* $Author: hansonr $

* $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $

* $Revision: 7273 $

*

* Copyright (C) 2007 Miguel, Bob, Jmol Development

*

* Contact: hansonr@stolaf.edu

*

*  This library is free software; you can redistribute it and/or

*  modify it under the terms of the GNU Lesser General Public

*  License as published by the Free Software Foundation; either

*  version 2.1 of the License, or (at your option) any later version.

*

*  This library 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

*  Lesser General License for more details.

*

*  You should have received a copy of the GNU Lesser General Public

*  License along with this library; if not, write to the Free Software

*  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.

*/

  //TODO -- need to escapeXml for text data

 

  final public static String JVXL_VERSION1 = "2.0";

  final public static String JVXL_VERSION_XML = "2.2";

 

  // 1.4 adds -nContours to indicate contourFromZero for MEP data mapped onto planes

  // 2.0 adds vertex/triangle compression when no grid is present

  // Jmol 11.7.25 -- recoded so that we do not create voxelData[nx][ny][nz] and instead

  //                 simply create a BitSet of length nx * ny * nz. This saves memory hugely.

  // 2.1 adds JvxlXmlReader

  // 2.2 adds color density Jmol 12.0.15/12.1.13

 

  public static String jvxlGetFile(VolumeData volumeData, JvxlData jvxlData,

                                   String[] title) {

    // for the simple writer

    int[] counts = volumeData.getVoxelCounts();

    jvxlData.nPointsX = counts[0];

    jvxlData.nPointsY = counts[1];

    jvxlData.nPointsZ = counts[2];

    jvxlData.jvxlVolumeDataXml = volumeData.setVolumetricXml();

    return jvxlGetFile(jvxlData, null, title, null, true, 1, null, null);

  }

  public static String jvxlGetFile(JvxlData jvxlData, MeshData meshData,

                                   String[] title, String msg,

                                   boolean includeHeader, int nSurfaces,

                                   String state, String comment) {

    return jvxlGetFileXml(jvxlData, meshData, title, msg, includeHeader, nSurfaces, state, comment);

   

    // version1 decomissioned because of jvxlExcluded[] performing so well

   

    //    if (meshData != null || jvxlData == null || jvxlData.asXml

    //      || jvxlData.vContours != null || jvxlData.contourValues != null

    //      || jvxlData.jvxlExcluded[0] != null || jvxlData.jvxlExcluded[1] != null )

    //  return jvxlGetFileXml(jvxlData, meshData, title, msg, includeHeader, nSurfaces, state, comment);

    //return jvxlGetFileVersion1(jvxlData, meshData, title, msg, includeHeader, nSurfaces, state, comment);

  }

  private static String jvxlGetFileXml(JvxlData jvxlData, MeshData meshData,

                                       String[] title, String msg,

                                       boolean includeHeader, int nSurfaces,

                                       String state, String comment) {

    StringBuffer data = new StringBuffer();

    if ("TRAILERONLY".equals(msg)) {

      XmlUtil.closeTag(data, "jvxlSurfaceSet");

      XmlUtil.closeTag(data, "jvxl");

      return data.toString();

    }

   

    boolean verticesOnly = (meshData != null);

    boolean isHeaderOnly = ("HEADERONLY".equals(msg));

    if (includeHeader) {

      XmlUtil.openDocument(data);

      XmlUtil.openTag(data, "jvxl", new String[] {

          "version", JVXL_VERSION_XML,

          "jmolVersion", jvxlData.version,

          "xmlns", "http://jmol.org/jvxl_schema",

          "xmlns:cml", "http://www.xml-cml.org/schema" });

      if (jvxlData.jvxlFileTitle != null)

        XmlUtil.appendCdata(data, "jvxlFileTitle", null, "\n" + jvxlData.jvxlFileTitle);

      if (jvxlData.moleculeXml != null)

        data.append(jvxlData.moleculeXml);

      String volumeDataXml = (verticesOnly ? null : jvxlData.jvxlVolumeDataXml);

      if (volumeDataXml == null)

        volumeDataXml = (new VolumeData()).setVolumetricXml();

      data.append(volumeDataXml);

      XmlUtil.openTag(data,"jvxlSurfaceSet",

          new String[] { "count", "" + (nSurfaces > 0 ? nSurfaces : 1) });

      if (isHeaderOnly)

        return data.toString();

    }

    StringBuffer sb;

    String type = (verticesOnly ? "pmesh"

        : jvxlData.jvxlPlane == null ? "isosurface" : "plane");

    // TODO: contours mentioned here? when discrete?

    if (jvxlData.jvxlColorData != null && jvxlData.jvxlColorData.length() > 0)

      type = "mapped " + type;

    XmlUtil.openTag(data, "jvxlSurface", new String[] { "type", type });

    data.append(jvxlGetInfo(jvxlData, verticesOnly, true));

    jvxlAppendCommandState(data, comment, state);

    if (title != null || msg != null && msg.length() > 0) {

      sb = new StringBuffer();

      if (msg != null && msg.length() > 0)

        sb.append(msg).append("\n");

      if (title != null)

        for (int i = 0; i < title.length; i++)

          sb.append(title[i]).append('\n');

      XmlUtil.appendCdata(data, "jvxlSurfaceTitle", null, sb.toString());

    }

    sb = new StringBuffer();

    XmlUtil.openTag(sb, "jvxlSurfaceData", (jvxlData.jvxlPlane == null ? null :

      new String[] { "plane", Escape.escape(jvxlData.jvxlPlane) }));

    if (verticesOnly) {

      jvxlAppendMeshXml(sb, jvxlData, meshData, true);

    } else if (jvxlData.jvxlPlane == null) {

      appendXmlEdgeData(sb, jvxlData);

      appendXmlColorData(sb, "jvxlColorData", jvxlData.jvxlColorData,

          jvxlData.isJvxlPrecisionColor, jvxlData.valueMappedToRed,

          jvxlData.valueMappedToBlue);

    } else {

      appendXmlColorData(sb, "jvxlColorData", jvxlData.jvxlColorData,

          jvxlData.isJvxlPrecisionColor, jvxlData.valueMappedToRed,

          jvxlData.valueMappedToBlue);

    }

    appendEncodedBitSetTag(sb, "jvxlInvalidatedVertexData", jvxlData.jvxlExcluded[1], -1);

    if (jvxlData.excludedVertexCount > 0) {

      appendEncodedBitSetTag(sb, "jvxlExcludedVertexData", jvxlData.jvxlExcluded[0], jvxlData.excludedVertexCount);

      appendEncodedBitSetTag(sb, "jvxlExcludedPlaneData", jvxlData.jvxlExcluded[2], -1);

    }

    appendEncodedBitSetTag(sb, "jvxlExcludedTriangleData", jvxlData.jvxlExcluded[3], jvxlData.excludedTriangleCount);

    XmlUtil.closeTag(sb, "jvxlSurfaceData");

    int len = sb.length();

    data.append(sb);

    if (jvxlData.vContours != null && jvxlData.vContours.length > 0) {

      jvxlEncodeContourData(jvxlData.vContours, data);

    }

    XmlUtil.closeTag(data, "jvxlSurface");

    if (includeHeader) {

      XmlUtil.closeTag(data, "jvxlSurfaceSet");

      XmlUtil.closeTag(data, "jvxl");

    }

    return jvxlSetCompressionRatio(data, jvxlData, len);

  }

  private static void appendEncodedBitSetTag(StringBuffer sb, String name, BitSet bs, int count) {

    if (count < 0)

      count = BitSetUtil.cardinalityOf(bs);

    if (count == 0)

      return;

