[jalview.git] / src / jalview / viewmodel / styles / ViewStyle.java

package jalview.viewmodel.styles;

import jalview.api.ViewStyleI;

import java.awt.Color;
import java.lang.reflect.Method;
import java.util.HashMap;

/**
 * A container for holding alignment view properties. View properties are
 * data-independent, which means they can be safely copied between views
 * involving different alignment data without causing exceptions in the
 * rendering system.
 * 
 * @author jprocter
 *
 */
public class ViewStyle implements ViewStyleI
{

  private boolean abovePIDThreshold = false;

  int charHeight;

  int charWidth;

  /**
   * gui state - changes to colour scheme propagated to all groups
   */
  private boolean colourAppliesToAllGroups;

  /**
   * colour according to the reference sequence defined on the alignment
   */
  private boolean colourByReferenceSeq = false;

  boolean conservationColourSelected = false;

  /**
   * show the reference sequence in the alignment view
   */
  private boolean displayReferenceSeq = false;

  private int increment;

  /**
   * display gap characters
   */
  boolean renderGaps = true;

  private boolean rightAlignIds = false;

  boolean scaleAboveWrapped = false;

  boolean scaleLeftWrapped = true;

  boolean scaleRightWrapped = true;

  boolean seqNameItalics;

  /**
   * show annotation tracks on the alignment
   */
  private boolean showAnnotation = true;

  /**
   * render each residue in a coloured box
   */
  boolean showBoxes = true;

  /**
   * Colour sequence text
   */
  boolean showColourText = false;

  /**
   * show blue triangles
   */
  boolean showHiddenMarkers = true;

  /**
   * show /start-end in ID panel
   */
  boolean showJVSuffix = true;

  /**
   * scale features height according to score
   */
  boolean showSeqFeaturesHeight;

  /**
   * display setting for showing/hiding sequence features on alignment view
   */
  boolean showSequenceFeatures = false;

  /**
   * display sequence symbols
   */
  boolean showText = true;

  /**
   * show non-conserved residues only
   */
  protected boolean showUnconserved = false;

  Color textColour = Color.black;

  Color textColour2 = Color.white;

  /**
   * PID or consensus threshold
   */
  int threshold;

  /**
   * threshold for switching between textColour & textColour2
   */
  int thresholdTextColour = 0;

  /**
   * upper case characters in sequence are shown in bold
   */
  boolean upperCasebold = false;

  public ViewStyle(ViewStyleI viewStyle)
  {
    ViewStyle.configureFrom(this, viewStyle);
  }

  public ViewStyle()
  {
  }

  private static HashMap<String, Method> getters, isErs, setters;
  static
  {
    getters = new HashMap<String, Method>();
    isErs = new HashMap<String, Method>();
    setters = new HashMap<String, Method>();
    // Match Getters and Setters
    for (Method m : ViewStyleI.class.getMethods())
    {
      if (m.getDeclaringClass() == ViewStyleI.class)
      {
        if (m.getName().startsWith("get"))
        {
          getters.put(m.getName().substring(3), m);
        }
        if (m.getName().startsWith("is"))
        {
          isErs.put(m.getName().substring(2), m);
        }
        if (m.getName().startsWith("set"))
        {
          setters.put(m.getName().substring(3), m);
        }
      }
    }
  }

  private static void configureFrom(ViewStyle us, ViewStyleI viewStyle)
  {
      // try and do the set thing
      for (String prop : setters.keySet())
      {
        Method getter = getters.get(prop);
        Method setter = setters.get(prop);
        if (getter == null)
        {
          getter = isErs.get(prop);
        }
      if (getter != null && setter != null)
      {
        try
        {
          setter.invoke(us, getter.invoke(viewStyle));
        } catch (Exception q)
        {
          System.err.println("Unexpected exception setting view property "
                  + prop + " by reflection");
          q.printStackTrace();
        }

      }
      }
  }

  private static boolean equivalent(ViewStyle us, ViewStyleI them)
  {
    // look for properties we can set
    for (String prop : setters.keySet())
    {
      Method getter = getters.get(prop);
      if (getter == null)
      {
        getter = isErs.get(prop);
      }
      if (getter != null)
      {
        try
        {
          if (!getter.invoke(them).equals(getter.invoke(us)))
          {
            return false;
          }
        } catch (Exception q)
        {
          System.err.println("Unexpected exception testing equivalence of property "
                  + prop + " by reflection");
          q.printStackTrace();
        }
      }
    }

    return true;
  }

  public boolean equals(ViewStyleI other)
  {
    return other == null ? false : equivalent(this, other);
  }

