X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=96b0757f179033d5ecd478e1acf51f8ff8961d57;hb=f2a83f0360d406859b80cc798099a9d270461bb3;hp=0128b9c8b66016653dcf72531da682381eca0aba;hpb=c2134e69548327ca932d37dc058fd44ab1cbfd50;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0128b9c..96b0757 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,115 +1,201 @@
/*
-* 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
-
-import java.util.*;
-
-import jalview.analysis.*;
+import jalview.analysis.AlignSeq;
+import jalview.api.DBRefEntryI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Vector;
+
+import fr.orsay.lri.varna.models.rna.RNA;
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class Sequence
- implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
SequenceI datasetSequence;
+
String name;
- private char [] sequence;
+
+ private char[] sequence;
+
String description;
+
int start;
+
int end;
- Vector pdbIds;
+
+ Vector pdbIds;
+
String vamsasId;
+
DBRefEntry[] dbrefs;
- /** This annotation is displayed below the alignment but the
- * positions are tied to the residues of this sequence */
- Vector annotation;
+ RNA rna;
+
+ /**
+ * This annotation is displayed below the alignment but the positions are tied
+ * to the residues of this sequence
+ *
+ * TODO: change to List<>
+ */
+ Vector annotation;
+
+ /**
+ * The index of the sequence in a MSA
+ */
+ int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
- public SequenceFeature[] sequenceFeatures;
+ private SequenceFeaturesI sequenceFeatureStore;
+
+ /*
+ * A cursor holding the approximate current view position to the sequence,
+ * as determined by findIndex or findPosition or findPositions.
+ * Using a cursor as a hint allows these methods to be more performant for
+ * large sequences.
+ */
+ private SequenceCursor cursor;
+ /*
+ * A number that should be incremented whenever the sequence is edited.
+ * If the value matches the cursor token, then we can trust the cursor,
+ * if not then it should be recomputed.
+ */
+ private int changeCount;
/**
* Creates a new Sequence object.
- *
- * @param name display name string
- * @param sequence string to form a possibly gapped sequence out of
- * @param start first position of non-gap residue in the sequence
- * @param end last position of ungapped residues (nearly always only used for display purposes)
+ *
+ * @param name
+ * display name string
+ * @param sequence
+ * string to form a possibly gapped sequence out of
+ * @param start
+ * first position of non-gap residue in the sequence
+ * @param end
+ * last position of ungapped residues (nearly always only used for
+ * display purposes)
*/
public Sequence(String name, String sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence.toCharArray();
- this.start = start;
- this.end = end;
- parseId();
- checkValidRange();
+ this();
+ initSeqAndName(name, sequence.toCharArray(), start, end);
}
- public Sequence(String name, char [] sequence, int start, int end)
+ public Sequence(String name, char[] sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
+ this();
+ initSeqAndName(name, sequence, start, end);
+ }
+
+ /**
+ * Stage 1 constructor - assign name, sequence, and set start and end fields.
+ * start and end are updated values from name2 if it ends with /start-end
+ *
+ * @param name2
+ * @param sequence2
+ * @param start2
+ * @param end2
+ */
+ protected void initSeqAndName(String name2, char[] sequence2, int start2,
+ int end2)
+ {
+ this.name = name2;
+ this.sequence = sequence2;
+ this.start = start2;
+ this.end = end2;
parseId();
checkValidRange();
}
- com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
- com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
- "[0-9]{1,}$");
-
+ /**
+ * If 'name' ends in /i-j, where i >= j > 0 are integers, extracts i and j as
+ * start and end respectively and removes the suffix from the name
+ */
void parseId()
{
- if (name==null)
+ if (name == null)
{
- System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ System.err.println(
+ "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signiature?
- if (limitrx.search(name))
+ int slashPos = name.lastIndexOf('/');
+ if (slashPos > -1 && slashPos < name.length() - 1)
{
- name = limitrx.left();
- endrx.search(limitrx.stringMatched());
- setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
- endrx.matchedFrom() - 1)));
- setEnd(Integer.parseInt(endrx.stringMatched()));
+ String suffix = name.substring(slashPos + 1);
+ String[] range = suffix.split("-");
+ if (range.length == 2)
+ {
+ try
+ {
+ int from = Integer.valueOf(range[0]);
+ int to = Integer.valueOf(range[1]);
+ if (from > 0 && to >= from)
+ {
+ name = name.substring(0, slashPos);
+ setStart(from);
+ setEnd(to);
+ checkValidRange();
+ }
+ } catch (NumberFormatException e)
+ {
+ // leave name unchanged if suffix is invalid
+ }
+ }
}
}
+ /**
+ * Ensures that 'end' is not before the end of the sequence, that is,
+ * (end-start+1) is at least as long as the count of ungapped positions. Note
+ * that end is permitted to be beyond the end of the sequence data.
