+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client 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 Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
package uk.ac.vamsas.objects.utils;\r
\r
import java.util.Vector;\r
import uk.ac.vamsas.objects.core.Seg;\r
\r
/**\r
- * Utilities for working with RangeType and MapType objects.\r
- * Derived from bitter experience.\r
+ * Utilities for working with RangeType and MapType objects. Derived from bitter\r
+ * experience.\r
+ * \r
* @author JimP\r
- *\r
+ * \r
*/\r
public class Range {\r
- static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getFactory().getLog(Range.class);\r
+ static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory\r
+ .getFactory().getLog(Range.class);\r
\r
/**\r
* get start<end range of segment, adjusting for inclusivity flag and\r
* polarity.\r
- *\r
+ * \r
* @param visSeg\r
- * @param ensureDirection when true - always ensure start is less than end.\r
- * @return int[] { start, end, direction} where direction==1 for range running from end to start.\r
+ * @param ensureDirection\r
+ * when true - always ensure start is less than end.\r
+ * @return int[] { start, end, direction} where direction==1 for range running\r
+ * from end to start.\r
*/\r
- public static int[] getSegRange(Seg visSeg, boolean ensureDirection)\r
- {\r
+ public static int[] getSegRange(Seg visSeg, boolean ensureDirection) {\r
boolean incl = visSeg.getInclusive();\r
// adjust for inclusive flag.\r
int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of\r
// region.\r
int start = visSeg.getStart() + (incl ? 0 : pol);\r
int end = visSeg.getEnd() + (incl ? 0 : -pol);\r
- if (ensureDirection && pol == -1)\r
- {\r
+ if (ensureDirection && pol == -1) {\r
// jalview doesn't deal with inverted ranges, yet.\r
int t = end;\r
end = start;\r
start = t;\r
}\r
- return new int[]\r
- {\r
- start, end, pol < 0 ? 1 : 0};\r
+ return new int[] { start, end, pol < 0 ? 1 : 0 };\r
}\r
\r
/**\r
* get real bounds of a RangeType's specification. start and end are an\r
- * inclusive range within which all segments and positions lie.\r
- * TODO: refactor to vamsas utils\r
+ * inclusive range within which all segments and positions lie. TODO: refactor\r
+ * to vamsas utils\r
+ * \r
* @param dseta\r
* @return int[] { start, end}\r
*/\r
- public static int[] getBounds(RangeType dseta)\r
- {\r
- if (dseta != null)\r
- {\r
+ public static int[] getBounds(RangeType dseta) {\r
+ if (dseta != null) {\r
int[] se = null;\r
- if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)\r
- {\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) {\r
+ throw new Error(\r
+ "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
}\r
- if (dseta.getSegCount() > 0)\r
- {\r
+ if (dseta.getSegCount() > 0) {\r
se = getSegRange(dseta.getSeg(0), true);\r
- for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)\r
- {\r
+ for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) {\r
int nse[] = getSegRange(dseta.getSeg(s), true);\r
- if (se[0] > nse[0])\r
- {\r
+ if (se[0] > nse[0]) {\r
se[0] = nse[0];\r
}\r
- if (se[1] < nse[1])\r
- {\r
+ if (se[1] < nse[1]) {\r
se[1] = nse[1];\r
}\r
}\r
}\r
- if (dseta.getPosCount() > 0)\r
- {\r
- // could do a polarity for pos range too. and pass back indication of discontinuities.\r
+ if (dseta.getPosCount() > 0) {\r
+ // could do a polarity for pos range too. and pass back indication of\r
+ // discontinuities.\r
int pos = dseta.getPos(0).getI();\r
- se = new int[]\r
- {\r
- pos, pos};\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
+ se = new int[] { pos, pos };\r
+ for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {\r
pos = dseta.getPos(p).getI();\r
- if (se[0] > pos)\r
- {\r
+ if (se[0] > pos) {\r
se[0] = pos;\r
}\r
- if (se[1] < pos)\r
- {\r
+ if (se[1] < pos) {\r
se[1] = pos;\r
}\r
}\r
}\r
\r
/**\r