  /**
   * @return the upperCasebold
   */
  @Override
  public boolean isUpperCasebold()
  {
    return upperCasebold;
  }

  /**
   * @param upperCasebold
   *          the upperCasebold to set
   */
  @Override
  public void setUpperCasebold(boolean upperCasebold)
  {
    this.upperCasebold = upperCasebold;
  }

  /**
   * flag for wrapping
   */
  boolean wrapAlignment = false;

  /**
   * number columns in wrapped alignment
   */
  int wrappedWidth;

  /**
   * GUI state
   * 
   * @return true if percent identity threshold is applied to shading
   */
  @Override
  public boolean getAbovePIDThreshold()
  {
    return abovePIDThreshold;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public int getCharHeight()
  {
    return charHeight;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public int getCharWidth()
  {
    return charWidth;
  }

  /**
   * 
   * 
   * @return flag indicating if colourchanges propagated to all groups
   */
  @Override
  public boolean getColourAppliesToAllGroups()
  {
    return colourAppliesToAllGroups;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getColourText()
  {
    return showColourText;
  }

  /**
   * GUI state
   * 
   * @return true if conservation based shading is enabled
   */
  @Override
  public boolean getConservationSelected()
  {
    return conservationColourSelected;
  }

  /**
   * GUI State
   * 
   * @return get scalar for bleaching colourschemes by conservation
   */
  @Override
  public int getIncrement()
  {
    return increment;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getScaleAboveWrapped()
  {
    return scaleAboveWrapped;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getScaleLeftWrapped()
  {
    return scaleLeftWrapped;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getScaleRightWrapped()
  {
    return scaleRightWrapped;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getShowBoxes()
  {
    return showBoxes;
  }

  @Override
  public boolean getShowHiddenMarkers()
  {
    return showHiddenMarkers;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getShowJVSuffix()
  {
    return showJVSuffix;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getShowText()
  {
    return showText;
  }

  @Override
  public boolean getShowUnconserved()
  {
    return showUnconserved;
  }

  /**
   * @return the textColour
   */
  @Override
  public Color getTextColour()
  {
    return textColour;
  }

  /**
   * @return the textColour2
   */
  @Override
  public Color getTextColour2()
  {
    return textColour2;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public int getThreshold()
  {
    return threshold;
  }

  /**
   * @return the thresholdTextColour
   */
  @Override
  public int getThresholdTextColour()
  {
    return thresholdTextColour;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public boolean getWrapAlignment()
  {
    return wrapAlignment;
  }

  /**
   * DOCUMENT ME!
   * 
   * @return DOCUMENT ME!
   */
  @Override
  public int getWrappedWidth()
  {
    return wrappedWidth;
  }

  @Override
  public boolean isColourByReferenceSeq()
  {
    return colourByReferenceSeq;
  }

  /**
   * @return the conservationColourSelected
   */
  @Override
  public boolean isConservationColourSelected()
  {
    return conservationColourSelected;
  }

  @Override
  public boolean isDisplayReferenceSeq()
  {
    return displayReferenceSeq;
  }

  /**
   * @return the renderGaps
   */
  @Override
  public boolean isRenderGaps()
  {
    return renderGaps;
  }

  @Override
  public boolean isRightAlignIds()
  {
    return rightAlignIds;
  }

  /**
   * @return the seqNameItalics
   */
  @Override
  public boolean isSeqNameItalics()
  {
    return seqNameItalics;
  }

  @Override
  public boolean isShowAnnotation()
  {
    return showAnnotation;
  }

  /**
   * @return the showColourText
   */
  @Override
  public boolean isShowColourText()
  {
    return showColourText;
  }

  /**
   * @return the showSeqFeaturesHeight
   */
  @Override
  public boolean isShowSeqFeaturesHeight()
  {
    return showSeqFeaturesHeight;
  }

  @Override
  public boolean isShowSequenceFeatures()
  {
    return showSequenceFeatures;
  }

  @Override
  public boolean isShowSequenceFeaturesHeight()
  {

    return showSeqFeaturesHeight;
  }

  /**
   * GUI state
   * 
   * 
   * @param b
   *          indicate if percent identity threshold is applied to shading
   */
  @Override
  public void setAbovePIDThreshold(boolean b)
  {
    abovePIDThreshold = b;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param h
   *          DOCUMENT ME!
   */
  @Override
  public void setCharHeight(int h)
  {
    this.charHeight = h;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param w
   *          DOCUMENT ME!
   */
  @Override
  public void setCharWidth(int w)
  {
    this.charWidth = w;
  }


