X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=fd3d89710fa95909ca678ee416bc7189ce550a5b;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=74f4cdabb14fe6db13a4bfa51c42a7dcdde653ac;hpb=25a836152d861ebf9db68a2fd2c52e39b0eeb200;p=jalview.git
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 74f4cda..fd3d897 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,20 +1,19 @@
/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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 .
*/
package jalview.datamodel;
@@ -29,13 +28,14 @@ public class ColumnSelection
{
Vector selected = new Vector();
- //Vector of int [] {startCol, endCol}
+ // Vector of int [] {startCol, endCol}
Vector hiddenColumns;
/**
* Add a column to the selection
- *
- * @param col index of column
+ *
+ * @param col
+ * index of column
*/
public void addElement(int col)
{
@@ -56,8 +56,9 @@ public class ColumnSelection
/**
* removes col from selection
- *
- * @param col index of column to be removed
+ *
+ * @param col
+ * index of column to be removed
*/
public void removeElement(int col)
{
@@ -71,8 +72,11 @@ public class ColumnSelection
/**
* removes a range of columns from the selection
- * @param start int - first column in range to be removed
- * @param end int - last col
+ *
+ * @param start
+ * int - first column in range to be removed
+ * @param end
+ * int - last col
*/
public void removeElements(int start, int end)
{
@@ -88,7 +92,7 @@ public class ColumnSelection
}
/**
- *
+ *
* @return Vector containing selected columns as Integers
*/
public Vector getSelected()
@@ -97,9 +101,10 @@ public class ColumnSelection
}
/**
- *
- * @param col index to search for in column selection
- *
+ *
+ * @param col
+ * index to search for in column selection
+ *
* @return true if Integer(col) is in selection.
*/
public boolean contains(int col)
@@ -109,19 +114,20 @@ public class ColumnSelection
/**
* Column number at position i in selection
- *
- * @param i index into selected columns
- *
+ *
+ * @param i
+ * index into selected columns
+ *
* @return column number in alignment
*/
public int columnAt(int i)
{
- return ( (Integer) selected.elementAt(i)).intValue();
+ return ((Integer) selected.elementAt(i)).intValue();
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int size()
@@ -131,7 +137,7 @@ public class ColumnSelection
/**
* rightmost selected column
- *
+ *
* @return rightmost column in alignment that is selected
*/
public int getMax()
@@ -151,7 +157,7 @@ public class ColumnSelection
/**
* Leftmost column in selection
- *
+ *
* @return column index of leftmost column in selection
*/
public int getMin()
@@ -171,9 +177,11 @@ public class ColumnSelection
/**
* propagate shift in alignment columns to column selection
- *
- * @param start beginning of edit
- * @param left shift in edit (+ve for removal, or -ve for inserts)
+ *
+ * @param start
+ * beginning of edit
+ * @param left
+ * shift in edit (+ve for removal, or -ve for inserts)
*/
public Vector compensateForEdit(int start, int change)
{
@@ -197,8 +205,7 @@ public class ColumnSelection
int[] region = (int[]) hiddenColumns.elementAt(i);
if (region[0] > start && start + change > region[1])
{
- deletedHiddenColumns.addElement(
- hiddenColumns.elementAt(i));
+ deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
hiddenColumns.removeElementAt(i);
i--;
@@ -226,10 +233,13 @@ public class ColumnSelection
}
/**
- * propagate shift in alignment columns to column selection
- * special version of compensateForEdit - allowing for edits within hidden regions
- * @param start beginning of edit
- * @param left shift in edit (+ve for removal, or -ve for inserts)
+ * propagate shift in alignment columns to column selection special version of
+ * compensateForEdit - allowing for edits within hidden regions
+ *
+ * @param start
+ * beginning of edit
+ * @param left
+ * shift in edit (+ve for removal, or -ve for inserts)
*/
private void compensateForDelEdits(int start, int change)
{
@@ -274,8 +284,9 @@ public class ColumnSelection
}
/**
- * Adjust hidden column boundaries based on a series of column
- * additions or deletions in visible regions.
+ * Adjust hidden column boundaries based on a series of column additions or
+ * deletions in visible regions.
+ *
* @param shiftrecord
* @return
*/
@@ -290,7 +301,7 @@ public class ColumnSelection
for (int i = 0, j = shifts.size(); i < j; i++)
{
int[] sh = (int[]) shifts.elementAt(i);
- //compensateForEdit(shifted+sh[0], sh[1]);
+ // compensateForEdit(shifted+sh[0], sh[1]);
compensateForDelEdits(shifted + sh[0], sh[1]);
shifted -= sh[1];
}
@@ -301,8 +312,9 @@ public class ColumnSelection
}
/**
- * removes intersection of position,length ranges in deletions
- * from the start,end regions marked in intervals.