- * map from a rangeType's internal frame to the referenced object's coordinate frame.\r
+ * map from a rangeType's internal frame to the referenced object's coordinate\r
+ * frame.\r
+ * \r
* @param dseta\r
* @return int [] { ref(pos)...} for all pos in rangeType's frame.\r
*/\r
- public static int[] getMapping(RangeType dseta)\r
- {\r
+ public static int[] getMapping(RangeType dseta) {\r
Vector posList = new Vector();\r
- if (dseta != null)\r
- {\r
+ if (dseta != null) {\r
int[] se = null;\r
- if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)\r
- {\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) {\r
+ throw new Error(\r
+ "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
}\r
- if (dseta.getSegCount() > 0)\r
- {\r
- for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)\r
- {\r
+ if (dseta.getSegCount() > 0) {\r
+ for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) {\r
se = getSegRange(dseta.getSeg(s), false);\r
int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);\r
- for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)\r
- {\r
+ for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) {\r
posList.add(new Integer(p));\r
}\r
}\r
- }\r
- else if (dseta.getPosCount() > 0)\r
- {\r
+ } else if (dseta.getPosCount() > 0) {\r
int pos = dseta.getPos(0).getI();\r
\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
+ for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {\r
pos = dseta.getPos(p).getI();\r
posList.add(new Integer(pos));\r
}\r
}\r
}\r
- if (posList != null && posList.size() > 0)\r
- {\r
+ if (posList != null && posList.size() > 0) {\r
int[] range = new int[posList.size()];\r
- for (int i = 0; i < range.length; i++)\r
- {\r
- range[i] = ( (Integer) posList.elementAt(i)).intValue();\r
+ for (int i = 0; i < range.length; i++) {\r
+ range[i] = ((Integer) posList.elementAt(i)).intValue();\r
}\r
posList.clear();\r
return range;\r
return null;\r
}\r
\r
- public static int[] getIntervals(RangeType range)\r
- {\r
- int[] intervals=null;\r
+ public static int[] getIntervals(RangeType range) {\r
+ int[] intervals = null;\r
Vector posList = new Vector();\r
- if (range != null)\r
- {\r
+ if (range != null) {\r
int[] se = null;\r
- if (range.getSegCount() > 0 && range.getPosCount() > 0)\r
- {\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
-}\r
- if (range.getSegCount() > 0)\r
- {\r
- for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)\r
- {\r
+ if (range.getSegCount() > 0 && range.getPosCount() > 0) {\r
+ throw new Error(\r
+ "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ }\r
+ if (range.getSegCount() > 0) {\r
+ for (int s = 0, sSize = range.getSegCount(); s < sSize; s++) {\r
se = getSegRange(range.getSeg(s), false);\r
posList.addElement(new Integer(se[0]));\r
posList.addElement(new Integer(se[1]));\r
}\r
- }\r
- else if (range.getPosCount() > 0)\r
- {\r
+ } else if (range.getPosCount() > 0) {\r
int pos = range.getPos(0).getI();\r
- for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)\r
- {\r
+ for (int p = 0, pSize = range.getPosCount(); p < pSize; p++) {\r
pos = range.getPos(p).getI();\r
posList.add(new Integer(pos));\r
posList.add(new Integer(pos));\r
}\r
}\r
}\r
- if (posList != null && posList.size() > 0)\r
- {\r
- intervals=new int[posList.size()];\r
+ if (posList != null && posList.size() > 0) {\r
+ intervals = new int[posList.size()];\r
java.util.Enumeration e = posList.elements();\r
- int i=0;\r
- while (e.hasMoreElements())\r
- {\r
- intervals[i++] = ((Integer)e.nextElement()).intValue();\r
+ int i = 0;\r
+ while (e.hasMoreElements()) {\r
+ intervals[i++] = ((Integer) e.nextElement()).intValue();\r
}\r
}\r
return intervals;\r
}\r
+\r
/**\r
* initialise a range type object from a set of start/end inclusive intervals\r
+ * \r
* @param mrt\r
* @param range\r
*/\r
- public static void initRangeType(RangeType mrt, int[] range)\r
- {\r
- for (int i=0; i<range.length; i+=2)\r
- {\r