+ */
void checkValidRange()
{
- if (end < 1)
+ // Note: JAL-774 :
+ // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
{
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
{
- if (!jalview.util.Comparison.isGap( sequence[j] ))
+ if (!Comparison.isGap(sequence[j]))
{
endRes++;
}
@@ -119,16 +205,29 @@ public class Sequence
endRes += start - 1;
}
- this.end = endRes;
+ if (end < endRes)
+ {
+ end = endRes;
+ }
}
}
/**
+ * default constructor
+ */
+ private Sequence()
+ {
+ sequenceFeatureStore = new SequenceFeatures();
+ }
+
+ /**
* Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ * @param sequence
+ * DOCUMENT ME!
*/
public Sequence(String name, String sequence)
{
@@ -136,53 +235,93 @@ public class Sequence
}
/**
- * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
- * but inherits any existing dataset sequence reference.
- * @param seq DOCUMENT ME!
+ * Creates a new Sequence object with new AlignmentAnnotations but inherits
+ * any existing dataset sequence reference. If non exists, everything is
+ * copied.
+ *
+ * @param seq
+ * if seq is a dataset sequence, behaves like a plain old copy
+ * constructor
*/
public Sequence(SequenceI seq)
{
this(seq, seq.getAnnotation());
}
+
/**
* Create a new sequence object with new features, DBRefEntries, and PDBIds
- * but inherits any existing dataset sequence reference, and duplicate of
- * any annotation that is present in the given annotation array.
- * @param seq the sequence to be copied
- * @param alAnnotation an array of annotation including some associated with seq
+ * but inherits any existing dataset sequence reference, and duplicate of any
+ * annotation that is present in the given annotation array.
+ *
+ * @param seq
+ * the sequence to be copied
+ * @param alAnnotation
+ * an array of annotation including some associated with seq
*/
public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
{
- this(seq.getName(),
- seq.getSequence(),
- seq.getStart(),
- seq.getEnd());
+ this();
+ initSeqFrom(seq, alAnnotation);
+ }
+
+ /**
+ * does the heavy lifting when cloning a dataset sequence, or coping data from
+ * dataset to a new derived sequence.
+ *
+ * @param seq
+ * - source of attributes.
+ * @param alAnnotation
+ * - alignment annotation present on seq that should be copied onto
+ * this sequence
+ */
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {
+ char[] oseq = seq.getSequence(); // returns a copy of the array
+ initSeqAndName(seq.getName(), oseq, seq.getStart(), seq.getEnd());
+
description = seq.getDescription();
- if (seq.getSequenceFeatures()!=null) {
- SequenceFeature[] sf = seq.getSequenceFeatures();
- for (int i=0; i ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
+ {
+ this.addPDBId(new PDBEntry(pdb));
}
}
}
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature[] features)
+ @Override
+ public void setSequenceFeatures(List features)
{
- sequenceFeatures = features;
+ if (datasetSequence != null)
+ {
+ datasetSequence.setSequenceFeatures(features);
+ return;
+ }
+ sequenceFeatureStore = new SequenceFeatures(features);
}
- public synchronized void addSequenceFeature(SequenceFeature sf)
+ @Override
+ public synchronized boolean addSequenceFeature(SequenceFeature sf)
{
- if (sequenceFeatures == null)
+ if (sf.getType() == null)
{
- sequenceFeatures = new SequenceFeature[0];
+ System.err.println("SequenceFeature type may not be null: "
+ + sf.toString());
+ return false;
}
- for (int i = 0; i < sequenceFeatures.length; i++)
+ if (datasetSequence != null)
{
- if (sequenceFeatures[i].equals(sf))
- {
- return;
- }
+ return datasetSequence.addSequenceFeature(sf);
}
- SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
- System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
- temp[sequenceFeatures.length] = sf;
-
- sequenceFeatures = temp;
+ return sequenceFeatureStore.add(sf);
}
+ @Override
public void deleteFeature(SequenceFeature sf)
{
- if(sequenceFeatures==null)
- {
- return;
- }
-
- int index=0;
- for (index = 0; index < sequenceFeatures.length; index++)
- {
- if (sequenceFeatures[index].equals(sf))
- {
- break;
- }
- }
-
-
- if(index==sequenceFeatures.length)
- {
- return;
- }
-
- int sfLength = sequenceFeatures.length;
- if(sfLength<2)
+ if (datasetSequence != null)
{
- sequenceFeatures = null;
+ datasetSequence.deleteFeature(sf);
}
else
{
- SequenceFeature[] temp = new SequenceFeature[sfLength-1];
