jspecview/common/JSViewer.java

package jspecview.common;

import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Map;
import java.util.Properties;

import org.jmol.api.GenericFileInterface;
import org.jmol.api.GenericGraphics;
import org.jmol.api.GenericPlatform;
import org.jmol.api.PlatformViewer;
import org.jmol.util.Logger;

import javajs.api.BytePoster;
import javajs.util.CU;
import javajs.util.Lst;
import javajs.util.OC;
import javajs.util.P3;
import javajs.util.PT;
import javajs.util.SB;
import jspecview.api.ExportInterface;
import jspecview.api.JSVFileHelper;
import jspecview.api.JSVMainPanel;
import jspecview.api.JSVPanel;
import jspecview.api.JSVPrintDialog;
import jspecview.api.JSVTree;
import jspecview.api.JSVTreeNode;
import jspecview.api.ScriptInterface;
import jspecview.api.VisibleInterface;
import jspecview.api.js.JSVAppletObject;
import jspecview.api.js.JSVToJSmolInterface;
import jspecview.common.Annotation.AType;
import jspecview.common.PanelData.LinkMode;
import jspecview.common.Spectrum.IRMode;
import jspecview.dialog.DialogManager;
import jspecview.dialog.JSVDialog;
import jspecview.exception.JSVException;
import jspecview.popup.JSVGenericPopup;
import jspecview.source.JDXReader;
import jspecview.source.JDXSource;
import jspecview.tree.SimpleTree;

/**
 * This class encapsulates all general functionality of applet and app. Most
 * methods include ScriptInterface parameter, which will be JSVAppletPrivate,
 * JSVAppletPrivatePro, or MainFrame.
 *
 * @author Bob Hanson hansonr@stolaf.edu
 *
 */
public class JSViewer implements PlatformViewer, BytePoster {

  public final static String sourceLabel = "Original...";

  public final static int FILE_OPEN_OK = 0;
  public final static int FILE_OPEN_ALREADY = -1;
  // private final static int FILE_OPEN_URLERROR = -2;
  public final static int FILE_OPEN_ERROR = -3;
  public final static int FILE_OPEN_NO_DATA = -4;
  public static final int OVERLAY_DIALOG = -1;
  public static final int OVERLAY_OFFSET = 99;
  public static final int PORTRAIT = 1; // Printable
  public static final int PAGE_EXISTS = 0;
  public static final int NO_SUCH_PAGE = 1;

  private static String testScript = "<PeakData  index=\"1\" title=\"\" model=\"~1.1\" type=\"1HNMR\" xMin=\"3.2915\" xMax=\"3.2965\" atoms=\"15,16,17,18,19,20\" multiplicity=\"\" integral=\"1\"> src=\"JPECVIEW\" file=\"http://SIMULATION/$caffeine\"";

  private final static int NLEVEL_MAX = 100;

  public ScriptInterface si;
  public GenericGraphics g2d;
  public JSVTree spectraTree;
  public JDXSource currentSource;
  public Lst<PanelNode> panelNodes;
  public ColorParameters parameters;
  public RepaintManager repaintManager;
  public JSVPanel selectedPanel;
  public JSVMainPanel mainPanel;
  public Properties properties; // application only
  public Lst<String> scriptQueue;
  public JSVFileHelper fileHelper;
  public JSVGenericPopup jsvpPopupMenu;
  private DialogManager dialogManager;
  private JSVDialog viewDialog;
  private JSVDialog overlayLegendDialog;

  private IRMode irMode = IRMode.NO_CONVERT;

  public boolean loadImaginary;
  public boolean interfaceOverlaid;
  public boolean autoIntegrate;
  public boolean autoShowLegend;
  public Boolean obscureTitleFromUser;
  //  public boolean allowCompoundMenu = true;
  public boolean allowMenu = true;
  public int initialStartIndex = -1;
  public int initialEndIndex = -1;

  public boolean isSingleThreaded;
  public boolean isApplet;
  public static boolean isJS, isSwingJS = false;
  public boolean isSigned;

  private String recentScript = "";

  public String appletName;
  public String fullName;
  public String syncID;
  public JSVAppletObject html5Applet; // will be an JavaScript object if this is JavaScript

  public Object display;

  private int maximumSize = Integer.MAX_VALUE;
  private int screenHeight, screenWidth;
  private int fileCount;
  private int nViews;
  private int scriptLevelCount;
  private String returnFromJmolModel;
  private String integrationRatios;

  public GenericPlatform apiPlatform;

  public static JSVToJSmolInterface jmolObject;

  public void setProperty(String key, String value) {
    if (properties != null)
      properties.setProperty(key, value);
  }

  public void setNode(PanelNode node) {
    if (node.jsvp != selectedPanel)
      si.siSetSelectedPanel(node.jsvp);
    si.siSendPanelChange();
    si.siNodeSet(node);
  }

  /**
   * @param si
   * @param isApplet
   * @param isJSApplet
   */
  public JSViewer(ScriptInterface si, boolean isApplet, boolean isJSApplet) {
    this.si = si;
    this.isApplet = isApplet;
    isJS = isApplet && isJSApplet;
    JSVToJSmolInterface jmol = null;

    /**
     * @j2sNative
     *
     * self.Jmol && (jmol = Jmol);
     *
     */
    {

    }
    jmolObject = jmol;
    this.isSigned = si.isSigned();
    apiPlatform = (GenericPlatform) getPlatformInterface("Platform");
    apiPlatform.setViewer(this, this.display);
    g2d = (GenericGraphics) getPlatformInterface("G2D");
    spectraTree = new SimpleTree(this);
    parameters = (ColorParameters) getPlatformInterface("Parameters");
    parameters.setName("applet");
    fileHelper = ((JSVFileHelper) getPlatformInterface("FileHelper")).set(this);
    isSingleThreaded = apiPlatform.isSingleThreaded();
    panelNodes = new Lst<PanelNode>();
    repaintManager = new RepaintManager(this);
    if (!isApplet)
      setPopupMenu(true, true);
  }

  private boolean popupAllowMenu = true;
  private boolean popupZoomEnabled = true;

  private String defaultLoadScript;

  public float nmrMaxY = Float.NaN;

  public void setPopupMenu(boolean allowMenu, boolean zoomEnabled) {
    popupAllowMenu = allowMenu;
    popupZoomEnabled = zoomEnabled;
  }

  public void showMenu(int x, int y) {
    if (!popupAllowMenu)
      return;
    if (jsvpPopupMenu == null) {
      try {
        jsvpPopupMenu = (JSVGenericPopup) getPlatformInterface("Popup");
        jsvpPopupMenu.jpiInitialize(this, isApplet ? "appletMenu" : "appMenu");
        jsvpPopupMenu.setEnabled(popupAllowMenu, popupZoomEnabled);
      } catch (Exception e) {
        Logger.error(e + " initializing popup menu");
        return;
      }
    }
    jsvpPopupMenu.jpiShow(x, y);
  }

  public boolean runScriptNow(String script) {
    System.out.println(checkScript(script));
    scriptLevelCount++;
    if (script == null)
      script = "";
    script = script.trim();
    if (script.startsWith("!"))
      script = script.substring(1).trim();
    else if (script.startsWith(">")) {
      Logger.error(script);
      return true;
    }
    if (script.indexOf("<PeakData") >= 0) {
      syncScript(script);
      return true;
    }
    Logger.info("RUNSCRIPT " + script);
    boolean isOK = true;
    int nErrorsLeft = 10;
    ScriptTokenizer commandTokens = new ScriptTokenizer(script, true);
    String msg = null;
    while (commandTokens != null && commandTokens.hasMoreTokens()
        && nErrorsLeft > 0 && isOK) {
      String token = commandTokens.nextToken();
      // now split the key/value pair