+ public static void initRangeType(RangeType mrt, int[] range) {\r
+ for (int i = 0; i < range.length; i += 2) {\r
Seg vSeg = new Seg();\r
vSeg.setStart(range[i]);\r
- vSeg.setEnd(range[i+1]);\r
+ vSeg.setEnd(range[i + 1]);\r
vSeg.setInclusive(true);\r
mrt.addSeg(vSeg);\r
}\r
\r
/**\r
* \r
- * @param maprange where the from range is the local mapped range, and the to range is the 'mapped' range in the MapRangeType\r
+ * @param maprange\r
+ * where the from range is the local mapped range, and the to range\r
+ * is the 'mapped' range in the MapRangeType\r
* @param default unit for local\r
* @param default unit for mapped\r
* @return MapList\r
*/\r
- public static MapList parsemapType(MapType maprange, int localu, int mappedu)\r
- {\r
+ public static MapList parsemapType(MapType maprange, int localu, int mappedu) {\r
MapList ml = null;\r
int[] localRange = getIntervals(maprange.getLocal());\r
int[] mappedRange = getIntervals(maprange.getMapped());\r
- long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu;\r
- long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit() : mappedu;\r
- ml = new MapList(localRange, mappedRange, (int)lu, (int)mu);\r
+ long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()\r
+ : localu;\r
+ long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit()\r
+ : mappedu;\r
+ ml = new MapList(localRange, mappedRange, (int) lu, (int) mu);\r
return ml;\r
}\r
+\r
/**\r
* Parse map with default units of 1,1\r
+ * \r
* @param map\r
* @return MapList representing map\r
*/\r
- public static MapList parsemapType(MapType map)\r
- {\r
- if (!map.getLocal().hasUnit() || !map.getMapped().hasUnit())\r
- {\r
- if (log.isDebugEnabled())\r
- { \r
- log.debug(\r
- "using default mapping length of 1:1 for map "\r
- +(map.isRegistered() ? map.getVorbaId().toString() : ("<no Id registered> "+map.toString())));\r
+ public static MapList parsemapType(MapType map) {\r
+ if (!map.getLocal().hasUnit() || !map.getMapped().hasUnit()) {\r
+ if (log.isDebugEnabled()) {\r
+ log.debug("using default mapping length of 1:1 for map "\r
+ + (map.isRegistered() ? map.getVorbaId().toString()\r
+ : ("<no Id registered> " + map.toString())));\r
}\r
}\r
- return parsemapType(map, 1, 1); \r
+ return parsemapType(map, 1, 1);\r
}\r
\r
/**\r
* initialise a MapType object from a MapList object.\r
+ * \r
* @param maprange\r
* @param ml\r
* @param setUnits\r
*/\r
- public static void initMapType(MapType maprange, MapList ml, boolean setUnits)\r
- {\r
+ public static void initMapType(MapType maprange, MapList ml, boolean setUnits) {\r
initMapType(maprange, ml, setUnits, false);\r
}\r
+\r
/**\r
* \r
* @param maprange\r
* @param ml\r
* @param setUnits\r
- * @param reverse - reverse MapList mapping for Local and Mapped ranges and units \r
+ * @param reverse\r
+ * - reverse MapList mapping for Local and Mapped ranges and units\r
*/\r
- public static void initMapType(MapType maprange, MapList ml, boolean setUnits, boolean reverse)\r
- {\r
+ public static void initMapType(MapType maprange, MapList ml,\r
+ boolean setUnits, boolean reverse) {\r
maprange.setLocal(new Local());\r
maprange.setMapped(new Mapped());\r
- if (!reverse)\r
- {\r
+ if (!reverse) {\r
initRangeType(maprange.getLocal(), ml.getFromRanges());\r
initRangeType(maprange.getMapped(), ml.getToRanges());\r
- } else {\r
- initRangeType(maprange.getLocal(), ml.getToRanges());\r
- initRangeType(maprange.getMapped(), ml.getFromRanges());\r
- }\r
- if (setUnits)\r
- {\r
- if (!reverse)\r
- { \r
+ } else {\r
+ initRangeType(maprange.getLocal(), ml.getToRanges());\r
+ initRangeType(maprange.getMapped(), ml.getFromRanges());\r
+ }\r
+ if (setUnits) {\r
+ if (!reverse) {\r
maprange.getLocal().setUnit(ml.getFromRatio());\r
maprange.getMapped().setUnit(ml.getToRatio());\r
} else {\r
}\r
}\r
\r
-}
\ No newline at end of file
+}\r
git://source.jalview.org / vamsas.git / blobdiff