- System.arraycopy(sequenceFeatures, 0, temp, 0, index);
-
- if(index getSequenceFeatures()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.getSequenceFeatures();
+ }
+ return sequenceFeatureStore.getAllFeatures();
+ }
+
+ @Override
+ public SequenceFeaturesI getFeatures()
{
- return sequenceFeatures;
+ return datasetSequence != null ? datasetSequence.getFeatures()
+ : sequenceFeatureStore;
}
- public void addPDBId(PDBEntry entry)
+ @Override
+ public boolean addPDBId(PDBEntry entry)
{
if (pdbIds == null)
{
- pdbIds = new Vector();
+ pdbIds = new Vector();
+ pdbIds.add(entry);
+ return true;
}
+ for (PDBEntry pdbe : pdbIds)
+ {
+ if (pdbe.updateFrom(entry))
+ {
+ return false;
+ }
+ }
pdbIds.addElement(entry);
+ return true;
}
/**
* DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
*/
- public void setPDBId(Vector id)
+ @Override
+ public void setPDBId(Vector id)
{
pdbIds = id;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public Vector getPDBId()
+ @Override
+ public Vector getAllPDBEntries()
{
- return pdbIds;
+ return pdbIds == null ? new Vector() : pdbIds;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public String getDisplayId(boolean jvsuffix)
{
StringBuffer result = new StringBuffer(name);
@@ -337,21 +470,24 @@ public class Sequence
}
/**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
+ * Sets the sequence name. If the name ends in /start-end, then the start-end
+ * values are parsed out and set, and the suffix is removed from the name.
+ *
+ * @param theName
*/
- public void setName(String name)
+ @Override
+ public void setName(String theName)
{
- this.name = name;
+ this.name = theName;
this.parseId();
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public String getName()
{
return this.name;
@@ -359,9 +495,11 @@ public class Sequence
/**
* DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
+ *
+ * @param start
+ * DOCUMENT ME!
*/
+ @Override
public void setStart(int start)
{
this.start = start;
@@ -369,9 +507,10 @@ public class Sequence
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getStart()
{
return this.start;
@@ -379,9 +518,11 @@ public class Sequence
/**
* DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
+ *
+ * @param end
+ * DOCUMENT ME!
*/
+ @Override
public void setEnd(int end)
{
this.end = end;
@@ -389,9 +530,10 @@ public class Sequence
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getEnd()
{
return this.end;
@@ -399,9 +541,10 @@ public class Sequence
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getLength()
{
return this.sequence.length;
@@ -409,39 +552,52 @@ public class Sequence
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
+ @Override
public void setSequence(String seq)
{
this.sequence = seq.toCharArray();
checkValidRange();
+ sequenceChanged();
}
-
+ @Override
public String getSequenceAsString()
{
return new String(sequence);
}
+ @Override
public String getSequenceAsString(int start, int end)
{
return new String(getSequence(start, end));
}
-
- public char [] getSequence()
+ @Override
+ public char[] getSequence()
{
- return sequence;
+ // return sequence;
+ return sequence == null ? null : Arrays.copyOf(sequence,
+ sequence.length);
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.SequenceI#getSequence(int, int)
*/
- public char [] getSequence(int start, int end)
+ @Override
+ public char[] getSequence(int start, int end)
{
- if (start<0)
- start=0;
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+ if (start < 0)
+ {
+ start = 0;
+ }
+ // JBPNote - left to user to pad the result here (TODO:Decide on this
+ // policy)
if (start >= sequence.length)
{
return new char[0];
@@ -452,26 +608,20 @@ public class Sequence
end = sequence.length;
}
- char [] reply = new char[end-start];
- System.arraycopy(sequence, start, reply, 0, end-start);
+ char[] reply = new char[end - start];
+ System.arraycopy(sequence, start, reply, 0, end - start);
return reply;
}
-
- /**
- * make a new Sequence object from start to end (including gaps) over this seqeunce
- * @param start int
- * @param end int
- * @return SequenceI
- */
+ @Override
public SequenceI getSubSequence(int start, int end)
{
if (start < 0)
{
start = 0;
}
- char [] seq = getSequence(start, end);
+ char[] seq = getSequence(start, end);
if (seq.length == 0)
{
return null;
@@ -481,27 +631,27 @@ public class Sequence
// JBPNote - this is an incomplete copy.
SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
nseq.setDescription(description);
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
- nseq.setDatasetSequence(datasetSequence);
+ nseq.setDatasetSequence(datasetSequence);
}
else
{
- nseq.setDatasetSequence(this);
+ nseq.setDatasetSequence(this);
}
return nseq;
}
/**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Returns the character of the aligned sequence at the given position (base
+ * zero), or space if the position is not within the sequence's bounds
+ *
+ * @return
*/
+ @Override
public char getCharAt(int i)
{
- if (i < sequence.length)
+ if (i >= 0 && i < sequence.length)
{
return sequence[i];
}
@@ -513,9 +663,11 @@ public class Sequence
/**
* DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
*/
+ @Override
public void setDescription(String desc)
{
this.description = desc;
@@ -523,488 +675,1249 @@ public class Sequence
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public String getDescription()
{
return this.description;
}
/**
- * Return the alignment position for a sequence position
- *
- * @param pos lying from start to end
- *
- * @return aligned position of residue pos
+ * {@inheritDoc}
*/
+ @Override
public int findIndex(int pos)
{
- // returns the alignment position for a residue
+ /*
+ * use a valid, hopefully nearby, cursor if available
+ */
+ if (isValidCursor(cursor))
+ {
+ return findIndex(pos, cursor);
+ }
+
int j = start;
int i = 0;
+ int startColumn = 0;
- while ( (i < sequence.length) && (j <= end) && (j <= pos))
+ /*
+ * traverse sequence from the start counting gaps; make a note of
+ * the column of the first residue to save in the cursor
+ */
+ while ((i < sequence.length) && (j <= end) && (j <= pos))
{
- if (!jalview.util.Comparison.isGap(sequence[i]))
+ if (!Comparison.isGap(sequence[i]))
{
+ if (j == start)
+ {
+ startColumn = i;
+ }
j++;
}
-
i++;
}
- if ( (j == end) && (j < pos))
+ if (j == end && j < pos)
{
return end + 1;
}
- else
- {
- return i;
- }
+
+ updateCursor(pos, i, startColumn);
+ return i;
}
/**
- * Returns the sequence position for an alignment position
- *
- * @param i column index in alignment (from 1)
- *
- * @return residue number for residue (left of and) nearest ith column
+ * Updates the cursor to the latest found residue and column position
+ *
+ * @param residuePos
+ * (start..)
+ * @param column
+ * (1..)
+ * @param startColumn
+ * column position of the first sequence residue
*/
- public int findPosition(int i)
+ protected void updateCursor(int residuePos, int column, int startColumn)
{
- int j = 0;
- int pos = start;
- int seqlen = sequence.length;
- while ( (j < i) && (j < seqlen))
+ /*
+ * preserve end residue column provided cursor was valid
+ */
+ int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+ if (residuePos == this.end)
{
- if (!jalview.util.Comparison.isGap( sequence[j] ))
- {
- pos++;
- }
-
- j++;
+ endColumn = column;
}
- return pos;
+ cursor = new SequenceCursor(this, residuePos, column, startColumn,
+ endColumn, this.changeCount);
}
/**
- * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
- *
- * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+ * Answers the aligned column position (1..) for the given residue position
+ * (start..) given a 'hint' of a residue/column location in the neighbourhood.
+ * The hint may be left of, at, or to the right of the required position.
+ *
+ * @param pos
+ * @param curs
+ * @return
*/
- public int[] gapMap()
+ protected int findIndex(int pos, SequenceCursor curs)
{
- String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
- GapChars, new String(sequence));
- int[] map = new int[seq.length()];
- int j = 0;
- int p = 0;
+ if (!isValidCursor(curs))
+ {
+ /*
+ * wrong or invalidated cursor, compute de novo
+ */
+ return findIndex(pos);
+ }
- while (j < sequence.length)
+ if (curs.residuePosition == pos)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ return curs.columnPosition;
+ }
+
+ /*
+ * move left or right to find pos from hint.position
+ */
+ int col = curs.columnPosition - 1; // convert from base 1 to 0-based array
+ // index
+ int newPos = curs.residuePosition;
+ int delta = newPos > pos ? -1 : 1;
+
+ while (newPos != pos)
+ {
+ col += delta; // shift one column left or right
