org.biopax.paxtools.io.sbgn.VNode Maven / Gradle / Ivy
package org.biopax.paxtools.io.sbgn;
import java.util.ArrayList;
import java.util.List;
import org.ivis.layout.LGraphObject;
import org.ivis.layout.LNode;
import org.ivis.layout.Updatable;
import org.sbgn.bindings.Glyph;
import org.sbgn.bindings.Bbox;
import org.ivis.layout.cose.CoSEGraph;
/**
* VNode Class
* @author: Istemi Bahceci
* */
class VNode implements Updatable
{
//Glyph attribute of this VNode
public Glyph glyph;
ArrayList stateGlyphs;
ArrayList infoGlyphs;
/*Glyph class types*/
private static final String MACROMOLECULE = "macromolecule";
private static final String UNIT_OF_INFORMATION = "unit of information";
private static final String STATE_VARIABLE = "state variable";
private static final String SOURCE_AND_SINK = "source and sink";
private static final String ASSOCIATION = "association";
private static final String DISSOCIATION = "dissociation";
private static final String OMITTED_PROCESS = "omitted process";
private static final String UNCERTAIN_PROCESS = "uncertain process";
private static final String SIMPLE_CHEMICAL = "simple chemical";
private static final String PROCESS = "process";
private static final String COMPLEX = "complex";
private static final String AND = "and";
private static final String OR = "or";
private static final String NOT = "not";
private static final String PHENOTYPE = "phenotype";
private static final String PERTURBING_AGENT = "perturbing agent";
private static final String TAG = "tag";
private static final String NUCLEIC_ACID_FEATURE = "nucleic acid feature";
private static final String UNSPECIFIED_ENTITY = "unspecified entity";
private static final String NONE = "NA";
// Constats used for determining "state of information" and "unit of information" glyph widths according to
// their labels
private static final int LOWERCASE_LETTER_PIXEL_WIDTH = 6;
private static final int UPPERCASE_LETTER_PIXEL_WIDTH = 9;
private static final int MAX_STATE_AND_INFO_WIDTH = 35;
private static final int MAX_STATE_AND_INFO_HEIGHT = 10;
private static final int OFFSET_BTW_INFO_GLYPHS = 5;
private static final int MAX_INFO_BOX_NUMBER = 4;
private static final int MAX_MACROMOLECULE_HEIGHT_WITH_INFO_BOXES = 25;
private static final int NON_SUPPORTED_GLYPH_OFFSET = 2;
/*Glyph Size Constants for layout*/
private static Bound SOURCE_AND_SINK_BOUND;
private static Bound LOGICAL_OPERATOR_BOUND;
private static Bound PROCESS_NODES_BOUND;
private static Bound MACROMOLECULE_BOUND;
private static Bound NUCLEIC_ACID_FEATURE_BOUND;
private static Bound SIMPLE_CHEMICAL_BOUND;
private static Bound UNSPECIFIED_ENTITY_BOUND;
private static Bound PHENOTYPE_BOUND;
private static Bound PERTURBING_AGENT_BOUND;
private static Bound TAG_BOUND;
private static Bound INFO_BOUND;
private static Bound STATE_BOUND;
private static Bound COMPLEX_BOUND;
/**
* Default Constructor, sets the geometry of the bounds which are attributes of this class
* @param g glyph
* */
public VNode(Glyph g)
{
SOURCE_AND_SINK_BOUND = new Bound(15,15);
LOGICAL_OPERATOR_BOUND = new Bound(15,15);
PROCESS_NODES_BOUND = new Bound(15,15);
MACROMOLECULE_BOUND = new Bound(48,25);
NUCLEIC_ACID_FEATURE_BOUND = new Bound(50,25);
SIMPLE_CHEMICAL_BOUND = new Bound(48,20);
UNSPECIFIED_ENTITY_BOUND = new Bound(40,40);
PHENOTYPE_BOUND = new Bound(50,20);
TAG_BOUND = new Bound(50,20);
PERTURBING_AGENT_BOUND = new Bound(50,20);
COMPLEX_BOUND = new Bound(48,20);
INFO_BOUND = new Bound(MAX_STATE_AND_INFO_WIDTH,MAX_STATE_AND_INFO_HEIGHT);
STATE_BOUND = new Bound(MAX_STATE_AND_INFO_WIDTH,MAX_STATE_AND_INFO_HEIGHT);
stateGlyphs = new ArrayList();
infoGlyphs = new ArrayList();
this.glyph = g;
/*
* need to add bbox objects
*/
Bbox b = new Bbox();
this.glyph.setBbox(b);
if (this.glyph.getClazz() == null)
this.glyph.setClazz(NONE);
this.setSizeAccordingToClass();
}
/**
* Function that will take place when VNode objects will update in layout process of ChiLay
*
* @param lGraphObj LGraphObject for whom the update will take place.
