X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=c7581d82b81b755852cafb8c6265e91bace4a332;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=aa27d253865423139a53bc403553c6952561bb1e;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index aa27d25..c7581d8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,27 +1,35 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
+ * 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 jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.List;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
@@ -29,7 +37,7 @@ import java.util.Vector;
* @author $author$
* @version $Revision$
*/
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
SequenceI datasetSequence;
@@ -43,20 +51,24 @@ public class Sequence implements SequenceI
int end;
- Vector pdbIds;
+ Vector pdbIds;
String vamsasId;
DBRefEntry[] dbrefs;
+ 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;
-
+ Vector annotation;
+
/**
- * The index of the sequence in a MSA
+ * The index of the sequence in a MSA
*/
int index = -1;
@@ -78,20 +90,30 @@ public class Sequence implements SequenceI
*/
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();
+ initSeqAndName(name, sequence.toCharArray(), start, end);
}
public Sequence(String name, char[] sequence, int start, int end)
{
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
+ 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();
}
@@ -109,7 +131,7 @@ public class Sequence implements SequenceI
.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signiature?
+ // Does sequence have the /start-end signature?
if (limitrx.search(name))
{
name = limitrx.left();
@@ -122,7 +144,8 @@ public class Sequence implements SequenceI
void checkValidRange()
{
- // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
+ // 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++)
@@ -137,7 +160,8 @@ public class Sequence implements SequenceI
endRes += start - 1;
}
- if (end();
}
- if (!pdbIds.contains(entry))
+ if (pdbIds.contains(entry))
+ {
+ updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+ }
+ else
{
pdbIds.addElement(entry);
}
}
+ private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+ {
+ if (newEntry.getFile() != null)
+ {
+ oldEntry.setFile(newEntry.getFile());
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector id)
+ @Override
+ public void setPDBId(Vector id)
{
pdbIds = id;
}
@@ -350,7 +408,8 @@ public class Sequence implements SequenceI
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId()
+ @Override
+ public Vector getAllPDBEntries()
{
return pdbIds;
}
@@ -480,7 +539,9 @@ public class Sequence implements SequenceI
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 >= sequence.length)
@@ -499,16 +560,7 @@ public class Sequence implements SequenceI
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)
@@ -577,13 +629,10 @@ public class Sequence implements SequenceI
return this.description;
}
- /**
- * Return the alignment position for a sequence position
- *
- * @param pos
- * lying from start to end
+ /*
+ * (non-Javadoc)
*
- * @return aligned position of residue pos
+ * @see jalview.datamodel.SequenceI#findIndex(int)
*/
public int findIndex(int pos)
{
@@ -611,14 +660,7 @@ public class Sequence implements SequenceI
}
}
- /**
- * 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
- */
+ @Override
public int findPosition(int i)
{
int j = 0;
@@ -665,11 +707,7 @@ public class Sequence implements SequenceI
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#findPositionMap()
- */
+ @Override
public int[] findPositionMap()
{
int map[] = new int[sequence.length];
@@ -689,33 +727,55 @@ public class Sequence implements SequenceI
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
- */
- public void deleteChars(int i, int j)
+ @Override
+ public List getInsertions()
{
- int newstart = start, newend = end;
- if (i >= sequence.length)
+ ArrayList map = new ArrayList();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
{
- return;
+ 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++;
}
-
- char[] tmp;
-
- if (j >= sequence.length)
+ if (lastj != -1)
{
- tmp = new char[i];
- System.arraycopy(sequence, 0, tmp, 0, i);
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
}
- else
+ return map;
+ }
+
+ @Override
+ public void deleteChars(int i, int j)
+ {
+ int newstart = start, newend = end;
+ if (i >= sequence.length || i < 0)
{
- tmp = new char[sequence.length - j + i];
- System.arraycopy(sequence, 0, tmp, 0, i);
- System.arraycopy(sequence, j, tmp, i, sequence.length - j);
+ 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)
@@ -726,7 +786,11 @@ public class Sequence implements SequenceI
}
else
{
- int sindex = findIndex(start) - 1;
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
if (sindex == s)
{
// delete characters including start of sequence
@@ -736,7 +800,11 @@ public class Sequence implements SequenceI
else
{
// delete characters after start.
- int eindex = findIndex(end) - 1;
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
if (eindex < j)
{
// delete characters at end of sequence
@@ -768,16 +836,7 @@ public class Sequence implements SequenceI
sequence = tmp;
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- * @param chop
- * DOCUMENT ME!
