Examples of java.util.BitSet.clear()

java.util.BitSet.clear()
Sets the bit specified by the index to false. @param bitIndex the index of the bit to be cleared. @exception IndexOutOfBoundsException if the specified index is negative. @since JDK1.0

      for (int i = bsBonds.nextSetBit(0); i >= 0; i = bsBonds.nextSetBit(i + 1)) {
        Atom atom1 = bonds[i].atom1;
        if (models[atom1.modelIndex].isModelKit)
          continue;
        bsA.clear();
        bsB.clear();
        bsA.set(atom1.index);
        bsB.set(bonds[i].getAtomIndex2());
        addStateScript("connect ", null, bsA, bsB, "delete", false, true);
      }
    }

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    }
    boolean nonbonded = (min == 0);
    for (i = atomCount; --i >= 0;) {
      int n = nBonded[i];
      if (n < min || n > max)
        bsResult.clear(i);
      else if (nonbonded && n == 0)
        bsResult.set(i);
    }
    return bsResult;
  }

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        " EXTRACT: ").append(Escape.escape(bs))
        .append("\n");
    BitSet bsAtoms = BitSetUtil.copy(bs);
    for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
      if (doTransform && atoms[i].isDeleted())
        bsAtoms.clear(i);
    BitSet bsBonds = getCovalentBondsForAtoms(bsAtoms);
    if (bsAtoms.cardinality() == 0)
      return "";
    boolean isOK = true;
    Quaternion q = (doTransform ? viewer.getRotationQuaternion() : null);

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    if (atomIndex < 0)
      return bs;
    BitSet bsToTest = new BitSet();
    bsToTest.or(bs0);
    if (atomIndexNot >= 0)
      bsToTest.clear(atomIndexNot);
    setBranch2dZ(atoms[atomIndex], bs, bsToTest, v, v0, v1);
    return bs;
  }


  private static void setBranch2dZ(Atom atom, BitSet bs,

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      return;
    // ...and it's a large model, to wireframe:
      sb.append("select ").append(Escape.escape(bs)).append(" & connected; wireframe only;");
    // ... and all non-biopolymer and not connected to stars...
    if (bs != bsAtoms) {
      bs2.clear();
      bs2.or(bsAtoms);
      bs2.andNot(bs);
      if (bs2.nextSetBit(0) >= 0)
        sb.append("select " + Escape.escape(bs2) + " & !connected;stars 0.5;");
    }

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    bs.set(0, nAttached);
    for (int i = 0; i < nAttached; i++)
      for (int j = 0; j < nPtrs; j++) {
        int[] a = angles[ptrs[j]];
        if (a[0] == i || a[1] == i)
          bs.clear(i);
      }
    return bs;
  }


  class AtomSorter implements Comparator {

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    if ("atomBitset" == propertyName) {
      BitSet atomset = (BitSet) value;
      atomIndex1 = atomset.nextSetBit(0);
      startCoord = modelSet.atoms[atomIndex1];
      atomset.clear(atomIndex1);
      propertyName = "endSet";
      //passes to endSet
    }


    if ("endSet" == propertyName) {

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              - (atoms[pt].screenDiameter >> 1)))
            break;
        if (j != m.atomCount) {
          pt = m.firstAtomIndex;
          for (int k = 0; k < m.atomCount; k++) {
            bsOK.clear(pt);
            atoms[pt++].screenZ = 0;
          }
        }
      }
    }

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          // note that in the case of navigation,
          // maxZ is set to Integer.MAX_VALUE.
          int r = (slabByAtom ? -1 : 1) * atom.screenDiameter / 2;
          if (atom.screenZ + r < minZ || atom.screenZ - r > maxZ
              || !g3d.isInDisplayRange(atom.screenX, atom.screenY)) {
            bsOK.clear(i);
            continue;
          }
        }
      }
      // note: above transform is required for all other renderings

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      int[]list = new int[12];
      int ptList = 0;
      for (int i = 0; i < triangles.length; i++) {
        int pt = triangles[i];
        if (bsPoints.get(pt)) {
          bsPoints.clear(pt);
          pts[ptList] = edgePoints[pt];
          list[pt] = (byte) ptList++;
        }          
        if (i % 4 == 2)
          i++;

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