+ if (col < 0 || col == sequence.length)
{
- map[p++] = j;
+ break;
+ }
+ if (!Comparison.isGap(sequence[col]))
+ {
+ newPos += delta;
}
-
- j++;
}
- return map;
+ col++; // convert back to base 1
+ updateCursor(pos, col, curs.firstColumnPosition);
+
+ return col;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
+ /**
+ * {@inheritDoc}
*/
- public void deleteChars(int i, int j)
+ @Override
+ public int findPosition(final int column)
{
- int newstart=start,newend=end;
- if (i >= sequence.length)
+ /*
+ * use a valid, hopefully nearby, cursor if available
+ */
+ if (isValidCursor(cursor))
{
- return;
+ return findPosition(column + 1, cursor);
}
+
+ // TODO recode this more naturally i.e. count residues only
+ // as they are found, not 'in anticipation'
+
+ /*
+ * traverse the sequence counting gaps; note the column position
+ * of the first residue, to save in the cursor
+ */
+ int firstResidueColumn = 0;
+ int lastPosFound = 0;
+ int lastPosFoundColumn = 0;
+ int seqlen = sequence.length;
- char [] tmp;
-
- if (j >= sequence.length)
- {
- tmp = new char[i];
- System.arraycopy(sequence,0,tmp,0,i);
- }
- else
+ if (seqlen > 0 && !Comparison.isGap(sequence[0]))
{
- tmp = new char[sequence.length-j+i];
- System.arraycopy(sequence,0,tmp,0,i);
- System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+ lastPosFound = start;
+ lastPosFoundColumn = 0;
}
- boolean createNewDs=false;
- for (int s = i; s < j; s++)
+
+ int j = 0;
+ int pos = start;
+
+ while (j < column && j < seqlen)
{
- if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ if (!Comparison.isGap(sequence[j]))
{
- if (createNewDs)
- {
- newend--;
- } else {
- int sindex = findIndex(start)-1;
- if (sindex==s)
+ lastPosFound = pos;
+ lastPosFoundColumn = j;
+ if (pos == this.start)
{
- // delete characters including start of sequence
- newstart = findPosition(j);
- break; // don't need to search for any more residue characters.
- } else {
- // delete characters after start.
- int eindex = findIndex(end)-1;
- if (eindex= sequence.length)
+ if (curs == null || curs.sequence != this || curs.token != changeCount)
{
- System.arraycopy(sequence, 0, tmp, 0, sequence.length);
- i = sequence.length;
+ return false;
}
- else
- {
- System.arraycopy(sequence, 0, tmp, 0, i);
- }
-
-
+ /*
+ * sanity check against range
+ */
+ if (curs.columnPosition < 0 || curs.columnPosition > sequence.length)
+ {
+ return false;
+ }
+ if (curs.residuePosition < start || curs.residuePosition > end)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Answers the sequence position (start..) for the given aligned column
+ * position (1..), given a hint of a cursor in the neighbourhood. The cursor
+ * may lie left of, at, or to the right of the column position.
+ *
+ * @param col
+ * @param curs
+ * @return
+ */
+ protected int findPosition(final int col, SequenceCursor curs)
+ {
+ if (!isValidCursor(curs))
+ {
+ /*
+ * wrong or invalidated cursor, compute de novo
+ */
+ return findPosition(col - 1);// ugh back to base 0
+ }
+
+ if (curs.columnPosition == col)
+ {
+ cursor = curs; // in case this method becomes public
+ return curs.residuePosition; // easy case :-)
+ }
+
+ if (curs.lastColumnPosition > 0 && curs.lastColumnPosition < col)
+ {
+ /*
+ * sequence lies entirely to the left of col
+ * - return last residue + 1
+ */
+ return end + 1;
+ }
+
+ if (curs.firstColumnPosition > 0 && curs.firstColumnPosition > col)
+ {
+ /*
+ * sequence lies entirely to the right of col
+ * - return first residue
+ */
+ return start;
+ }
+
+ // todo could choose closest to col out of column,
+ // firstColumnPosition, lastColumnPosition as a start point
+
+ /*
+ * move left or right to find pos from cursor position
+ */
+ int firstResidueColumn = curs.firstColumnPosition;
+ int column = curs.columnPosition - 1; // to base 0
+ int newPos = curs.residuePosition;
+ int delta = curs.columnPosition > col ? -1 : 1;
+ boolean gapped = false;
+ int lastFoundPosition = curs.residuePosition;
+ int lastFoundPositionColumn = curs.columnPosition;
+
+ while (column != col - 1)
+ {
+ column += delta; // shift one column left or right
+ if (column < 0 || column == sequence.length)
+ {
+ break;
+ }
+ gapped = Comparison.isGap(sequence[column]);
+ if (!gapped)
+ {
