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package jalview.io.vamsas; |
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import jalview.io.VamsasAppDatastore; |
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import jalview.util.MessageManager; |
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import java.util.List; |
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import java.util.Vector; |
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import uk.ac.vamsas.client.Vobject; |
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import uk.ac.vamsas.objects.core.Local; |
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import uk.ac.vamsas.objects.core.MapType; |
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import uk.ac.vamsas.objects.core.Mapped; |
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import uk.ac.vamsas.objects.core.RangeType; |
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import uk.ac.vamsas.objects.core.Seg; |
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@author |
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| 0% |
Uncovered Elements: 192 (192) |
Complexity: 55 |
Complexity Density: 0.52 |
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public abstract class Rangetype extends DatastoreItem |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public Rangetype()... |
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{ |
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super(); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public Rangetype(VamsasAppDatastore datastore)... |
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{ |
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super(datastore); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public Rangetype(VamsasAppDatastore datastore, Vobject vobj,... |
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Class jvClass) |
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{ |
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super(datastore, vobj, jvClass); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public Rangetype(VamsasAppDatastore datastore, Object jvobj, Class vClass)... |
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{ |
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super(datastore, jvobj, vClass); |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 43 (43) |
Complexity: 12 |
Complexity Density: 0.52 |
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protected int[] getBounds(RangeType dseta)... |
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{ |
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if (dseta != null) |
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{ |
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int[] se = null; |
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if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) |
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{ |
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throw new Error(MessageManager.getString( |
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"error.invalid_vamsas_rangetype_cannot_resolve_lists")); |
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} |
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if (dseta.getSegCount() > 0) |
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{ |
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se = getSegRange(dseta.getSeg(0), true); |
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for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) |
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{ |
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int nse[] = getSegRange(dseta.getSeg(s), true); |
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if (se[0] > nse[0]) |
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{ |
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se[0] = nse[0]; |
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} |
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if (se[1] < nse[1]) |
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{ |
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se[1] = nse[1]; |
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} |
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} |
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} |
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if (dseta.getPosCount() > 0) |
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{ |
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int pos = dseta.getPos(0).getI(); |
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se = new int[] { pos, pos }; |
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for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) |
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{ |
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pos = dseta.getPos(p).getI(); |
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if (se[0] > pos) |
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{ |
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se[0] = pos; |
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} |
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if (se[1] < pos) |
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{ |
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se[1] = pos; |
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} |
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} |
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} |
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return se; |
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} |
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return null; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 45 (45) |
Complexity: 14 |
Complexity Density: 0.61 |
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protected int[] getMapping(RangeType dseta)... |
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{ |
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Vector posList = new Vector(); |
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if (dseta != null) |
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{ |
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int[] se = null; |
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if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) |
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{ |
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throw new Error(MessageManager.getString( |
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"error.invalid_vamsas_rangetype_cannot_resolve_lists")); |
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} |
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if (dseta.getSegCount() > 0) |
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{ |
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for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) |
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{ |
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se = getSegRange(dseta.getSeg(s), false); |
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int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1); |
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for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) |
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{ |
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posList.add(Integer.valueOf(p)); |
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} |
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} |
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} |
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else if (dseta.getPosCount() > 0) |
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{ |
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int pos = dseta.getPos(0).getI(); |
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for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) |
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{ |
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pos = dseta.getPos(p).getI(); |
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posList.add(Integer.valueOf(pos)); |
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} |
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} |
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} |
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if (posList != null && posList.size() > 0) |
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{ |
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int[] range = new int[posList.size()]; |
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for (int i = 0; i < range.length; i++) |
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{ |
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range[i] = ((Integer) posList.elementAt(i)).intValue(); |
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} |
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posList.clear(); |
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return range; |
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} |
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return null; |
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} |
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| 0% |
Uncovered Elements: 40 (40) |
Complexity: 11 |
Complexity Density: 0.46 |
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protected int[] getIntervals(RangeType range)... |
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{ |
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int[] intervals = null; |
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Vector posList = new Vector(); |