    StringBuffer sb1 = new StringBuffer("\n ");

    jvxlEncodeBitSet(bs, -1, sb1);

    XmlUtil.appendTag(sb, name, new String[] {

        "bsEncoding", "base90+35",

        "count", "" + count,

        "len", "" + bs.length() },

        jvxlCompressString(sb1.toString(), true));

  }

  private static String jvxlSetCompressionRatio(StringBuffer data,

                                                JvxlData jvxlData, int len) {

    String s = data.toString();

    int r = (int) (jvxlData.nBytes > 0 ? ((float) jvxlData.nBytes) / len

        : ((float) (jvxlData.nPointsX

          * jvxlData.nPointsY * jvxlData.nPointsZ * 13)) / len);

    return TextFormat.simpleReplace(s, "#RATIO#", (r > 0 ? "" + r : "?"));

  }

  private static void appendXmlEdgeData(StringBuffer sb, JvxlData jvxlData) {

    XmlUtil.appendTag(sb, "jvxlEdgeData", new String[] {

        "count", "" + (jvxlData.jvxlEdgeData.length() - 1),

        "encoding", "base90f1",

        "bsEncoding", "base90+35c",

        "isXLowToHigh", "" + jvxlData.isXLowToHigh,

        "data", jvxlCompressString(jvxlData.jvxlEdgeData, true) }, "\n"

        + jvxlCompressString(jvxlData.jvxlSurfaceData, true));

  }

  private static void jvxlAppendCommandState(StringBuffer data, String cmd,

                                             String state) {

    if (cmd != null)

      XmlUtil.appendCdata(data, "jvxlIsosurfaceCommand", null,

          "\n" + (cmd.indexOf("#") < 0 ? cmd : cmd.substring(0, cmd.indexOf("#"))) + "\n");

    if (state != null) {

      if (state.indexOf("** XML ** ") >=0) {

        state = TextFormat.split(state, "** XML **")[1].trim();

        XmlUtil.appendTag(data, "jvxlIsosurfaceState",  "\n" + state + "\n");

      } else {

        XmlUtil.appendCdata(data, "jvxlIsosurfaceState", null, "\n" + state + "\n");

      }

    }

  }

  private static void appendXmlColorData(StringBuffer sb, String key,

                                         String data,

                                         boolean isPrecisionColor,

                                         float value1,

                                         float value2) {

    int n;

    if (data == null || (n = data.length() - 1) < 0)

      return;

    if (isPrecisionColor)

      n /= 2;

    XmlUtil.appendTag(sb, key, new String[] {

        "count", "" + n,

        "encoding", "base90f" + (isPrecisionColor ? "2" : "1"),

        "min", "" + value1,

        "max", "" + value2,

        "data", jvxlCompressString(data, true) }, null);

  }

 

  public static String jvxlGetInfo(JvxlData jvxlData) {

    return jvxlGetInfo(jvxlData, jvxlData.vertexDataOnly, true);

  }

  public static String jvxlGetInfo(JvxlData jvxlData, boolean verticesOnly, boolean notVersion1) {

    if (jvxlData.jvxlSurfaceData == null)

      return "";

    List attribs = new ArrayList();

    

    int nSurfaceInts = jvxlData.nSurfaceInts;// jvxlData.jvxlSurfaceData.length();

    int bytesUncompressedEdgeData = (verticesOnly ? 0

        : jvxlData.jvxlEdgeData.length() - 1);

    int nColorData = (jvxlData.jvxlColorData == null ? -1 : (jvxlData.jvxlColorData.length() - 1));

    if (!verticesOnly) {

      // informational only:

      addAttrib(attribs, "\n  cutoff", "" + jvxlData.cutoff);

      addAttrib(attribs, "\n  isCutoffAbsolute", "" + jvxlData.isCutoffAbsolute);

      addAttrib(attribs, "\n  pointsPerAngstrom", "" + jvxlData.pointsPerAngstrom);

      int n = jvxlData.jvxlSurfaceData.length()

          + bytesUncompressedEdgeData + nColorData + 1;

      if (n > 0)

        addAttrib(attribs, "\n  nBytesData", "" + n);

      //TODO: these should only be for information purposes, but are not:

      addAttrib(attribs, "\n  isXLowToHigh", "" + jvxlData.isXLowToHigh);

      if (jvxlData.jvxlPlane == null) {

        addAttrib(attribs, "\n  nSurfaceInts", "" + nSurfaceInts);

        addAttrib(attribs, "\n  nBytesUncompressedEdgeData", "" + bytesUncompressedEdgeData);

      }

      if (nColorData > 0)

        addAttrib(attribs, "\n  nBytesUncompressedColorData", "" + nColorData); // TODO: later?

    }

    //next is for information only -- will be superceded by "encoding" attribute of jvxlColorData

    if (jvxlData.isJvxlPrecisionColor)

      addAttrib(attribs, "\n  precisionColor", "true");

    if (jvxlData.colorDensity)

      addAttrib(attribs, "\n  colorDensity", "true");

    if (jvxlData.jvxlPlane == null) {

      if (jvxlData.isContoured) {

        addAttrib(attribs, "\n  contoured", "true");

        addAttrib(attribs, "\n  colorMapped", "true");

      } else if (jvxlData.isBicolorMap) {

        addAttrib(attribs, "\n  bicolorMap", "true");

      } else if (nColorData > 0) {

        addAttrib(attribs, "\n  colorMapped", "true");

      }

      if (jvxlData.vContours != null && jvxlData.vContours.length > 0)

        addAttrib(attribs, "\n  nContourData", "" + jvxlData.vContours.length);

    } else {

      if (jvxlData.scale3d != 0)

        addAttrib(attribs, "\n  scale3d", "" + jvxlData.scale3d);

      if (nColorData > 0)

        addAttrib(attribs, "\n  colorMapped", "true");

      addAttrib(attribs, "\n  plane", Escape.escape(jvxlData.jvxlPlane));

    }

    jvxlData.excludedVertexCount = BitSetUtil.cardinalityOf(jvxlData.jvxlExcluded[0]);

    jvxlData.excludedTriangleCount = BitSetUtil .cardinalityOf(jvxlData.jvxlExcluded[3]);

    if (jvxlData.excludedVertexCount > 0)

      addAttrib(attribs, "\n  nExcludedVertexes", "" + jvxlData.excludedVertexCount);

    if (jvxlData.excludedTriangleCount > 0)

      addAttrib(attribs, "\n  nExcludedTriangles", "" + jvxlData.excludedTriangleCount);

    int n = BitSetUtil.cardinalityOf(jvxlData.jvxlExcluded[1]);

    if (n > 0)

      addAttrib(attribs, "\n  nInvalidatedVertexes", "" + n);

    if (jvxlData.isContoured) {

      if (jvxlData.contourValues == null || jvxlData.contourColixes == null) {

        if (jvxlData.vContours == null)

          addAttrib(attribs, "\n  nContours", "" + Math.abs(jvxlData.nContours));

      } else {

        if (jvxlData.jvxlPlane != null)

          addAttrib(attribs, "\n  contoured", "true");

        addAttrib(attribs, "\n  nContours", "" + jvxlData.contourValues.length);

        addAttrib(attribs, "\n  contourValues", Escape.escapeArray(jvxlData.contourValuesUsed == null ? jvxlData.contourValues : jvxlData.contourValuesUsed));

        addAttrib(attribs, "\n  contourColors", jvxlData.contourColors);

      }

    }

    // ... mappedDataMin mappedDataMax valueMappedToRed valueMappedToBlue ...

