Examples of org.jmol.modelset.Measurement

org.jmol.modelset.Measurement

  private void setColor(short colix) {
    if (bsColixSet == null)
      bsColixSet = new BitSet();
      if (bsSelected == null)
        this.colix = colix;
    Measurement mt;
    for (int i = measurements.size(); --i >= 0; )
      if ((mt = (Measurement) measurements.get(i)) != null
          && (bsSelected != null && bsSelected.get(i) || bsSelected == null
              && (colix == Graphics3D.INHERIT_ALL || mt.getColix() == Graphics3D.INHERIT_ALL))) {
        mt.setColix(colix);
        bsColixSet.set(i);
      }
  }

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  private void toggle(Measurement m) {
    rangeMinMax[0] = Float.MAX_VALUE;
    //toggling one that is hidden should be interpreted as DEFINE
    int i = find(m);
    Measurement mt;
    if (i >= 0 && !(mt = (Measurement) measurements.get(i)).isHidden()) // delete it and all like it
      define(i, mt, true, false, false);
    else // define OR turn on if measureAllModels
      define(-1, m, false, true, false);
    setIndices();

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  private void toggleOn(int[] indices) {
    rangeMinMax[0] = Float.MAX_VALUE;
    //toggling one that is hidden should be interpreted as DEFINE
    bsSelected = new BitSet();
    define(Integer.MIN_VALUE, new Measurement(modelSet, indices, null, defaultTickInfo), false, true, true);
    setIndices();
    reformatDistances();
  }

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    setIndices();
  }


  private void delete(Object value) {
    if (value instanceof int[]) {
      define(Integer.MIN_VALUE, new Measurement(modelSet, (int[])value, null, null), true, false, false);
      return;
    }
    if ((value instanceof Integer))
      deleteMeasurement(((Integer)value).intValue());   
  }

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      ((Measurement) measurements.get(i)).setHidden(false);
      if (doSelect)
        bsSelected.set(i);
      return;
    }
    Measurement measureNew = new Measurement(modelSet, m, value, colix,
        strFormat, measurementCount);
    measurements.add(measureNew);
    viewer.setStatusMeasuring("measureCompleted", measurementCount++,
        measureNew.toVector().toString(), measureNew.getValue());
  }

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    }
    return info;
  }
  
  private Hashtable getInfo(int index) {
    Measurement m = (Measurement) measurements.get(index);
    int count = m.getCount();
    Hashtable info = new Hashtable();
    info.put("index", new Integer(index));
    info.put("type", (count == 2 ? "distance" : count == 3 ? "angle"
        : "dihedral"));
    info.put("strMeasurement", m.getString());
    info.put("count", new Integer(count));
    info.put("value", new Float(m.getValue()));
    TickInfo tickInfo = m.getTickInfo();
    if (tickInfo != null) {
      info.put("ticks", tickInfo.ticks);
      if (tickInfo.scale != null)
        info.put("tickScale", tickInfo.scale);
      if (tickInfo.tickLabelFormats != null)
        info.put("tickLabelFormats", tickInfo.tickLabelFormats);
      if (!Float.isNaN(tickInfo.first))
        info.put("tickStart", new Float(tickInfo.first));
    }
    List atomsInfo = new ArrayList();
    for (int i = 1; i <= count; i++) {
      Hashtable atomInfo = new Hashtable();
      int atomIndex = m.getAtomIndex(i);
      atomInfo.put("_ipt", new Integer(atomIndex));
      atomInfo.put("coord", Escape.escape(m.getAtom(i)));
      atomInfo.put("atomno", new Integer(atomIndex < 0 ? -1 : atoms[atomIndex].getAtomNumber()));
      atomInfo.put("info", (atomIndex < 0 ? "<point>" : atoms[atomIndex].getInfo()));
      atomsInfo.add(atomInfo);
    }
    info.put("atoms", atomsInfo);

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  void setVisibilityInfo() {
    BitSet bsModels = viewer.getVisibleFramesBitSet();
    out:
    for (int i = measurementCount; --i >= 0; ) {
      Measurement m = ((Measurement) measurements.get(i));
      m.setVisible(false);
      if(mad == 0 || m.isHidden())
        continue;
      for (int iAtom = m.getCount(); iAtom > 0; iAtom--) {
        int atomIndex = m.getAtomIndex(iAtom);
        if (atomIndex >= 0) {
          if (!modelSet.atoms[atomIndex].isClickable())
            continue out;
        } else {
          int modelIndex = m.getAtom(iAtom).modelIndex;
          if (modelIndex >= 0 && !bsModels.get(modelIndex))
            continue out;
        }
      }
      m.setVisible(true);
    }
  }

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    appendCmd(commands, getFontCommand("measures", font3d));
    int nHidden = 0;
    Hashtable temp = new Hashtable();
    BitSet bs = new BitSet(measurementCount);
    for (int i = 0; i < measurementCount; i++) {
      Measurement m = ((Measurement) measurements.get(i));
      if (m.isHidden()) {
        nHidden++;
        bs.set(i);
      }
      if (bsColixSet != null && bsColixSet.get(i))
        setStateInfo(temp, i, getColorCommand("measure", m.getColix()));
      if (m.getStrFormat() != null)
        setStateInfo(temp, i, "measure "
            + Escape.escape(m.getStrFormat()));
    }
    if (nHidden > 0)
      if (nHidden == measurementCount)
        appendCmd(commands, "measures off; # lines and numbers off");
      else

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    return commands.toString();
  }
  
  private String getState(int index) {
    Measurement m = ((Measurement) measurements.get(index));
    int count = m.getCount();
    StringBuffer sb = new StringBuffer("measure");
    TickInfo tickInfo = m.getTickInfo();
    if (tickInfo != null)
      FontLineShape.addTickInfo(sb, tickInfo, true);
    for (int i = 1; i <= count; i++)
      sb.append(" ").append(m.getLabel(i, true, true));
    sb.append("; # " + getInfoAsString(index));
    return sb.toString();
  }

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    clearBox();
    boolean showMeasurementLabels = viewer.getShowMeasurementLabels();
    boolean dynamicMeasurements = viewer.getDynamicMeasurements();
    measures.setVisibilityInfo();
    for (int i = measures.measurementCount; --i >= 0;) {
      Measurement m = (Measurement) measures.measurements.get(i);
      if (dynamicMeasurements || m.isDynamic())
        m.refresh();
      if (!m.isVisible())
        continue;
      colix = m.getColix();
      if (colix == 0)
        colix = measures.colix;
      if (colix == 0)
        colix = viewer.getColixBackgroundContrast();
      g3d.setColix(colix);
      renderMeasurement(m.getCount(), m, showMeasurementLabels);
    }
  }

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Related Classes of org.jmol.modelset.Measurement

org.jmol.shape.Measures

org.jmol.shape.MeasuresRenderer

org.jmol.util.Point3fi

java.util.ArrayList

javax.vecmath.AxisAngle4f

javax.vecmath.Vector3f

java.util.List

javax.vecmath.Point3f

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