/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
getDataset().addSequence(ds);
}
}
-
sequences.addElement(snew);
+
+ hiddenSequences.adjustHeightSequenceAdded();
}
return groups;
}
- /** Takes out columns consisting entirely of gaps (-,.," ")
- */
- public void removeGaps()
- {
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();
- int j, jSize = seqs.length;
-
- int width = 0;
- for (int i = 0; i < jSize; i++)
- {
- if (seqs[i].getLength() > width)
- {
- width = seqs[i].getLength();
- }
- }
-
- int startCol = -1, endCol = -1;
- boolean delete = true;
- for (int i = 0; i < width; i++)
- {
- delete = true;
-
- for (j = 0; j < jSize; j++)
- {
- if (seqs[j].getLength() > i)
- {
- if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
- {
- if(delete)
- endCol = i;
-
- delete = false;
- break;
- }
- }
- }
-
- if(delete && startCol==-1)
- {
- startCol = i;
- }
-
-
- if (!delete && startCol > -1)
- {
- deleteColumns(seqs, startCol, endCol);
- width -= (endCol - startCol);
- i -= (endCol - startCol);
- startCol = -1;
- endCol = -1;
- }
- }
-
- if (delete && startCol > -1)
- {
- deleteColumns(seqs, startCol, endCol);
- }
- }
-
- /** Removes a range of columns (start to end inclusive).
- *
- * @param seqs Sequences to remove columns from
- * @param start Start column in the alignment
- * @param end End column in the alignment
- */
- public void deleteColumns(SequenceI [] seqs, int start, int end)
- {
- for(int i=0; i<seqs.length; i++)
- seqs[i].deleteChars(start, end);
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void trimLeft(int i)
- {
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();
- int j, jSize = seqs.length;
- for (j = 0; j < jSize; j++)
- {
- int newstart = seqs[j].findPosition(i);
-
- if(i>seqs[j].getLength())
- {
- sequences.removeElement(seqs[j]);
- j--;
- jSize--;
- }
- else
- {
- seqs[j].setStart(newstart);
- seqs[j].setSequence(seqs[j].getSequence().substring(i));
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void trimRight(int i)
- {
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();
- int j, jSize = seqs.length;
- for (j = 0; j < jSize; j++)
- {
- int newend = seqs[j].findPosition(i);
-
- seqs[j].setEnd(newend);
- if(seqs[j].getLength()>i)
- seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));
- }
- }
-
/**
* DOCUMENT ME!
*
*/
public void deleteSequence(SequenceI s)
{
- for (int i = 0; i < getHeight(); i++)
- {
- if (getSequenceAt(i) == s)
- {
- deleteSequence(i);
- }
- }
+ deleteSequence(findIndex(s));
}
/**
*/
public void deleteSequence(int i)
{
+ if(i>0 && i<getHeight())
+ {
sequences.removeElementAt(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
+ }
}
while (i < sequences.size())
{
- Sequence s = (Sequence)getSequenceAt(i);
- s.hiddenSequences = null;
+ SequenceI s = getSequenceAt(i);
s.setColor(java.awt.Color.white);
i++;
}
{
if (groups.contains(g))
{
- //remove any hidden representatives
- // for(int i=0; i<g.getsiz
- // g.getSequences()
groups.removeElement(g);
}
}
return maxLength;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getMaxIdLength()
- {
- int max = 0;
- int i = 0;
-
- while (i < sequences.size())
- {
- SequenceI seq = getSequenceAt(i);
- String tmp = seq.getName() + "/" + seq.getStart() + "-" +
- seq.getEnd();
-
- if (tmp.length() > max)
- {
- max = tmp.length();
- }
-
- i++;
- }
-
- return max;
- }
/**
* DOCUMENT ME!
return gapCharacter;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getAAFrequency()
- {
- return AAFrequency.calculate(sequences, 0, getWidth());
- }
/**
* DOCUMENT ME!
for (int i=0; i<sequences.size(); i++) {
alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
}
- return new CigarArray(alseqs);
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
}
}