*/
public class Sequence implements SequenceI
{
- SequenceI datasetSequence;
- String name;
- private String sequence;
- String description;
- int start;
- int end;
- Color color = Color.white;
- 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;
-
- /** 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.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- */
- public Sequence(String name, String sequence, int start, int end)
- {
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
+ SequenceI datasetSequence;
+ String name;
+ private String sequence;
+ String description;
+ int start;
+ int end;
+ Color color = Color.white;
+ 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;
+
+ /** 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.
+ *
+ * @param name DOCUMENT ME!
+ * @param sequence DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ */
+ public Sequence(String name, String sequence, int start, int end)
+ {
+ this.name = name;
+ this.sequence = sequence;
+ this.start = start;
+ this.end = end;
- parseId();
+ parseId();
- checkValidRange();
- }
+ checkValidRange();
+ }
- com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
- com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
- "[0-9]{1,}$");
+ com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+ "[/][0-9]{1,}[-][0-9]{1,}$");
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+ "[0-9]{1,}$");
- void parseId()
+ void parseId()
+ {
+ // Does sequence have the /start-end signiature?
+ if (limitrx.search(name))
{
- // Does sequence have the /start-end signiature?
- if(limitrx.search(name))
- {
- name = limitrx.left();
- endrx.search(limitrx.stringMatched());
- setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));
- setEnd( Integer.parseInt( endrx.stringMatched() ));
- }
+ name = limitrx.left();
+ endrx.search(limitrx.stringMatched());
+ setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
+ endrx.matchedFrom() - 1)));
+ setEnd(Integer.parseInt(endrx.stringMatched()));
}
+ }
- void checkValidRange()
+ void checkValidRange()
+ {
+ if (end < 1)
{
- if (end < 1)
+ int endRes = 0;
+ char ch;
+ for (int j = 0; j < sequence.length(); j++)
{
- int endRes = 0;
- char ch;
- for (int j = 0; j < sequence.length(); j++)
+ ch = sequence.charAt(j);
+ if (!jalview.util.Comparison.isGap( (ch)))
{
- ch = sequence.charAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
- {
- endRes++;
- }
+ endRes++;
}
- if (endRes > 0)
- {
- endRes += start - 1;
- }
-
- this.end = endRes;
- }
-
- }
-
- /**
- * Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
- */
- public Sequence(String name, String sequence)
- {
- this(name, sequence, 1, -1);
- }
-
- /**
- * Creates a new Sequence object.
- *
- * @param seq DOCUMENT ME!
- */
- public Sequence(SequenceI seq)
- {
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature [] features)
- {
- sequenceFeatures = features;
- }
-
- public synchronized void addSequenceFeature(SequenceFeature sf)
- {
- if(sequenceFeatures==null)
- {
- sequenceFeatures = new SequenceFeature[0];
}
-
- for(int i=0; i<sequenceFeatures.length; i++)
+ if (endRes > 0)
{
- if(sequenceFeatures[i].equals(sf))
- {
- return;
- }
+ endRes += start - 1;
}
- SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
- System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
- temp[sequenceFeatures.length] = sf;
-
- sequenceFeatures = temp;
+ this.end = endRes;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceFeature [] getSequenceFeatures()
- {
- return sequenceFeatures;
- }
-
- public void addPDBId(PDBEntry entry)
- {
- if(pdbIds == null)
- pdbIds = new Vector();
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param name DOCUMENT ME!
+ * @param sequence DOCUMENT ME!
