From f047ab25cc45bfc9d130f67d2c56a940751d9c91 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 28 Sep 2023 17:39:51 +0100 Subject: [PATCH] JAL-3858 improved contactInterval computation and added detailed test coverage for ContactGeometry - contactInterval.cStart/cEnd and pStart/pEnd are now base-0 inclusive ranges, always less than contactHeight and graphHeight - change in mapFor behaviour so cStart/cEnd and pStart/pEnd are always just one mapped range, not as many as requested to cover mapFor(pFrom,pTo) --- src/jalview/gui/AnnotationPanel.java | 264 +++++++++++------------- src/jalview/renderer/ContactGeometry.java | 139 +++++++++++-- src/jalview/renderer/ContactMapRenderer.java | 8 +- test/jalview/renderer/ContactGeometryTest.java | 176 ++++++++++++++++ 4 files changed, 419 insertions(+), 168 deletions(-) create mode 100644 test/jalview/renderer/ContactGeometryTest.java diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index ee4c327..f01d7be 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -648,144 +648,152 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, clicked.graphHeight); - ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset, - yOffset); - /** - * start and end range corresponding to the row range under the mouse at - * column currentX - */ - int fr, to; - fr = Math.min(cXci.cStart, cXci.cEnd); - to = Math.max(cXci.cStart, cXci.cEnd); - - // double click selects the whole group - if (evt.getClickCount() == 2) + ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset); + if (cXci != null) { - ContactMatrixI matrix = av.getContactMatrix(clicked); + /** + * start and end range corresponding to the row range under the mouse at + * column currentX + */ + int fr, to; + fr = Math.min(cXci.cStart, cXci.cEnd); + to = Math.max(cXci.cStart, cXci.cEnd); - if (matrix != null) + // double click selects the whole group + if (evt.getClickCount() == 2) { - // simplest approach is to select all group containing column - if (matrix.hasGroups()) + ContactMatrixI matrix = av.getContactMatrix(clicked); + + if (matrix != null) { - SequenceI rseq = clicked.sequenceRef; - BitSet grp = new BitSet(); - grp.or(matrix.getGroupsFor(currentX)); - // TODO: cXci needs to be mapped to real groups - for (int c = fr; c <= to; c++) + // simplest approach is to select all group containing column + if (matrix.hasGroups()) { - BitSet additionalGrp = matrix.getGroupsFor(c); - grp.or(additionalGrp); - } + SequenceI rseq = clicked.sequenceRef; + BitSet grp = new BitSet(); + grp.or(matrix.getGroupsFor(currentX)); + // TODO: cXci needs to be mapped to real groups + for (int c = fr; c <= to; c++) + { + BitSet additionalGrp = matrix.getGroupsFor(c); + grp.or(additionalGrp); + } - HiddenColumns hc = av.getAlignment().getHiddenColumns(); - ColumnSelection cs = av.getColumnSelection(); - - for (int p=grp.nextSetBit(0); p >= 0; p = grp - .nextSetBit(p + 1)) - { - if (matrix instanceof MappableContactMatrixI) + HiddenColumns hc = av.getAlignment().getHiddenColumns(); + ColumnSelection cs = av.getColumnSelection(); + + for (int p = grp.nextSetBit(0); p >= 0; p = grp + .nextSetBit(p + 1)) { - // find the end of this run of set bits - int nextp = grp.nextClearBit(p)-1; - int[] pos = ((MappableContactMatrixI)matrix).getMappedPositionsFor(rseq, p,nextp); - p=nextp; - - if (pos!