    //TODO: again, these really should not be necessary here

    float min = (jvxlData.mappedDataMin == Float.MAX_VALUE ? 0f

        : jvxlData.mappedDataMin);

    float blue = (jvxlData.isColorReversed ? jvxlData.valueMappedToRed : jvxlData.valueMappedToBlue);

    float red = (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue : jvxlData.valueMappedToRed);

    if (jvxlData.jvxlColorData != null && jvxlData.jvxlColorData.length() > 0 && !jvxlData.isBicolorMap) {

      addAttrib(attribs, "\n  dataMinimum", "" + min);

      addAttrib(attribs, "\n  dataMaximum", "" + jvxlData.mappedDataMax);

      addAttrib(attribs, "\n  valueMappedToRed", "" + red);

      addAttrib(attribs, "\n  valueMappedToBlue", "" + blue);

    }

    //TODO: confusing flag insideOut:

    if (jvxlData.insideOut)

      addAttrib(attribs, "\n  insideOut", "true");

   

    // rest is information only:

    if (jvxlData.isXLowToHigh)

      addAttrib(attribs, "\n  note", "progressive JVXL+ -- X values read from low(0) to high("

              + (jvxlData.nPointsX - 1) + ")");

    addAttrib(attribs, "\n  xyzMin", Escape.escape(jvxlData.boundingBox[0]));

    addAttrib(attribs, "\n  xyzMax", Escape.escape(jvxlData.boundingBox[1]));

    addAttrib(attribs, "\n  approximateCompressionRatio", "#RATIO#:1");

    addAttrib(attribs, "\n  jmolVersion", jvxlData.version);

   

    StringBuffer info = new StringBuffer();

    XmlUtil.openTag(info, "jvxlSurfaceInfo", attribs.toArray());

    XmlUtil.closeTag(info, "jvxlSurfaceInfo");

    return info.toString();

  }

 

  private static void addAttrib(List attribs, String name, String value) {

    attribs.add(new String[] { name, value });

  }

  public static final int CONTOUR_NPOLYGONS = 0;

  public static final int CONTOUR_BITSET = 1;

  public static final int CONTOUR_VALUE = 2;

  public static final int CONTOUR_COLIX = 3;

  public static final int CONTOUR_COLOR = 4;

  public static final int CONTOUR_FDATA = 5;

  public static final int CONTOUR_POINTS = 6; // must be last

  /**

   * contour data are appended to a string buffer in the form of a

   * <jmolContourData count="[nContours]">

   *   <jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>

   *   <jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>

   *   <jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>

   *   ...

   * </jmolContourData>

   *

   * One presumes an ordered set of triangles.

   * The contour intersects these triangles along two edges or at two vertices.

   * (see IsosurfaceMesh for details)

   * Each contour is a List containing:

   *   0 Integer number of polygons (length of BitSet)

   *   1 BitSet of critical triangles

   *   2 Float value

   *   3 int[] [colorArgb]

   *   4 StringBuffer containing encoded data for each segment:

   *     char type ('3', '6', '5') indicating which two edges

   *       of the triangle are connected:

   *         '3' 0x011 AB-BC

   *         '5' 0x101 AB-CA

   *         '6' 0x110 BC-CA

   *     char fraction along first edge (jvxlFractionToCharacter)

   *     char fraction along second edge (jvxlFractionToCharacter)

   *   5- stream of pairs of points for rendering (created

   *

   *

   * @param contours

   * @param sb

   */

  private static void jvxlEncodeContourData(List[] contours, StringBuffer sb) {

    XmlUtil.openTag(sb, "jvxlContourData", new String[] { "count", "" + contours.length });

    for (int i = 0; i < contours.length; i++) {

      if (contours[i].size() < CONTOUR_POINTS)

        continue;

      int nPolygons = ((Integer) contours[i]

          .get(CONTOUR_NPOLYGONS)).intValue();

      StringBuffer sb1 = new StringBuffer("\n");

      BitSet bs = (BitSet) contours[i].get(CONTOUR_BITSET);

      jvxlEncodeBitSet(bs, nPolygons, sb1);

      XmlUtil.appendTag(sb, "jvxlContour", new String[] {

          "index", "" + i,

          "value", "" + contours[i].get(CONTOUR_VALUE),

          "color", Escape.escapeColor(((int[]) contours[i]

              .get(CONTOUR_COLOR))[0]),

          "count", "" + bs.length(),

          "encoding", "base90iff1",

          "bsEncoding", "base90+35c",

          "data", jvxlCompressString(contours[i].get(CONTOUR_FDATA).toString(), true) },

          jvxlCompressString(sb1.toString(), true));

    }

    XmlUtil.closeTag(sb, "jvxlContourData");

  }

  /**

   * Interpret fractional data in terms of actual vertex positions and

   * create the elements of a List in List[] vContours starting at

   * the CONTOUR_POINTS position.

   * 

   * @param v

   * @param polygonIndexes

   * @param vertices

   */

  public static void set3dContourVector(List v, int[][] polygonIndexes, Point3f[] vertices) {

    // we must add points only after the MarchingCubes process has completed.

    if (v.size() < CONTOUR_POINTS)

      return;

    StringBuffer fData = (StringBuffer) v.get(CONTOUR_FDATA);

    BitSet bs = (BitSet) v.get(CONTOUR_BITSET);

    //int nPolygons = ((Integer)v.get(CONTOUR_NPOLYGONS)).intValue();

    int pt = 0;

    int nBuf = fData.length();

    int type = 0;

    char c1 = ' ';

    char c2 = ' ';

    for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {

      int[] vertexIndexes = polygonIndexes[i];

      while (pt < nBuf && !Character.isDigit(c1 = fData.charAt(pt++))) {

        // skip non-digit data

      }

      type = ((int) c1) - 48;

      while (pt < nBuf && Character.isWhitespace(c1 = fData.charAt(pt++))) {

        // skip whitespace

      }

      while (pt < nBuf && Character.isWhitespace(c2 = fData.charAt(pt++))) {

        // skip whitespace

      }

      float f1 = jvxlFractionFromCharacter(c1, defaultEdgeFractionBase, defaultEdgeFractionRange, 0);

      float f2 = jvxlFractionFromCharacter(c2, defaultEdgeFractionBase, defaultEdgeFractionRange, 0);

      int i1, i2, i3, i4;

      /*

       *     char type ('3', '6', '5') indicating which two edges

       *       of the triangle are connected:

       *         '3' 0x011 AB-BC

       *         '5' 0x101 AB-CA

       *         '6' 0x110 BC-CA

       */

      if ((type & 1) == 0) { //BC-CA

        i1 = vertexIndexes[1];

        i2 = i3 = vertexIndexes[2];

        i4 = vertexIndexes[0];

      } else { //AB-BC or //AB-CA

        i1 = vertexIndexes[0];

        i2 = vertexIndexes[1];

        if ((type & 2) != 0) {

          i3 = i2;

          i4 = vertexIndexes[2];

        } else {

          i3 = vertexIndexes[2];

          i4 = i1;         

        }

      }

      v.add(getContourPoint(vertices, i1, i2, f1));

      v.add(getContourPoint(vertices, i3, i4, f2));

    }

  }

  private static Point3f getContourPoint(Point3f[] vertices, int i, int j, float f) {

    Point3f pt = new Point3f();

    pt.set(vertices[j]);

    pt.sub(vertices[i]);

    pt.scale(f);

    pt.add(vertices[i]);

    return pt;

  }

  /**

   * appends an integer (3, 5, or 6) representing two sides of a triangle ABC --

   * AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges

   * for the intersection point base-90-encoded. This version is single precision.