      ScriptTokenizer eachParam = new ScriptTokenizer(token, false);
      String key = ScriptToken.getKey(eachParam);
      if (key == null)
        continue;
      ScriptToken st = ScriptToken.getScriptToken(key);
      String value = ScriptToken.getValue(st, eachParam, token);
      // System.out.println("KEY-> " + key + " VALUE-> " + value + " : " + st);
      try {
        switch (st) {
        case UNKNOWN:
          Logger.info("Unrecognized parameter: " + key);
          --nErrorsLeft;
          break;
        default:
          if (selectedPanel == null)
            break;// probably a startup option for the applet
          parameters.set(pd(), st, value);
          si.siUpdateBoolean(st, Parameters.isTrue(value));
          break;
        case PEAKCALLBACKFUNCTIONNAME:
        case SYNCCALLBACKFUNCTIONNAME:
        case COORDCALLBACKFUNCTIONNAME:
        case LOADFILECALLBACKFUNCTIONNAME:
          si.siExecSetCallback(st, value);
          break;
        case DEFAULTLOADSCRIPT:
          value = PT.rep(value, "''", "\"");
          defaultLoadScript = (value.length() > 0 ? value : null);
          break;
        case DEFAULTNMRNORMALIZATION:
          nmrMaxY = PT.parseFloat(value);
          break;
        case AUTOINTEGRATE:
          autoIntegrate = Parameters.isTrue(value);
          break;
        case CLOSE:
          execClose(value);
          break;
        case DEBUG:
          Logger
              .setLogLevel(value.toLowerCase().equals("high") ? Logger.LEVEL_DEBUGHIGH
                  : Parameters.isTrue(value) ? Logger.LEVEL_DEBUG
                      : Logger.LEVEL_INFO);
          break;
        case GETPROPERTY:
          Map<String, Object> info = (selectedPanel == null ? null
              : getPropertyAsJavaObject(value));
          if (info != null)
            selectedPanel.showMessage(PT.toJSON(null, info), value);
          break;
        case HELP:
          execHelp(value);
          break;
        case HIDDEN:
          si.siExecHidden(Parameters.isTrue(value));
          break;
        case INTEGRATIONRATIOS:
          integrationRatios = value;
          execIntegrate(null);
          break;
        case INTERFACE:
          interfaceOverlaid = checkOvelayInterface(value);
          break;
        case INTEGRALOFFSET:
        case INTEGRALRANGE:
          execSetIntegralParameter(st, Double.parseDouble(value));
          break;
        case INVERTY:
          execZoom("invertY");
          break;
        case JMOL:
          si.syncToJmol(value);
          break;
        case JSV:
          syncScript(PT.trimQuotes(value));
          break;
        case LOAD:
          if (value.length() == 0) {
            if (defaultLoadScript != null)
              runScriptNow(defaultLoadScript);
            break;
          }
          execLoad(value, (defaultLoadScript == null ? "" : defaultLoadScript
              + ";")
              + commandTokens.getRemainingScript());
          msg = (selectedPanel == null ? null : si.siLoaded(value));
          commandTokens = null;
          break;
        case LOADIMAGINARY:
          loadImaginary = Parameters.isTrue(value);
          break;
        case PEAK:
          execPeak(value);
          break;
        case PEAKLIST:
          execPeakList(value);
          break;
        case SCALEBY:
          scaleSelectedBy(panelNodes, value);
          break;
        case SCRIPT:
          if (value.equals("") || value.toLowerCase().startsWith("inline")) {
            execScriptInline(value);
          } else {
            String s = JSVFileManager.getFileAsString(value);
            if (s != null && scriptLevelCount < NLEVEL_MAX)
              runScriptNow(s);
          }
          break;
        case SELECT:
          execSelect(value);
          break;
        case SPECTRUM:
        case SPECTRUMNUMBER:
          if (!setSpectrum(value))
            isOK = false;
          break;
        case STACKOFFSETY:
          execOverlayOffsetY(PT.parseInt("" + PT.parseFloat(value)));
          break;
        case TEST:
          si.siExecTest(value);
          break;
        case OVERLAY: // deprecated
        case VIEW:
          execView(value, true);
          break;
        case HIGHLIGHT:
          isOK = highlight(token);
          break;
        case FINDX:
        case GETSOLUTIONCOLOR:
        case INTEGRATION:
        case INTEGRATE:
        case IRMODE:
        case LABEL:
        case LINK:
        case OVERLAYSTACKED:
        case PRINT:
        case SETPEAK:
        case SETX:
        case SHIFTX:
        case SHOWERRORS:
        case SHOWMEASUREMENTS:
        case SHOWMENU:
        case SHOWKEY:
        case SHOWPEAKLIST:
        case SHOWINTEGRATION:
        case SHOWPROPERTIES:
        case SHOWSOURCE:
        case YSCALE:
        case WRITE:
        case ZOOM:
          if (isClosed()) {
            isOK = false;
            break;
          }
          switch (st) {
          default:
            break;
          case FINDX:
            pd().findX(null, Double.parseDouble(value));
            break;
          case GETSOLUTIONCOLOR:
            show("solutioncolor" + value.toLowerCase());
            break;
          case INTEGRATION:
          case INTEGRATE:
            execIntegrate(value);
            break;
          case IRMODE:
            execIRMode(value);
            break;
          case LABEL:
            pd().addAnnotation(ScriptToken.getTokens(value));
            break;
          case LINK:
            pd().linkSpectra(LinkMode.getMode(value));
            break;
          case OVERLAYSTACKED:
            pd().splitStack(!Parameters.isTrue(value));
            break;
          case PRINT:
            msg = execWrite(null);
            break;
          case SETPEAK:
          case SETX:
          case SHIFTX:
            execShiftSpectrum(st, token);
            break;
          case SHOWERRORS:
            show("errors");
            break;
          case SHOWINTEGRATION:
            pd().showAnnotation(AType.Integration,
                Parameters.getTFToggle(value));
            // execIntegrate(null);
            break;
          case SHOWKEY:
            setOverlayLegendVisibility(Parameters.getTFToggle(value), true);
            break;
          case SHOWMEASUREMENTS:
            pd().showAnnotation(AType.Measurements,
                Parameters.getTFToggle(value));
            break;
          case SHOWMENU:
            showMenu(Integer.MIN_VALUE, 0);
            break;
          case SHOWPEAKLIST:
            pd().showAnnotation(AType.PeakList, Parameters.getTFToggle(value));
            break;
          case SHOWPROPERTIES:
            show("properties");
            break;
          case SHOWSOURCE:
            show("source");
            break;
          case YSCALE:
            setYScale(value);
            break;
          case WINDOW:
            si.siNewWindow(Parameters.isTrue(value), false);
            break;
          case WRITE:
            msg = execWrite(value);
            break;
          case ZOOM:
            isOK = execZoom(value);
            break;
          }
          break;
        }
      } catch (Exception e) {
        msg = e.toString();
        Logger.error(e.toString());
        isOK = false;
        --nErrorsLeft;
      }
    }
    scriptLevelCount--;
    si.siExecScriptComplete(msg, true);
    return isOK;
  }

  private void execShiftSpectrum(ScriptToken st, String script) {
    Lst<String> tokens = ScriptToken.getTokens(script);
    double xOld = Double.NaN;
    double xNew = Double.NaN;
    switch (tokens.size()) {
    case 2:
      String value = tokens.get(1);
      if (value.equals(""))
        value = "?";
      xNew = value.equalsIgnoreCase("NONE") ? Double.MAX_VALUE : value
          .equalsIgnoreCase("?") ? Double.NaN : Double.parseDouble(value);
      break;
    case 3:
      xOld = Double.parseDouble(tokens.get(1));
      xNew = Double.parseDouble(tokens.get(2));
      break;
    default:
      Double.parseDouble(""); // throw an exception
    }
    int mode = 0;
    switch (st) {
    case SETPEAK:
      mode = GraphSet.SHIFT_PEAK;
      break;
    case SETX:
      mode = GraphSet.SHIFT_SETX;
      break;
    case SHIFTX:
      mode = GraphSet.SHIFT_X;
      if (Double.isNaN(xNew))
        Double.parseDouble(""); // throw an exception -- SHIFT by itself not
                                // allowed
      break;
    default:
      return;
    }
    pd().shiftSpectrum(mode, xOld, xNew);
  }

  private void execClose(String value) {
    boolean fromScript = (!value.startsWith("!"));
    if (!fromScript)
      value = value.substring(1);
    close(PT.trimQuotes(value));
    if (!fromScript || panelNodes.size() == 0)
      si.siValidateAndRepaint(true);
  }

  public boolean checkOvelayInterface(String value) {
    return (value.equalsIgnoreCase("single") || value
        .equalsIgnoreCase("overlay"));
  }

  private void execPeak(String value) {
    try {
      Lst<String> tokens = ScriptToken.getTokens(PT.rep(value, "#", "INDEX="));
      value = " type=\"" + tokens.get(0).toUpperCase() + "\" _match=\""
          + PT.trimQuotes(tokens.get(1).toUpperCase()) + "\"";
      if (tokens.size() > 2 && tokens.get(2).equalsIgnoreCase("all"))
        value += " title=\"ALL\"";
      processPeakPickEvent(new PeakInfo(value), false); // false == true here
    } catch (Exception e) {
      // ignore
    }
  }

  private void execPeakList(String value) {
    ColorParameters p = parameters;
    Boolean b = Parameters.getTFToggle(value);
    if (value.indexOf("=") < 0) {
      if (!isClosed())
        pd().getPeakListing(null, b);
    } else {
      Lst<String> tokens = ScriptToken.getTokens(value);
      double threshold = p.peakListThreshold;
      String interp = p.peakListInterpolation;
      try {
        for (int i = tokens.size(); --i >= 0;) {
          String token = tokens.get(i);
          int pt = token.indexOf("=");
          if (pt <= 0)
            continue;
          String key = token.substring(0, pt);
          value = token.substring(pt + 1);
          if (key.startsWith("thr")) {
            threshold = Double.valueOf(value).doubleValue();
          } else if (key.startsWith("int")) {
            interp = (value.equalsIgnoreCase("none") ? "NONE" : "parabolic");
          }
        }
        p.peakListThreshold = threshold;
        p.peakListInterpolation = interp;
        if (!isClosed())
          pd().getPeakListing(p, Boolean.TRUE);
      } catch (Exception e) {
        // ignore
      }
    }
  }