+ * removes intersection of position,length ranges in deletions from the
+ * start,end regions marked in intervals.
+ *
* @param deletions
* @param intervals
* @return
@@ -389,7 +401,8 @@ public class ColumnSelection
}
}
}
- return pruned; // true if any interval was removed or modified by operations.
+ return pruned; // true if any interval was removed or modified by
+ // operations.
}
private boolean pruneColumnList(Vector deletion, Vector list)
@@ -400,7 +413,7 @@ public class ColumnSelection
int i = 0, j = list.size();
while (i < j && s <= t)
{
- int c = ( (Integer) list.elementAt(i++)).intValue();
+ int c = ((Integer) list.elementAt(i++)).intValue();
if (sr[0] <= c)
{
if (sr[1] + sr[0] >= c)
@@ -422,8 +435,9 @@ public class ColumnSelection
}
/**
- * remove any hiddenColumns or selected columns and shift remaining
- * based on a series of position, range deletions.
+ * remove any hiddenColumns or selected columns and shift remaining based on a
+ * series of position, range deletions.
+ *
* @param deletions
*/
public void pruneDeletions(ShiftList deletions)
@@ -457,9 +471,11 @@ public class ColumnSelection
}
/**
- * This Method is used to return all the HiddenColumn regions
- * less than the given index.
- * @param end int
+ * This Method is used to return all the HiddenColumn regions less than the
+ * given index.
+ *
+ * @param end
+ * int
* @return Vector
*/
public Vector getHiddenColumns()
@@ -469,7 +485,9 @@ public class ColumnSelection
/**
* Return absolute column index for a visible column index
- * @param column int column index in alignment view
+ *
+ * @param column
+ * int column index in alignment view
* @return alignment column index for column
*/
public int adjustForHiddenColumns(int column)
@@ -490,9 +508,12 @@ public class ColumnSelection
}
/**
- * Use this method to find out where a visible column is in the alignment
- * when hidden columns exist
- * @param hiddenColumn int
+ * Use this method to find out where a column will appear in the visible
+ * alignment when hidden columns exist. If the column is not visible, then the
+ * left-most visible column will always be returned.
+ *
+ * @param hiddenColumn
+ * int
* @return int
*/
public int findColumnPosition(int hiddenColumn)
@@ -501,22 +522,21 @@ public class ColumnSelection
if (hiddenColumns != null)
{
int index = 0;
- int gaps = 0;
+ int[] region;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ region = (int[]) hiddenColumns.elementAt(index++);
if (hiddenColumn > region[1])
{
result -= region[1] + 1 - region[0];
}
- index++;
+ } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+ if (hiddenColumn > region[0] && hiddenColumn < region[1])
+ {
+ return region[0] + hiddenColumn - result;
}
- while (index < hiddenColumns.size());
-
- result -= gaps;
}
-
- return result;
+ return result; // return the shifted position after removing hidden columns.
}
/**
@@ -540,8 +560,7 @@ public class ColumnSelection
gaps += region[1] + 1 - region[0];
result = region[1] + 1;
index++;
- }
- while (index < hiddenRegion + 1);
+ } while (index < hiddenRegion + 1);
result -= gaps;
}
@@ -550,10 +569,11 @@ public class ColumnSelection
}
/**
- * THis method returns the rightmost limit of a
- * region of an alignment with hidden columns.
- * In otherwords, the next hidden column.
- * @param index int
+ * THis method returns the rightmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the next hidden column.
+ *
+ * @param index
+ * int
*/
public int getHiddenBoundaryRight(int alPos)
{
@@ -569,8 +589,7 @@ public class ColumnSelection
}
index++;
- }
- while (index < hiddenColumns.size());
+ } while (index < hiddenColumns.size());
}
return alPos;
@@ -578,10 +597,11 @@ public class ColumnSelection
}
/**
- * This method returns the leftmost limit of a
- * region of an alignment with hidden columns.
- * In otherwords, the previous hidden column.
- * @param index int
+ * This method returns the leftmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the previous hidden column.