   *

   * type     f1     f2

   *  3       AB     BC

   *  5       AB     CA

   *  6       BC     CA

   *

   * @param type

   * @param f1 -- character-encoded fraction

   * @param f2 -- character-encoded fraction

   * @param fData

   */

  public static void appendContourTriangleIntersection(int type, float f1, float f2, StringBuffer fData) {

    fData.append(type);

    fData.append(jvxlFractionAsCharacter(f1));

    fData.append(jvxlFractionAsCharacter(f2));   

  }

 

  /**

   *

   * @param jvxlData

   * @param vertexValues

   */

  public static void jvxlCreateColorData(JvxlData jvxlData, float[] vertexValues) {

    if (vertexValues == null) {

      jvxlData.jvxlColorData = "";

      return;

    }

    boolean writePrecisionColor = jvxlData.isJvxlPrecisionColor;

    boolean doTruncate = jvxlData.isTruncated;

    int colorFractionBase = jvxlData.colorFractionBase;

    int colorFractionRange = jvxlData.colorFractionRange;

    float valueBlue = jvxlData.valueMappedToBlue;

    float valueRed = jvxlData.valueMappedToRed;

    int vertexCount = (jvxlData.saveVertexCount > 0 ? jvxlData.saveVertexCount

        : jvxlData.vertexCount);

    float min = jvxlData.mappedDataMin;

    float max = jvxlData.mappedDataMax;

    StringBuffer list1 = new StringBuffer();

    StringBuffer list2 = new StringBuffer();

    for (int i = 0; i < vertexCount; i++) {

      float value = vertexValues[i];

      if (doTruncate)

        value = (value > 0 ? 0.999f : -0.999f);

      if (writePrecisionColor)

        jvxlAppendCharacter2(value, min, max, colorFractionBase,

            colorFractionRange, list1, list2);

      else

        list1.append(jvxlValueAsCharacter(value, valueRed, valueBlue,

            colorFractionBase, colorFractionRange));

    }

    jvxlData.jvxlColorData = list1.append(list2).append('\n').toString();

  }

  /* ******************************************************************

   *

   * JVXL 2.0 encoding of vertices, triangles, and vertex values:

   *

   * <jvxlSurfaceData>

   *   <jvxlTriangleData data="!]][[_]]Y`WbVa^]]] ... cZ_T^ZdUdTc!^[Dv][Bx-43,+44,]-55,f+43,_W`Z^X`Z ...">

   *   </jvxlTriangleData>

   *   <jvxlVertexData min="(15.218472, -28.304049, 34.71112)" max="(97.8228, 54.011948, 109.95208)" data=0HY0HZ0HZ0HY0H[0GZ0IZ0IZ0H[0FZ...">

   *   </jvxlVertexData>

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CBB@@>@?@>>?>~11 =~4 ::;9:::===:<<<:;;>=~6 <=<<===;<=<=<====<<====<<==AAAA@caadc_ae]^^`outuqtwpv!]!!``![!ilcllc>~4 yxwxuyyywyywy>>a`XYZ[Y^_]_]a^c[[Ydbdca```acbb^`__Y[W!]fffed]!]!!XZfe][^[![Z[!!!![[[!aZcXXXZffeec`hcYXce`eednqmmfeYYkienoilkYWWYW!!bdqrmlZfj777a_^`_^]]]]^!]![!!!]_!]^``]]]^A~4 BBA]!]~4 ::99;;:89;<;<;<;9::]!!]]!!!!?D?@??:;;::;<9;9:;~5 :;;:>>=>=~7 >>>====>===<===???>>===A>>>>=>=~13 >~7 ==>=<=?><<<=<<<==>??<?==<<?@@=??<=<<==<<=~7 <~4 ;<<<==<<==<<=<<====<~12 =<~10 =<<;<~6 >=<==>===<~11 =<~11 =<~4 ==<=<~4 ===<~5 =<~5 =<=~7 <=<<=<~6 =~6 <===<~5 ;~5 <<;~5 <;;:::;;;::;:;::;:;::;~4 :;:~5 ;;<;<~4 =~8 <===<>=>==>=>><<;<===<=<==<=????>AA@AAA@A??>>??=>>?A:A:A:~8 <=;<;;;:;;A;::B:BBA::::???=<<>?>===<<<<==;<=<====>>>;;:<;;>==<=<;~5 ?@A???@@@ABA??=>=>@@B?>>>>==>?>==>==>>=><<>=>;;<=::;;:~4 ;~9 <<=<;~9 <;<<<;~4 <~4 ;<<;<;~12 ::;~9 <~8 ===::;;;<:<~4 ;<~4 ;;:;:::9;:~4 9::9998:9988;~10 9;;;:;;;;::;;;;:;;;:;;:9::;::8=~5 <~4 =<=<<<===<~5 ===<~6 ;<====<====<<<<=~9 >=<~4 ==<<=~5 <====;<<==<;<~5 ==<==<?@?>>===??==@~5 ?@?;=<~5 ==<<==;<<<==>=>=~4 >===>===>>>=>?=?>~4 ===>>>>====<~4 ===<<;<>>?=~5 ??==?=<<;;;;::899:889:~4 ;<;<;<;:;;;;RRSRSTSQQSSTSSPQQQRQPPRTRBCDBDBDDFCDBDBBD??@DCCC==-1<=CD1484:0<?A?C-BD;===:../0=<~14 =<>==>>=<====<=<==<~6 ==>><@>?@DD<?@B?DBD~4 EEGEGDDED?=DHGFDEEFEGHHHGGGFHHHEH<3<<<72>~4 =>>>>====>~4 ====>~5 ====>><=>~5 <<====1052==>=~7 >~6 @A@@@?@@?A??>A@AAA@>>>>?>>@~4 ??>@???@@@??@~5 ??@>~13 =>>===>~5 ?>>?>==>>>>?>~6 ?>>=~4 >=>=~8 ??>>>==???==>~9 ?>=~4 >>>??>><<=<<<>=>>=~4 <~8 ====>==<====><>>>>==>>=>=><=<~8 ?>?>>=>=>=>~16 ?~9 ===>>>>=>====<<=<>===<<<=<=????>~16 ?>>>D~4 CD>~9 D~8 B@A@A??CD?>?>>>?>>DDCD??A???>??>?~4 >>>>?>???>~11 =>~14 ?~12 >>=>?=?==>>==>>?>>>EDEDDD>~6 ===>>=>>>>====<<<<==<<<<==DCDFEDGFGDFGCEBAC?@@CB@??@??@?>>>???A??<=<===<<===<~5 =<~5 =<<>~7 A~10 B~11 AAB~9 AAA@AAA@?@@@?BA~5 BBBCCBB?>>@?>~10 ??><<==<<;:;::;<;;:;;;:;;:~5 ;=:;<~9 ====<=;<<<<=<<=<~7 ;~20 <~9 ;<~16 =<<<==<~11 ;<~19 ===<<=<<<<=<==<<=<=<<=<=<<==<<<=<~10 =~18 <=<=~4 <===<=<<<==<~11 =>>=;:;==>==>>=~6 >>?>>>???>~4 ?>?>?>=?~5 =>???>>??<<<=>><=<>=><~4 =<=~6 <~4 =<<=;;==>>>>=~4 >>????>?>=>~6 <<=~8 >==>>==?>@~4 A>??>@?>?@BB>>??AA@AB@@A@??>?@@===>=~4 >~4 =~6 <<<<=~6 BBCCBCCB~4 A~6 @ABAA@AAA@A@@@@>~5 ?>>????>????>?>>>??>=><=>?;;;<<=<=>>??;<==<<<<=<~14 ;<;<<<;;<<;;;;<;;<~4 ;~4 ?>><<=>=G~15 C~4 DECBDDBEEDDCDCCCBBBBCBBDCC@@@BB@@?>?>@??=>=?>?>@?@=?<?>?<<??<;<?>>?=:>=>>====>===87;A9;>>;<~6 >>==<===:~5 @:~7 @@A::::<=~25 >>;<=;:~4 ??>??=>=:<??=::=@=;=<;<<;;<~8 ::<=~6 <@?>==<>>>?@?>=~4 ;=;<<<;<;;;<<<??@~8 A@?@~19 =~5 <><==>=@>>><=>~11 =<=>>AAA@><<<<A@ABB;;<<;<?@=@@@<<???=??>=??>??>??@@=>~4 ?>BBB<=;;;;B;@>=>~4 ==>>=~12 ;=<====<:;<;<::<<==>~5 :~5 <;<;;;;<>>>I>><;<==>;;<;;<<=>==><<<:~4 ;99:99:<;<;<;~11 <;<<<;<;;:;;;<<<::<???<<==><<<==><@???@>=<~6 @@<<<<@>>==<>=>==<~25 >~10 <<=<<>=>>>=~5 <=>===<==>~5 ====<<<<=~4 <~5 =<=<===<=<=<=<;~9 =>>==><<=;;;=>;<<??=>=>?=><<<<;=887788878~4 7~4 88777999:99889988989899998999::99:~6 ;;::;::;<<<;~7 <;::::9998878898:9:87778787778<<<<;<;<;;:;;;:;;:;;;:~4 99::::8::99::999::899897899:788:9:9<~7 ;<<<;<:;<~6 ;;;:::9999;:;8:9<<==<===<<<=<<=~4 <==<<<<=<=<<<;;<<===<<<<===;<;=<;;:;;;;:;<::;89::8:::8:::8787:::79:9:99989:9:;:;;;:;;<;;;;<~7 ;<99;;:">

