-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-public class DBRefEntry\r
-{\r
- String source, version, accessionId;\r
-\r
- public DBRefEntry(String source, String version, String accessionId)\r
- {\r
- this.source = source;\r
- this.version = version;\r
- this.accessionId = accessionId;\r
- }\r
-\r
- public String getSource()\r
- {\r
- return source;\r
- }\r
-\r
- public String getVersion()\r
- {\r
- return version;\r
- }\r
-\r
- public String getAccessionId()\r
- {\r
- return accessionId;\r
- }\r
-\r
-}\r
+/*
+ * 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;
+
+public class DBRefEntry
+{
+ String source="", version="", accessionId="";
+ /**
+ * maps from associated sequence to the database sequence's coordinate system
+ */
+ Mapping map=null;
+ public DBRefEntry() {
+
+ }
+ public DBRefEntry(String source, String version, String accessionId)
+ {
+ this.source = source;
+ this.version = version;
+ this.accessionId = accessionId;
+ }
+ public boolean equals(DBRefEntry entry) {
+ if (entry==this)
+ return true;
+ if (entry==null)
+ return false;
+ if ((source!=null && entry.source!=null && source.equals(entry.source))
+ &&
+ (accessionId!=null && entry.accessionId!=null && accessionId.equals(entry.accessionId))
+ &&
+ (version!=null && entry.version!=null && version.equals(entry.version))
+ &&
+ ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
+ return true;
+ }
+ return false;
+ }
+ public String getSource()
+ {
+ return source;
+ }
+
+ public String getVersion()
+ {
+ return version;
+ }
+
+ public String getAccessionId()
+ {
+ return accessionId;
+ }
+/**
+ * @param accessionId the accessionId to set
+ */
+public void setAccessionId(String accessionId) {
+ this.accessionId = accessionId;
+}
+/**
+ * @param source the source to set
+ */
+public void setSource(String source) {
+ this.source = source;
+}
+/**
+ * @param version the version to set
+ */
+public void setVersion(String version) {
+ this.version = version;
+}
+/**
+ * @return the map
+ */
+public Mapping getMap() {
+ return map;
+}
+/**
+ * @param map the map to set
+ */
+public void setMap(Mapping map) {
+ this.map = map;
+}
+}
--- /dev/null
+package jalview.datamodel;\r
+\r
+import jalview.util.MapList;\r
+\r
+public class Mapping {\r
+ /**\r
+ * Contains the\r
+ * start-end pairs mapping from \r
+ * the associated sequence to the \r
+ * sequence in the database \r
+ * coordinate system\r
+ * it also takes care of step difference between coordinate systems\r
+ */\r
+ MapList map=null;\r
+ /**\r
+ * The seuqence that map maps the associated seuqence to (if any).\r
+ */\r
+ SequenceI to=null;\r
+ public Mapping(MapList map) {\r
+ super();\r
+ this.map = map;\r
+ }\r
+ /**\r
+ * create a new mapping from\r
+ * @param exon int[] {start,end,start,end} series on associated sequence\r
+ * @param is int[] {start,end,...} ranges on the reference frame being mapped to\r
+ * @param i step size on associated sequence\r
+ * @param j step size on mapped frame\r
+ */\r
+ public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)\r
+ {\r
+ map = new MapList(exon, is, i, j);\r
+ }\r
+\r
+ /**\r
+ * @return the map\r
+ */\r
+ public MapList getMap() {\r
+ return map;\r
+ }\r
+\r
+ /**\r
+ * @param map the map to set\r
+ */\r
+ public void setMap(MapList map) {\r
+ this.map = map;\r
+ }\r
+ public boolean equals(Mapping other) {\r
+ if (other==null)\r
+ return false;\r
+ if (other==this)\r
+ return true;\r
+ if ((map!=null && other.map==null) || (map==null && other.map!=null))\r
+ return false;\r
+ if (map.equals(other.map))\r
+ return true;\r
+ return false;\r
+ }\r
+ /**\r
+ * get the 'initial' position in the associated\r
+ * sequence for a position in the mapped reference frame\r
+ * @param mpos\r
+ * @return\r
+ */\r