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if (range != null) |
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{ |
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int[] se = null; |
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if (range.getSegCount() > 0 && range.getPosCount() > 0) |
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{ |
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throw new Error(MessageManager.getString( |
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"error.invalid_vamsas_rangetype_cannot_resolve_lists")); |
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} |
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if (range.getSegCount() > 0) |
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{ |
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for (int s = 0, sSize = range.getSegCount(); s < sSize; s++) |
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{ |
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se = getSegRange(range.getSeg(s), false); |
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posList.addElement(Integer.valueOf(se[0])); |
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posList.addElement(Integer.valueOf(se[1])); |
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} |
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} |
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else if (range.getPosCount() > 0) |
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{ |
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int pos = range.getPos(0).getI(); |
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for (int p = 0, pSize = range.getPosCount(); p < pSize; p++) |
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{ |
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pos = range.getPos(p).getI(); |
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posList.add(Integer.valueOf(pos)); |
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posList.add(Integer.valueOf(pos)); |
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} |
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} |
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} |
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if (posList != null && posList.size() > 0) |
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{ |
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intervals = new int[posList.size()]; |
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java.util.Enumeration e = posList.elements(); |
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int i = 0; |
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while (e.hasMoreElements()) |
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{ |
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intervals[i++] = ((Integer) e.nextElement()).intValue(); |
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} |
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} |
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return intervals; |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
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protected void initRangeType(RangeType mrt, List<int[]> ranges)... |
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{ |
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for (int[] range : ranges) |
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{ |
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Seg vSeg = new Seg(); |
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vSeg.setStart(range[0]); |
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vSeg.setEnd(range[1]); |
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vSeg.setInclusive(true); |
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mrt.addSeg(vSeg); |
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} |
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} |
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@param |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
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0 |
protected jalview.util.MapList parsemapType(MapType maprange, int localu,... |
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int mappedu) |
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{ |
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jalview.util.MapList ml = null; |
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int[] localRange = getIntervals(maprange.getLocal()); |
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int[] mappedRange = getIntervals(maprange.getMapped()); |
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long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() |
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: localu; |
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long mu = maprange.getMapped().hasUnit() |
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? maprange.getMapped().getUnit() |
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: mappedu; |
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ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, |
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(int) mu); |
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return ml; |
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} |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 4 |
Complexity Density: 1.33 |
|
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0 |
protected jalview.util.MapList parsemapType(MapType map)... |
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{ |
272 |
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if (!map.getLocal().hasUnit() || map.getMapped().hasUnit()) |
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{ |
274 |
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jalview.bin.Cache.log |
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.warn("using default mapping length of 1:1 for map " |
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+ (map.isRegistered() ? map.getVorbaId().toString() |
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: ("<no Id registered> " + map.toString()))); |
278 |
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} |
279 |
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return parsemapType(map, 1, 1); |
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} |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
289 |
0 |
protected void initMapType(MapType maprange, jalview.util.MapList ml,... |
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boolean setUnits) |
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{ |
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initMapType(maprange, ml, setUnits, false); |
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} |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 23 (23) |
Complexity: 5 |
Complexity Density: 0.33 |
|
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0 |
protected void initMapType(MapType maprange, jalview.util.MapList ml,... |
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boolean setUnits, boolean reverse) |
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{ |
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if (ml == null) |
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{ |
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throw new Error( |
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"Implementation error. MapList is null for initMapType."); |
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} |
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maprange.setLocal(new Local()); |
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maprange.setMapped(new Mapped()); |
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0 |
if (!reverse) |
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{ |
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initRangeType(maprange.getLocal(), ml.getFromRanges()); |
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initRangeType(maprange.getMapped(), ml.getToRanges()); |
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} |
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else |
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{ |
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initRangeType(maprange.getLocal(), ml.getToRanges()); |
321 |
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initRangeType(maprange.getMapped(), ml.getFromRanges()); |
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} |
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if (setUnits) |
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{ |
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if (!reverse) |
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{ |
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maprange.getLocal().setUnit(ml.getFromRatio()); |
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maprange.getMapped().setUnit(ml.getToRatio()); |
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} |
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else |
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{ |
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maprange.getLocal().setUnit(ml.getToRatio()); |
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maprange.getMapped().setUnit(ml.getFromRatio()); |
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} |
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336 |
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337 |
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} |
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} |
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} |