   *   </jvxlColorData>

   * </jvxlSurfaceData>

   *

   *

   **********************************************************/

  private static void jvxlAppendMeshXml(StringBuffer sb,

                                        JvxlData jvxlData, MeshData meshData, boolean escapeXml) {

    int[] vertexIdNew = new int[meshData.vertexCount];

    if (appendXmlTriangleData(sb, meshData.polygonIndexes,

        meshData.polygonCount, vertexIdNew, escapeXml))

      appendXmlVertexData(sb, jvxlData, vertexIdNew,

          meshData.vertices, meshData.vertexValues, meshData.vertexCount,

          meshData.polygonColorData, meshData.polygonCount,

          jvxlData.jvxlColorData.length() > 0, escapeXml);

  }

  /**

   * encode triangle data -- [ia ib ic]  [ia ib ic]  [ia ib ic] ...

   * algorithm written by Bob Hanson, 11/2008. The principle is that

   * not all vertices may be represented -- we only need the

   * used vertices here. Capitalizing on the fact that triangle sets

   * tend to have common edges and similar numbers for sequential triangles.

   *

   * a) Renumbering vertices as they appear in the triangle set

   *

   *    [2456 2457 2458] [2456 2459 2458]

   *   

   *   becomes

   *   

   *    [   1    2    3] [   1    4    3]

   *

   * b) This allows efficient encoding of differences, not absolute numbers.

   *

   *        0    1    2     -2    3   -1

   *       

   * c) Which can then be represented often using a single ASCII character.

   *    I chose \ to be 0, and replace that with !.

   *   

   *    ASCII:

   *    -30       -20       -10         0       +10       +20       +30     

   *    <=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|

   *   

   *    So the above sequence would simply be:

   *   

   *      !]^Z_[

   *

   *    When the range falls outside of +/-32, we simply use a number.

   *    When a positive number follows another number, we add a "+" to it.

   *   

   *      !]^Z_[-33+250]230-210]]

   *     

   *    Preliminary trials indicated that on average a triangle

   *    can be encoded in about 7 bytes, or roughly half the 12 bytes

   *    necessary for standard binary encoding of integers. The advantage

   *    here is that we have an ASCII-readable file and no little-/big-endian issue.

   *

   * @param sb

   * @param triangles

   * @param nData

   * @param vertexIdNew

   * @param escapeXml

   * @return (triangles are present)

   */

  private static boolean appendXmlTriangleData(StringBuffer sb, int[][] triangles, int nData,

                                              int[] vertexIdNew, boolean escapeXml) {

    StringBuffer list1 = new StringBuffer();

    int ilast = 1;

    int p = 0;

    int inew = 0;

    boolean addPlus = false;

    int nTri = 0;

    for (int i = 0; i < nData;) {

      if (triangles[i] == null) {

        i++;

        continue;

      }

      int idata = triangles[i][p];

      if (vertexIdNew[idata] > 0) {

        idata = vertexIdNew[idata];

      } else {

        idata = vertexIdNew[idata] = ++inew;

      }

      int diff = idata - ilast;

      ilast = idata;

      if (diff == 0) {

        list1.append('!');

        addPlus = false;

      } else if (diff > 32) {

        if (addPlus)

          list1.append('+');

        list1.append(diff);

        addPlus = true;

      } else if (diff < -32) {

        list1.append(diff);

        addPlus = true;

      } else {

        list1.append((char) ('\\' + diff));

        addPlus = false;

      }

      if (++p % 3 == 0) {

        p = 0;

        i++;

        nTri++;

      }

    }

    if (list1.length() == 0)

      return false;

    XmlUtil.appendTag(sb, "jvxlTriangleData", new String[] {

        "count", "" + nTri,

        "encoding", "jvxltdiff",

        "data" , jvxlCompressString(list1.toString(), escapeXml) }, null);

    return true;

  }

  /**

   * encode the vertex data. This must be done AFTER encoding the triangles,

   * because the triangles redefine the order of vertices.

   *

   * Bob Hanson 11/2008

   *

   * If another program has created the triangles, we probably do not

   * know the grid that was used for Marching Cubes, or quite possibly

   * no grid was used. In that case, we just save the vertex/triangle/value

   * data in a compact form. 

   *

   * For the  we use an extension of the way edge points are encoded.

   * We simply identify the minimum and maximum x, y, and z coordinates and

   * then express the point as a fraction along each of those directions.

   * Thus, the x, y, and z coordinate are within the interval [0,1].

   * 

   * We opt for the two-byte double-precision JVXL character compression.

   * This allows a 1 part in 8100 resolution, which is plenty for these

   * purposes.

   *

   * The tag will indicate the minimum and maximum values:

   *

   *   <jvxlVertexData

   *      count="150"

   *      min="(15.218472, -28.304049, 34.71112)"

   *      max="(97.8228, 54.011948, 109.95208)"

   *      data="....">

   *   </jvxlVertexData>

   *

   * The resultant string is really two strings of length nData

   * where the first string lists the "high" part of the positions,

   * and the second string lists the "low" part of the positions.