+ public int getPosition(int mpos) \r
+ {\r
+ if (map!=null) {\r
+ int[] mp = map.shiftTo(mpos);\r
+ if (mp!=null)\r
+ {\r
+ return mp[0];\r
+ }\r
+ }\r
+ return mpos;\r
+ }\r
+ public int[] getWord(int mpos) {\r
+ if (map!=null) {\r
+ int[] mp=map.shiftTo(mpos);\r
+ if (mp!=null) {\r
+ return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)}; \r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ /**\r
+ * width of mapped unit in associated sequence \r
+ * \r
+ */\r
+ public int getWidth() {\r
+ if (map!=null) {\r
+ return map.getFromRatio();\r
+ }\r
+ return 1;\r
+ }\r
+\r
+ /**\r
+ * width of unit in mapped reference frame\r
+ * @return\r
+ */\r
+ public int getMappedWidth() {\r
+ if (map!=null) {\r
+ return map.getToRatio();\r
+ }\r
+ return 1;\r
+ }\r
+ /**\r
+ * get mapped position in the associated\r
+ * reference frame for position pos in the\r
+ * associated sequence.\r
+ * @param pos\r
+ * @return\r
+ */\r
+ public int getMappedPosition(int pos) {\r
+ if (map!=null) {\r
+ int[] mp = map.shiftFrom(pos);\r
+ if (mp!=null)\r
+ {\r
+ return mp[0];\r
+ }\r
+ }\r
+ return pos;\r
+ }\r
+ public int[] getMappedWord(int pos) {\r
+ if (map!=null) {\r
+ int[] mp = map.shiftFrom(pos);\r
+ if (mp!=null)\r
+ {\r
+ return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)};\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ /**\r
+ * locates the region of feature f in the associated sequence's reference frame \r
+ * @param f\r
+ * @return one or more features corresponding to f\r
+ */\r
+ public SequenceFeature[] locateFeature(SequenceFeature f)\r
+ {\r
+ // this is a stopgap - features broken over exon boundaries will not be\r
+ // broken into a collection of feature fragments.\r
+ // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence\r
+ // need a function like int [] fromrange = map.getRange(from,to)\r
+ // need to make subgrouped sequence features.\r
+ if (true) {\r
+ if (map!=null) {\r
+ int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());\r
+ SequenceFeature[] vf = new SequenceFeature[frange.length/2];\r
+ for (int i=0,v=0;i<frange.length;i+=2) {\r
+ vf[v] = new SequenceFeature(f);\r
+ vf[v].setBegin(frange[i]);\r
+ vf[v].setEnd(frange[i+1]);\r
+ if (frange.length>2)\r
+ vf[v].setDescription(f.getDescription() +"\nPart "+v);\r
+ }\r
+ return vf;\r
+ }\r
+ }\r
+ if (false){\r
+ int[] word = getWord(f.getBegin());\r
+ if (word[0]<word[1]) \r
+ {\r
+ f.setBegin(word[0]);\r
+ } else {\r
+ f.setBegin(word[1]);\r
+ }\r
+ word = getWord(f.getEnd());\r
+ if (word[0]>word[1]) \r
+ {\r
+ f.setEnd(word[0]);\r
+ } else {\r
+ f.setEnd(word[1]);\r
+ }\r
+ }\r
+ // give up and just return the feature.\r
+ return new SequenceFeature[] { f };\r
+ }\r
+ \r
+ /**\r
+ * return a series of contigs on the associated sequence corresponding to\r
+ * the from,to interval on the mapped reference frame\r
+ * @param from\r
+ * @param to\r
+ * @return\r
+ */\r
+ public int[] locateRange(int from, int to) {\r
+ //TODO\r
+ return null;\r
+ }\r
+ /**\r
+ * return a series of contigs on the mapped reference frame corresponding to\r
+ * the from,to interval on the associated sequence\r
+ * @param from\r
+ * @param to\r
+ * @return\r
+ */\r
+ public int[] locateMappedRange(int from, int to) {\r
+ //TODO \r
+ return null;\r
+ }\r
+}\r
*/
public class MapList
{
+ /* (non-Javadoc)
+ * @see java.lang.Object#clone()
+ */
+ protected Object clone() throws CloneNotSupportedException {
+ // TODO Auto-generated method stub
+ return super.clone();
+ }
+ /* (non-Javadoc)
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ public boolean equals(MapList obj) {
+ if (obj==this)
+ return true;
+ if (obj!=null && obj.fromRatio==fromRatio && obj.toRatio==toRatio
+ && obj.fromShifts!=null && obj.toShifts!=null) {
+ Iterator i,j;