=null) + if (matrix instanceof MappableContactMatrixI) { - for (int pos_p = pos[0];pos_p<=pos[1];pos_p++) + // find the end of this run of set bits + int nextp = grp.nextClearBit(p) - 1; + int[] pos = ((MappableContactMatrixI) matrix) + .getMappedPositionsFor(rseq, p, nextp); + p = nextp; + + if (pos != null) { - int col = rseq.findIndex(pos_p)-1; - if (col>=0 && (!av.hasHiddenColumns() || hc.isVisible(col))) + for (int pos_p = pos[0]; pos_p <= pos[1]; pos_p++) { - cs.addElement(col); + int col = rseq.findIndex(pos_p) - 1; + if (col >= 0 && (!av.hasHiddenColumns() + || hc.isVisible(col))) + { + cs.addElement(col); + } } } } - } else { - int offp = (rseq != null) - ? rseq.findIndex(rseq.getStart() - 1 + p) - : p; - - if (!av.hasHiddenColumns() || hc.isVisible(offp)) + else { - cs.addElement(offp); + int offp = (rseq != null) + ? rseq.findIndex(rseq.getStart() - 1 + p) + : p; + + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + cs.addElement(offp); + } } } } - } - // possible alternative for interactive selection - threshold - // gives 'ceiling' for forming a cluster - // when a row+column is selected, farthest common ancestor less - // than thr is used to compute cluster + // possible alternative for interactive selection - threshold + // gives 'ceiling' for forming a cluster + // when a row+column is selected, farthest common ancestor less + // than thr is used to compute cluster - } - } - else - { - // select corresponding range in segment under mouse - { - int[] rng = forCurrentX.getMappedPositionsFor(fr, to); - if (rng != null) - { - av.getColumnSelection().addRangeOfElements(rng, true); } - av.getColumnSelection().addElement(currentX); } - // PAE SPECIFIC - // and also select everything lower than the max range adjacent - // (kind of works) - if (evt.isControlDown() - && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) + else { - int c = fr; - ContactRange cr = forCurrentX.getRangeFor(fr, to); - double cval; - // TODO: could use GraphLine instead of arbitrary picking - // TODO: could report mean/median/variance for partitions - // (contiguous selected vs unselected regions and inter-contig - // regions) - // controls feathering - what other elements in row/column - // should we select - double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15; - while (c >= 0) + // select corresponding range in segment under mouse { - cval = forCurrentX.getContactAt(c); - if (// cr.getMin() <= cval && - cval <= thresh) + int[] rng = forCurrentX.getMappedPositionsFor(fr, to); + if (rng != null) { - int[] cols = forCurrentX.getMappedPositionsFor(c, c); - if (cols != null) - { - av.getColumnSelection().addRangeOfElements(cols, true); - } - else - { - break; - } + av.getColumnSelection().addRangeOfElements(rng, true); } - c--; + av.getColumnSelection().addElement(currentX); } - c = to; - while (c < forCurrentX.getContactHeight()) + // PAE SPECIFIC + // and also select everything lower than the max range adjacent + // (kind of works) + if (evt.isControlDown() + && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) { - cval = forCurrentX.getContactAt(c); - if (// cr.getMin() <= cval && - cval <= thresh) + int c = fr; + ContactRange cr = forCurrentX.getRangeFor(fr, to); + double cval; + // TODO: could use GraphLine instead of arbitrary picking + // TODO: could report mean/median/variance for partitions + // (contiguous selected vs unselected regions and inter-contig + // regions) + // controls feathering - what other elements in row/column + // should we select + double thresh = cr.getMean() + + (cr.getMax() - cr.getMean()) * .15; + while (c >= 0) { - int[] cols = forCurrentX.getMappedPositionsFor(c, c); - if (cols != null) + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= thresh) { - av.getColumnSelection().addRangeOfElements(cols, true); + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } + else + { + break; + } } + c--; } - else + c = to; + while (c < forCurrentX.getContactHeight()) { - break; - } - c++; + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= thresh) + { + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } + } + else + { + break; + } + c++; + } } + } } } @@ -1076,23 +1084,21 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (forFromX != null && forToX != null) { - ContactGeometry lastXcgeom = new ContactGeometry(forFromX, - cma.graphHeight); - ContactGeometry.contactInterval lastXci = lastXcgeom - .mapFor(rowIndex[1], rowIndex[1] + deltaY); - - ContactGeometry cXcgeom = new ContactGeometry(forToX, + // FIXME will need two ContactGeometry objects when handling contact matrices with differing numbers of rows at each + // column + ContactGeometry xcgeom = new ContactGeometry(forFromX, cma.graphHeight); - ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1], - rowIndex[1] + deltaY); + ContactGeometry.contactInterval lastXci = xcgeom + .mapFor(rowIndex[1]); + ContactGeometry.contactInterval cXci = xcgeom.mapFor(rowIndex[1] + deltaY); // mark rectangular region formed by drag jalview.bin.Console.trace("Matrix Selection from last(" + fromXc + ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])"); int fr, to; - fr = Math.min(lastXci.cStart, lastXci.cEnd); - to = Math.max(lastXci.cStart, lastXci.cEnd); + fr = Math.min(lastXci.cStart, cXci.cStart); + to = Math.max(lastXci.cEnd, cXci.cEnd); int[] mappedPos = forFromX.getMappedPositionsFor(fr, to); if (mappedPos != null) { @@ -1110,33 +1116,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // } // else { - av.getColumnSelection().addElement(c); - } - } - } - // and again for most recent corner of drag - fr = Math.min(cXci.cStart, cXci.cEnd); - to = Math.max(cXci.cStart, cXci.cEnd); - mappedPos = forFromX.getMappedPositionsFor(fr, to); - if (mappedPos != null) - { - for (int pair = 0; pair < mappedPos.length; pair += 2) - { - jalview.bin.Console.trace("Marking " + fr + " to " + to - + " mapping to sequence positions " + mappedPos[pair] - + " to " + mappedPos[pair + 1]); - for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++) - { - // if (cma.sequenceRef != null) - // { - // int col = - // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c); - // av.getColumnSelection().addElement(col); - // } - // else - { - av.getColumnSelection().addElement(c); - } + av.getColumnSelection().addElement(c-1); } } } diff --git a/src/jalview/renderer/ContactGeometry.java b/src/jalview/renderer/ContactGeometry.java index 9fd4de6..a1443c8 100644 --- a/src/jalview/renderer/ContactGeometry.java +++ b/src/jalview/renderer/ContactGeometry.java @@ -1,6 +1,8 @@ package jalview.renderer; +import java.util.Arrays; import java.util.Iterator; +import java.util.List; import jalview.datamodel.ColumnSelection; import jalview.datamodel.ContactListI; @@ -19,21 +21,45 @@ public class ContactGeometry final ContactListI contacts; + /** + * how many pixels per contact (1..many) + */ final int pixels_step; + /** + * how many contacts per pixel (many > 0) + */ final double contacts_per_pixel; + /** + * number of contacts being mapped + */ final int contact_height; + /** + * number of pixels to map contact_height to + */ final int graphHeight; + /** + * number of contacts for each pixel_step - to last whole contact + */ + final double contacts_step; + + final int lastStep; + + /** + * Bean used to map from a range of contacts to a range of pixels + * @param contacts + * @param graphHeight Number of pixels to map given range of contacts + */ public ContactGeometry(final ContactListI contacts, int graphHeight) { this.contacts = contacts; this.graphHeight = graphHeight; contact_height = contacts.getContactHeight(); // fractional number of contacts covering each pixel - contacts_per_pixel = (graphHeight < 1) ? contact_height + contacts_per_pixel = (graphHeight <= 1) ? contact_height : ((double) contact_height) / ((double) graphHeight); if (contacts_per_pixel >= 1) @@ -47,6 +73,8 @@ public class ContactGeometry pixels_step = (int) Math .ceil(((double) graphHeight) / (double) contact_height); } + contacts_step = pixels_step*contacts_per_pixel; + lastStep = (int) Math.min((double)graphHeight, ((double)graphHeight)/((double)pixels_step)); } public class contactInterval @@ -69,6 +97,22 @@ public class ContactGeometry public final int pEnd; + @Override + public boolean equals(Object obj) + { + if (obj == null || !(obj instanceof contactInterval)) + { + return false; + } + contactInterval them = (contactInterval) obj; + return cStart == them.cStart && cEnd == them.cEnd && pEnd == them.pEnd + && pStart == them.pStart; + } + @Override + public String toString() + { + return "Contacts ["+cStart+","+cEnd+"] : Pixels ["+pStart+","+pEnd+"]"; + } } /** @@ -100,7 +144,7 @@ public class ContactGeometry { // TODO: turn into function on hiddenColumns and create test !! Iterator viscont = hiddenColumns.getVisContigsIterator( - mappedRange[p], mappedRange[p + 1], false); + -1+mappedRange[p], -1+mappedRange[p + 1], false); containsHidden = !viscont.hasNext(); if (!containsHidden) { @@ -112,8 +156,8 @@ public class ContactGeometry } else { - rowsel = columnSelection.intersects(mappedRange[p], - mappedRange[p + 1]); + rowsel = columnSelection.intersects(-1+mappedRange[p], + -1+mappedRange[p + 1]); } } return rowsel; @@ -121,21 +165,56 @@ public class ContactGeometry } /** + * Return mapped cell intersecting pStart \ + * + * FIXME: REDUNDANT METHOD - COULD DELETE FIXME: OR RE-IMPLEMENT AS EFFICIENT + * RANGE QUERY * * @param pStart + * [0..) * @param pEnd - * @return range for + * @return nearest full cell containing pStart - does not set + * contactInterval.pEnd or cEnd to equivalent position on pEnd ! */ public contactInterval mapFor(int pStart, int pEnd) { - int cStart = (int) Math.floor(pStart * contacts_per_pixel); - contactInterval ci = new contactInterval(cStart, - (int) Math.min(contact_height, - Math.ceil( - cStart + (pEnd - pStart) * contacts_per_pixel)), - pStart, pEnd); - - return ci; + if (pStart < 0) + { + pStart = 0; + } + if (pEnd < pStart) + { + pEnd = pStart; + } + if (pEnd >= graphHeight) + { + pEnd = graphHeight - 1; + } + if (pStart >= graphHeight) + { + pStart = graphHeight - pixels_step; + } + int step = Math.floorDiv(pStart, pixels_step); + return findStep(step); + } + + /** + * + * @param step + * [0..) n steps covering height and contactHeight + * @return contactInterval for step, or null if out of bounds + */ + contactInterval findStep(int step) + { + if (step < 0 || step > lastStep) + { + return null; + } + return new contactInterval((int) Math.floor(contacts_step * step), + -1 + (int) Math.min(contact_height, + Math.floor(contacts_step * (step + 1))), + pixels_step * step, + Math.min(graphHeight, (step + 1) * pixels_step) - 1); } /** @@ -146,15 +225,31 @@ public class ContactGeometry */ public contactInterval mapFor(int pCentre) { - int pStart = Math.max(pCentre - pixels_step, 0); - int pEnd = Math.min(pStart + pixels_step, graphHeight); - int cStart = (int) Math.floor(pStart * contacts_per_pixel); - contactInterval ci = new contactInterval(cStart, - (int) Math.min(contact_height, - Math.ceil(cStart + (pixels_step) * contacts_per_pixel)), - pStart, pEnd); - - return ci; + if (pCentre >= graphHeight + pixels_step) + { + return null; + } + int step = Math.floorDiv(pCentre, pixels_step); + return findStep(step); + } + + public List allSteps() + { + contactInterval[] array = new contactInterval[lastStep + 1]; + int csum = 0, psum = 0; + for (int i = 0; i <= lastStep; i++) + { + array[i] = findStep(i); + csum += 1 + array[i].cEnd - array[i].cStart; + psum += 1 + array[i].pEnd - array[i].pStart; + } + if (csum != contact_height || psum != graphHeight) + { + System.err.println("csum = " + csum + " not " + contact_height + "\n" + + "psum = " + psum + " not " + graphHeight); + return null; + } + return Arrays.asList(array); } public Iterator iterateOverContactIntervals( diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java index d1eb2f4..af8838c 100644 --- a/src/jalview/renderer/ContactMapRenderer.java +++ b/src/jalview/renderer/ContactMapRenderer.java @@ -178,14 +178,14 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI for (int ht = 0, botY = topY - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step) { - ContactGeometry.contactInterval ci = cgeom.mapFor(ht, - ht + cgeom.pixels_step); + ContactGeometry.contactInterval ci = cgeom.mapFor(ht); // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel); // cend = (int) Math.min(contact_height, // Math.ceil(cstart + contacts_per_pixel * pixels_step)); Color col; - boolean rowsel = false, containsHidden = false; + boolean rowsel = false; + boolean containsHidden = false; if (columnSelection != null) { rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, @@ -226,7 +226,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI g.setColor(col); if (cgeom.pixels_step > 1) { - g.fillRect(x * charWidth, botY+ht, charWidth, 1 + cgeom.pixels_step); + g.fillRect(x * charWidth, botY+ht, charWidth, cgeom.pixels_step); } else { diff --git a/test/jalview/renderer/ContactGeometryTest.java b/test/jalview/renderer/ContactGeometryTest.java new file mode 100644 index 0000000..6e38e89 --- /dev/null +++ b/test/jalview/renderer/ContactGeometryTest.java @@ -0,0 +1,176 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview 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 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.renderer; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNotEquals; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertTrue; + +import org.testng.annotations.Test; + +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactRange; +import jalview.datamodel.Mapping; +import jalview.datamodel.SeqDistanceContactMatrix; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.MapList; +import jalview.util.StringUtils; +import jalview.ws.datamodel.MappableContactMatrixI; + +public class ContactGeometryTest +{ + @Test(groups="Functional") + public void testCoverageofRange() + { + // a really dumb test to make sure we really cover the requested pixel and + // contactList range for any dimension of each + for (int range = 12; range < 2000; range += 35) + { + StringBuilder sb = new StringBuilder(); + while (sb.length() < range) + { + sb.append("c"); + } + SequenceI sq = new Sequence("a", sb.toString()); + MappableContactMatrixI cm = new SeqDistanceContactMatrix(range); + AlignmentAnnotation cm_aan = sq.addContactList(cm); + ContactListI cl = sq.getContactListFor(cm_aan, 10); + assertNotNull(cl); + for (int ht = range / 2; ht < range * 3; ht++) + { + ContactGeometry clgeom = new ContactGeometry(cl, ht); + assertNotNull(clgeom.allSteps()); + } + } + } + @Test(groups = "Functional") + public void testContactGeometry() + { + SequenceI sq = new Sequence("a", "SSSQ"); + MappableContactMatrixI cm = new SeqDistanceContactMatrix(4); + AlignmentAnnotation cm_aan = sq.addContactList(cm); + checkConsistencyFor(sq,cm_aan); + // Also check all is good when there's a sequence mapping involved + MappableContactMatrixI newcm=cm.liftOver(sq, + new Mapping(sq, new