/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
+ * 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
+ */
package jalview.datamodel;
-import java.awt.*;
-
import java.util.*;
+import jalview.analysis.*;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class Sequence implements SequenceI
+public class Sequence
+ implements SequenceI
{
SequenceI datasetSequence;
String name;
- private String sequence;
+ private char[] sequence;
String description;
int start;
int end;
/** DOCUMENT ME!! */
public SequenceFeature[] sequenceFeatures;
- /** This array holds hidden sequences
- * of which this sequence is the representitive member of a group
- */
- SequenceGroup hiddenSequences;
-
/**
* Creates a new Sequence object.
*
public Sequence(String name, String sequence, int start, int end)
{
this.name = name;
- this.sequence = sequence;
+ this.sequence = sequence.toCharArray();
this.start = start;
this.end = end;
-
parseId();
+ checkValidRange();
+ }
+ public Sequence(String name, char[] sequence, int start, int end)
+ {
+ this.name = name;
+ this.sequence = sequence;
+ this.start = start;
+ this.end = end;
+ parseId();
checkValidRange();
}
if (end < 1)
{
int endRes = 0;
- char ch;
- for (int j = 0; j < sequence.length(); j++)
+ for (int j = 0; j < sequence.length; j++)
{
- ch = sequence.charAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
endRes++;
}
*/
public Sequence(SequenceI seq)
{
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ this(seq.getName(),
+ seq.getSequence(),
+ seq.getStart(),
+ seq.getEnd());
+ description = seq.getDescription();
}
/**
public void deleteFeature(SequenceFeature sf)
{
- if(sequenceFeatures==null)
+ if (sequenceFeatures == null)
+ {
return;
+ }
- int index=0;
+ int index = 0;
for (index = 0; index < sequenceFeatures.length; index++)
{
if (sequenceFeatures[index].equals(sf))
}
}
-
- if(index==sequenceFeatures.length)
+ if (index == sequenceFeatures.length)
+ {
return;
+ }
int sfLength = sequenceFeatures.length;
- if(sfLength<2)
+ if (sfLength < 2)
{
sequenceFeatures = null;
}
else
{
- SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+ SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
System.arraycopy(sequenceFeatures, 0, temp, 0, index);
- if(index<sfLength)
+ if (index < sfLength)
+ {
System.arraycopy(sequenceFeatures,
index + 1,
temp,
- index, sequenceFeatures.length - index -1);
+ index, sequenceFeatures.length - index - 1);
+ }
sequenceFeatures = temp;
}
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
+ {
pdbIds = new Vector();
+ }
pdbIds.addElement(entry);
}
*/
public int getLength()
{
- return this.sequence.length();
+ return this.sequence.length;
}
/**
*/
public void setSequence(String seq)
{
- this.sequence = seq;
+ this.sequence = seq.toCharArray();
checkValidRange();
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence()
+ public String getSequenceAsString()
{
- return this.sequence;
+ return new String(sequence);
+ }
+
+ public String getSequenceAsString(int start, int end)
+ {
+ return new String(getSequence(start, end));
+ }
+
+ public char[] getSequence()
+ {
+ return sequence;
}
/**
*
* @return DOCUMENT ME!
*/
- public String getSequence(int start, int end)
+ public char[] getSequence(int start, int end)
{
// JBPNote - left to user to pad the result here (TODO:Decide on this policy)
- if (start >= sequence.length())
+ if (start >= sequence.length)
{
- return "";
+ return new char[0];
}
- if (end >= sequence.length())
+ if (end >= sequence.length)
{
- end = sequence.length();
+ end = sequence.length;
}
- return this.sequence.substring(start, end);
+ char[] reply = new char[end - start];
+ System.arraycopy(sequence, start, reply, 0, end - start);
+
+ return reply;
}
/**
public SequenceI getSubSequence(int start, int end)
{
if (start < 0)
+ {
start = 0;
- String seq = getSequence(start, end);
- if (seq == "")
+ }
+ char[] seq = getSequence(start, end);
+ if (seq.length == 0)
+ {
return null;
+ }
int nstart = findPosition(start);
int nend = findPosition(end) - 1;
// JBPNote - this is an incomplete copy.
SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
nseq.setDescription(description);
- nseq.setDatasetSequence(getDatasetSequence());
+ if (datasetSequence != null)
+ {
+ nseq.setDatasetSequence(datasetSequence);
+ }
+ else
+ {
+ nseq.setDatasetSequence(this);
+ }
return nseq;
}
*/
public char getCharAt(int i)
{
- if (i < sequence.length())
+ if (i < sequence.length)
{
- return sequence.charAt(i);
+ return sequence[i];
}
else
{
int j = start;
int i = 0;
- while ( (i < sequence.length()) && (j <= end) && (j <= pos))
+ while ( (i < sequence.length) && (j <= end) && (j <= pos))
{
- if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+ if (!jalview.util.Comparison.isGap(sequence[i]))
{
j++;
}
{
int j = 0;
int pos = start;
- int seqlen = sequence.length();
+ int seqlen = sequence.length;
while ( (j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
pos++;
}
public int[] gapMap()
{
String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
- GapChars, sequence);
+ GapChars, new String(sequence));
int[] map = new int[seq.length()];
int j = 0;
int p = 0;
- while (j < sequence.length())
+ while (j < sequence.length)
{
- if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
map[p++] = j;
}
* DOCUMENT ME!