  private boolean highlight(String value) {
    Lst<String> tokens = ScriptToken.getTokens(value);
    int n = tokens.size();
    switch (n) {
    case 3:
    case 5:
    case 6:
    case 7:
      break;
    case 2:
    case 4:
      if (tokens.get(n - 1).equalsIgnoreCase("OFF"))
        break;
      //$FALL-THROUGH$
    default:
      return false;
    }
    if (!isClosed()) {
      float x1 = PT.parseFloat(n > 1 ? tokens.get(1) : "");
      float x2 = PT.parseFloat(n > 2 ? tokens.get(2) : "");
      int r = getRGB(n > 3 ? tokens.get(3) : "100");
      int g = getRGB(n > 4 ? tokens.get(4) : "100");
      int b = getRGB(n > 5 ? tokens.get(5) : "100");
      int a = getRGB(n > 6 ? tokens.get(6) : "100");
      if (Float.isNaN(x1) || Float.isNaN(x2)) {
        pd().removeAllHighlights();
      } else {
        pd().removeHighlight(x1, x2);
        if (a < 0)
          a = 150;
        if (r >= 0 && g >= 0 && b >= 0)
          pd().addHighlight(null, x1, x2, null, r, g, b, a);
      }
      repaint(true);
    }
    return true;
  }

  private int getRGB(String s) {
    float f = PT.parseFloat(s);
    return (int) (Float.isNaN(f) ? -1 : f > 1 ? f : f * 255);
  }

  private boolean execZoom(String value) {
    double x1 = 0, x2 = 0, y1 = 0, y2 = 0;
    value = PT.rep(value, " - ", " ").replace(',', ' ');
    Lst<String> tokens = ScriptToken.getTokens(value);
    switch (tokens.size()) {
    default:
      return false;
    case 0:
      ScaleData v = pd().getCurrentGraphSet().getCurrentView();
      value = Math.round(v.minXOnScale * 100) / 100f + ","
          + Math.round(v.maxXOnScale * 100) / 100f;
      value = selectedPanel.getInput("Enter zoom range x1 x2", "Zoom", value);
      return (value == null || execZoom(value));
    case 1:
      value = tokens.get(0);
      if (value.equalsIgnoreCase("next")) {
        pd().nextView();
      } else if (value.toLowerCase().startsWith("prev")) {
        pd().previousView();
      } else if (value.equalsIgnoreCase("out")) {
        pd().resetView();
      } else if (value.equalsIgnoreCase("clear")) {
        pd().clearAllView();
      } else if (value.equalsIgnoreCase("invertY")) {
        pd().getCurrentGraphSet().invertYAxis();
      }
      return true;
    case 2:
      x1 = Double.parseDouble(tokens.get(0));
      x2 = Double.parseDouble(tokens.get(1));
      break;
    case 3:
      String xy = tokens.get(0);
      if (xy.equalsIgnoreCase("X")) {
        x1 = Double.parseDouble(tokens.get(1));
        x2 = Double.parseDouble(tokens.get(2));
      } else if (xy.equalsIgnoreCase("Y")) {
        y1 = Double.parseDouble(tokens.get(1));
        y2 = Double.parseDouble(tokens.get(2));
      }
      break;
    case 4:
      x1 = Double.parseDouble(tokens.get(0));
      y1 = Double.parseDouble(tokens.get(1));
      x2 = Double.parseDouble(tokens.get(2));
      y2 = Double.parseDouble(tokens.get(3));
    }
    pd().setZoom(x1, y1, x2, y2);
    return true;
  }

  private void scaleSelectedBy(Lst<PanelNode> nodes, String value) {
    try {
      double f = Double.parseDouble(value);
      for (int i = nodes.size(); --i >= 0;)
        nodes.get(i).pd().scaleSelectedBy(f);
    } catch (Exception e) {
    }
  }

  public PanelData pd() {
    return (selectedPanel == null ? null : selectedPanel.getPanelData());
  }

  private boolean isClosed() {
    return (pd() == null);
  }

  private void execSelect(String value) {
    if (value.startsWith("ID ")) {
      if (!isClosed())
        try {
          pd().selectSpectrum(null, "ID", PT.trimQuotes(value.substring(3)),
              true);
        } catch (Exception e) {
          //
        }
      return;
    }
    Lst<PanelNode> nodes = panelNodes;
    for (int i = nodes.size(); --i >= 0;)
      nodes.get(i).pd().selectFromEntireSet(Integer.MIN_VALUE);
    Lst<Spectrum> speclist = new Lst<Spectrum>();
    fillSpecList(value, speclist, false);
    // not sure where this is going...
  }

  public void execView(String value, boolean fromScript) {
    if (value.equals("")) {
      checkOverlay();
      return;
    }
    Lst<Spectrum> speclist = new Lst<Spectrum>();
    String strlist = fillSpecList(value, speclist, true);
    if (speclist.size() > 0)
      si.siOpenDataOrFile(null, strlist, speclist, strlist, -1, -1, false,
          null, null);
    if (!fromScript) {
      si.siValidateAndRepaint(false);
    }
  }

  private void execIRMode(String value) {
    IRMode mode = IRMode.getMode(value); // T, A, or TOGGLE
    String type = pd().getSpectrum().dataType;
    for (int i = panelNodes.size(); --i >= 0;)
      panelNodes.get(i).pd().setIRMode(mode, type);
    setIRmode(value);
    // jsvp.doRepaint();
  }

  private void execIntegrate(String value) {
    if (isClosed())
      return;
    pd().checkIntegral(parameters, value);
    if (integrationRatios != null)
      pd().setIntegrationRatios(integrationRatios);
    integrationRatios = null; // one time only
    repaint(true);
  }

  private void repaint(boolean andTaintAll) {
    selectedPanel.doRepaint(andTaintAll);
  }

  @SuppressWarnings("incomplete-switch")
  private void execSetIntegralParameter(ScriptToken st, double value) {
    ColorParameters p = parameters;
    switch (st) {
    case INTEGRALRANGE:
      p.integralRange = value;
      break;
    case INTEGRALOFFSET:
      p.integralOffset = value;
      break;
    }
    if (!isClosed())
      pd().checkIntegral(parameters, "update");
  }

  private void setYScale(String value) {
    Lst<String> tokens = ScriptToken.getTokens(value);
    int pt = 0;
    boolean isAll = false;
    if (tokens.size() > 1 && tokens.get(0).equalsIgnoreCase("ALL")) {
      isAll = true;
      pt++;
    }
    double y1 = Double.parseDouble(tokens.get(pt++));
    double y2 = Double.parseDouble(tokens.get(pt));
    if (isAll) {
      Spectrum spec = pd().getSpectrum();
      for (int i = panelNodes.size(); --i >= 0;) {
        PanelNode node = panelNodes.get(i);
        if (node.source != currentSource)
          continue;
        if (Spectrum.areXScalesCompatible(spec, node.getSpectrum(), false,
            false))
          node.pd().setZoom(0, y1, 0, y2);
      }
    } else {
      pd().setZoom(0, y1, 0, y2);
    }
  }

  private boolean overlayLegendVisible;

  private void setOverlayLegendVisibility(Boolean tftoggle, boolean doSet) {
    if (doSet)
      overlayLegendVisible = (tftoggle == null ? !overlayLegendVisible
          : tftoggle == Boolean.TRUE);
    PanelNode node = PanelNode.findNode(selectedPanel, panelNodes);
    for (int i = panelNodes.size(); --i >= 0;)
      showOverlayLegend(panelNodes.get(i), panelNodes.get(i) == node
          && overlayLegendVisible);
  }

  private void showOverlayLegend(PanelNode node, boolean visible) {
    JSVDialog legend = node.legend;
    if (legend == null && visible) {
      legend = node.setLegend(node.pd().getNumberOfSpectraInCurrentSet() > 1
          && node.pd().getNumberOfGraphSets() == 1 ? getDialog(
          AType.OverlayLegend, null) : null);
    }
    if (legend != null)
      legend.setVisible(visible);
  }

  // / from JavaScript

  /**
   * incoming script processing of <PeakAssignment file="" type="xxx"...> record
   * from Jmol
   *
   * @param peakScript
   */

  public void syncScript(String peakScript) {
    if (peakScript.equals("TEST"))
      peakScript = testScript;
    Logger.info("JSViewer.syncScript Jmol>JSV " + peakScript);
    if (peakScript.indexOf("<PeakData") < 0) {
      if (peakScript.startsWith("JSVSTR:")) {
        si.syncToJmol(peakScript);
        return;
      }
      runScriptNow(peakScript);
      if (peakScript.indexOf("#SYNC_PEAKS") >= 0)
        syncPeaksAfterSyncScript();
      return;
    }
    Logger.info(">>toJSV>> " + peakScript);
    String sourceID = PT.getQuotedAttribute(peakScript, "sourceID");
    String type, model, file, jmolSource, index, atomKey;
    if (sourceID == null) {
      // todo: why the quotes??
      //peakScript = PT.rep(peakScript, "\\\"", "");
      file = PT.getQuotedAttribute(peakScript, "file");
      index = PT.getQuotedAttribute(peakScript, "index");
      if (file == null || index == null)
        return;
      file = PT.rep(file, "#molfile", "");// Jmol has loaded the model from the cache
      model = PT.getQuotedAttribute(peakScript, "model");
      jmolSource = PT.getQuotedAttribute(peakScript, "src");
      String modelSent = (jmolSource != null && jmolSource.startsWith("Jmol") ? null
          : returnFromJmolModel);
      if (model != null && modelSent != null && !model.equals(modelSent)) {
        Logger.info("JSV ignoring model " + model + "; should be " + modelSent);
        return;
      }
      returnFromJmolModel = null;
      if (panelNodes.size() == 0 || !checkFileAlreadyLoaded(file)) {
        Logger.info("file " + file
            + " not found -- JSViewer closing all and reopening");
        si.siSyncLoad(file);
      }
      type = PT.getQuotedAttribute(peakScript, "type");
      atomKey = null;
    } else {
      file = null;
      index = model = sourceID;
      atomKey = "," + PT.getQuotedAttribute(peakScript, "atom") + ",";
      type = "ID";
      jmolSource = sourceID; //??
    }