+ newPos += delta;
+ lastFoundPosition = newPos;
+ lastFoundPositionColumn = column + 1;
+ if (lastFoundPosition == this.start)
+ {
+ firstResidueColumn = column + 1;
+ }
+ }
+ }
+
+ if (cursor == null || lastFoundPosition != cursor.residuePosition)
+ {
+ updateCursor(lastFoundPosition, lastFoundPositionColumn,
+ firstResidueColumn);
+ }
+
+ /*
+ * hack to give position to the right if on a gap
+ * or beyond the length of the sequence (see JAL-2562)
+ */
+ if (delta > 0 && (gapped || column >= sequence.length))
+ {
+ newPos++;
+ }
+
+ return newPos;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Range findPositions(int fromColumn, int toColumn)
+ {
+ if (toColumn < fromColumn || fromColumn < 1)
+ {
+ return null;
+ }
+
+ /*
+ * find the first non-gapped position, if any
+ */
+ int firstPosition = 0;
+ int col = fromColumn - 1;
+ int length = sequence.length;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col]))
+ {
+ firstPosition = findPosition(col++);
+ break;
+ }
+ col++;
+ }
+
+ if (firstPosition == 0)
+ {
+ return null;
+ }
+
+ /*
+ * find the last non-gapped position
+ */
+ int lastPosition = firstPosition;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col++]))
+ {
+ lastPosition++;
+ }
+ }
+
+ return new Range(firstPosition, lastPosition);
+ }
+
+ /**
+ * Returns an int array where indices correspond to each residue in the
+ * sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+ * residues in SequenceI object
+ */
+ @Override
+ public int[] gapMap()
+ {
+ String seq = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, new String(sequence));
+ int[] map = new int[seq.length()];
+ int j = 0;
+ int p = 0;
+
+ while (j < sequence.length)
+ {
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ map[p++] = j;
+ }
+
+ j++;
+ }
+
+ return map;
+ }
+
+ @Override
+ public int[] findPositionMap()
+ {
+ int map[] = new int[sequence.length];
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ map[j] = pos;
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ pos++;
+ }
+
+ j++;
+ }
+ return map;
+ }
+
+ @Override
+ public List getInsertions()
+ {
+ ArrayList map = new ArrayList();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
+ {
+ lastj = j;
+ }
+ }
+ else
+ {
+ if (lastj != -1)
+ {
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
+ }
+ }
+ j++;
+ }
+ if (lastj != -1)
+ {
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
+ }
+ return map;
+ }
+
+ @Override
+ public BitSet getInsertionsAsBits()
+ {
+ BitSet map = new BitSet();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
+ {
+ lastj = j;
+ }
+ }
+ else
+ {
+ if (lastj != -1)
+ {
+ map.set(lastj, j);
+ lastj = -1;
+ }
+ }
+ j++;
+ }
+ if (lastj != -1)
+ {
+ map.set(lastj, j);
+ lastj = -1;
+ }
+ return map;
+ }
+
+ @Override
+ public void deleteChars(int i, int j)
+ {
+ int newstart = start, newend = end;
+ if (i >= sequence.length || i < 0)
+ {
+ return;
+ }
+
+ char[] tmp = StringUtils.deleteChars(sequence, i, j);
+ boolean createNewDs = false;
+ // TODO: take a (second look) at the dataset creation validation method for
+ // the very large sequence case
+ int eindex = -1, sindex = -1;
+ boolean ecalc = false, scalc = false;
+ for (int s = i; s < j; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ {
+ if (createNewDs)
+ {
+ newend--;
+ }
+ else
+ {
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
+ if (sindex == s)
+ {
+ // delete characters including start of sequence
+ newstart = findPosition(j);
+ break; // don't need to search for any more residue characters.
+ }
+ else
+ {
+ // delete characters after start.
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
+ if (eindex < j)
+ {
+ // delete characters at end of sequence
+ newend = findPosition(i - 1);
+ break; // don't need to search for any more residue characters.
+ }
+ else
+ {
+ createNewDs = true;
+ newend--; // decrease end position by one for the deleted residue
+ // and search further
+ }
+ }
+ }
+ }
+ }
+ // deletion occured in the middle of the sequence
+ if (createNewDs && this.datasetSequence != null)
+ {
+ // construct a new sequence
+ Sequence ds = new Sequence(datasetSequence);
+ // TODO: remove any non-inheritable properties ?
+ // TODO: create a sequence mapping (since there is a relation here ?)
