+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.util.Vector;
* create a new mapping from
*
* @param to
- * the sequence being mapped
+ * the sequence being mapped
* @param exon
- * int[] {start,end,start,end} series on associated sequence
+ * int[] {start,end,start,end} series on associated sequence
* @param is
- * int[] {start,end,...} ranges on the reference frame being mapped
- * to
+ * int[] {start,end,...} ranges on the reference frame being
+ * mapped to
* @param i
- * step size on associated sequence
+ * step size on associated sequence
* @param j
- * step size on mapped frame
+ * step size on mapped frame
*/
public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
{
/**
* @param map
- * the map to set
+ * the map to set
*/
public void setMap(MapList map)
{
* gets boundary in direction of mapping
*
* @param position
- * in mapped reference frame
+ * in mapped reference frame
* @return int{start, end} positions in associated sequence (in direction of
* mapped word)
*/
if (map != null)
{
int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
- if (frange==null)
+ if (frange == null)
{
// JBPNote - this isprobably not the right thing to doJBPHack
return null;
vf[v].setBegin(frange[i]);
vf[v].setEnd(frange[i + 1]);
if (frange.length > 2)
- vf[v].setDescription(f.getDescription() + "\nPart " + (v+1));
+ vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
}
return vf;
}
for (int vc = 0; vc < viscontigs.length; vc += 2)
{
// find a mapped range in this visible region
- int[] mpr = locateMappedRange(1+viscontigs[vc], viscontigs[vc + 1]-1);
+ int[] mpr = locateMappedRange(1 + viscontigs[vc],
+ viscontigs[vc + 1] - 1);
if (mpr != null)
{
for (int m = 0; m < mpr.length; m += 2)
}
}
}
- int[] from = new int[fromRange.size()*2];
- int[] to = new int[toRange.size()*2];
+ int[] from = new int[fromRange.size() * 2];
+ int[] to = new int[toRange.size() * 2];
int[] r;
- for (int f=0,fSize=fromRange.size(); f<fSize; f++)
+ for (int f = 0, fSize = fromRange.size(); f < fSize; f++)
{
r = (int[]) fromRange.elementAt(f);
- from[f*2] = r[0];
- from[f*2+1] = r[1];
+ from[f * 2] = r[0];
+ from[f * 2 + 1] = r[1];
}
- for (int f=0,fSize=toRange.size(); f<fSize; f++)
+ for (int f = 0, fSize = toRange.size(); f < fSize; f++)
{
r = (int[]) toRange.elementAt(f);
- to[f*2] = r[0];
- to[f*2+1] = r[1];
+ to[f * 2] = r[0];
+ to[f * 2 + 1] = r[1];
}
- copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+ copy.setMap(new MapList(from, to, map.getFromRatio(), map
+ .getToRatio()));
}
return copy;
}
+
public static void main(String[] args)
{
/**
- * trite test of the intersectVisContigs method
- * for a simple DNA -> Protein exon map and a range of visContigs
+ * trite test of the intersectVisContigs method for a simple DNA -> Protein
+ * exon map and a range of visContigs
*/
- MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
+ MapList fk = new MapList(new int[]
+ { 1, 6, 8, 13, 15, 23 }, new int[]
+ { 1, 7 }, 3, 1);
Mapping m = new Mapping(fk);
- Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
- Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
- System.out.println(""+m_1.map.getFromRanges());
-
-
+ Mapping m_1 = m.intersectVisContigs(new int[]
+ { fk.getFromLowest(), fk.getFromHighest() });
+ Mapping m_2 = m.intersectVisContigs(new int[]
+ { 1, 7, 11, 20 });
+ System.out.println("" + m_1.map.getFromRanges());
+
}
+
/**
* get the sequence being mapped to - if any
+ *
* @return null or a dataset sequence
*/
public SequenceI getTo()
{
return to;
}
+
/**
* set the dataset sequence being mapped to if any
+ *
* @param tto
*/
public void setTo(SequenceI tto)
to = tto;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable
to = null;
super.finalize();
}
-
+
}
git://source.jalview.org / jalview.git / blobdiff