X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=42559c620ad74ca9837f73da38af6dca0eb9ec91;hb=85024c0dee90b249ba1e03dc991ce0a4d0156cda;hp=c47414223229826273bff0563c30006ef2bd3887;hpb=d7563d2df09ba5146008951448b941a69bf74744;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c474142..42559c6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
+ * 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 .
*/
package jalview.datamodel;
@@ -22,17 +21,27 @@ import java.util.*;
import jalview.analysis.*;
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
*/
-public class Alignment
- implements AlignmentI
+/**
+ * @author JimP
+ *
+ */
+public class Alignment implements AlignmentI
{
protected Alignment dataset;
+
protected Vector sequences;
+
protected Vector groups = new Vector();
+
protected char gapCharacter = '-';
+
protected int type = NUCLEOTIDE;
+
public static final int PROTEIN = 0;
+
public static final int NUCLEOTIDE = 1;
/** DOCUMENT ME!! */
@@ -64,8 +73,9 @@ public class Alignment
}
- /** Make an alignment from an array of Sequences.
- *
+ /**
+ * Make an alignment from an array of Sequences.
+ *
* @param sequences
*/
public Alignment(SequenceI[] seqs)
@@ -75,20 +85,25 @@ public class Alignment
/**
* Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
+ *
+ * @param seqs
+ * SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs)
{
- SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
- new ColumnSelection(), null);
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+ gapCharacter, new ColumnSelection(), null);
initAlignment(seqs);
}
/**
- * Make a new alignment from an CigarArray
- * JBPNote - can only do this when 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
+ * Make a new alignment from an CigarArray JBPNote - can only do this when
+ * 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
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
@@ -98,7 +113,7 @@ public class Alignment
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getSequences()
@@ -108,7 +123,7 @@ public class Alignment
public SequenceI[] getSequencesArray()
{
- if (sequences==null)
+ if (sequences == null)
return null;
SequenceI[] reply = new SequenceI[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
@@ -120,14 +135,15 @@ public class Alignment
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public SequenceI getSequenceAt(int i)
{
- if (i < sequences.size())
+ if (i>-1 && i < sequences.size())
{
return (SequenceI) sequences.elementAt(i);
}
@@ -135,8 +151,9 @@ public class Alignment
return null;
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
* @param snew
*/
public void addSequence(SequenceI snew)
@@ -156,17 +173,22 @@ public class Alignment
snew = adding;
}
}
- if (sequences==null) {
- initAlignment(new SequenceI[] { snew });
- } else {
+ if (sequences == null)
+ {
+ initAlignment(new SequenceI[]
+ { snew });
+ }
+ else
+ {
sequences.addElement(snew);
}
- if (hiddenSequences!=null)
+ if (hiddenSequences != null)
hiddenSequences.adjustHeightSequenceAdded();
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
* @param snew
*/
public void setSequenceAt(int i, SequenceI snew)
@@ -179,7 +201,7 @@ public class Alignment
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getGroups()
@@ -189,8 +211,8 @@ public class Alignment
public void finalize()
{
- if(getDataset()!=null)
- getDataset().finalize();
+ if (getDataset() != null)
+ getDataset().removeAlignmentRef();
dataset = null;
sequences = null;
@@ -199,11 +221,23 @@ public class Alignment
hiddenSequences = null;
}
+ /**
+ * decrement the alignmentRefs counter by one and call finalize if it goes to
+ * zero.
+ */
+ private void removeAlignmentRef()
+ {
+ if (--alignmentRefs == 0)
+ {
+ finalize();
+ }
+ }
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
*/
public void deleteSequence(SequenceI s)
{
@@ -212,8 +246,9 @@ public class Alignment
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
*/
public void deleteSequence(int i)
{
@@ -242,9 +277,10 @@ public class Alignment
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public SequenceGroup[] findAllGroups(SequenceI s)
@@ -307,10 +343,71 @@ public class Alignment
}
/**
- * 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;
+ }
+ }
+
public void deleteAllGroups()
{
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
groups.removeAllElements();
}
@@ -319,6 +416,7 @@ public class Alignment
{
if (groups.contains(g))
{
+ removeAnnotationForGroup(g);
groups.removeElement(g);
}
}
@@ -326,11 +424,55 @@ public class Alignment
/** */
public SequenceI findName(String name)
{
- int i = 0;
+ return findName(name, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ */
+ public SequenceI findName(String token, boolean b)
+ {
+ return findName(null, token, b);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * boolean)
+ */
+ public SequenceI findName(SequenceI startAfter, String token, boolean b)
+ {
+ int i = 0;
+ SequenceI sq = null;
+ String sqname = null;
+ if (startAfter != null)
+ {
+ // try to find the sequence in the alignment
+ boolean matched = false;
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i++) == startAfter)
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
+ }
while (i < sequences.size())
{
- if (getSequenceAt(i).getName().equals(name))
+ sq = getSequenceAt(i);
+ sqname = sq.getName();
+ if (sqname.equals(token) // exact match
+ || (b && // allow imperfect matches - case varies
+ (sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
}
@@ -365,7 +507,11 @@ public class Alignment
}
- /** */
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
public int findIndex(SequenceI s)
{
int i = 0;
@@ -383,9 +529,30 @@ public class Alignment
return -1;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ public int findIndex(SearchResults results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
+ {
+ return i;
+ }
+ i++;
+ }
+ return -1;
+ }
+
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getHeight()
@@ -395,7 +562,7 @@ public class Alignment
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getWidth()
@@ -415,8 +582,9 @@ public class Alignment
/**
* DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gc)
{
@@ -425,17 +593,14 @@ public class Alignment
for (int i = 0; i < sequences.size(); i++)
{
Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence(seq.getSequenceAsString()
- .replace('.', gc)
- .replace('-', gc)
- .replace(' ', gc)
- );
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
@@ -443,27 +608,47 @@ public class Alignment
return gapCharacter;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned()
*/
public boolean isAligned()
{
- int width = getWidth();
+ return isAligned(false);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ 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;
+ }
}
}
return true;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
*/
public boolean deleteAnnotation(AlignmentAnnotation aa)
{
@@ -481,36 +666,65 @@ public class Alignment
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
- boolean swap=false;
+ boolean swap = false;
int tIndex = 0;
for (int i = 0; i < aSize; i++)
{
if (annotations[i] == aa)
{
- swap=true;
+ swap = true;
continue;
}
- if (tIndex= 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];
+ }
}
}
@@ -568,7 +794,7 @@ public class Alignment
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
@@ -607,7 +833,7 @@ public class Alignment
// Create a new dataset for this alignment.