    PeakInfo pi = selectPanelByPeak(file, index, atomKey);
    PanelData pd = pd();
    pd.selectSpectrum(file, type, model, true);
    si.siSendPanelChange();
    pd.addPeakHighlight(pi);
    repaint(true);
    // round trip this so that Jmol highlights all equivalent atoms
    // and appropriately starts or clears vibration
    if (jmolSource == null || (pi != null && pi.getAtoms() != null))
      si.syncToJmol(jmolSelect(pi));
  }

  private void syncPeaksAfterSyncScript() {
    JDXSource source = currentSource;
    if (source == null)
      return;
    try {
      String file = "file=" + PT.esc(source.getFilePath());
      Lst<PeakInfo> peaks = source.getSpectra().get(0).getPeakList();
      SB sb = new SB();
      sb.append("[");
      int n = peaks.size();
      for (int i = 0; i < n; i++) {
        String s = peaks.get(i).toString();
        s = s + " " + file;
        sb.append(PT.esc(s));
        if (i > 0)
          sb.append(",");
      }
      sb.append("]");
      si.syncToJmol("Peaks: " + sb);
    } catch (Exception e) {
      // ignore bad structures -- no spectrum
    }
  }

  private boolean checkFileAlreadyLoaded(String fileName) {
    if (isClosed())
      return false;
    if (pd().hasFileLoaded(fileName))
      return true;
    for (int i = panelNodes.size(); --i >= 0;)
      if (panelNodes.get(i).pd().hasFileLoaded(fileName)) {
        si.siSetSelectedPanel(panelNodes.get(i).jsvp);
        return true;
      }
    return false;
  }

  /**
   * @param file
   * @param index
   * @param atomKey
   * @return PeakInfo entry if appropriate
   */
  private PeakInfo selectPanelByPeak(String file, String index, String atomKey) {
    if (panelNodes == null)
      return null;
    PeakInfo pi = null;
    for (int i = panelNodes.size(); --i >= 0;)
      panelNodes.get(i).pd().addPeakHighlight(null);
    pi = pd().selectPeakByFileIndex(file, index, atomKey);
    if (pi != null) {
      // found in current panel
      setNode(PanelNode.findNode(selectedPanel, panelNodes));
    } else {
      // must look elsewhere
      for (int i = panelNodes.size(); --i >= 0;) {
        PanelNode node = panelNodes.get(i);
        if ((pi = node.pd().selectPeakByFileIndex(file, index, atomKey)) != null) {
          setNode(node);
          break;
        }
      }
    }
    return pi;
  }

  /**
   * this method is called as a result of the user clicking on a peak
   * (eventObject instanceof PeakPickEvent) or from PEAK command execution
   *
   * @param eventObj
   * @param isApp
   */
  public void processPeakPickEvent(Object eventObj, boolean isApp) {
    // trouble here is with round trip when peaks are clicked in rapid
    // succession.

    PeakInfo pi;
    if (eventObj instanceof PeakInfo) {
      // this is a call from the PEAK command, above.
      pi = (PeakInfo) eventObj;
      PeakInfo pi2 = pd().findMatchingPeakInfo(pi);
      if (pi2 == null) {
        if (!"ALL".equals(pi.getTitle()))
          return;
        PanelNode node = null;
        for (int i = 0; i < panelNodes.size(); i++)
          if ((pi2 = panelNodes.get(i).pd().findMatchingPeakInfo(pi)) != null) {
            node = panelNodes.get(i);
            break;
          }
        if (node == null)
          return;
        setNode(node);
      }
      pi = pi2;
    } else {
      PeakPickEvent e = ((PeakPickEvent) eventObj);
      si.siSetSelectedPanel((JSVPanel) e.getSource());
      pi = e.getPeakInfo();
    }
    pd().addPeakHighlight(pi);
    // the above line is what caused problems with GC/MS selection
    syncToJmol(pi);
    // System.out.println(Thread.currentThread() +
    // "processPeakEvent --selectSpectrum " + pi);
    if (pi.isClearAll()) // was not in app version??
      repaint(false);
    else
      pd().selectSpectrum(pi.getFilePath(), pi.getType(), pi.getModel(), true);
    si.siCheckCallbacks(pi.getTitle());
  }

  void newStructToJmol(String data) {
    Logger.info("sending new structure to Jmol:\n" + data);
    si.syncToJmol("struct:" + data);
  }

  private void syncToJmol(PeakInfo pi) {
    repaint(true);
    returnFromJmolModel = pi.getModel();
    si.syncToJmol(jmolSelect(pi));
  }

  public void sendPanelChange() {
    PanelData pd = pd();
    Spectrum spec = pd.getSpectrum();
    PeakInfo pi = spec.getSelectedPeak();
    if (pi == null)
      pi = spec.getModelPeakInfoForAutoSelectOnLoad();
    if (pi == null)
      pi = spec.getBasePeakInfo();
    pd.addPeakHighlight(pi);
    Logger.info(Thread.currentThread() + "JSViewer sendFrameChange "
        + selectedPanel);
    syncToJmol(pi);
  }

  private String jmolSelect(PeakInfo pi) {
    String script = ("IR".equals(pi.getType()) || "RAMAN".equals(pi.getType()) ? "vibration ON; selectionHalos OFF;"
        : "vibration OFF; selectionhalos "
            + (pi.getAtoms() == null ? "OFF" : "ON"));
    return "Select: " + pi + " script=\"" + script + " \" sourceID=\""
        + pd().getSpectrum().sourceID + "\"";
  }

  public Map<String, Object> getPropertyAsJavaObject(String key) {

    Map<String, Object> map = new Hashtable<String, Object>();

    if ("SOURCEID".equalsIgnoreCase(key)) {
      // get current spectrum ID
      map.put(key, (pd() == null ? "" : pd().getSpectrum().sourceID));
      return map;
    }
    if (key != null && key.startsWith("DATA_")) {
      // mol, json, xml, jcamp -- most recent only
      map.put(key, "" + JSVFileManager.cacheGet(key.substring(5)));
      return map;
    }

    boolean isAll = false;
    if (key != null && key.toUpperCase().startsWith("ALL ")
        || "all".equalsIgnoreCase(key)) {
      key = key.substring(3).trim();
      isAll = true;
    }
    if ("".equals(key))
      key = null;
    if ("NAMES".equalsIgnoreCase(key) || "KEYS".equalsIgnoreCase(key))
      key = "";
    Map<String, Object> map0 = pd().getInfo(true, key);
    if (!isAll && map0 != null)
      return map0;
    if (map0 != null)
      map.put("current", map0);
    Lst<Map<String, Object>> info = new Lst<Map<String, Object>>();
    for (int i = 0; i < panelNodes.size(); i++) {
      JSVPanel jsvp = panelNodes.get(i).jsvp;
      if (jsvp == null)
        continue;
      info.addLast(panelNodes.get(i).getInfo(key));
    }
    map.put("items", info);
    return map;
  }

  public String getCoordinate() {
    if (!isClosed()) {
      Coordinate coord = pd().getClickedCoordinate();
      if (coord != null)
        return coord.getXVal() + " " + coord.getYVal();
    }
    return "";
  }

  /**
   * originally in MainFrame, this method takes the OVERLAY command option and
   * converts it to a list of spectra
   *
   * @param value
   * @param speclist
   * @param isView
   * @return comma-separated list, for the title
   */
  private String fillSpecList(String value, Lst<Spectrum> speclist,
                              boolean isView) {

    String prefix = "1.";
    Lst<String> list;
    Lst<String> list0 = null;
    boolean isNone = (value.equalsIgnoreCase("NONE"));
    if (isNone || value.equalsIgnoreCase("all"))
      value = "*";
    if (value.indexOf("*") < 0) {
      // replace "3.1.1" with "3.1*1"
      String[] tokens = value.split(" ");
      SB sb = new SB();
      for (int i = 0; i < tokens.length; i++) {
        int pt = tokens[i].indexOf('.');
        if (pt != tokens[i].lastIndexOf('.'))
          tokens[i] = tokens[i].substring(0, pt + 1)
              + tokens[i].substring(pt + 1).replace('.', '_');
        sb.append(tokens[i]).append(" ");
      }
      value = sb.toString().trim();
    }
    if (value.equals("*")) {
      list = ScriptToken.getTokens(PanelNode
          .getSpectrumListAsString(panelNodes));
    } else if (value.startsWith("\"") || value.startsWith("'")) {
      list = ScriptToken.getTokens(value);
    } else {
      value = PT.rep(value, "_", " _ ");
      value = PT.rep(value, "-", " - ");
      list = ScriptToken.getTokens(value);
      list0 = ScriptToken.getTokens(PanelNode
          .getSpectrumListAsString(panelNodes));
      if (list0.size() == 0)
        return null;
    }