+ ds.deleteChars(i, j);
+ datasetSequence = ds;
+ }
+ start = newstart;
+ end = newend;
+ sequence = tmp;
+ sequenceChanged();
+ }
+
+ @Override
+ public void insertCharAt(int i, int length, char c)
+ {
+ char[] tmp = new char[sequence.length + length];
+
+ if (i >= sequence.length)
+ {
+ System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+ i = sequence.length;
+ }
+ else
+ {
+ System.arraycopy(sequence, 0, tmp, 0, i);
+ }
+
int index = i;
while (length > 0)
{
- tmp[ index++ ] = c;
+ tmp[index++] = c;
length--;
}
if (i < sequence.length)
{
- System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+ System.arraycopy(sequence, i, tmp, index, sequence.length - i);
}
sequence = tmp;
+ sequenceChanged();
}
+ @Override
public void insertCharAt(int i, char c)
{
insertCharAt(i, 1, c);
}
+ @Override
public String getVamsasId()
{
return vamsasId;
}
+ @Override
public void setVamsasId(String id)
{
vamsasId = id;
}
- public void setDBRef(DBRefEntry[] dbref)
+ @Override
+ public void setDBRefs(DBRefEntry[] dbref)
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ datasetSequence.setDBRefs(dbref);
+ return;
+ }
dbrefs = dbref;
+ if (dbrefs != null)
+ {
+ DBRefUtils.ensurePrimaries(this);
+ }
}
- public DBRefEntry[] getDBRef()
+ @Override
+ public DBRefEntry[] getDBRefs()
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRefs();
+ }
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
+ if (datasetSequence != null)
+ {
+ datasetSequence.addDBRef(entry);
+ return;
+ }
+
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
}
- int i, iSize = dbrefs.length;
-
- for(i=0; i();
+ }
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
}
-
- this.annotation.addElement(annotation);
annotation.setSequenceRef(this);
}
+ @Override
public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
{
- if(this.annotation!=null)
+ if (this.annotation != null)
{
this.annotation.removeElement(annotation);
- if(this.annotation.size()==0)
+ if (this.annotation.size() == 0)
+ {
this.annotation = null;
+ }
}
}
-
/**
- * test if this is a valid candidate for another
- * sequence's dataset sequence.
- *
+ * test if this is a valid candidate for another sequence's dataset sequence.
+ *
*/
private boolean isValidDatasetSequence()
{
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
- return false;
+ return false;
}
- for (int i=0;i subset = new Vector();
+ Enumeration e = annotation.elements();
while (e.hasMoreElements())
{
- AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
- if (ann.label!=null && ann.label.equals(label))
+ AlignmentAnnotation ann = e.nextElement();
+ if (ann.label != null && ann.label.equals(label))
{
subset.addElement(ann);
}
}
- if (subset.size()==0)
+ if (subset.size() == 0)
{
return null;
}
AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
- int i=0;
+ int i = 0;
e = subset.elements();
while (e.hasMoreElements())
{
- anns[i++] = (AlignmentAnnotation) e.nextElement();
+ anns[i++] = e.nextElement();
}
subset.removeAllElements();
return anns;
}
+ @Override
public boolean updatePDBIds()
{
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
// TODO: could merge DBRefs
return datasetSequence.updatePDBIds();
}
- if (dbrefs==null || dbrefs.length==0)
+ if (dbrefs == null || dbrefs.length == 0)
{
return false;
}
- Vector newpdb = new Vector();
- for (int i=0; i sfs = entry.getSequenceFeatures();
+ for (SequenceFeature feature : sfs)
{
- PDBEntry pdbe = new PDBEntry();
- pdbe.setId(dbrefs[i].getAccessionId());
- if (pdbIds==null || pdbIds.size()==0)
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+ : new SequenceFeature[] { new SequenceFeature(feature) };
+ if (sf != null)
{
- newpdb.addElement(pdbe);
- } else {
- Enumeration en = pdbIds.elements();
- boolean matched=false;
- while (!matched && en.hasMoreElements())
+ for (int sfi = 0; sfi < sf.length; sfi++)
{
- PDBEntry anentry = (PDBEntry) en.nextElement();
- if (anentry.getId().equals(pdbe.getId()))
- {
- matched=true;
- }
+ addSequenceFeature(sf[sfi]);
}
- if (!matched)
+ }
+ }
+ }
+
+ // transfer PDB entries
+ if (entry.getAllPDBEntries() != null)
+ {
+ Enumeration e = entry.getAllPDBEntries().elements();
+ while (e.hasMoreElements())
+ {
+ PDBEntry pdb = e.nextElement();
+ addPDBId(pdb);
+ }
+ }
+ // transfer database references
+ DBRefEntry[] entryRefs = entry.getDBRefs();
+ if (entryRefs != null)
+ {
+ for (int r = 0; r < entryRefs.length; r++)
+ {
+ DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+ if (newref.getMap() != null && mp != null)
+ {
+ // remap ref using our local mapping
+ }
+ // we also assume all version string setting is done by dbSourceProxy
+ /*