+ for (i=fromShifts.iterator(),j=obj.fromShifts.iterator(); i.hasNext();) {
+ int[] mi=(int[]) i.next();
+ if (!j.hasNext())
+ return false;
+ int[] mj=(int[]) j.next();
+ if (mi[0]!=mj[0] || mi[1]!=mj[1])
+ return false;
+ }
+ if (j.hasNext())
+ return false;
+ for (i=toShifts.iterator(),j=obj.toShifts.iterator(); i.hasNext();) {
+ int[] mi=(int[]) i.next();
+ if (!j.hasNext())
+ return false;
+ int[] mj=(int[]) j.next();
+ if (mi[0]!=mj[0] || mi[1]!=mj[1])
+ return false;
+ }
+ if (j.hasNext())
+ return false;
+ return true;
+ }
+ return false;
+ }
public Vector fromShifts;
public Vector toShifts;
int fromRatio; // number of steps in fromShifts to one toRatio unit
int toRatio; // number of steps in toShifts to one fromRatio
+ /**
+ * lowest and highest value in the from Map
+ */
+ int[] fromRange=null;
+ /**
+ * lowest and highest value in the to Map
+ */
+ int[] toRange=null;
+ public int getFromRatio()
+ {
+ return fromRatio;
+ }
+ public int getToRatio()
+ {
+ return toRatio;
+ }
+ public int getFromLowest() {
+ return fromRange[0];
+ }
+ public int getFromHighest() {
+ return fromRange[1];
+ }
+ public int getToLowest() {
+ return toRange[0];
+ }
+ public int getToHighest() {
+ return toRange[1];
+ }
+ private void ensureRange(int[] limits, int pos) {
+ if (limits[0]>pos)
+ limits[0]=pos;
+ if (limits[1]<pos)
+ limits[1]=pos;
+ }
public MapList(int from[], int to[], int fromRatio, int toRatio)
{
+ fromRange=new int[] { from[0],from[1] };
+ toRange=new int[] { to[0],to[1] };
+
fromShifts = new Vector();
- for (int i = 0; i < from.length; i += 2)
- {
+ for (int i=0;i<from.length; i+=2)
+ {
+ ensureRange(fromRange, from[i]);
+ ensureRange(fromRange, from[i+1]);
+
fromShifts.add(new int[]
- {from[i], from[i + 1]});
+ {from[i], from[i + 1]});
}
toShifts = new Vector();
- for (int i = 0; i < to.length; i += 2)
+ for (int i=0;i<to.length; i+=2)
{
+ ensureRange(toRange, to[i]);
+ ensureRange(toRange, to[i+1]);
toShifts.add(new int[]
- {to[i], to[i + 1]});
+ {to[i], to[i + 1]});
}
- this.fromRatio = fromRatio;
- this.toRatio = toRatio;
+ this.fromRatio=fromRatio;
+ this.toRatio=toRatio;
}
-
/**
* get all mapped positions from 'from' to 'to'
* @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
{
return posMap(fromShifts, fromRatio, toShifts, toRatio);
}
-
/**
* get all mapped positions from 'to' to 'from'
* @return int[to position]=position mapped in from
*/
public int[][] makeToMap()
{
- return posMap(toShifts, toRatio, fromShifts, fromRatio);
+ return posMap(toShifts,toRatio, fromShifts, fromRatio);
}
-
/**
* construct an int map for intervals in intVals
* @param intVals
* @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
*/
private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
- int toRatio)
+ int toRatio)
{
Iterator iv = intVals.iterator();
if (!iv.hasNext())
{
return null;
}
- int[] intv = (int[]) iv.next();
- int from = intv[0], to = intv[1];
+ int[] intv=(int[]) iv.next();
+ int from=intv[0],to=intv[1];
if (from > to)
{
from = intv[1];
- to = intv[0];
+ to=intv[0];
}
while (iv.hasNext())
{
intv = (int[]) iv.next();
- if (intv[0] < from)
+ if (intv[0]<from)
{
- from = intv[0];
+ from=intv[0];
}
- if (intv[1] < from)
+ if (intv[1]<from)
{
- from = intv[1];
+ from=intv[1];
}
- if (intv[0] > to)
+ if (intv[0]>to)
{
- to = intv[0];
+ to=intv[0];
}
- if (intv[1] > to)
+ if (intv[1]>to)
{
- to = intv[1];
+ to=intv[1];
}
}
- int tF = 0, tT = 0;
- int mp[][] = new int[to - from + 2][];
+ int tF=0,tT=0;
+ int mp[][] = new int[to-from+2][];
for (int i = 0; i < mp.length; i++)
{
- int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
+ int[] m = shift(i+from,intVals,ratio,toIntVals, toRatio);
if (m != null)
{
if (i == 0)
{
- tF = tT = m[0];
+ tF=tT=m[0];
}
else
{
if (m[0] < tF)
{
- tF = m[0];
+ tF=m[0];
}