    String id0 = (isClosed() ? prefix : PanelNode.findNode(selectedPanel,
        panelNodes).id);
    id0 = id0.substring(0, id0.indexOf(".") + 1);
    SB sb = new SB();
    int n = list.size();
    String idLast = null;
    for (int i = 0; i < n; i++) {
      String id = list.get(i);
      double userYFactor = Double.NaN;
      int isubspec = -1;
      if (i + 1 < n && list.get(i + 1).equals("*")) {
        i += 2;
        userYFactor = Double.parseDouble(list.get(i));
      } else if (i + 1 < n && list.get(i + 1).equals("_")) {
        i += 2;
        isubspec = Integer.parseInt(list.get(i));
      }
      if (id.equals("-")) {
        if (idLast == null)
          idLast = list0.get(0);
        id = (i + 1 == n ? list0.get(list0.size() - 1) : list.get(++i));
        if (!id.contains("."))
          id = id0 + id;
        int pt = 0;
        while (pt < list0.size() && !list0.get(pt).equals(idLast))
          pt++;
        pt++;
        while (pt < list0.size() && !idLast.equals(id)) {
          PanelNode node = PanelNode.findNodeById((idLast = list0.get(pt++)),
              panelNodes);
          speclist.addLast(node.pd().getSpectrumAt(0));
          sb.append(",").append(idLast);
        }
        continue;
      }
      PanelNode node;
      if (id.startsWith("'") && id.endsWith("'"))
        id = "\"" + PT.trim(id, "'") + "\"";
      if (id.startsWith("\"")) {
        id = PT.trim(id, "\"");
        int pn = panelNodes.size();
        for (int j = 0; j < pn; j++) {
          node = panelNodes.get(j);
          if (node.fileName != null && node.fileName.startsWith(id)
              || node.frameTitle != null && node.frameTitle.startsWith(id)) {
            addSpecToList(node.pd(), userYFactor, -1, speclist, isView);
            sb.append(",").append(node.id);
          }
        }
        continue;
      }
      if (!id.contains("."))
        id = id0 + id;
      node = PanelNode.findNodeById(id, panelNodes);
      if (node == null)
        continue;
      idLast = id;
      addSpecToList(node.pd(), userYFactor, isubspec, speclist, isView);
      sb.append(",").append(id);
      if (isubspec > 0)
        sb.append(".").appendI(isubspec);
    }
    if (isView && speclist.size() > 0) {
      PanelNode node = PanelNode.findNodeById(sb.substring(1), panelNodes);
      if (node != null) {
        setNode(node); // was "fromTree true"
        // possibility of a problem here -- we are not communicating with Jmol
        // our model changes.
        speclist.clear();
      }
    }
    return (isNone ? "NONE" : sb.length() > 0 ? sb.toString().substring(1)
        : null);
  }

  private void addSpecToList(PanelData pd, double userYFactor, int isubspec,
                             Lst<Spectrum> list, boolean isView) {
    if (isView) {
      Spectrum spec = pd.getSpectrumAt(0);
      spec.setUserYFactor(Double.isNaN(userYFactor) ? 1 : userYFactor);
      pd.addToList(isubspec - 1, list);
    } else {
      pd.selectFromEntireSet(isubspec - 1);
    }
  }

  public int getSolutionColor(boolean asFitted) {
    Spectrum spectrum = pd().getSpectrum();
    VisibleInterface vi = (spectrum.canShowSolutionColor() ? (VisibleInterface) JSViewer
        .getInterface("jspecview.common.Visible") : null);
    return (vi == null ? -1 : vi.getColour(spectrum, asFitted));
  }

  public int openDataOrFile(Object data, String name, Lst<Spectrum> specs,
                            String strUrl, int firstSpec, int lastSpec,
                            boolean isAppend, String id) {
    if ("NONE".equals(name)) {
      close("View*");
      return FILE_OPEN_OK;
    }
    si.writeStatus("");
    String filePath = null;
    String newPath = null;
    String fileName = null;
    boolean isView = false;
    if (strUrl != null && strUrl.startsWith("cache://")) {
      /**
       * @j2sNative
       *
       *            data = Jmol.Cache.get(name = strUrl);
       *
       */
      {
      }
    }
    GenericFileInterface file = null;
    if (data != null) {
      try {
        fileName = name;
        newPath = filePath = JSVFileManager.getFullPathName(name);
      } catch (JSVException e) {
        // ok...
      }
    } else if (specs != null) {
      isView = true;
      newPath = fileName = filePath = "View" + (++nViews);
    } else if (strUrl != null) {
      try {
        file = apiPlatform.newFile(strUrl);
        // System.out.println("strURL=" + strUrl);
        // System.out.println("JSVFileManager.appletDocumentBase=" +
        // JSVFileManager.appletDocumentBase);
        URL u = new URL(JSVFileManager.appletDocumentBase, strUrl, null);
        // System.out.println("u=" + u);
        filePath = u.toString();
        recentURL = filePath;
        fileName = JSVFileManager.getTagName(filePath);
        // System.out.println("fileName=" + fileName);
      } catch (MalformedURLException e) {
        fileName = file.getName();
        newPath = filePath = file.getFullPath();
        recentURL = null;
      }
    }
    // if (!isView)
    int pt = -1;
    if ((pt = PanelNode.isOpen(panelNodes, filePath)) >= 0
        || (pt = PanelNode.isOpen(panelNodes, strUrl)) >= 0) {
      if (isView) {
        --nViews;
        setNode(panelNodes.get(pt)); // was fromTree true
      } else {
        si.writeStatus(filePath + " is already open");
      }
      return FILE_OPEN_ALREADY;
    }
    if (!isAppend && !isView)
      close("all"); // with CHECK we may still need to do this
    si.setCursor(GenericPlatform.CURSOR_WAIT);
    try {
      si.siSetCurrentSource(isView ? JDXSource.createView(specs) : JDXReader
          .createJDXSource(file, data, filePath,
              obscureTitleFromUser == Boolean.TRUE, loadImaginary, firstSpec,
              lastSpec, nmrMaxY));

    } catch (Exception e) {
      /**
       * @j2sNative alert(e.toString())
       */
      {
    	  e.printStackTrace();
        Logger.error(e.toString());
        if (Logger.debugging)
          e.printStackTrace();
        si.writeStatus(e.getMessage());
      }
      si.setCursor(GenericPlatform.CURSOR_DEFAULT);
      if (isApplet) {
        selectedPanel.showMessage(e.toString(), "Error Opening File");
      }
      return FILE_OPEN_ERROR;
    }
    si.setCursor(GenericPlatform.CURSOR_DEFAULT);
    System.gc();
    if (newPath == null) {
      newPath = currentSource.getFilePath();
      if (newPath != null)
        fileName = newPath.substring(newPath.lastIndexOf("/") + 1);
    } else {
      currentSource.setFilePath(newPath);
    }
    if (id == null && !isView)
      id = newPath;
    if (id != null)
      currentSource.setID(id);
    si.siSetLoaded(fileName, newPath);

    Spectrum spec = currentSource.getJDXSpectrum(0);
    if (spec == null) {
      return FILE_OPEN_NO_DATA;
    }

    specs = currentSource.getSpectra();
    Spectrum.process(specs, irMode);

    boolean autoOverlay = interfaceOverlaid
        || spec.isAutoOverlayFromJmolClick();

    boolean combine = isView || autoOverlay && currentSource.isCompoundSource;
    if (combine) {
      combineSpectra((isView ? strUrl : null));
    } else {
      splitSpectra();
    }
    pd().setTaintedAll();
    if (!isView)
      si.siUpdateRecentMenus(filePath);
    return FILE_OPEN_OK;
  }

  public void close(String value) {
    // close * > 1 "close all except one spectrum."
    // close SIMULATIONS > 1 "close simulations until no more than one spectrum is present,
    // or all simulations if that is not possible."
    int n0 = 0;
    int pt = (value == null ? -2 : value.indexOf(">"));
    if (pt > 0) {
      n0 = PT.parseInt(value.substring(pt + 1).trim());
      value = value.substring(0, pt).trim();
    }
    if ("*".equals(value))
      value = "all";
    boolean isAll = (value == "all");
    if (value == null || n0 == 0 && value.equalsIgnoreCase("all")) {
      closeSource(null);
      return;
    }
    boolean isViews = value.equalsIgnoreCase("views");
    Lst<JDXSource> list = new Lst<JDXSource>();
    JDXSource source;
    value = value.replace('\\', '/');
    int n = panelNodes.size();
    int nMax = n - n0;
    if (value.endsWith("*")) {
      value = value.substring(0, value.length() - 1);
      for (int i = n; --i >= 0;)
        if (panelNodes.get(i).fileName.startsWith(value))
          list.addLast(panelNodes.get(i).source);
    } else if (value.equalsIgnoreCase("selected")) {
      JDXSource lastSource = null;
      for (int i = n; --i >= 0;) {
        source = panelNodes.get(i).source;
        if (panelNodes.get(i).isSelected
            && (lastSource == null || lastSource != source))
          list.addLast(source);
        lastSource = source;
      }
    } else if (isAll || isViews || value.equalsIgnoreCase("simulations")) {
      for (int n1 = 0, i = n; --i >= 0 && n1 < nMax;)
        if (isAll ? true : isViews ? panelNodes.get(i).isView : panelNodes
            .get(i).isSimulation) {
          list.addLast(panelNodes.get(i).source);
          n1++;
        }
    } else {
      source = (value.length() == 0 ? currentSource : PanelNode
          .findSourceByNameOrId(value, panelNodes));
      if (source != null)
        list.addLast(source);
    }
    for (int i = list.size(); --i >= 0;)
      closeSource(list.get(i));
    if (selectedPanel == null && panelNodes.size() > 0)
      si.siSetSelectedPanel(PanelNode.getLastFileFirstNode(panelNodes));
  }

