ * (exons)
+ */
+ return alignAs(al, false, true);
+ }
+
+ /**
+ * Align this alignment 'the same as' the given one. Mapped sequences only are
+ * realigned. If both of the same type (nucleotide/protein) then align both
+ * identically. If this is nucleotide and the other is protein, make 3 gaps
+ * for each gap in the protein sequences. If this is protein and the other is
+ * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+ * nucleotide bases. If this is protein and the other is nucleotide, gaps
+ * protein to match the relative ordering of codons in the nucleotide.
+ *
+ * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+ * regions are preserved. Gaps that connect introns to exons are treated
+ * conservatively, i.e. only preserved if both intron and exon gaps are
+ * preserved.
+ *
+ * @param al
+ * @param preserveMappedGaps
+ * if true, gaps within and between mapped codons are preserved
+ * @param preserveUnmappedGaps
+ * if true, gaps within and between unmapped codons are preserved
+ */
+ // @Override
+ public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ // TODO should this method signature be the one in the interface?
+ int count = 0;
+ boolean thisIsNucleotide = this.isNucleotide();
+ boolean thatIsProtein = !al.isNucleotide();
+ if (!thatIsProtein && !thisIsNucleotide)
+ {
+ return AlignmentUtils.alignProteinAsDna(this, al);
+ }
+
+ char thisGapChar = this.getGapCharacter();
+ String gap = thisIsNucleotide && thatIsProtein ? String
+ .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
+ : String.valueOf(thisGapChar);
+
+ // TODO handle intron regions? Needs a 'holistic' alignment of dna,
+ // not just sequence by sequence. But how to 'gap' intron regions?
+
+ /*
+ * Get mappings from 'that' alignment's sequences to this.
+ */
+ for (SequenceI alignTo : getSequences())
+ {
+ count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
+ preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
+ }
+ return count;
+ }
+
+ /**
+ * Returns the alignment in Fasta format. Behaviour of this method is not
+ * guaranteed between versions.
+ */
+ @Override
+ public String toString()
+ {
+ return new FastaFile().print(getSequencesArray());
+ }
+
+ /**
+ * Returns the set of distinct sequence names. No ordering is guaranteed.
+ */
+ @Override
+ public Set getSequenceNames()
+ {
+ Set names = new HashSet();
+ for (SequenceI seq : getSequences())
+ {
+ names.add(seq.getName());
+ }
+ return names;
+ }
+
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if ((seq.getEnd() - seq.getStart()) > 0)
+ {
+ hasValidSeq = true;
+ break;
+ }
+ }
+ return hasValidSeq;
+ }
}