+ *
+ * @param index
+ * int
*/
public int getHiddenBoundaryLeft(int alPos)
{
@@ -597,8 +617,7 @@ public class ColumnSelection
}
index--;
- }
- while (index > -1);
+ } while (index > -1);
}
return alPos;
@@ -609,7 +628,7 @@ public class ColumnSelection
{
while (size() > 0)
{
- int column = ( (Integer) getSelected().firstElement()).intValue();
+ int column = ((Integer) getSelected().firstElement()).intValue();
hideColumns(column);
}
@@ -637,7 +656,7 @@ public class ColumnSelection
else if (end < region[0] && start < region[0])
{
hiddenColumns.insertElementAt(new int[]
- {start, end}, i);
+ { start, end }, i);
added = true;
break;
}
@@ -650,15 +669,17 @@ public class ColumnSelection
else if (!added)
{
hiddenColumns.addElement(new int[]
- {start, end});
+ { start, end });
}
}
/**
- * This method will find a range of selected columns
- * around the column specified
- * @param res int
+ * This method will find a range of selected columns around the column
+ * specified
+ *
+ * @param res
+ * int
*/
public void hideColumns(int col)
{
@@ -742,6 +763,7 @@ public class ColumnSelection
/**
* Copy constructor
+ *
* @param copy
*/
public ColumnSelection(ColumnSelection copy)
@@ -782,7 +804,7 @@ public class ColumnSelection
}
public String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
+ SequenceI[] seqs)
{
int i, iSize = seqs.length;
String selection[] = new String[iSize];
@@ -843,10 +865,13 @@ public class ColumnSelection
/**
* return all visible segments between the given start and end boundaries
- *
- * @param start (first column inclusive from 0)
- * @param end (last column - not inclusive)
- * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end vstart)
{
visiblecontigs.addElement(new int[]
- {vstart, hideStart - 1});
+ { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
@@ -880,7 +905,7 @@ public class ColumnSelection
if (vstart < end)
{
visiblecontigs.addElement(new int[]
- {vstart, end - 1});
+ { vstart, end - 1 });
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
@@ -896,32 +921,40 @@ public class ColumnSelection
else
{
return new int[]
- {
- start, end - 1};
+ { start, end - 1 };
}
}
/**
- * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
* @param alignmentAnnotation
*/
public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- makeVisibleAnnotation(-1,-1,alignmentAnnotation);
+ makeVisibleAnnotation(-1, -1, alignmentAnnotation);
}
+
/**
- * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
- * @param start remove any annotation to the right of this column
- * @param end remove any annotation to the left of this column
- * @param alignmentAnnotation the annotation to operate on
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param alignmentAnnotation
+ * the annotation to operate on
*/
- public void makeVisibleAnnotation(int start, int end, AlignmentAnnotation alignmentAnnotation)
+ public void makeVisibleAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
{
- if (alignmentAnnotation.annotations==null)
+ if (alignmentAnnotation.annotations == null)
{
return;
}
- if (start==end && end==-1)
+ if (start == end && end == -1)
{
start = 0;
end = alignmentAnnotation.annotations.length;
@@ -929,81 +962,93 @@ public class ColumnSelection
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector annels = new Vector();
- Annotation[] els = null;
- Vector regions = getHiddenColumns();
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd,w=0;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
+ Vector annels = new Vector();
+ Annotation[] els = null;
+ Vector regions = getHiddenColumns();
+ int blockStart = start, blockEnd = end;
+ int[] region;
+ int hideStart, hideEnd, w = 0;
- if (hideStart < start)
- {
- continue;
- }
+ for (int j = 0; j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
+ if (hideStart < start)
+ {
+ continue;
+ }
- if (blockStart > blockEnd)
- {
- break;
- }
+ blockStart = Math.min(blockStart, hideEnd + 1);
+ blockEnd = Math.min(blockEnd, hideStart);
- annels.addElement(els = new Annotation[blockEnd-blockStart]);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
- w+=els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
+ if (blockStart > blockEnd)
+ {
+ break;
}
- if (end > blockStart)
+ annels.addElement(els = new Annotation[blockEnd - blockStart]);
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+ 0, els.length);
+ w += els.length;
+ blockStart = hideEnd + 1;
+ blockEnd = end;
+ }
+
+ if (end > blockStart)
+ {
+ annels.addElement(els = new Annotation[end - blockStart + 1]);
+ if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
{
- annels.addElement(els = new Annotation[end-blockStart+1]);
- if (end-blockStart+1<=alignmentAnnotation.annotations.length)
- {
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
- } else {
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, (end-blockStart+1));
- }
- w+=els.length;
+ // copy just the visible segment of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0, els.length);
}
- if (w==0)
- return;
- Enumeration e = annels.elements();
- alignmentAnnotation.annotations = new Annotation[w];
- w=0;
- while (e.hasMoreElements())
+ else
{
- Annotation[] chnk = (Annotation[]) e.nextElement();
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);
- w+=chnk.length;
+ // copy to the end of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0,
+ (alignmentAnnotation.annotations.length - blockStart));
}
- } else {
+ w += els.length;
+ }
+ if (w == 0)
+ return;
+ Enumeration e = annels.elements();
+ alignmentAnnotation.annotations = new Annotation[w];
+ w = 0;
+ while (e.hasMoreElements())
+ {
+ Annotation[] chnk = (Annotation[]) e.nextElement();
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
+ }
+ }
+ else
+ {
alignmentAnnotation.restrict(start, end);
}
}
/**
- * Invert the column selection from first to end-1.