  public void execLoad(String value, String script) {
    JSVAppletObject applet = html5Applet;
    boolean isID = false;
    /**
     * When part of a view set, route all internal database requests through
     * this.html5Applet._search.
     *
     * @j2sNative
     *
     *            isID = (applet && applet._viewSet != null && !value.startsWith("ID"));
     *
     */
    if (isID) {
      // note that this was not functional, as it was missing {}
      applet._search(value);
      return;
    }
    // load   (alone) just runs defaultLoadScript
    // load ID "xx"...
    Lst<String> tokens = ScriptToken.getTokens(value);
    String filename = tokens.get(0);
    String id = null;
    int pt = 0;
    if (filename.equalsIgnoreCase("ID")) {
      id = PT.trimQuotes(tokens.get(1));
      filename = tokens.get(2);
      pt = 2;
    }
    boolean isAppend = filename.equalsIgnoreCase("APPEND");
    boolean isCheck = filename.equalsIgnoreCase("CHECK");
    if (isAppend || isCheck)
      pt++;
    if (pt > 0)
      filename = tokens.get(pt);
    if (script == null)
      script = defaultLoadScript;
    if (filename.equals("?")) {
      openFileFromDialog(isAppend, false, null, script);
      return;
    }
    if (filename.equals("http://?")) {
      openFileFromDialog(isAppend, true, null, null);
      return;
    }
    if (filename.equals("$?") || filename.equals("$H1?")) {
      openFileFromDialog(isAppend, true, "H1", null);
      return;
    }
    if (filename.equals("$C13?")) {
      openFileFromDialog(isAppend, true, "C13", null);
      return;
    }
    boolean isH1 = filename.equalsIgnoreCase("MOL")
        || filename.equalsIgnoreCase("H1");
    boolean isC13 = filename.equalsIgnoreCase("C13");
    if (isH1 || isC13)
      filename = JSVFileManager.SIMULATION_PROTOCOL + (isH1 ? "H1/" : "C13/")
          + "MOL=" + PT.trimQuotes(tokens.get(++pt));
    if (!isCheck && !isAppend) {
      if (filename.equals("\"\"") && currentSource != null)
        filename = currentSource.getFilePath();
      close("all");
    }
    filename = PT.trimQuotes(filename);
    boolean isSimulation = filename.startsWith("$");
    if (isSimulation) {
      if (!filename.startsWith("$H1") && !filename.startsWith("$C13"))
        filename = "$H1/" + filename.substring(1);
      filename = JSVFileManager.SIMULATION_PROTOCOL + filename.substring(1);
    }
    int firstSpec = (pt + 1 < tokens.size() ? Integer.valueOf(tokens.get(++pt))
        .intValue() : -1);
    int lastSpec = (pt + 1 < tokens.size() ? Integer.valueOf(tokens.get(++pt))
        .intValue() : firstSpec);
    si.siOpenDataOrFile(null, null, null, filename, firstSpec, lastSpec,
        isAppend, script, id);
    if (isSimulation) {
      close("views");
      execView("*", true);
    }
  }

  public void combineSpectra(String name) {
    JDXSource source = currentSource;
    Lst<Spectrum> specs = source.getSpectra();
    boolean haveSimulation = false;
    for (int i = specs.size(); --i >= 0;)
      if (specs.get(i).isSimulation) {
        haveSimulation = true;
        break;
      }

    JSVPanel jsvp = si.siGetNewJSVPanel2(specs);
    jsvp.setTitle(source.getTitle());
    if (jsvp.getTitle().equals("")) {
      jsvp.getPanelData().setViewTitle(source.getFilePath());
      jsvp.setTitle(name);
    }
    si.siSetPropertiesFromPreferences(jsvp, true);
    spectraTree.createTree(++fileCount, source, new JSVPanel[] { jsvp })
        .getPanelNode().isView = true;
    PanelNode node = PanelNode.findNode(selectedPanel, panelNodes);
    node.setFrameTitle(name);
    node.isView = true;
    if (autoShowLegend && pd().getNumberOfGraphSets() == 1)
      node.setLegend(getDialog(AType.OverlayLegend, null));
    si.siSetMenuEnables(node, false);
    if (haveSimulation)
      pd().splitStack(true);
  }

  public void closeSource(JDXSource source) {
    // Remove nodes and dispose of frames
    JSVTreeNode rootNode = spectraTree.getRootNode();
    String fileName = (source == null ? null : source.getFilePath());
    Lst<JSVTreeNode> toDelete = new Lst<JSVTreeNode>();
    Enumeration<?> enume = rootNode.children();
    while (enume.hasMoreElements()) {
      JSVTreeNode node = (JSVTreeNode) enume.nextElement();
      if (fileName == null
          || node.getPanelNode().source.matchesFilePath(fileName)) {
        Logger.info("Closing " + node.getPanelNode().source.getFilePath());
        for (Enumeration<?> e = node.children(); e.hasMoreElements();) {
          JSVTreeNode childNode = (JSVTreeNode) e.nextElement();
          toDelete.addLast(childNode);
          panelNodes.removeObj(childNode.getPanelNode());
        }
        toDelete.addLast(node);
        if (fileName != null)
          break;
      }
    }

    spectraTree.deleteNodes(toDelete);
    if (source == null) {
      // jsvpPopupMenu.dispose();
      if (currentSource != null)
        currentSource.dispose();
      currentSource = null;
      // jsvpPopupMenu.dispose();
      if (selectedPanel != null)
        selectedPanel.dispose();
    } else {
      // setFrameAndTreeNode(panelNodes.size() - 1);
    }

    if (currentSource == source) {
      si.siSetSelectedPanel(null);
      si.siSetCurrentSource(null);
    }

    int max = 0;
    for (int i = 0; i < panelNodes.size(); i++) {
      float f = PT.parseFloat(panelNodes.get(i).id);
      if (f >= max + 1)
        max = (int) Math.floor(f);
    }
    fileCount = max;
    System.gc();
    if (Logger.debugging)
      Logger.checkMemory();
    si.siSourceClosed(source);
  }

  public void setFrameAndTreeNode(int i) {
    if (panelNodes == null || i < 0 || i >= panelNodes.size())
      return;
    setNode(panelNodes.get(i));
  }

  public PanelNode selectFrameNode(JSVPanel jsvp) {
    // Find Node in SpectraTree and select it
    PanelNode node = PanelNode.findNode(jsvp, panelNodes);
    if (node == null)
      return null;
    spectraTree.setPath(spectraTree.newTreePath(node.treeNode.getPath()));
    setOverlayLegendVisibility(null, false);
    return node;
  }

  private boolean setSpectrum(String value) {
    if (value.indexOf('.') >= 0) {
      PanelNode node = PanelNode.findNodeById(value, panelNodes);
      if (node == null)
        return false;
      setNode(node);
    } else {
      int n = PT.parseInt(value);
      if (n <= 0) {
        checkOverlay();
        return false;
      }
      setFrameAndTreeNode(n - 1);
    }
    return true;
  }

  public void splitSpectra() {
    JDXSource source = currentSource;
    Lst<Spectrum> specs = source.getSpectra();
    JSVPanel[] panels = new JSVPanel[specs.size()];
    JSVPanel jsvp = null;
    for (int i = 0; i < specs.size(); i++) {
      Spectrum spec = specs.get(i);
      jsvp = si.siGetNewJSVPanel(spec);
      si.siSetPropertiesFromPreferences(jsvp, true);
      panels[i] = jsvp;
    }
    // arrange windows in ascending order
    spectraTree.createTree(++fileCount, source, panels);
    si.siGetNewJSVPanel(null); // end of operation
    PanelNode node = PanelNode.findNode(selectedPanel, panelNodes);
    si.siSetMenuEnables(node, true);
  }

  public void selectedTreeNode(JSVTreeNode node) {
    if (node == null) {
      return;
    }
    if (node.isLeaf()) {
      setNode(node.getPanelNode());
    } else {
      System.out.println("not a leaf");
    }
    si.siSetCurrentSource(node.getPanelNode().source);
  }

  public void dispose() {
    fileHelper = null;
    if (viewDialog != null)
      viewDialog.dispose();
    viewDialog = null;
    if (overlayLegendDialog != null)
      overlayLegendDialog.dispose();
    overlayLegendDialog = null;

    if (jsvpPopupMenu != null) {
      jsvpPopupMenu.jpiDispose();
      jsvpPopupMenu = null;
    }
    if (panelNodes != null)
      for (int i = panelNodes.size(); --i >= 0;) {
        panelNodes.get(i).dispose();
        panelNodes.removeItemAt(i);
      }
  }