+ */
+ public Sequence(String name, String sequence)
+ {
+ this(name, sequence, 1, -1);
+ }
- pdbIds.addElement(entry);
- }
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public Sequence(SequenceI seq)
+ {
+ this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ }
- /**
- * DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
- */
- public void setPDBId(Vector id)
- {
- pdbIds = id;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void setSequenceFeatures(SequenceFeature[] features)
+ {
+ sequenceFeatures = features;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getPDBId()
+ public synchronized void addSequenceFeature(SequenceFeature sf)
+ {
+ if (sequenceFeatures == null)
{
- return pdbIds;
+ sequenceFeatures = new SequenceFeature[0];
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDisplayId(boolean jvsuffix)
+ for (int i = 0; i < sequenceFeatures.length; i++)
{
- StringBuffer result = new StringBuffer(name);
- if (jvsuffix)
+ if (sequenceFeatures[i].equals(sf))
{
- result.append("/" + start + "-" + end);
+ return;
}
-
- return result.toString();
}
- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- */
- public void setName(String name)
- {
- this.name = name;
- this.parseId();
- }
+ SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+ temp[sequenceFeatures.length] = sf;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName()
- {
- return this.name;
- }
+ sequenceFeatures = temp;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- */
- public void setStart(int start)
- {
- this.start = start;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceFeature[] getSequenceFeatures()
+ {
+ return sequenceFeatures;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStart()
- {
- return this.start;
- }
+ public void addPDBId(PDBEntry entry)
+ {
+ if (pdbIds == null)
+ pdbIds = new Vector();
- /**
- * DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
- */
- public void setEnd(int end)
- {
- this.end = end;
- }
+ pdbIds.addElement(entry);
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEnd()
- {
- return this.end;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ */
+ public void setPDBId(Vector id)
+ {
+ pdbIds = id;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getLength()
- {
- return this.sequence.length();
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getPDBId()
+ {
+ return pdbIds;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- public void setSequence(String seq)
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayId(boolean jvsuffix)
+ {
+ StringBuffer result = new StringBuffer(name);
+ if (jvsuffix)
{
- this.sequence = seq;
- checkValidRange();
+ result.append("/" + start + "-" + end);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence()
- {
- return this.sequence;
- }
+ return result.toString();
+ }
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence(int start, int end)
- {
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
- if (start >= sequence.length())
- {
- return "";
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setName(String name)
+ {
+ this.name = name;
+ this.parseId();
+ }
- if (end >= sequence.length())
- {
- end = sequence.length();
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName()
+ {
+ return this.name;
+ }
- return this.sequence.substring(start, end);
- }
- /**
- * make a new Sequence object from start to end (including gaps) over this seqeunce
- * @param start int
- * @param end int
- * @return SequenceI
- */
- public SequenceI getSubSequence(int start, int end) {
- if (start<0)
- start = 0;
- String seq = getSequence(start, end);
- if (seq=="")
- 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.setDatasetSequence(getDatasetSequence());
- return nseq;
- }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getCharAt(int i)
- {
- if (i < sequence.length())
- {
- return sequence.charAt(i);
- }
- else
- {
- return ' ';
- }
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ */
+ public void setStart(int start)
+ {
+ this.start = start;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
- */
- public void setDescription(String desc)
- {
- this.description = desc;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStart()
+ {
+ return this.start;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDescription()
- {
- return this.description;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param end DOCUMENT ME!
+ */
+ public void setEnd(int end)
+ {
+ this.end = end;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int findIndex(int pos)
- {
- // returns the alignment position for a residue
- int j = start;
- int i = 0;
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEnd()
+ {
+ return this.end;
+ }
- while ((i < sequence.length()) && (j <= end) && (j <= pos))
- {
- if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
- {
- j++;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getLength()
+ {
+ return this.sequence.length();
+ }
- i++;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public void setSequence(String seq)
+ {
+ this.sequence = seq;
+ checkValidRange();
+ }
- if ((j == end) && (j < pos))
- {
- return end + 1;
- }
- else
- {
- return i;
- }
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSequence()
+ {
+ return this.sequence;
+ }
- /**
- * 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
- */
- public int findPosition(int i)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSequence(int start, int end)
+ {
+ // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+ if (start >= sequence.length())
{
- int j = 0;
- int pos = start;
- int seqlen=sequence.length();
- while ((j < i) && (j < seqlen))
- {
- if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
- {
- pos++;
- }
-
- j++;
- }
-
- return pos;
+ return "";
}
- /**
- * 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
- */
- public int[] gapMap()
+ if (end >= sequence.length())
{
- String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
- int[] map = new int[seq.length()];
- int j = 0;
- int p = 0;
-
- while (j < sequence.length())
- {
- if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
- {
- map[p++] = j;
- }
-
- j++;
- }
-
- return map;
+ end = sequence.length();
}
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i)
- {
- if (i >= sequence.length())
- {
- return;
- }
+ return this.sequence.substring(start, end);
+ }
- sequence = sequence.substring(0, i) + sequence.substring(i + 1);
- }
+ /**
+ * make a new Sequence object from start to end (including gaps) over this seqeunce
+ * @param start int
+ * @param end int
+ * @return SequenceI
+ */
+ public SequenceI getSubSequence(int start, int end)
+ {
+ if (start < 0)
+ start = 0;
+ String seq = getSequence(start, end);
+ if (seq == "")
+ 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.setDatasetSequence(getDatasetSequence());
+ return nseq;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void deleteChars(int i, int j)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getCharAt(int i)
+ {
+ if (i < sequence.length())
{
- if (i >= sequence.length())
- {
- return;
- }
-
- if (j >= sequence.length())
- {
- sequence = sequence.substring(0, i);
- }
- else
- {
- sequence = sequence.substring(0, i) + sequence.substring(j);
- }
+ return sequence.charAt(i);
}
-
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- * @param chop DOCUMENT ME!
