Examples of java.util.BitSet.nextSetBit()

java.util.BitSet.nextSetBit()
ate on index i here } @param fromIndex the index to start checking from (inclusive). @return the index of the next set bit. @throws IndexOutOfBoundsException if the specified index is negative. @since 1.4

    if (nModelsDeleted == 0)
      return null;


    // clear references to this frame if it is a dataFrame


    for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1))
      clearDataFrameReference(i);


    BitSet bsDeleted;
    if (nModelsDeleted == modelCount) {
      bsDeleted = getModelAtomBitSetIncludingDeleted(-1, true);

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  public void recalculatePositionDependentQuantities(BitSet bs) {
    if (getHaveStraightness())
      calculateStraightness();
    recalculateLeadMidpointsAndWingVectors(-1);
    BitSet bsModels = getModelBitSet(bs, false);
    for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1))
      shapeManager.refreshShapeTrajectories(i, viewer.getModelUndeletedAtomsBitSet(i));
  }


  public void connect(float[][] connections) {
    // array of [index1 index2 order diameter energy]

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  public void recalculatePositionDependentQuantities(BitSet bs) {
    if (getHaveStraightness())
      calculateStraightness();
    recalculateLeadMidpointsAndWingVectors(-1);
    BitSet bsModels = getModelBitSet(bs, false);
    for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1))
      shapeManager.refreshShapeTrajectories(i, viewer.getModelUndeletedAtomsBitSet(i));
  }


  public void connect(float[][] connections) {
    // array of [index1 index2 order diameter energy]

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        continue; 
      }
      float energy = (f.length > 4 ? f[4] : 0);
      bondAtoms(atoms[index1], atoms[index2], order, mad, null, energy, true);
    }
    if (bsDelete.nextSetBit(0) >= 0)
      deleteBonds(bsDelete, false);
  }


}

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          AminoPolymer ap = (AminoPolymer) bioPolymers[i];
          sbSummary.append(ap.dumpSummary(labels[i]));
          sb.append(reports[i]).append(
              ap.dumpTags("$.1: " + String.valueOf(labels[i]), bsBad, 2));
        }
      if (bsBad.nextSetBit(0) >= 0)
        sb
            .append("\nNOTE: '!' indicates a residue that is missing a backbone carbonyl oxygen atom.\n");
      sb.append("\n").append("SUMMARY:" + sbSummary);
    }

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    int nSets = meshData.nSets;
    BitSet pocketSet = new BitSet(nSets);
    BitSet ss;
    for (int i = 0; i < nSets; i++)
      if ((ss = meshData.surfaceSet[i]) != null)
        for (int j = ss.nextSetBit(0); j >= 0; j = ss.nextSetBit(j + 1))
          if (Float.isNaN(meshData.vertexValues[j])) {
            pocketSet.set(i);
            //System.out.println("pocket " + i + " " + j + " " + surfaceSet[i]);
            break;
          }

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    int nSets = meshData.nSets;
    BitSet pocketSet = new BitSet(nSets);
    BitSet ss;
    for (int i = 0; i < nSets; i++)
      if ((ss = meshData.surfaceSet[i]) != null)
        for (int j = ss.nextSetBit(0); j >= 0; j = ss.nextSetBit(j + 1))
          if (Float.isNaN(meshData.vertexValues[j])) {
            pocketSet.set(i);
            //System.out.println("pocket " + i + " " + j + " " + surfaceSet[i]);
            break;
          }

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        if (nAtoms == 0)
          return;
        if (nAtoms > 1)
          modelIndex = 0;
        ptLastAtom = i;
        indices[i + 1] = bs.nextSetBit(0);
      } else {
        if (pts == null)
          pts = new Point3fi[4];
        pts[i] = (Point3fi)obj;
        indices[i + 1] = -2 - i;

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    if (thisAtomIndex < 0) {
      nextMeasure(thispt + 1, ptLastAtom, m, thisModel);
      return;
    }
    boolean haveNext = false;
    for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
      if (i == thisAtomIndex)
        continue;
      int modelIndex = atoms[i].getModelIndex();
      if (thisModel >= 0) {
        if (thispt == 0)

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      return;
    int j = script.indexOf("})", i);
    if (j < 0)
      return;
    BitSet bs = Escape.unescapeBitset(script.substring(i + 3, j + 1));
    modelIndex = (bs == null ? -1 : bs.nextSetBit(0));
    iHaveModelIndex = (modelIndex >= 0);
  }
  
  protected void setStatusPicked(int flag, Point3f v) {
    // for draw and isosurface

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