*
* @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i)
- {
- if (i >= sequence.length())
- {
- return;
- }
-
- sequence = sequence.substring(0, i) + sequence.substring(i + 1);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
* @param j DOCUMENT ME!
*/
public void deleteChars(int i, int j)
{
- if (i >= sequence.length())
+ if (i >= sequence.length)
{
return;
}
- if (j >= sequence.length())
+ char[] tmp;
+
+ if (j >= sequence.length)
{
- sequence = sequence.substring(0, i);
+ tmp = new char[i];
+ System.arraycopy(sequence, 0, tmp, 0, i);
}
else
{
- sequence = sequence.substring(0, i) + sequence.substring(j);
+ tmp = new char[sequence.length - j + i];
+ System.arraycopy(sequence, 0, tmp, 0, i);
+ System.arraycopy(sequence, j, tmp, i, sequence.length - j);
+ }
+
+ if (this.datasetSequence != null)
+ {
+ for (int s = i; s < j; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ {
+
+ Sequence ds = new Sequence(name,
+ AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ this.getSequenceAsString()
+ ),
+ start,
+ end);
+ ds.setDescription(description);
+ }
+ break;
+ }
}
+
+ sequence = tmp;
+
}
/**
*/
public void insertCharAt(int i, int length, char c)
{
- StringBuffer tmp;
+ char[] tmp = new char[sequence.length + length];
- if (i >= sequence.length())
+ if (i >= sequence.length)
{
- tmp = new StringBuffer(sequence);
+ System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+ i = sequence.length;
}
else
- tmp = new StringBuffer(sequence.substring(0, i));
+ {
+ System.arraycopy(sequence, 0, tmp, 0, i);
+ }
+ int index = i;
while (length > 0)
{
- tmp.append(c);
+ tmp[index++] = c;
length--;
}
- if (i < sequence.length())
+ if (i < sequence.length)
{
- tmp.append(sequence.substring(i));
+ System.arraycopy(sequence, i, tmp, index, sequence.length - i);
}
- sequence = tmp.toString();
+ sequence = tmp;
}
public void insertCharAt(int i, char c)
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
+ {
dbrefs = new DBRefEntry[0];
+ }
int i, iSize = dbrefs.length;
- for(i=0; i<iSize; i++)
- if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
- && dbrefs[i].getSource().equals(entry.getSource())
- && dbrefs[i].getVersion().equals(entry.getVersion()))
+ for (i = 0; i < iSize; i++)
+ {
+ if (dbrefs[i].getAccessionId().equals(entry.getAccessionId())
+ && dbrefs[i].getSource().equals(entry.getSource())
+ && dbrefs[i].getVersion().equals(entry.getVersion()))
{
return;
}
+ }
DBRefEntry[] temp = new DBRefEntry[iSize + 1];
System.arraycopy(dbrefs, 0, temp, 0, iSize);
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 ret;
}
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
+ {
this.annotation = new Vector();
+ }
this.annotation.addElement(annotation);
}
- public SequenceGroup getHiddenSequences()
- {
- return hiddenSequences;
- }
-
- public void addHiddenSequence(SequenceI seq)
+ /**
+ * test if this is a valid candidate for another
+ * sequence's dataset sequence.
+ *
+ */
+ private boolean isValidDatasetSequence()
{
- if (hiddenSequences == null)
+ if (datasetSequence != null)
{
- hiddenSequences = new SequenceGroup();
+ return false;
}
- hiddenSequences.addSequence(seq, false);
+ for (int i = 0; i < sequence.length; i++)
+ {
+ if (jalview.util.Comparison.isGap(sequence[i]))
+ {
+ return false;
+ }
+ }
+ return true;
}
- public void showHiddenSequence(SequenceI seq)
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SequenceI#deriveSequence()
+ */
+ public SequenceI deriveSequence()
{
- hiddenSequences.deleteSequence(seq, false);
- if (hiddenSequences.getSize(false) < 1)
+ SequenceI seq = new Sequence(name, sequence, start, end);
+ seq.setDescription(description);
+ if (datasetSequence != null)
+ {
+ seq.setDatasetSequence(datasetSequence);
+ }
+ else
{
- hiddenSequences = null;
+ if (isValidDatasetSequence())
+ {
+ seq.setDatasetSequence(this);
+ }
}
+ return seq;
}
-}
-
+}