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package jalview.renderer; |
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import java.util.Arrays; |
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import java.util.Iterator; |
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import java.util.List; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.ContactListI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.renderer.ContactGeometry.contactInterval; |
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@author |
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| 68.2% |
Uncovered Elements: 28 (88) |
Complexity: 27 |
Complexity Density: 0.53 |
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public class ContactGeometry |
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{ |
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final ContactListI contacts; |
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final int pixels_step; |
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final double contacts_per_pixel; |
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final int contact_height; |
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final int graphHeight; |
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final double contacts_step; |
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final int lastStep; |
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@param |
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@param |
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| 92.3% |
Uncovered Elements: 1 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
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145566 |
public ContactGeometry(final ContactListI contacts, int graphHeight)... |
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{ |
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this.contacts = contacts; |
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this.graphHeight = graphHeight; |
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contact_height = contacts.getContactHeight(); |
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contacts_per_pixel = (graphHeight <= 1) ? contact_height |
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: ((double) contact_height) / ((double) graphHeight); |
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if (contacts_per_pixel >= 1) |
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{ |
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pixels_step = 1; |
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} |
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else |
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{ |
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pixels_step = (int) Math |
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.ceil(((double) graphHeight) / (double) contact_height); |
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} |
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contacts_step = pixels_step * contacts_per_pixel; |
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lastStep = (int) Math.min((double) graphHeight, |
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((double) graphHeight) / ((double) pixels_step)); |
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} |
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| 85.7% |
Uncovered Elements: 2 (14) |
Complexity: 5 |
Complexity Density: 0.56 |
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public class contactInterval |
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{ |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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147149644 |
public contactInterval(int cStart, int cEnd, int pStart, int pEnd)... |
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{ |
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this.cStart = cStart; |
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this.cEnd = cEnd; |
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this.pStart = pStart; |
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this.pEnd = pEnd; |
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} |
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public final int cStart; |
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public final int cEnd; |
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public final int pStart; |
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public final int pEnd; |
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| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
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@Override... |
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public boolean equals(Object obj) |
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{ |
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if (obj == null || !(obj instanceof contactInterval)) |
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{ |
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return false; |
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} |
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contactInterval them = (contactInterval) obj; |
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return cStart == them.cStart && cEnd == them.cEnd && pEnd == them.pEnd |
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&& pStart == them.pStart; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String toString() |
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{ |
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return "Contacts [" + cStart + "," + cEnd + "] : Pixels [" + pStart |
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+ "," + pEnd + "]"; |
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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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| 50% |
Uncovered Elements: 12 (24) |
Complexity: 9 |
Complexity Density: 0.64 |
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167447 |
boolean intersects(contactInterval ci, ColumnSelection columnSelection,... |
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HiddenColumns hiddenColumns, boolean visibleOnly) |
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{ |
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boolean rowsel = false; |
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final int[] mappedRange = contacts.getMappedPositionsFor(ci.cStart, |
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ci.cEnd); |
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if (mappedRange == null) |
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{ |
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return false; |
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} |
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for (int p = 0; p < mappedRange.length && !rowsel; p += 2) |
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{ |
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boolean containsHidden = false; |
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if (visibleOnly && hiddenColumns != null |
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&& hiddenColumns.hasHiddenColumns()) |
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{ |
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Iterator<int[]> viscont = hiddenColumns.getVisContigsIterator( |
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-1 + mappedRange[p], -1 + mappedRange[p + 1], false); |
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containsHidden = !viscont.hasNext(); |
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if (!containsHidden) |
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{ |
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for (int[] interval = viscont.next(); viscont |
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.hasNext(); rowsel |= columnSelection |
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.intersects(interval[p], interval[p + 1])) |
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; |
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} |
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} |
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else |
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{ |
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167451 |
rowsel = columnSelection.intersects(-1 + mappedRange[p], |
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-1 + mappedRange[p + 1]); |
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} |
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} |
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return rowsel; |
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} |
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@param |
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@param |
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@return |
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| 66.7% |
Uncovered Elements: 6 (18) |
Complexity: 5 |
Complexity Density: 0.5 |
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public contactInterval mapFor(int pStart, int pEnd)... |
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{ |
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if (pStart < 0) |
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pStart = 0; |
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} |
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if (pEnd < pStart) |
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{ |
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pEnd = pStart; |
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} |
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if (pEnd >= graphHeight) |
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{ |
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pEnd = graphHeight - 1; |
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} |
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if (pStart >= graphHeight) |
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{ |
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pStart = graphHeight - pixels_step; |
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} |
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int step = Math.floorDiv(pStart, pixels_step); |
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return findStep(step); |
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} |
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@param |
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@return |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
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147149649 |
contactInterval findStep(int step)... |
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{ |
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147149649 |
if (step < 0 || step > lastStep) |
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{ |
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return null; |
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} |
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return new contactInterval((int) Math.floor(contacts_step * step), |
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-1 + (int) Math.min(contact_height, |
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Math.floor(contacts_step * (step + 1))), |
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pixels_step * step, |
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Math.min(graphHeight, (step + 1) * pixels_step) - 1); |
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} |
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@param |
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@return |
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| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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167530 |
public contactInterval mapFor(int pCentre)... |
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{ |
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167530 |
if (pCentre >= graphHeight + pixels_step) |
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{ |
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return null; |
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} |
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int step = Math.floorDiv(pCentre, pixels_step); |
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167530 |
return findStep(step); |
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} |
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| 78.6% |
Uncovered Elements: 3 (14) |
Complexity: 4 |
Complexity Density: 0.4 |
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141374 |
public List<contactInterval> allSteps()... |
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{ |
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141374 |
contactInterval[] array = new contactInterval[lastStep + 1]; |
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141374 |
int csum = 0, psum = 0; |
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147123408 |
for (int i = 0; i <= lastStep; i++) |
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{ |
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146982034 |
array[i] = findStep(i); |
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csum += 1 + array[i].cEnd - array[i].cStart; |
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psum += 1 + array[i].pEnd - array[i].pStart; |
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} |
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if (csum != contact_height || psum != graphHeight) |
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{ |
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System.err.println("csum = " + csum + " not " + contact_height + "\n" |
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+ "psum = " + psum + " not " + graphHeight); |
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return null; |
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} |
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return Arrays.asList(array); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
public Iterator<contactInterval> iterateOverContactIntervals(... |
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int graphHeight) |
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{ |
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return null; |
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} |
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} |