+ * if (!newref.getSource().equalsIgnoreCase(dbSource)) {
+ * newref.setSource(dbSource); }
+ */
+ addDBRef(newref);
+ }
+ }
+ }
+
+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ @Override
+ public int getIndex()
+ {
+ return index;
+ }
+
+ /**
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
+ *
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
+ */
+ @Override
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ @Override
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ @Override
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ @Override
+ public List getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List result = new ArrayList();
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (ann.calcId != null && ann.calcId.equals(calcId)
+ && ann.label != null && ann.label.equals(label))
+ {
+ result.add(ann);
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() != null)
+ {
+ return getDatasetSequence().getPDBEntry(pdbIdStr);
+ }
+ if (pdbIds == null)
+ {
+ return null;
+ }
+ List entries = getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public List getPrimaryDBRefs()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.getPrimaryDBRefs();
+ }
+ if (dbrefs == null || dbrefs.length == 0)
+ {
+ return Collections.emptyList();
+ }
+ synchronized (dbrefs)
+ {
+ List primaries = new ArrayList();
+ DBRefEntry[] tmp = new DBRefEntry[1];
+ for (DBRefEntry ref : dbrefs)
+ {
+ if (!ref.isPrimaryCandidate())
+ {
+ continue;
+ }
+ if (ref.hasMap())
+ {
+ MapList mp = ref.getMap().getMap();
+ if (mp.getFromLowest() > start || mp.getFromHighest() < end)
{
- newpdb.addElement(pdbe);
+ // map only involves a subsequence, so cannot be primary
+ continue;
}
}
+ // whilst it looks like it is a primary ref, we also sanity check type
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
+ .equals(DBRefUtils.getCanonicalName(ref.getSource())))
+ {
+ // PDB dbrefs imply there should be a PDBEntry associated
+ // TODO: tighten PDB dbrefs
+ // formally imply Jalview has actually downloaded and
+ // parsed the pdb file. That means there should be a cached file
+ // handle on the PDBEntry, and a real mapping between sequence and
+ // extracted sequence from PDB file
+ PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+ if (pdbentry != null && pdbentry.getFile() != null)
+ {
+ primaries.add(ref);
+ }
+ continue;
+ }
+ // check standard protein or dna sources
+ tmp[0] = ref;
+ DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+ if (res != null && res[0] == tmp[0])
+ {
+ primaries.add(ref);
+ continue;
+ }
}
+ return primaries;
}
- if (newpdb.size()>0)
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List findFeatures(int fromColumn, int toColumn,
+ String... types)
+ {
+ int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
+ int endPos = fromColumn == toColumn ? startPos
+ : findPosition(toColumn - 1);
+
+ List result = getFeatures().findFeatures(startPos,
+ endPos, types);
+
+ /*
+ * if end column is gapped, endPos may be to the right,
+ * and we may have included adjacent or enclosing features;
+ * remove any that are not enclosing, non-contact features
+ */
+ boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+ && Comparison.isGap(sequence[toColumn - 1]);
+ if (endPos > this.end || endColumnIsGapped)
{
- Enumeration en = newpdb.elements();
- while (en.hasMoreElements())
+ ListIterator it = result.listIterator();
+ while (it.hasNext())
{
- addPDBId((PDBEntry) en.nextElement());
+ SequenceFeature sf = it.next();
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int featureStartColumn = findIndex(sfBegin);
+ if (featureStartColumn > toColumn)
+ {
+ it.remove();
+ }
+ else if (featureStartColumn < fromColumn)
+ {
+ int featureEndColumn = sfEnd == sfBegin ? featureStartColumn
+ : findIndex(sfEnd);
+ if (featureEndColumn < fromColumn)
+ {
+ it.remove();
+ }
+ else if (featureEndColumn > toColumn && sf.isContactFeature())
+ {
+ /*
+ * remove an enclosing feature if it is a contact feature
+ */
+ it.remove();
+ }
+ }
}
- return true;
}
- return false;
+
+ return result;
}
-}
+ /**
+ * Invalidates any stale cursors (forcing recalculation) by incrementing the
+ * token that has to match the one presented by the cursor
+ */
+ @Override
+ public void sequenceChanged()
+ {
+ changeCount++;
+ }
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public int replace(char c1, char c2)
+ {
+ if (c1 == c2)
+ {
+ return 0;
+ }
+ int count = 0;
+ synchronized (sequence)
+ {
+ for (int c = 0; c < sequence.length; c++)
+ {
+ if (sequence[c] == c1)
+ {
+ sequence[c] = c2;
+ count++;
+ }
+ }
+ }
+ if (count > 0)
+ {
+ sequenceChanged();
+ }
+ return count;
+ }
+}