- */
- public void insertCharAt(int i, char c)
+ else
{
- String tmp = new String(sequence);
+ return ' ';
+ }
+ }
- if (i < sequence.length())
- {
- sequence = tmp.substring(0, i) + String.valueOf(c) +
- tmp.substring(i);
- }
- else
- {
- // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
- char[] ch = new char[(1 + i) - sequence.length()];
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void setDescription(String desc)
+ {
+ this.description = desc;
+ }
- for (int j = 0, k = ch.length; j < k; j++)
- ch[j] = c;
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return this.description;
+ }
- sequence = tmp + String.valueOf(ch);
- }
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pos DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int findIndex(int pos)
+ {
+ // returns the alignment position for a residue
+ int j = start;
+ int i = 0;
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c)
+ while ( (i < sequence.length()) && (j <= end) && (j <= pos))
{
- this.color = c;
- }
+ if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+ {
+ j++;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor()
- {
- return color;
+ i++;
}
- public String getVamsasId()
+ if ( (j == end) && (j < pos))
{
- return vamsasId;
+ return end + 1;
}
-
- public void setVamsasId(String id)
+ else
{
- vamsasId = id;
+ return i;
}
+ }
- public void setDBRef(DBRefEntry [] dbref)
+ /**
+ * 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
+ */
+ public int findPosition(int i)
+ {
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length();
+ while ( (j < i) && (j < seqlen))
{
- dbrefs = dbref;
- }
+ if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
+ {
+ pos++;
+ }
- public DBRefEntry [] getDBRef()
- {
- return dbrefs;
+ j++;
}
- public void addDBRef(DBRefEntry entry)
- {
- if(dbrefs == null)
- dbrefs = new DBRefEntry[0];
+ return pos;
+ }
- DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
- System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+ /**
+ * 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
+ */
+ public int[] gapMap()
+ {
+ String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
+ GapChars, sequence);
+ int[] map = new int[seq.length()];
+ int j = 0;
+ int p = 0;
- temp[temp.length-1] = entry;
+ while (j < sequence.length())
+ {
+ if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+ {
+ map[p++] = j;
+ }
- dbrefs = temp;
+ j++;
}
- public void setDatasetSequence(SequenceI seq)
+ return map;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ public void deleteCharAt(int i)
+ {
+ if (i >= sequence.length())
{
- datasetSequence = seq;
+ return;
}
- public SequenceI getDatasetSequence()
+ 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())
{
- return datasetSequence;
+ return;
}
- public AlignmentAnnotation [] getAnnotation()
+ if (j >= sequence.length())
{
- 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;
+ sequence = sequence.substring(0, i);
}
-
- public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+ else
{
- if(this.annotation==null)
- this.annotation = new Vector();
-
- this.annotation.addElement( annotation );
+ sequence = sequence.substring(0, i) + sequence.substring(j);
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ * @param chop DOCUMENT ME!