- * leaves hiddenColumns untouched (and unselected)
+ * Invert the column selection from first to end-1. leaves hiddenColumns
+ * untouched (and unselected)
+ *
* @param first
* @param end
*/
public void invertColumnSelection(int first, int width)
{
- boolean hasHidden = hiddenColumns!=null && hiddenColumns.size()>0;
- for(int i=first; i 0;
+ for (int i = first; i < width; i++)
{
+ if (contains(i))
+ {
removeElement(i);
- }
+ }
else
{
if (!hasHidden || isVisible(i))
@@ -1011,6 +1056,203 @@ public class ColumnSelection
addElement(i);
}
}
- }
+ }
+ }
+
+ /**
+ * add in any unselected columns from the given column selection, excluding
+ * any that are hidden.
+ *
+ * @param colsel
+ */
+ public void addElementsFrom(ColumnSelection colsel)
+ {
+ if (colsel != null && colsel.size() > 0)
+ {
+ Enumeration e = colsel.getSelected().elements();
+ while (e.hasMoreElements())
+ {
+ Object eo = e.nextElement();
+ if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+ {
+ if (!selected.contains(eo))
+ {
+ selected.addElement(eo);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * set the selected columns the given column selection, excluding any columns
+ * that are hidden.
+ *
+ * @param colsel
+ */
+ public void setElementsFrom(ColumnSelection colsel)
+ {
+ selected = new Vector();
+ if (colsel.selected != null && colsel.selected.size() > 0)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ // only select visible columns in this columns selection
+ selected = new Vector();
+ addElementsFrom(colsel);
+ }
+ else
+ {
+ // add everything regardless
+ Enumeration en = colsel.selected.elements();
+ while (en.hasMoreElements())
+ {
+ selected.addElement(en.nextElement());
+ }
+ }
+ }
+ }
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * @param al
+ * - alignment to have gaps inserted into it
+ * @param input
+ * - alignment view where sequence corresponding to profileseq is
+ * first entry
+ * @return new Column selection for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public static ColumnSelection propagateInsertions(SequenceI profileseq,
+ Alignment al, AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ // return propagateInsertions(profileseq, al, )
+ char gc = al.getGapCharacter();
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+ ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+ SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
+ nview.propagateInsertions(profileseq, al, origseq);
+ return nview;
+ }
+
+ /**
+ *
+ * @param profileseq
+ * - sequence in al which corresponds to origseq
+ * @param al
+ * - alignment which is to have gaps inserted into it
+ * @param origseq
+ * - sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ public void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ SequenceI origseq)
+ {
+ char gc = al.getGapCharacter();
+ // recover mapping between sequence's non-gap positions and positions
+ // mapping to view.
+ pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
+ int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
+ int spos = 0;
+ int offset = 0;
+ // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ // alandcolsel[0])[0].gapMap()))
+ // add profile to visible contigs
+ for (int v = 0; v < viscontigs.length; v += 2)
+ {
+ if (viscontigs[v] > spos)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= spos + offset)
+ {
+ // pad sequence
+ int diff = spos + offset - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = spos + offset - sq.length() - 1) > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ }
+ }
+ sq += sb.toString();
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, spos + offset) + sb.toString()
+ + sq.substring(spos + offset));
+ }
+ }
+ }
+ // offset+=sb.length();
+ }
+ spos = viscontigs[v + 1] + 1;
+ }
+ if ((offset + spos) < profileseq.getLength())
+ {
+ // pad the final region with gaps.
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj == profileseq)
+ {
+ continue;
+ }
+ String sq = sqobj.getSequenceAsString();
+ // pad sequence
+ int diff = origseq.getLength() - sq.length();
+ while (diff > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ diff = origseq.getLength() - sq.length();
+ }
+ }
+ }
}
}