// Can only be done once, if dataset is not null
// This will not be performed
- Sequence[] seqs = new Sequence[getHeight()];
+ SequenceI[] seqs = new SequenceI[getHeight()];
SequenceI currentSeq;
for (int i = 0; i < getHeight(); i++)
{
@@ -618,17 +844,7 @@ public class Alignment
}
else
{
- seqs[i] = new Sequence(currentSeq.getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- currentSeq.getSequenceAsString()
- ),
- currentSeq.getStart(),
- currentSeq.getEnd());
- seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
- seqs[i].setDescription(currentSeq.getDescription());
- getSequenceAt(i).setSequenceFeatures(null);
- getSequenceAt(i).setDatasetSequence(seqs[i]);
+ seqs[i] = currentSeq.createDatasetSequence();
}
}
@@ -638,6 +854,20 @@ public class Alignment
{
dataset = data;
}
+ dataset.addAlignmentRef();
+ }
+
+ /**
+ * reference count for number of alignments referencing this one.
+ */
+ int alignmentRefs = 0;
+
+ /**
+ * increase reference count to this alignment.
+ */
+ private void addAlignmentRef()
+ {
+ alignmentRefs++;
}
public Alignment getDataset()
@@ -649,7 +879,7 @@ public class Alignment
{
boolean modified = false;
- //Remove excess gaps from the end of alignment
+ // Remove excess gaps from the end of alignment
int maxLength = -1;
SequenceI current;
@@ -658,8 +888,8 @@ public class Alignment
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
{
- if (j > maxLength && !jalview.util.Comparison.isGap(
- current.getCharAt(j)))
+ if (j > maxLength
+ && !jalview.util.Comparison.isGap(current.getCharAt(j)))
{
maxLength = j;
break;
@@ -670,16 +900,14 @@ public class Alignment
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size();
- i++)
+ for (int i = 0; i < sequences.size(); i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
if (cLength < maxLength)
{
- current.insertCharAt(cLength,
- maxLength - cLength, gapCharacter);
+ current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
modified = true;
}
else if (current.getLength() > maxLength)
@@ -690,6 +918,111 @@ public class Alignment
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
+ */
+ 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;
+ }
+
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
@@ -700,7 +1033,7 @@ public class Alignment
SeqCigar alseqs[] = new SeqCigar[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
- alseqs[i] = new SeqCigar( (SequenceI) sequences.elementAt(i));
+ alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
}
CigarArray cal = new CigarArray(alseqs);
cal.addOperation(CigarArray.M, getWidth());
@@ -709,15 +1042,15 @@ public class Alignment
public void setProperty(Object key, Object value)
{
- if(alignmentProperties==null)
+ if (alignmentProperties == null)
alignmentProperties = new Hashtable();
- alignmentProperties.put(key,value);
+ alignmentProperties.put(key, value);
}
public Object getProperty(Object key)
{
- if(alignmentProperties!=null)
+ if (alignmentProperties != null)
return alignmentProperties.get(key);
else
return null;
@@ -727,26 +1060,35 @@ public class Alignment
{
return alignmentProperties;
}
- AlignedCodonFrame[] codonFrameList=null;
- /* (non-Javadoc)
- * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+
+ AlignedCodonFrame[] codonFrameList = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
*/
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons==null)
+ if (codons == null)
return;
- if (codonFrameList==null)
+ if (codonFrameList == null)
{
- codonFrameList = new AlignedCodonFrame[] { codons };
+ codonFrameList = new AlignedCodonFrame[]
+ { codons };
return;
}
- AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+ AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
t[codonFrameList.length] = codons;
codonFrameList = t;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
public AlignedCodonFrame getCodonFrame(int index)
@@ -754,27 +1096,32 @@ public class Alignment
return codonFrameList[index];
}
- /* (non-Javadoc)
- * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
- if (seq==null || codonFrameList==null)
+ if (seq == null || codonFrameList == null)
return null;
- Vector cframes=new Vector();
- for (int f=0;f