   *

   * @param sb

   * @param jvxlData

   * @param vertexIdNew

   * @param vertices

   * @param vertexValues

   * @param vertexCount

   * @param polygonColorData

   * @param polygonCount

   * @param addColorData

   * @param escapeXml

   */

  private static void appendXmlVertexData(StringBuffer sb,

                                            JvxlData jvxlData,

                                            int[] vertexIdNew,

                                            Point3f[] vertices,

                                            float[] vertexValues,

                                            int vertexCount,

                                            String polygonColorData,

                                            int polygonCount,

                                            boolean addColorData, boolean escapeXml) {

    int colorFractionBase = jvxlData.colorFractionBase;

    int colorFractionRange = jvxlData.colorFractionRange;

    Point3f p;

    Point3f min = jvxlData.boundingBox[0];

    Point3f max = jvxlData.boundingBox[1];

    StringBuffer list1 = new StringBuffer();

    StringBuffer list2 = new StringBuffer();

    int[] vertexIdOld = new int[vertexCount];

    for (int i = 0; i < vertexCount; i++)

      if (vertexIdNew[i] > 0) // not all vertices may be in triangle -- that's OK

        vertexIdOld[vertexIdNew[i] - 1] = i;

    for (int i = 0; i < vertexCount; i++) {

      p = vertices[vertexIdOld[i]];

      jvxlAppendCharacter2(p.x, min.x, max.x, colorFractionBase,

          colorFractionRange, list1, list2);

      jvxlAppendCharacter2(p.y, min.y, max.y, colorFractionBase,

          colorFractionRange, list1, list2);

      jvxlAppendCharacter2(p.z, min.z, max.z, colorFractionBase,

          colorFractionRange, list1, list2);

    }

    list1.append(list2);

    XmlUtil.appendTag(sb, "jvxlVertexData", new String[] {

        "count", "" + vertexCount,

        "min", Escape.escape(min),

        "max", Escape.escape(max),

        "encoding", "base90xyz2",

        "data", jvxlCompressString(list1.toString(), escapeXml) }, null);

    if (polygonColorData != null)

      XmlUtil.appendTag(sb, "jvxlPolygonColorData", new String[] {

          "encoding", "jvxlnc",

          "count", "" + polygonCount}, "\n" + polygonColorData);

    if (!addColorData)

      return;

    // now add the color data, again as a double-precision value.

    list1 = new StringBuffer();

    list2 = new StringBuffer();

    for (int i = 0; i < vertexCount; i++) {

      float value = vertexValues[vertexIdOld[i]];

      jvxlAppendCharacter2(value, jvxlData.mappedDataMin,

          jvxlData.mappedDataMax, colorFractionBase, colorFractionRange, list1,

          list2);

    }

    appendXmlColorData(sb, "jvxlColorData", list1.append(list2).append("\n").toString(), true,

        jvxlData.valueMappedToRed, jvxlData.valueMappedToBlue);

  }

  ////////// character - fraction encoding and decoding

 

  // NEVER change the numbers for these next defaults

 

  final public static int defaultEdgeFractionBase = 35; //#$%.......

  final public static int defaultEdgeFractionRange = 90;

  final public static int defaultColorFractionBase = 35;

  final public static int defaultColorFractionRange = 90;

  /* character-encoding of factions in base 90:

   *

   * characters ASC(35) - ASC(124) are used for this encoding with the

   * exception of ASC(92)'\\', which is encoded as ASC(33)'!'.

   * ASC(125)'}' is reserved for "NaN".

   * Double-quote is not in this range, but '<' and '>' are, so this

   * is only XML-safe when quoted as an attribute.

   *

   */

  public static char jvxlFractionAsCharacter(float fraction) {

    return jvxlFractionAsCharacter(fraction, defaultEdgeFractionBase, defaultEdgeFractionRange); 

  }

 

  public static char jvxlFractionAsCharacter(float fraction, int base, int range) {

    if (fraction > 0.9999f)

      fraction = 0.9999f;

    else if (Float.isNaN(fraction))

      fraction = 1.0001f;

    int ich = (int) (fraction * range + base);

    if (ich < base)

      return (char) base;

    if (ich == 92)

      return 33; // \ --> !

    //if (logCompression)

    //Logger.info("fac: " + fraction + " --> " + ich + " " + (char) ich);

    return (char) ich;

  }

  private static void jvxlAppendCharacter2(float value, float min, float max,

                                           int base, int range,

                                           StringBuffer list1,

                                           StringBuffer list2) {

    float fraction = (min == max ? value : (value - min) / (max - min));

    char ch1 = jvxlFractionAsCharacter(fraction, base, range);

    list1.append(ch1);

    fraction -= jvxlFractionFromCharacter(ch1, base, range, 0);

    list2.append(jvxlFractionAsCharacter(fraction * range, base, range));

  }

  public static float jvxlFractionFromCharacter(int ich, int base, int range,

                                                float fracOffset) {

    if (ich == base + range)

      return Float.NaN;

    if (ich < base)

      ich = 92; // ! --> \

    float fraction = (ich - base + fracOffset) / range;

    if (fraction < 0f)

      return 0f;

    if (fraction > 1f)

      return 0.999999f;

    // System.out.println("ffc: " + fraction + " <-- " + ich + " " + (char)

    // ich);

    return fraction;

  }

  public static float jvxlFractionFromCharacter2(int ich1, int ich2, int base,

                                          int range) {

    float fraction = jvxlFractionFromCharacter(ich1, base, range, 0);

    float remains = jvxlFractionFromCharacter(ich2, base, range, 0.5f);

    return fraction + remains / range;

  }

  public static char jvxlValueAsCharacter(float value, float min, float max, int base,

                                   int range) {

    float fraction = (min == max ? value : (value - min) / (max - min));

    return jvxlFractionAsCharacter(fraction, base, range);

  }

  protected static float jvxlValueFromCharacter2(int ich, int ich2, float min,

                                                 float max, int base, int range) {

    float fraction = jvxlFractionFromCharacter2(ich, ich2, base, range);

    return (max == min ? fraction : min + fraction * (max - min));

  }

  // /// differential bitset encoding and decoding (Bob Hanson hansonr@stolaf.edu for Jmol)

  public static int jvxlEncodeBitSet0(BitSet bs, int nPoints, StringBuffer sb) {

    // nunset nset nunset ...

    // for repeated numbers:

    // 3 3 3 3 3 3 3 becomes 3 -6

    int dataCount = 0;

    int prevCount = -1;

    int nPrev = 0;

    if (nPoints < 0)

      nPoints = bs.length();

    int n = 0;

    boolean isset = false;

    int lastPoint = nPoints - 1;

   

    for (int i = 0; i < nPoints; ++i) {

      if (isset == bs.get(i)) {

        dataCount++;

      } else {

        if (dataCount == prevCount && i != lastPoint) {

          nPrev++;

        } else {

          if (nPrev > 0) {

            sb.append(' ').append(-nPrev);

            nPrev = 0;

            n++;

          }

          sb.append(' ').append(dataCount);

          n++;

          prevCount = dataCount;

        }

        dataCount = 1;

        isset = !isset;

      }

    }

    sb.append(' ').append(dataCount).append('\n');

    return n;

  }

 

   

  public static int jvxlEncodeBitSet(BitSet bs, int nPoints, StringBuffer sb) {

    //if (false)

      //return jvxlEncodeBitSet0(bs, nPoints, sb);

    int dataCount = 0;

    int n = 0;

    boolean isset = false;

    if (nPoints < 0)

      nPoints = bs.length();

    if (nPoints == 0)

      return 0;

    sb.append("-");

    for (int i = 0; i < nPoints; ++i) {

      if (isset == bs.get(i)) {

        dataCount++;