MapList(new int[] + { 1, 4 }, new int[] { 1, 4 }, 1, 1))); + AlignmentAnnotation mapped_cm = sq.addContactList(newcm); + checkConsistencyFor(sq,mapped_cm); + } + // Do some asserts for a sequence and a contact matrix + private void checkConsistencyFor(SequenceI sq, AlignmentAnnotation cm_aan) + { + int col=1; + ContactListI cl = sq.getContactListFor(cm_aan, col); + assertNotNull(cl); + assertEquals(cl.getContactHeight(),4); + + // Map contacts 0 to 3 to a tiny range and check + ContactGeometry testee = new ContactGeometry(cl,2); + assertEquals(testee.contacts_per_pixel,2d); + ContactGeometry.contactInterval lastInterval = testee.mapFor(1); + assertEquals(lastInterval.cStart,2); + assertEquals(lastInterval.cEnd,3); + assertEquals(lastInterval.pStart,1); + assertEquals(lastInterval.pEnd,1); + ContactGeometry.contactInterval another = testee.mapFor(1,2); + assertEquals(lastInterval,another); + // Also check for a big pixel range + testee = new ContactGeometry(cl, 395); + lastInterval = testee.mapFor(390, 395); // 395 is one over limit. + assertNotNull(lastInterval); + assertEquals(lastInterval.cEnd,3); + assertEquals(lastInterval.pEnd,394); + // Map contacts 0 to 3 to Pixels 0-9, 10-19, 20-29, 30-39 + testee = new ContactGeometry(cl, 40); + + // verify mapping from pixel to contacts + + // renderer thinks base 0 for pixel coordinates + // contact coordinates are base 1 + for (int p = 0; p < 40; p++) + { + int expectC=(p / 10); + int expectP=(expectC)*10; + ContactGeometry.contactInterval ci_at = testee.mapFor(p), + ci_from = testee.mapFor(p, p); + assertNotNull(ci_at); + // mapFor and map should locate the same pixel window + assertEquals(ci_at.cStart, expectC,"Different cStart at position "+p); + assertEquals(ci_at.cEnd, expectC,"Different cEnd at position "+p); + assertEquals(ci_at.pStart,expectP, "Different pStart at position "+p); + assertEquals(ci_at.pEnd,expectP+9, "Different pEnd at position "+p); + + assertEquals(ci_from,ci_at, "Different contactIntervals at position "+p); + // also test getRangeFor + ContactRange cr = cl.getRangeFor(ci_at.cStart, ci_at.cEnd); + assertEquals(cr.getFrom_column(),cr.getTo_column()); + assertEquals((double) cr.getMean(),(double)Math.abs(col-cr.getFrom_column()), "Didn't resolve expected value at position "+p); + } + + ContactGeometry.contactInterval ci_at0 = testee.mapFor(0); + ContactGeometry.contactInterval ci_at9 = testee.mapFor(9); + assertNotNull(ci_at9); + + assertEquals(ci_at0,ci_at9); + + // Adjacent cell + ContactGeometry.contactInterval ci_at10 = testee.mapFor(10); + assertNotNull(ci_at10); + ContactGeometry.contactInterval ci_at11 = testee.mapFor(11); + assertNotNull(ci_at11); + + assertEquals(ci_at11,ci_at10,"Off-by-one in ContactGeometry mapping."); + + assertNotEquals(ci_at0,ci_at10,"Expected adjacent cells to be not equal."); + + // verify adjacent window is mapped + assertEquals(ci_at11.cStart,ci_at9.cStart+1); + + assertEquals(ci_at9.cEnd+1,ci_at11.cStart); + assertEquals(ci_at9.cEnd+1,ci_at11.cEnd); + + // verify interval/intersection + // column selection is base 0 + ColumnSelection cs = new ColumnSelection(); + cs.addElement(2); + + boolean mask = false; + do + { + assertFalse(testee.intersects(ci_at0, cs, null, mask)); + assertFalse(testee.intersects(ci_at11, cs, null, mask)); + assertTrue(testee.intersects(testee.mapFor(21), cs, null, mask)); + assertFalse(testee.intersects(testee.mapFor(31), cs, null, mask)); + cs.addElement(3); + assertTrue(testee.intersects(testee.mapFor(31), cs, null, mask)); + cs.removeElement(2); + assertFalse(testee.intersects(testee.mapFor(21), cs, null, mask)); + mask = !mask; + } while (!mask); + + } +} -- 1.7.10.2