  public void runScript(String script) {
    if (scriptQueue == null)
      si.siProcessCommand(script);
    else
      scriptQueue.addLast(script);
  }

  public void requestRepaint() {
    if (selectedPanel != null)
      repaintManager.refresh();
  }

  public void repaintDone() {
    repaintManager.repaintDone();
  }

  public void checkOverlay() {
    if (mainPanel != null)
      markSelectedPanels(panelNodes, mainPanel.getCurrentPanelIndex());
    viewDialog = getDialog(AType.Views, null);
  }

  private void markSelectedPanels(Lst<PanelNode> panelNodes, int ip) {
    for (int i = panelNodes.size(); --i >= 0;)
      panelNodes.get(i).isSelected = (ip == i);
  }

  private int recentStackPercent = 5;

  private void execOverlayOffsetY(int offset) {
    if (offset == Integer.MIN_VALUE) {
      if (selectedPanel == null)
        return;
      String soffset = selectedPanel.getInput(
          "Enter a vertical offset in percent for stacked plots", "Overlay", ""
              + recentStackPercent);
      float f = PT.parseFloat(soffset);
      if (Float.isNaN(f))
        return;
      offset = (int) f;
    }
    recentStackPercent = offset;
    parameters.viewOffset = offset;
    if (isClosed())
      pd().setYStackOffsetPercent(offset);
  }

  private void execScriptInline(String script) {
    if (script.length() > 0)
      script = script.substring(6).trim();
    if (script.length() == 0)
      script = selectedPanel.getInput("Enter a JSpecView script", "Script",
          recentScript);
    if (script == null)
      return;
    recentScript = script;
    runScriptNow(script);
  }

  // / called by JSmol JavaScript

  public void setDisplay(Object canvas) {
    // used by JSmol/HTML5 when a canvas is resized
    apiPlatform.setViewer(this, display = canvas);
    int[] wh = new int[2];
    apiPlatform.getFullScreenDimensions(canvas, wh);
    setScreenDimension(wh[0], wh[1]);
  }

  public void setScreenDimension(int width, int height) {
    // There is a bug in Netscape 4.7*+MacOS 9 when comparing dimension objects
    // so don't try dim1.equals(dim2)
    height = Math.min(height, maximumSize);
    width = Math.min(width, maximumSize);
    if (screenWidth == width && screenHeight == height)
      return;
    // System.out.println("HMM " + width + " " + height + " " + maximumSize);
    resizeImage(width, height);
  }

  void resizeImage(int width, int height) {
    if (width > 0) {
      screenWidth = width;
      screenHeight = height;
    } else {
      width = (screenWidth == 0 ? screenWidth = 500 : screenWidth);
      height = (screenHeight == 0 ? screenHeight = 500 : screenHeight);
    }
    g2d.setWindowParameters(width, height);
  }

  /**
   * for JavaScript only; this is the call to draw the spectrum
   *
   */
  public void updateJS() {
    if (selectedPanel != null)
      selectedPanel.paintComponent(apiPlatform.getGraphics(null));
  }

  /**
   * called by JSmol.js mouse event
   *
   * @param id
   * @param x
   * @param y
   * @param modifiers
   * @param time
   * @return t/f
   */
  public boolean processMouseEvent(int id, int x, int y, int modifiers,
                                   long time) {
    return (selectedPanel != null && selectedPanel.processMouseEvent(id, x, y,
        modifiers, time));
  }

  public void processTwoPointGesture(float[][][] touches) {
    if (!isClosed())
      selectedPanel.processTwoPointGesture(touches);
  }

  public JSVAppletObject getApplet() {
    return html5Applet;
  }

  /**
   * @param fileName
   * @param flags
   */
  public void openFileAsyncSpecial(String fileName, int flags) {
    String ans = (currentSource == null ? "NO" : getDialogManager()
        .getDialogInput(this,
            "Do you want to append this file? (Answer NO to replace.)",
            "Drag/Drop Action", DialogManager.QUESTION_MESSAGE, null, null,
            "YES"));
    if (ans == null)
      return;
    String pre = (ans.toLowerCase().startsWith("y") ? "append" : "");
    String post = (pre == "" ? "" : "; view *");
    runScript("load " + pre + " \"" + fileName + "\"" + post);
  }

  public int getHeight() {
    return screenHeight;
  }

  public int getWidth() {
    return screenWidth;
  }

  public Object getPlatformInterface(String type) {
    return getInterface("jspecview." + (isJS ? "js2d.Js" : "java.Awt") + type);
  }

  public DialogManager getDialogManager() {
    if (dialogManager != null)
      return dialogManager;
    dialogManager = (DialogManager) getPlatformInterface("DialogManager");
    //Interface.getInterface("jspecview.awtjs2d.JsDialogManager");
    return dialogManager.set(this);
  }

  public JSVDialog getDialog(AType type, Spectrum spec) {
    String root = "jspecview.dialog.";
    switch (type) {
    case Integration:
      return ((JSVDialog) getInterface(root + "IntegrationDialog")).setParams(
          "Integration for " + spec, this, spec);
    case Measurements:
      return ((JSVDialog) getInterface(root + "MeasurementsDialog")).setParams(
          "Measurements for " + spec, this, spec);
    case PeakList:
      return ((JSVDialog) getInterface(root + "PeakListDialog")).setParams(
          "Peak List for " + spec, this, spec);
    case OverlayLegend:
      return overlayLegendDialog = ((JSVDialog) getInterface(root
          + "OverlayLegendDialog")).setParams(pd().getViewTitle(), this, null);
    case Views:
      return viewDialog = ((JSVDialog) getInterface(root + "ViewsDialog"))
          .setParams("View/Combine/Close Spectra", this, null);
    default:
      return null;
    }
  }

  private void show(String what) {
    getDialogManager();
    if (what.equals("properties")) {
      dialogManager.showProperties(null, pd().getSpectrum());
    } else if (what.equals("errors")) {
      dialogManager.showSourceErrors(null, currentSource);
    } else if (what.equals("source")) {
      if (currentSource == null) {
        if (panelNodes.size() > 0)
          dialogManager.showMessageDialog(null, "Please Select a Spectrum",
              "Select Spectrum", DialogManager.ERROR_MESSAGE);
        return;
      }
      dialogManager.showSource(this, pd().getSpectrum());
    } else if (what.startsWith("solutioncolorfill")) {
      if (what.indexOf("all") >= 0) {
        for (int i = panelNodes.size(); --i >= 0;)
          panelNodes.get(i).pd().setSolutionColor(what);
      } else {
        pd().setSolutionColor(what);
      }
    } else if (what.startsWith("solutioncolor")) {
      String msg = getSolutionColorStr(what.indexOf("false") < 0);
      msg = "background-color:rgb(" + msg
          + ")'><br />Predicted Solution Colour- RGB(" + msg + ")<br /><br />";
      if (isJS) {
        dialogManager.showMessage(this, "<div style='width:100%;height:100%;"
            + msg + "</div>", "Predicted Colour");
      } else {
        selectedPanel.showMessage("<html><body style='" + msg
            + "</body></html>", "Predicted Colour");
      }
    }
  }

  private PrintLayout lastPrintLayout;
  private Object offWindowFrame;

  public PrintLayout getDialogPrint(boolean isJob) {
    if (!isJS)
      try {
        PrintLayout pl = ((JSVPrintDialog) getPlatformInterface("PrintDialog"))
            .set(offWindowFrame, lastPrintLayout, isJob).getPrintLayout();
        if (pl != null)
          lastPrintLayout = pl;
        return pl;
      } catch (Exception e) {
      }
    return new PrintLayout(pd());
  }

  public void setIRmode(String mode) {
    if (mode.equals("AtoT")) {
      irMode = IRMode.TO_TRANS;
    } else if (mode.equals("TtoA")) {
      irMode = IRMode.TO_ABS;
    } else {
      irMode = IRMode.getMode(mode);
    }
  }

  public int getOptionFromDialog(String[] items, String title, String label) {
    return getDialogManager().getOptionFromDialog(null, items, selectedPanel,
        title, label);
  }

  public String print(String fileName) {
    return execWrite("PDF \"" + fileName + "\"");
  }

  private String execWrite(String value) {
    if (isJS && value == null)
      value = "PDF";
    String msg = ((ExportInterface) JSViewer
        .getInterface("jspecview.export.Exporter")).write(this,
        value == null ? null : ScriptToken.getTokens(value), false);
    si.writeStatus(msg);
    return msg;
  }

  public String export(String type, int n) {
    if (type == null)
      type = "XY";
    PanelData pd = pd();
    int nMax = pd.getNumberOfSpectraInCurrentSet();
    if (n < -1 || n >= nMax)
      return "Maximum spectrum index (0-based) is " + (nMax - 1) + ".";
    Spectrum spec = (n < 0 ? pd.getSpectrum() : pd.getSpectrumAt(n));
    try {
      return ((ExportInterface) JSViewer
          .getInterface("jspecview.export.Exporter")).exportTheSpectrum(this,
          ExportType.getType(type), null, spec, 0,
          spec.getXYCoords().length - 1, null, type.equalsIgnoreCase("PDF"));
    } catch (Exception e) {
      Logger.error(e.toString());
      return null;
    }
  }

  @Override
  public String postByteArray(String fileName, byte[] bytes) {
    return JSVFileManager.postByteArray(fileName, bytes);
  }