      } else {

         jvxlAppendEncodedNumber(sb, dataCount, defaultEdgeFractionBase, defaultEdgeFractionRange);

        n++;

        dataCount = 1;

        isset = !isset;

      }

    }

    jvxlAppendEncodedNumber(sb, dataCount, defaultEdgeFractionBase, defaultEdgeFractionRange);

    sb.append('\n');

    return n;

  }

  public static void jvxlAppendEncodedNumber(StringBuffer sb, int n, int base, int range) {

    boolean isInRange = (n < range);

    if (n == 0)

      sb.append((char) base);

    else if (!isInRange)

      sb.append((char)(base + range));

    while (n > 0) {

      int n1 = n / range;

      int x = base + n - n1 * range;

      if (x == 92)

        x = 33;  // \ --> !

      sb.append((char) x);

      n = n1;

    }

    if (!isInRange)

      sb.append(" ");

  }

  public static BitSet jvxlDecodeBitSet(String data, int base, int range) {

    BitSet bs = new BitSet();

    int dataCount = 0;

    int ptr = 0;

    boolean isset = false;

    int[] next = new int[1];

    while ((dataCount = jvxlParseEncodedInt(data, base, range, next)) != Integer.MIN_VALUE) {

      if (isset)

        bs.set(ptr, ptr + dataCount);

      ptr += dataCount;

      isset = !isset;

    }

    return bs;

  }

  public static int jvxlParseEncodedInt(String str, int offset, int base, int[] next) {

    boolean digitSeen = false;

    int value = 0;

    int ich = next[0];

    int ichMax = str.length();

    if (ich < 0)

      return Integer.MIN_VALUE;

    while (ich < ichMax && Character.isWhitespace(str.charAt(ich)))

      ++ich;

    if (ich >= ichMax)

      return Integer.MIN_VALUE;

    int factor = 1;

    boolean isLong = (str.charAt(ich) == (offset + base));

    if (isLong)

      ich++;

    while (ich < ichMax && !Character.isWhitespace(str.charAt(ich))) {

      int i = str.charAt(ich);

      if (i < offset)

        i = 92;   // ! --> \

      value += (i - offset) * factor;

      digitSeen = true;

      ++ich;

      if (!isLong)

        break;

      factor *= base;

    }

    if (!digitSeen)

      value = Integer.MIN_VALUE;

    next[0] = ich;

    return value;

  }

  public static BitSet jvxlDecodeBitSet(String data) {

    if (data.startsWith("-"))

      return jvxlDecodeBitSet(jvxlUncompressString(data.substring(1)), defaultEdgeFractionBase, defaultEdgeFractionRange);

    // nunset nset nunset ...

    BitSet bs = new BitSet();

    int dataCount = 0;

    int lastCount = 0;

    int nPrev = 0;

    int ptr = 0;

    boolean isset = false;

    int[] next = new int[1];

    while (true) {

      dataCount = (nPrev++ < 0 ? dataCount : Parser.parseInt(data, next));

      if (dataCount == Integer.MIN_VALUE)

        break;

      if (dataCount < 0) {

        nPrev = dataCount;

        dataCount = lastCount;

        continue;

      }

      if (isset)

        bs.set(ptr, ptr + dataCount);

      ptr += dataCount;

      lastCount = dataCount;

      isset = !isset;

    }

    return bs;

  }

 

  /////// string data compression/decompression

 

  public static String jvxlCompressString(String data, boolean escapeXml) {

   

   

    /* just a simple compression, but allows 2000-6000:1 CUBE:JVXL for planes!

     *

     *   "X~nnn " means "nnn copies of character X"

     *  

     *   ########## becomes "#~10 "

     *  

     *   ~ is not encoded, as it is ASC(126), outside the range of 33--125.

     *  

     *   for escaping XML, we also do:

     *

     *   < becomes "~;0 "

     *   & becomes "~%0 "

     *  

     *   and repeats of those become:

     *  

     *   "~;nnn "

     *   "~%nnn "

     *

     */

    if (data.indexOf("~") >= 0)

      return data;

    StringBuffer dataOut = new StringBuffer();

    char chLast = '\0';

    boolean escaped = false;

    boolean lastEscaped = false;

    int nLast = 0;

    int n = data.length();

    for (int i = 0; i <= n; i++) {

      char ch = (i == n ? '\0' : data.charAt(i));

      switch (ch) {

      case '\n':

      case '\r':

        continue;

      case '&':

      case '<':

        escaped = escapeXml;

        break;

      default:

        escaped = false;

      }

      if (ch == chLast) {

        ++nLast;

        ch = '\0';

      } else if (nLast > 0 || lastEscaped) {

        if (nLast < 4 && !lastEscaped || chLast == ' '

            || chLast == '\t') {

          while (--nLast >= 0)

            dataOut.append(chLast);

        } else {

          if (lastEscaped)

            lastEscaped = false;

          else

            dataOut.append('~');

          dataOut.append(nLast);

          dataOut.append(' ');

        }

        nLast = 0;

      }

      if (ch != '\0') {

        if (escaped) {

          lastEscaped = true;

          escaped = false;

          dataOut.append('~');

          chLast = ch;

          --ch;

        } else {

          chLast = ch;         

        }

        dataOut.append(ch);

      }

    }

   

    return dataOut.toString();

  }

  public static String jvxlUncompressString(String data) {

    if (data.indexOf("~") < 0)

      return data;

    StringBuffer dataOut = new StringBuffer();

    char chLast = '\0';

    int[] next = new int[1];

    for (int i = 0; i < data.length(); i++) {

      char ch = data.charAt(i);

      if (ch == '~') {

        next[0] = ++i;

        switch (ch = data.charAt(i)) {

        case ';':

        case '%':

          next[0]++;

          dataOut.append(chLast = ++ch);

          //fall through

        case '1':

        case '2':

        case '3':

        case '4':

        case '5':

        case '6':

        case '7':

        case '8':

        case '9':

          int nChar = Parser.parseInt(data, next);

          for (int c = 0; c < nChar; c++)

            dataOut.append(chLast);

          i = next[0];

          continue;

        case '~':

          --i;

          break;

        default:

          Logger.error("Error uncompressing string " + data.substring(0, i) + "?");

        }

      }

      dataOut.append(ch);

      chLast = ch;

    }

    return dataOut.toString();

  }

  // VERSION 1 methods -- deprecated but still available through Jmol 11.9.18

 

  public static void jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData v, StringBuffer bs) {

    jvxlCreateHeader(v, Integer.MAX_VALUE, null, null,  bs);

  }

  public static void jvxlCreateHeader(VolumeData v, int nAtoms,

                                         Point3f[] atomXyz, int[] atomNo,

                                         StringBuffer sb) {

    // if the StringBuffer comes in non-empty, it should have two lines

    // that do not start with # already present.

    v.setVolumetricXml();

    if (sb.length() == 0)

      sb.append("Line 1\nLine 2\n");

    sb.append(nAtoms == Integer.MIN_VALUE ? "+2"

        : nAtoms == Integer.MAX_VALUE ? "-2" : "" + (-nAtoms))

      .append(' ')

      .append(v.volumetricOrigin.x).append(' ')

      .append(v.volumetricOrigin.y).append(' ')

      .append(v.volumetricOrigin.z).append(" ANGSTROMS\n");

    for (int i = 0; i < 3; i++)

      sb.append(v.voxelCounts[i]).append(' ')