if (m[0] > tT)
{
- tT = m[0];
+ tT=m[0];
}
}
}
mp[i] = m;
}
int[][] map = new int[][]
- {
+ {
new int[]
- {
- from, to, tF, tT}, new int[to - from + 2]};
+ {
+ from, to, tF, tT}, new int[to - from + 2]};
map[0][2] = tF;
map[0][3] = tT;
{
if (mp[i] != null)
{
- map[1][i] = mp[i][0] - tF;
+ map[1][i] = mp[i][0]-tF;
}
else
{
}
return map;
}
-
/**
* addShift
* @param pos start position for shift (in original reference frame)
* @param shift length of shift
*
- public void addShift(int pos, int shift)
- {
+ public void addShift(int pos, int shift)
+ {
int sidx = 0;
int[] rshift=null;
- while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+ while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
sidx++;
if (sidx==shifts.size())
shifts.insertElementAt(new int[] { pos, shift}, sidx);
else
rshift[1]+=shift;
- }
+ }
*/
/**
* shift from pos to To(pos)
*
* @param pos int
- * @return int shifted position in To, frameshift in From
+ * @return int shifted position in To, frameshift in From, direction of mapped symbol in To
*/
public int[] shiftFrom(int pos)
{
/**
* inverse of shiftFrom - maps pos in To to a position in From
* @param pos (in To)
- * @return shifted position in From, frameshift in To
+ * @return shifted position in From, frameshift in To, direction of mapped symbol in From
*/
public int[] shiftTo(int pos)
{
return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
}
-
/**
- *
+ *
* @param fromShifts
* @param fromRatio
* @param toShifts
* @return
*/
private int[] shift(int pos, Vector fromShifts, int fromRatio,
- Vector toShifts, int toRatio)
+ Vector toShifts, int toRatio)
{
int[] fromCount = countPos(fromShifts.iterator(), pos);
- if (fromCount == null)
+ if (fromCount==null)
{
return null;
}
- int fromRemainder = (fromCount[0] - 1) % fromRatio;
- int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
+ int fromRemainder=(fromCount[0]-1) % fromRatio;
+ int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
int[] toPos = countToPos(toShifts.iterator(), toCount);
- if (toPos == null)
+ if (toPos==null)
{
return null; // throw new Error("Bad Mapping!");
}
//System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
return new int[]
- {
- toPos[0], fromRemainder};
+ {
+ toPos[0], fromRemainder, toPos[1]};
}
-
/**
* count how many positions pos is along the series of intervals.
* @param intVals
*/
private int[] countPos(Iterator intVals, int pos)
{
- int count = 0, intv[];
+ int count=0,intv[];
while (intVals.hasNext())
{
- intv = (int[]) intVals.next();
+ intv = (int[])intVals.next();
if (intv[0] <= intv[1])
{
if (pos >= intv[0] && pos <= intv[1])
{
return new int[]
- {
+ {
count + pos - intv[0] + 1, +1};
}
else
{
- count += intv[1] - intv[0] + 1;
+ count+=intv[1]-intv[0]+1;
}
}
else
if (pos >= intv[1] && pos <= intv[0])
{
return new int[]
- {
+ {
count + intv[0] - pos + 1, -1};
}
else
{
- count += intv[0] - intv[1] + 1;
+ count+=intv[0]-intv[1]+1;
}
}
}
return null;
}
-
/**
* count out pos positions into a series of intervals and return the position
* @param intVals
private int[] countToPos(Iterator intVals, int pos)
{
int count = 0, diff = 0, intv[] =
- {
+ {
0, 0};
while (intVals.hasNext())
{
- intv = (int[]) intVals.next();
- diff = intv[1] - intv[0];
+ intv = (int[])intVals.next();
+ diff = intv[1]-intv[0];
if (diff >= 0)
{
if (pos <= count + 1 + diff)
{
return new int[]
- {
+ {
pos - count - 1 + intv[0], +1};
}
else
{
- count += 1 + diff;
+ count+=1+diff;
}
}
else
if (pos <= count + 1 - diff)
{
return new int[]
- {
+ {
intv[0] - (pos - count - 1), -1};
}
else
{
- count += 1 - diff;
+ count+=1-diff;
}
}
}
- return null; //(diff<0) ? (intv[1]-1) : (intv[0]+1);
+ return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
+ }
+ /**
+ * find series of intervals mapping from start-end in the From map.