  @SuppressWarnings("resource")
  public OC getOutputChannel(String fileName, boolean isBinary)
      throws Exception {
    OutputStream os = null;
    /**
     * in JavaScript, this will be a string buffer or byte array
     *
     * @j2sNative
     *
     *            while (fileName.startsWith("/")) fileName =
     *            fileName.substring(1);
     *
     *
     */
    {
      os = (fileName == null || fileName.equals(";base64,") ? null
          : new FileOutputStream(fileName));
    }
    return new OC().setParams(this, fileName, !isBinary, os);
  }

  public static Object getInterface(String name) {
    try {
      Class<?> x = Class.forName(name);
      return (x == null ? null : x.newInstance());
    } catch (Exception e) {
      Logger.error("Interface.java Error creating instance for " + name
          + ": \n" + e);
      return null;
    }
  }

  public void showMessage(String msg) {
    if (selectedPanel != null && msg != null)
      selectedPanel.showMessage(msg, null);
  }

  public void openFileFromDialog(boolean isAppend, boolean isURL,
                                 String simulationType, String script) {
    String url = null;
    if (simulationType != null) {
      url = fileHelper.getUrlFromDialog(
          "Enter the name or identifier of a compound", recentSimulation);
      if (url == null)
        return;
      recentSimulation = url;
      url = "$" + simulationType + "/" + url;
    } else if (isURL) {
      url = fileHelper.getUrlFromDialog("Enter the URL of a JCAMP-DX File",
          recentURL == null ? recentOpenURL : recentURL);
      if (url == null)
        return;
      recentOpenURL = url;
    } else {
      Object[] userData = new Object[] { Boolean.valueOf(isAppend), script };
      GenericFileInterface file = fileHelper.showFileOpenDialog(mainPanel,
          userData);
      // note that in JavaScript this will be asynchronous and file will be null.
      if (file != null)
        url = file.getFullPath();
      // it is not necessary to run the script in Java; we are not loading asynchronously
    }
    if (url != null)
      runScriptNow("load " + (isAppend ? "APPEND " : "") + "\"" + url + "\""
          + (script == null ? "" : ";" + script));
  }

  private String recentOpenURL = "http://";
  private String recentURL;
  private String recentSimulation = "tylenol";

  /**
   * Opens and displays a file
   *
   * @param fileName
   * @param closeFirst
   *
   */
  public void openFile(String fileName, boolean closeFirst) {
    if (closeFirst && panelNodes != null) {
      JDXSource source = PanelNode.findSourceByNameOrId(
          (new File(fileName)).getAbsolutePath(), panelNodes);
      if (source != null)
        closeSource(source);
    }
    si.siOpenDataOrFile(null, null, null, fileName, -1, -1, true,
        defaultLoadScript, null);

  }

  public int selectPanel(JSVPanel jsvp, Lst<PanelNode> panelNodes) {
    int iPanel = -1;
    if (panelNodes != null) {
      for (int i = panelNodes.size(); --i >= 0;) {
        JSVPanel j = panelNodes.get(i).jsvp;
        if (j == jsvp) {
          iPanel = i;
        } else {
          j.setEnabled(false);
          j.setFocusable(false);
          j.getPanelData().closeAllDialogsExcept(AType.NONE);
        }
      }
      markSelectedPanels(panelNodes, iPanel);
    }
    return iPanel;
  }

  public void checkAutoIntegrate() {
    if (autoIntegrate)
      pd().integrateAll(parameters);
  }

  /**
   * Parses the JavaScript call parameters and executes them accordingly
   *
   * @param params
   *        String
   */
  public void parseInitScript(String params) {
    if (params == null)
      params = "";
    ScriptTokenizer allParamTokens = new ScriptTokenizer(params, true);
    if (Logger.debugging) {
      Logger.info("Running in DEBUG mode");
    }
    while (allParamTokens.hasMoreTokens()) {
      String token = allParamTokens.nextToken();
      // now split the key/value pair
      ScriptTokenizer eachParam = new ScriptTokenizer(token, false);
      String key = eachParam.nextToken();
      if (key.equalsIgnoreCase("SET"))
        key = eachParam.nextToken();
      key = key.toUpperCase();
      ScriptToken st = ScriptToken.getScriptToken(key);
      String value = ScriptToken.getValue(st, eachParam, token);
      //if (Logger.debugging)
      Logger.info("KEY-> " + key + " VALUE-> " + value + " : " + st);
      try {
        switch (st) {
        default:
          parameters.set(null, st, value);
          break;
        case UNKNOWN:
          break;
        case APPLETID:
          fullName = appletName + "__" + (appletName = value) + "__";
          JSVAppletObject applet = null;
          /**
           * @j2sNative
           *
           *            self.Jmol && (applet = Jmol._applets[value]);
           *
           *
           */
          {
          }
          this.html5Applet = applet;
          break;
        case AUTOINTEGRATE:
          autoIntegrate = Parameters.isTrue(value);
          break;
        case COMPOUNDMENUON:
          // not implemented          allowCompoundMenu = Boolean.parseBoolean(value);
          break;
        case APPLETREADYCALLBACKFUNCTIONNAME:
        case COORDCALLBACKFUNCTIONNAME:
        case LOADFILECALLBACKFUNCTIONNAME:
        case PEAKCALLBACKFUNCTIONNAME:
        case SYNCCALLBACKFUNCTIONNAME:
          si.siExecSetCallback(st, value);
          break;
        case ENDINDEX:
          initialEndIndex = Integer.parseInt(value);
          break;
        case INTERFACE:
          checkOvelayInterface(value);
          break;
        case IRMODE:
          setIRmode(value);
          break;
        case MENUON:
          allowMenu = Boolean.parseBoolean(value);
          break;
        case OBSCURE:
          if (obscureTitleFromUser == null) // once only
            obscureTitleFromUser = Boolean.valueOf(value);
          break;
        case STARTINDEX:
          initialStartIndex = Integer.parseInt(value);
          break;
        // case SPECTRUMNUMBER:
        // initialSpectrumNumber = Integer.parseInt(value);
        // break;
        case SYNCID:
          fullName = appletName + "__" + (syncID = value) + "__";
          break;
        }
      } catch (Exception e) {
      }
    }
  }

  public String getSolutionColorStr(boolean asFit) {
    P3 pt = CU.colorPtFromInt(getSolutionColor(asFit), null);
    return (int) pt.x + "," + (int) pt.y + "," + (int) pt.z;
  }

  public String checkCommandLineForTip(char c, String cmd, boolean oneLineOnly) {
    boolean isHelp = (c == '\1');
    if (!isHelp && c != '\0') {
      if (c != '\t' && (c == '\n' || c < 32 || c > 126))
        return null;
      cmd += (Character.isISOControl(c) ? "" : "" + c);
    }
    String tip;
    if (cmd.indexOf(";") >= 0)
      cmd = cmd.substring(cmd.lastIndexOf(";") + 1);
    String ret = null;
    while (cmd.startsWith(" "))
      cmd = cmd.substring(1);
    if (cmd.length() == 0 && !isHelp) {
      tip = "";
    } else {
      Lst<String> tokens = ScriptToken.getTokens(cmd);
      if (tokens.size() == 0 && !isHelp)
        return "";
      boolean isExact = (cmd.endsWith(" ") || tokens.size() > 1 && oneLineOnly);
      Lst<ScriptToken> list = ScriptToken.getScriptTokenList(
          tokens.size() == 0 ? null : tokens.get(0), isExact);// || isHelp && tokens.size() > 0);
      switch (list.size()) {
      case 0:
        tip = "?";
        break;
      case 1:
        ScriptToken st = list.get(0);
        tip = st.getTip();
        try {
          if (tip.indexOf("TRUE") >= 0)
            tip = " (" + parameters.getBoolean(st) + ")";
          else if (st.name().indexOf("COLOR") >= 0)
            tip = " (" + CU.toRGBHexString(parameters.getElementColor(st))
                + ")";
          else
            tip = "";
        } catch (Exception e) {
          return null;
        }
        if (c == '\t' || isExact || !oneLineOnly) {
          tip = st.name() + " " + st.getTip() + tip + " " + st.getDescription();
          if (c == '\t')
            ret = st.name() + " ";
          break;
        }
        tip = st.name() + " " + tip;
        break;
      default:
        tip = ScriptToken.getNameList(list);
      }
    }
    if (oneLineOnly) {
      si.writeStatus(tip);
    } else {
      ret = tip;
    }
    return ret;
  }

  public String checkScript(String script) {
    return checkCommandLineForTip('\0', script, false);
  }

  private void execHelp(String value) {
    String s = checkCommandLineForTip('\1', value, false);
    if (s.indexOf(" ") < 0 && s.indexOf(",") > 0) {
      String[] tokens = PT.split(s, ",");
      Arrays.sort(tokens);
      s = "";
      for (int i = 0; i < tokens.length; i++) {
        ScriptToken st = ScriptToken.getScriptToken(tokens[i]);
        s += tokens[i] + " " + st.getTip() + "\n  " + st.getDescription()
            + "\n\n";
      }
      getDialogManager().showMessage(null, s, "HELP " + value);
    } else {
      selectedPanel.showMessage(s, "Help " + value);
    }
    System.out.println(s);
  }

}