        .append(v.volumetricVectors[i].x).append(' ')

        .append(v.volumetricVectors[i].y).append(' ')

        .append(v.volumetricVectors[i].z).append('\n');

    if (nAtoms != Integer.MAX_VALUE && nAtoms != Integer.MIN_VALUE) {

      nAtoms = Math.abs(nAtoms);

      for (int i = 0, n = 0; i < nAtoms; i++)

        sb.append((n = Math.abs(atomNo[i])) + " " + n + ".0 "

            + atomXyz[i].x + " " + atomXyz[i].y + " " + atomXyz[i].z + "\n");

      return;

    }

    Point3f pt = new Point3f(v.volumetricOrigin);

    sb.append("1 1.0 ").append(pt.x).append(' ').append(pt.y).append(' ')

        .append(pt.z).append(" //BOGUS H ATOM ADDED FOR JVXL FORMAT\n");

    for (int i = 0; i < 3; i++)

      pt.scaleAdd(v.voxelCounts[i] - 1, v.volumetricVectors[i], pt);

    sb.append("2 2.0 ").append(pt.x).append(' ').append(pt.y).append(' ')

        .append(pt.z).append(" //BOGUS He ATOM ADDED FOR JVXL FORMAT\n");

  }

  /*

  private static String jvxlGetFileVersion1(JvxlData jvxlData,

                                            MeshData meshData, String[] title,

                                            String msg, boolean includeHeader,

                                            int nSurfaces, String state,

                                            String comment) {

    // pre-XML

    if ("TRAILERONLY".equals(msg))

      return "";

    StringBuffer data = new StringBuffer();

    if (includeHeader) {

      String s = jvxlData.jvxlFileHeader

          + (nSurfaces > 0 ? -nSurfaces : -1) +" " + jvxlData.edgeFractionBase + " "

          + jvxlData.edgeFractionRange + " " + jvxlData.colorFractionBase + " "

          + jvxlData.colorFractionRange + " Jmol voxel format version " +  JVXL_VERSION1 + "\n";

      if (s.indexOf("#JVXL") != 0)

        data.append("#JVXL").append(jvxlData.isXLowToHigh ? "+" : "").append(

            " VERSION ").append(JVXL_VERSION1).append("\n");

      data.append(s);

    }

    if ("HEADERONLY".equals(msg))

      return data.toString();

    data.append("# ").append(msg).append('\n');

    if (title != null)

      for (int i = 0; i < title.length; i++)

        data.append("# ").append(title[i]).append('\n');

    state = (state == null ? "" : " rendering:" + state);

    String definitionLine = jvxlGetDefinitionLineVersion1(jvxlData);

    data.append(definitionLine).append(state).append('\n');

    StringBuffer sb = new StringBuffer();

    String colorData = (jvxlData.jvxlColorData == null ? "" : jvxlData.jvxlColorData);

    // if (jvxlData.vertexDataOnly) {  // see XML version

    //  sb.append("<jvxlSurfaceData>\n");

    //  jvxlAppendMeshXml(sb, jvxlData, meshData, false);

    //  sb.append("</jvxlSurfaceData>\n");

    //} else 

    if (jvxlData.jvxlPlane == null) {

      if (jvxlData.jvxlEdgeData == null)

        return "";

      //no real point in compressing this unless it's a sign-based coloring

      sb.append(jvxlData.jvxlSurfaceData);

      sb.append(jvxlCompressString(jvxlData.jvxlEdgeData, false)).append('\n').append(

          jvxlCompressString(colorData, false)).append('\n');

    } else if (colorData != null) {

      sb.append(jvxlCompressString(colorData, false)).append('\n');

    }

    int len = sb.length();

    data.append(sb);

    if (includeHeader) {

      if (msg != null && !jvxlData.vertexDataOnly)

        data.append("#-------end of jvxl file data-------\n");

      data.append(jvxlGetInfo(jvxlData, false)).append('\n');

        jvxlAppendCommandState(data, comment, state, false);

      if (includeHeader)

        XmlUtil.appendTag(data, "jvxlFileTitle", null, null, jvxlData.jvxlFileTitle, false, true);

    }

    return jvxlSetCompressionRatio(data, jvxlData, len);

  }

  private static String jvxlGetDefinitionLineVersion1(JvxlData jvxlData) {

    String definitionLine =

    //(jvxlData.vContours == null ? ""  : "#+contourlines\n")+

       jvxlData.cutoff + " ";

    //  optional comment line for compatibility with earlier Jmol versions:

    //  #+contourlines (no longer used -- see XML version)

    //  cutoff       nInts     (+/-)bytesEdgeData (+/-)bytesColorData

    //               param1              param2         param3   

    //                 |                   |              |

    //   when          |                   |        >  0 ==> jvxlDataIsColorMapped

    //   when          |                   |       == -1 ==> not color mapped

    //   when          |                   |        < -1 ==> jvxlDataIsPrecisionColor   

    //   when        == -1     &&   == -1 ==> noncontoured plane

    //   when        == -1     &&   == -2 ==> contourable plane

    //   when        < -1*     &&    >  0 ==> contourable functionXY

    //   when        > 0       &&    <  0 ==> jvxlDataisBicolorMap

    //  nInts saved as -1 - nInts

    if (jvxlData.jvxlSurfaceData == null)

      return "";

    int nSurfaceInts = jvxlData.nSurfaceInts;// jvxlData.jvxlSurfaceData.length();

    int bytesUncompressedEdgeData = (jvxlData.vertexDataOnly ? 0

        : jvxlData.jvxlEdgeData.length() - 1);

    int nColorData = (jvxlData.jvxlColorData == null ? -1 : (jvxlData.jvxlColorData.length() - 1));

    if (jvxlData.jvxlPlane == null) {

      if (jvxlData.isContoured) {

        definitionLine += (-1 - nSurfaceInts) + " " + bytesUncompressedEdgeData;

      } else if (jvxlData.isBicolorMap) {

        definitionLine += (nSurfaceInts) + " " + (-bytesUncompressedEdgeData);

      } else {

        definitionLine += nSurfaceInts + " " + bytesUncompressedEdgeData;

      }

      definitionLine += " "

          + (jvxlData.isJvxlPrecisionColor && nColorData != -1 ? -nColorData

              : nColorData);

    } else {

      String s = " " + jvxlData.jvxlPlane.x + " " + jvxlData.jvxlPlane.y + " "

          + jvxlData.jvxlPlane.z + " " + jvxlData.jvxlPlane.w;

      definitionLine += (jvxlData.isContoured ? "-1 -2 " + (-nColorData)

          : "-1 -1 " + nColorData)

          + s;

    }

    if (jvxlData.isContoured) {

      if (jvxlData.contourValues == null || jvxlData.contourColixes == null) {

        definitionLine += " " + jvxlData.nContours;

      } else {

        definitionLine += " " + Escape.escapeArray(jvxlData.contourValues)

            + " \"" + jvxlData.contourColors + "\"";

      }

    }

    // ... mappedDataMin mappedDataMax valueMappedToRed valueMappedToBlue ...

    float min = (jvxlData.mappedDataMin == Float.MAX_VALUE ? 0f

        : jvxlData.mappedDataMin);

    definitionLine += " " + min + " " + jvxlData.mappedDataMax + " "

        + jvxlData.valueMappedToRed + " " + jvxlData.valueMappedToBlue;

    if (jvxlData.insideOut) {

      definitionLine += " insideOut";

    }

    return definitionLine;

  }

  */