Package edu.stanford.genetics.treeview

Examples of edu.stanford.genetics.treeview.ConfigNode

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    }
    PluginManager.getPluginManager().pluginAssignConfigNodes(getGlobalConfig().getNode("Plugins"));
  }
 
  private void dealWithRegistration() {
    ConfigNode node = getGlobalConfig().getNode("Registration");
    if (node != null) {
      try {
        edu.stanford.genetics.treeview.reg.RegEngine.verify(node);
        getGlobalConfig().store();
      } catch (Exception e) {
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    /**
     * returns String [] of preset names for display
     */
    public String[] getPresetNames()
    {
        ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
        String astring[] = new String[aconfigNode.length];
    KaryoColorSet temp = new KaryoColorSet("TempColorSet");
    for (int i = 0; i < aconfigNode.length; i++) {
      temp.bindConfig(aconfigNode[i]);
            astring[i] = temp.getName();
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            astring[i] = temp.getName();
    }
    return astring;
    }
  public int getNumPresets() {
        ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
    return aconfigNode.length;
  }
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  public int getNumPresets() {
        ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
    return aconfigNode.length;
  }
  public String toString() {
        ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
    KaryoColorSet tmp = new KaryoColorSet();
    String ret = "Default is " + getPresetNames() [getDefaultIndex()] + " index " + getDefaultIndex() + "\n";
    for (int index = 0; index < aconfigNode.length; index++) {
      tmp.bindConfig(aconfigNode[index]);
      ret += tmp.toString() +"\n";
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    /**
     * returns the color set for the ith preset
     * or null, if any exceptions are thrown.
     */
    public KaryoColorSet getColorSet(int index) {
        ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
    try {
      KaryoColorSet ret = new KaryoColorSet();
      ret.bindConfig(aconfigNode[index]);
      return ret;
    } catch (Exception e) {
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    /**
     * returns the color set for this name
     * or null, if name not found in kids
     */
   public KaryoColorSet getColorSet(String name) {
     ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
     KaryoColorSet ret = new KaryoColorSet();
     for (int i = 0; i < aconfigNode.length; i++) {
     ret.bindConfig(aconfigNode[i]);
     if (name.equals(ret.getName()))  {
       return ret;
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    }

    }

  public void removeColorSet(int i) {
     ConfigNode aconfigNode[] = root.fetch("KaryoColorSet");
     root.remove(aconfigNode[i]);
  }
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    /**
     * returns String [] of preset names for display
     */
    public String[] getPresetNames()
    {
        ConfigNode aconfigNode[] = root.fetch("ScatterColorSet");
        String astring[] = new String[aconfigNode.length];
    ScatterColorSet temp = new ScatterColorSet("TempColorSet");
    for (int i = 0; i < aconfigNode.length; i++) {
      temp.bindConfig(aconfigNode[i]);
            astring[i] = temp.getName();
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            astring[i] = temp.getName();
    }
    return astring;
    }
  public int getNumPresets() {
        ConfigNode aconfigNode[] = root.fetch("ScatterColorSet");
    return aconfigNode.length;
  }
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  public int getNumPresets() {
        ConfigNode aconfigNode[] = root.fetch("ScatterColorSet");
    return aconfigNode.length;
  }
  public String toString() {
        ConfigNode aconfigNode[] = root.fetch("ScatterColorSet");
    ScatterColorSet tmp = new ScatterColorSet();
    String ret = "Default is " + getPresetNames() [getDefaultIndex()] + " index " + getDefaultIndex() + "\n";
    for (int index = 0; index < aconfigNode.length; index++) {
      tmp.bindConfig(aconfigNode[index]);
      ret += tmp.toString() +"\n";
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Related Classes of edu.stanford.genetics.treeview.ConfigNode

  • edu.stanford.genetics.treeview.app.LinkedViewApp
  • edu.stanford.genetics.treeview.plugin.karyoview.KaryoColorPresets
  • edu.stanford.genetics.treeview.plugin.scatterview.ScatterColorPresets
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