- */
+ @Override
public void insertCharAt(int i, int length, char c)
{
char[] tmp = new char[sequence.length + length];
@@ -807,26 +866,31 @@ public class Sequence implements SequenceI
sequence = tmp;
}
+ @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;
}
+ @Override
public void setDBRef(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
+ @Override
public DBRefEntry[] getDBRef()
{
if (dbrefs == null && datasetSequence != null
@@ -837,6 +901,7 @@ public class Sequence implements SequenceI
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
@@ -869,37 +934,37 @@ public class Sequence implements SequenceI
dbrefs = temp;
}
+ @Override
public void setDatasetSequence(SequenceI seq)
{
datasetSequence = seq;
}
+ @Override
public SequenceI getDatasetSequence()
{
return datasetSequence;
}
+ @Override
public AlignmentAnnotation[] getAnnotation()
{
- if (annotation == null)
- {
- return null;
- }
-
- AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
- for (int r = 0; r < ret.length; r++)
- {
- ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
- }
+ return annotation == null ? null : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
+ }
- return ret;
+ @Override
+ public boolean hasAnnotation(AlignmentAnnotation ann)
+ {
+ return annotation == null ? false : annotation.contains(ann);
}
+ @Override
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
{
- this.annotation = new Vector();
+ this.annotation = new Vector();
}
if (!this.annotation.contains(annotation))
{
@@ -914,7 +979,9 @@ public class Sequence implements SequenceI
{
this.annotation.removeElement(annotation);
if (this.annotation.size() == 0)
+ {
this.annotation = null;
+ }
}
}
@@ -938,11 +1005,7 @@ public class Sequence implements SequenceI
return true;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deriveSequence()
- */
+ @Override
public SequenceI deriveSequence()
{
SequenceI seq = new Sequence(this);
@@ -990,9 +1053,20 @@ public class Sequence implements SequenceI
// move database references onto dataset sequence
datasetSequence.setDBRef(getDBRef());
setDBRef(null);
- datasetSequence.setPDBId(getPDBId());
+ datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ for (AlignmentAnnotation aa : annotation)
+ {
+ AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+ _aa.sequenceRef = datasetSequence;
+ _aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(_aa);
+ }
+ }
}
return datasetSequence;
}
@@ -1015,16 +1089,14 @@ public class Sequence implements SequenceI
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] != null)
+ {
addAlignmentAnnotation(annotations[i]);
+ }
}
}
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
- */
+ @Override
public AlignmentAnnotation[] getAnnotation(String label)
{
if (annotation == null || annotation.size() == 0)
@@ -1057,6 +1129,7 @@ public class Sequence implements SequenceI
return anns;
}
+ @Override
public boolean updatePDBIds()
{
if (datasetSequence != null)
@@ -1110,13 +1183,7 @@ public class Sequence implements SequenceI
return false;
}
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
- * jalview.datamodel.Mapping)
- */
+ @Override
public void transferAnnotation(SequenceI entry, Mapping mp)
{
if (datasetSequence != null)
@@ -1137,8 +1204,7 @@ public class Sequence implements SequenceI
for (int si = 0; si < sfs.length; si++)
{
SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
- : new SequenceFeature[]
- { new SequenceFeature(sfs[si]) };
+ : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
if (sf != null && sf.length > 0)
{
for (int sfi = 0; sfi < sf.length; sfi++)
@@ -1150,9 +1216,9 @@ public class Sequence implements SequenceI
}
// transfer PDB entries
- if (entry.getPDBId() != null)
+ if (entry.getAllPDBEntries() != null)
{
- Enumeration e = entry.getPDBId().elements();
+ Enumeration e = entry.getAllPDBEntries().elements();
while (e.hasMoreElements())
{
PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -1181,16 +1247,78 @@ public class Sequence implements SequenceI
}
/**
- * @return The index (zero-based) on this sequence in the MSA.
- * It returns {@code -1} if this information is not available.
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
*/
- public int getIndex() { return index; }
-
+ public int getIndex()
+ {
+ return index;
+ }
+
/**
- * Defines the position of this sequence in the MSA.
- * Use the value {@code -1} if this information is undefined.
+ * 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)
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
*/
- public void setIndex(int value) { index = value; }
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ 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;
+ }
+
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() == null
+ || getDatasetSequence().getAllPDBEntries() == null)
+ {
+ return null;
+ }
+ List entries = getDatasetSequence().getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+
}