  /**
   * @param value
   *          indicating if subsequent colourscheme changes will be propagated
   *          to all groups
   */
  @Override
  public void setColourAppliesToAllGroups(boolean b)
  {
    colourAppliesToAllGroups = b;
  }

  @Override
  public void setColourByReferenceSeq(boolean colourByReferenceSeq)
  {
    this.colourByReferenceSeq = colourByReferenceSeq;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param state
   *          DOCUMENT ME!
   */
  @Override
  public void setColourText(boolean state)
  {
    showColourText = state;
  }

  /**
   * @param conservationColourSelected
   *          the conservationColourSelected to set
   */
  @Override
  public void setConservationColourSelected(
          boolean conservationColourSelected)
  {
    this.conservationColourSelected = conservationColourSelected;
  }

  /**
   * GUI state
   * 
   * @param b
   *          enable conservation based shading
   */
  @Override
  public void setConservationSelected(boolean b)
  {
    conservationColourSelected = b;
  }

  @Override
  public void setDisplayReferenceSeq(boolean displayReferenceSeq)
  {
    this.displayReferenceSeq = displayReferenceSeq;
  }

  /**
   * 
   * @param inc
   *          set the scalar for bleaching colourschemes according to degree of
   *          conservation
   */
  @Override
  public void setIncrement(int inc)
  {
    increment = inc;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param state
   *          DOCUMENT ME!
   */
  @Override
  public void setRenderGaps(boolean state)
  {
    renderGaps = state;
  }

  @Override
  public void setRightAlignIds(boolean rightAlignIds)
  {
    this.rightAlignIds = rightAlignIds;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param b
   *          DOCUMENT ME!
   */
  @Override
  public void setScaleAboveWrapped(boolean b)
  {
    scaleAboveWrapped = b;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param b
   *          DOCUMENT ME!
   */
  @Override
  public void setScaleLeftWrapped(boolean b)
  {
    scaleLeftWrapped = b;
  }

  /**
   * 
   * 
   * @param scaleRightWrapped
   *          - true or false
   */

  @Override
  public void setScaleRightWrapped(boolean b)
  {
    scaleRightWrapped = b;
  }

  @Override
  public void setSeqNameItalics(boolean italics)
  {
    seqNameItalics = italics;
  }

  @Override
  public void setShowAnnotation(boolean b)
  {
    showAnnotation = b;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param state
   *          DOCUMENT ME!
   */
  @Override
  public void setShowBoxes(boolean state)
  {
    showBoxes = state;
  }

  /**
   * @param showColourText
   *          the showColourText to set
   */
  @Override
  public void setShowColourText(boolean showColourText)
  {
    this.showColourText = showColourText;
  }

  @Override
  public void setShowHiddenMarkers(boolean show)
  {
    showHiddenMarkers = show;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param b
   *          DOCUMENT ME!
   */
  @Override
  public void setShowJVSuffix(boolean b)
  {
    showJVSuffix = b;
  }

  @Override
  public void setShowSeqFeaturesHeight(boolean selected)
  {
    showSeqFeaturesHeight = selected;

  }

  /**
   * set the flag
   * 
   * @param b
   *          features are displayed if true
   */
  @Override
  public void setShowSequenceFeatures(boolean b)
  {
    showSequenceFeatures = b;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param state
   *          DOCUMENT ME!
   */
  @Override
  public void setShowText(boolean state)
  {
    showText = state;
  }

  @Override
  public void setShowUnconserved(boolean showunconserved)
  {
    showUnconserved = showunconserved;
  }

  /**
   * @param textColour
   *          the textColour to set
   */
  @Override
  public void setTextColour(Color textColour)
  {
    this.textColour = textColour;
  }

  /**
   * @param textColour2
   *          the textColour2 to set
   */
  @Override
  public void setTextColour2(Color textColour2)
  {
    this.textColour2 = textColour2;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param thresh
   *          DOCUMENT ME!
   */
  @Override
  public void setThreshold(int thresh)
  {
    threshold = thresh;
  }

  /**
   * @param thresholdTextColour
   *          the thresholdTextColour to set
   */
  @Override
  public void setThresholdTextColour(int thresholdTextColour)
  {
    this.thresholdTextColour = thresholdTextColour;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param state
   *          DOCUMENT ME!
   */
  @Override
  public void setWrapAlignment(boolean state)
  {
    wrapAlignment = state;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param w
   *          DOCUMENT ME!
   */
  @Override
  public void setWrappedWidth(int w)
  {
    this.wrappedWidth = w;
  }

  @Override
  public boolean sameStyle(ViewStyleI them)
  {
    return equivalent(this, them);
  }
}