+ */
+ public void insertCharAt(int i, int length, char c)
+ {
+ StringBuffer tmp;
- public SequenceGroup getHiddenSequences()
+ if (i >= sequence.length())
{
- return hiddenSequences;
+ length = i - sequence.length() + 1;
+ tmp = new StringBuffer(sequence);
}
+ else
+ tmp = new StringBuffer(sequence.substring(0, i));
- public void addHiddenSequence(SequenceI seq)
+ while (length > 0)
{
- if(hiddenSequences==null)
- {
- hiddenSequences = new SequenceGroup();
- }
- hiddenSequences.addSequence(seq, false);
+ tmp.append(c);
+ length--;
}
- public void showHiddenSequence(SequenceI seq)
+ if (i < sequence.length())
{
- hiddenSequences.deleteSequence(seq, false);
- if (hiddenSequences.getSize(false) < 1)
- {
- hiddenSequences = null;
- }
+ tmp.append(sequence.substring(i));
}
- public void changeCase(boolean toUpper, int start, int end)
- {
- StringBuffer newSeq = new StringBuffer();
+ sequence = tmp.toString();
+ }
- if(end>sequence.length())
- end = sequence.length();
+ public void insertCharAt(int i, char c)
+ {
+ insertCharAt(i, 1, c);
+ }
- if (start > 0)
- {
- newSeq.append(sequence.substring(0, start));
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ */
+ public void setColor(Color c)
+ {
+ this.color = c;
+ }
- if (toUpper)
- newSeq.append(sequence.substring(start, end).toUpperCase());
- else
- newSeq.append(sequence.substring(start, end).toLowerCase());
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color getColor()
+ {
+ return color;
+ }
- if (end < sequence.length())
- newSeq.append(sequence.substring(end));
+ public String getVamsasId()
+ {
+ return vamsasId;
+ }
- sequence = newSeq.toString();
- }
+ public void setVamsasId(String id)
+ {
+ vamsasId = id;
+ }
- public void toggleCase(int start, int end)
- {
- StringBuffer newSeq = new StringBuffer();
+ public void setDBRef(DBRefEntry[] dbref)
+ {
+ dbrefs = dbref;
+ }
- if(end>sequence.length())
- end = sequence.length();
+ public DBRefEntry[] getDBRef()
+ {
+ return dbrefs;
+ }
- if (start > 0)
- {
- newSeq.append(sequence.substring(0, start));
- }
+ public void addDBRef(DBRefEntry entry)
+ {
+ if (dbrefs == null)
+ dbrefs = new DBRefEntry[0];
- char nextChar;
- for(int c=start; c<end; c++)
- {
- nextChar = sequence.charAt(c);
- if(Character.isLetter(nextChar))
- {
- if(Character.isUpperCase(nextChar))
- nextChar = Character.toLowerCase(nextChar);
- else
- nextChar = Character.toUpperCase(nextChar);
- }
+ DBRefEntry[] temp = new DBRefEntry[dbrefs.length + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+ temp[temp.length - 1] = entry;
- newSeq.append(nextChar);
- }
+ dbrefs = temp;
+ }
- if (end < sequence.length())
- newSeq.append(sequence.substring(end));
+ public void setDatasetSequence(SequenceI seq)
+ {
+ datasetSequence = seq;
+ }
- sequence = newSeq.toString();
- }
+ public SequenceI getDatasetSequence()
+ {
+ return datasetSequence;
+ }
- public SequenceI getSubSequence(int start)
+ public AlignmentAnnotation[] getAnnotation()
{
- int e=getLength();
- if (start>=e)
+ if (annotation == null)
return null;
- return getSubSequence(start, getLength());
- }
- public int removeGaps() {
- if (sequence!=null)
- return removeGaps(0, getLength());
- return 0;
+ AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
+ for (int r = 0; r < ret.length; r++)
+ ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+
+ return ret;
}
- public int removeGaps(int start, int end) {
- int jSize = getLength();
- int oSize=jSize;
- if (jSize<=start)
- return 0;
- if (end>jSize)
- end = jSize;
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ if (this.annotation == null)
+ this.annotation = new Vector();
- // Removing a range is much quicker than removing gaps
- // one by one for long sequences
- int j = start;
- int rangeStart=-1, rangeEnd=-1;
+ this.annotation.addElement(annotation);
+ }
- do
+ public SequenceGroup getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ public void addHiddenSequence(SequenceI seq)
+ {
+ if (hiddenSequences == null)
{
- if (jalview.util.Comparison.isGap(getCharAt(j)))
- {
- if(rangeStart==-1)
- {
- rangeStart = j;
- rangeEnd = j+1;
- }
- else
- {
- rangeEnd++;
- }
- j++;
- }
- else
- {
- if(rangeStart>-1)
- {
- deleteChars(rangeStart, rangeEnd);
- j-=rangeEnd-rangeStart;
- jSize-=rangeEnd-rangeStart;
- rangeStart = -1;
- rangeEnd = -1;
- }
- else
- j++;
- }
+ hiddenSequences = new SequenceGroup();
}
- while (j < end && j < jSize);
- if(rangeStart>-1)
+ hiddenSequences.addSequence(seq, false);
+ }
+
+ public void showHiddenSequence(SequenceI seq)
+ {
+ hiddenSequences.deleteSequence(seq, false);
+ if (hiddenSequences.getSize(false) < 1)
{
- deleteChars(rangeStart, rangeEnd);
- jSize-=rangeEnd-rangeStart;
+ hiddenSequences = null;
}
- return oSize-jSize; // number of deleted characters.
}
-
}
+
+
git://source.jalview.org / jalview.git / commitdiff