+ * @param start position in to map
+ * @param end position in to map
+ * @return series of ranges in from map
+ */
+ public int[] locateInFrom(int start, int end) {
+ // inefficient implementation
+ int fromStart[] = shiftTo(start);
+ int fromEnd[] = shiftTo(end);
+ if (fromStart==null || fromEnd==null)
+ return null;
+ int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
+ return iv;
}
+ /**
+ * find series of intervals mapping from start-end in the to map.
+ * @param start position in from map
+ * @param end position in from map
+ * @return series of ranges in to map
+ */
+ public int[] locateInTo(int start, int end) {
+ // inefficient implementation
+ int toStart[] = shiftFrom(start);
+ int toEnd[] = shiftFrom(end);
+ if (toStart==null || toEnd==null)
+ return null;
+ int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
+ return iv;
+ }
+ /**
+ * like shift - except returns the intervals in the given vector of shifts which were spanned
+ * in traversing fromStart to fromEnd
+ * @param fromShifts2
+ * @param fromStart
+ * @param fromEnd
+ * @param fromRatio2
+ * @return
+ */
+ private int[] getIntervals(Vector fromShifts2, int[] fromStart, int[] fromEnd, int fromRatio2)
+ {
+ // correct for word direction for start and end
+ int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
+ int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
+ Iterator intv = fromShifts2.iterator();
+ int iv[],i=0,fs=-1,fe=-1; // containing intervals
+ while (intv.hasNext() && (fs==-1 || fe==-1)) {
+ iv = (int[]) intv.next();
+ if (iv[0]<=iv[1]) {
+ if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
+ fs = i;
+ }
+ if (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
+ fe = i;
+ }
+ } else {
+ if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
+ fs = i;
+ }
+ if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
+ fe = i;
+ }
+ }
+ i++;
+ }
+ if (fs==fe && fe==-1)
+ return null;
+ Vector ranges=new Vector();
+ if (fs<=fe) {
+ intv = fromShifts2.iterator();
+ i=0;
+ while (i<fs) {
+ intv.next();
+ i++;
+ }
+ // truncate initial interval
+ iv = (int[]) intv.next();
+ iv = new int[] { iv[0], iv[1]};// clone
+ if (i==fs)
+ iv[0] = startpos;
+ while (i!=fe) {
+ ranges.addElement(iv); // add initial range
+ iv = (int[]) intv.next(); // get next interval
+ iv = new int[] { iv[0], iv[1]};// clone
+ i++;
+ }
+ if (i==fe)
+ iv[1] = endpos;
+ ranges.addElement(iv); // add only - or final range
+ } else {
+ // walk from end of interval.
+ i=fromShifts2.size()-1;
+ while (i>fs) {
+ i--;
+ }
+ iv = (int[]) fromShifts2.elementAt(i);
+ iv = new int[] { iv[1], iv[0]};// reverse and clone
+ // truncate initial interval
+ if (i==fs)
+ {
+ iv[0] = startpos;
+ }
+ while (i!=fe) {
+ ranges.addElement(iv); // add (truncated) reversed interval
+ iv = (int[]) fromShifts2.elementAt(--i);
+ iv = new int[] { iv[1], iv[0] }; // reverse and clone
+ }
+ if (i==fe) {
+ // interval is already reversed
+ iv[1] = endpos;
+ }
+ ranges.addElement(iv); // add only - or final range
+ }
+ // create array of start end intervals.
+ int[] range = null;
+ if (ranges!=null && ranges.size()>0)
+ {
+ range = new int[ranges.size()*2];
+ intv = ranges.iterator();
+ i=0;
+ while (intv.hasNext())
+ {
+ iv = (int[]) intv.next();
+ range[i++] = iv[0];
+ range[i++] = iv[1];
+ intv.remove();
+ }
+ }
+ return range;
+ }
+ /**
+ * test routine. not incremental.
+ * @param ml
+ * @param fromS
+ * @param fromE
+ */
public static void testMap(MapList ml, int fromS, int fromE)
{
for (int from = 1; from <= 25; from++)
{
- int[] too = ml.shiftFrom(from);
- System.out.print("ShiftFrom(" + from + ")==");
- if (too == null)
+ int[] too=ml.shiftFrom(from);
+ System.out.print("ShiftFrom("+from+")==");
+ if (too==null)
{
System.out.print("NaN\n");
}
else
{
- System.out.print(too[0] + " % " + too[1]);
+ System.out.print(too[0]+" % "+too[1]+" ("+too[2]+")");
System.out.print("\t+--+\t");
- int[] toofrom = ml.shiftTo(too[0]);
+ int[] toofrom=ml.shiftTo(too[0]);
if (toofrom != null)
{
- if (toofrom[0] != from)
+ if (toofrom[0]!=from)
{
System.err.println("Mapping not reflexive:" + from + " " + too[0] +
- "->" + toofrom[0]);
+ "->" + toofrom[0]);
}
System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
- toofrom[1]);
+ toofrom[1]+" ("+toofrom[2]+")");
}
else
{
System.out.println("ShiftTo(" + too[0] + ")==" +
- "NaN! - not Bijective Mapping!");
+ "NaN! - not Bijective Mapping!");
}
}
}
int mmap[][] = ml.makeFromMap();
System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
- mmap[0][2] + " " + mmap[0][3] + " ");
+ mmap[0][2] + " " + mmap[0][3] + " ");
+ for (int i = 1; i <= mmap[1].length; i++)
+ {
+ if (mmap[1][i - 1] == -1)
+ {
+ System.out.print(i+"=XXX");
+
+ }
+ else
+ {
+ System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+ }
+ if (i % 20==0)
+ {
+ System.out.print("\n");
+ }
+ else
+ {
+ System.out.print(",");
+ }
+ }
+ //test range function
+ System.out.print("\nTest locateInFrom\n");
+ {
+ int f=mmap[0][2],t=mmap[0][3];
+ while (f<t) {
+ System.out.println("Range "+f+" to "+t);
+ int rng[] = ml.locateInFrom(f,t);
+ if (rng!=null)
+ {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\nReversed\n");
+ rng = ml.locateInFrom(t,f);
+ if (rng!=null)
+ {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\n");
+ f++;t--;
+ }
+ }
+ System.out.print("\n");
+ mmap = ml.makeToMap();
+ System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
+ mmap[0][2] + " " + mmap[0][3] + " ");
for (int i = 1; i <= mmap[1].length; i++)
{
if (mmap[1][i - 1] == -1)
{
- System.out.print(i + "=XXX");
+ System.out.print(i+"=XXX");
}
else
{
- System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+ System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
}
- if (i % 20 == 0)
+ if (i % 20==0)
{
System.out.print("\n");
}
}
}
System.out.print("\n");
+ //test range function
+ System.out.print("\nTest locateInTo\n");
+ {
+ int f=mmap[0][2],t=mmap[0][3];
+ while (f<t) {
+ System.out.println("Range "+f+" to "+t);
+ int rng[] = ml.locateInTo(f,t);
+ if (rng!=null) {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\nReversed\n");
+ rng = ml.locateInTo(t,f);
+ if (rng!=null)
+ {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ f++; t--;
+ System.out.print("\n");
+ }
+ }
+
}
public static void main(String argv[])
{
MapList ml = new MapList(new int[]
- {1, 5, 10, 15, 25, 20},
- new int[]
- {51, 1}, 1, 3);
+ {1, 5, 10, 15, 25, 20},
+ new int[]
+ {51, 1}, 1, 3);
MapList ml1 = new MapList(new int[]
- {1, 3, 17, 4},
- new int[]
- {51, 1}, 1, 3);
-
+ {1, 3, 17, 4},
+ new int[]
+ {51, 1}, 1, 3);
+ MapList ml2 = new MapList(new int[] { 1, 60 },
+ new int[] { 1, 20 }, 3, 1);
// test internal consistency
int to[] = new int[51];
- MapList.testMap(ml, 1, 25);
+ MapList.testMap(ml, 1, 60);
/*
- for (int from=1; from<=51; from++) {
- int[] too=ml.shiftTo(from);
- int[] toofrom=ml.shiftFrom(too[0]);
- System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
- }*/
+ for (int from=1; from<=51; from++) {
+ int[] too=ml.shiftTo(from);
+ int[] toofrom=ml.shiftFrom(too[0]);
+ System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
+ }*/
System.out.print("Success?\n"); // if we get here - something must be working!
}
}
git://source.jalview.org / jalview.git / commitdiff