*/
public void update(LGraphObject lGraphObj)
{
if (lGraphObj instanceof CoSEGraph)
{
return;
}
LNode lNode = (LNode)lGraphObj;
this.glyph.getBbox().setX((float) lNode.getLeft());
this.glyph.getBbox().setY((float) lNode.getTop());
this.placeStateAndInfoGlyphs();
}
/**
* Sets the bound of this VNode by given width and height
* @param w new width
* @param h new height
*/
public void setBounds(float w, float h)
{
this.glyph.getBbox().setW(w);
this.glyph.getBbox().setH(h);
}
/**
* Chooses a proper bound for this VNode according to its class.
*/
public void setSizeAccordingToClass()
{
String glyphClass = this.glyph.getClazz();
//If glyph class is not specified return here
if (glyphClass.equalsIgnoreCase(NONE))
return;
if (glyphClass.equalsIgnoreCase(SOURCE_AND_SINK))
{
setBounds(SOURCE_AND_SINK_BOUND.getWidth(), SOURCE_AND_SINK_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(AND) || glyphClass.equalsIgnoreCase(OR) || glyphClass.equalsIgnoreCase(NOT))
{
setBounds(LOGICAL_OPERATOR_BOUND.getWidth(), LOGICAL_OPERATOR_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(ASSOCIATION) || glyphClass.equalsIgnoreCase(DISSOCIATION) || glyphClass.equalsIgnoreCase(OMITTED_PROCESS) ||
glyphClass.equalsIgnoreCase(UNCERTAIN_PROCESS) || glyphClass.equalsIgnoreCase(PROCESS))
{
setBounds(PROCESS_NODES_BOUND.getWidth(), PROCESS_NODES_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(SIMPLE_CHEMICAL))
{
setBounds(SIMPLE_CHEMICAL_BOUND.getWidth(), SIMPLE_CHEMICAL_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(UNSPECIFIED_ENTITY))
{
setBounds(UNSPECIFIED_ENTITY_BOUND.getWidth(), UNSPECIFIED_ENTITY_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(MACROMOLECULE))
{
setBounds(MACROMOLECULE_BOUND.getWidth(), MACROMOLECULE_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(NUCLEIC_ACID_FEATURE))
{
setBounds(NUCLEIC_ACID_FEATURE_BOUND.getWidth(), NUCLEIC_ACID_FEATURE_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(STATE_VARIABLE))
{
setBounds(STATE_BOUND.getWidth(), STATE_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(UNIT_OF_INFORMATION))
{
setBounds(INFO_BOUND.getWidth(), INFO_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(PHENOTYPE))
{
setBounds(PHENOTYPE_BOUND.getWidth(), PHENOTYPE_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(PERTURBING_AGENT))
{
setBounds(PERTURBING_AGENT_BOUND.getWidth(), PERTURBING_AGENT_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(TAG))
{
setBounds(TAG_BOUND.getWidth(), TAG_BOUND.getHeight());
}
else if (glyphClass.equalsIgnoreCase(COMPLEX))
{
setBounds(COMPLEX_BOUND.getWidth(), COMPLEX_BOUND.getHeight());
}
if( this.glyph.getClone() != null )
{
Bbox glyphBbox = this.glyph.getBbox();
setBounds(3*glyphBbox.getW()/4, 3*glyphBbox.getH()/4);
}
if (glyphClass.equalsIgnoreCase(MACROMOLECULE) || glyphClass.equalsIgnoreCase(NUCLEIC_ACID_FEATURE) || glyphClass.equalsIgnoreCase(SIMPLE_CHEMICAL) || glyphClass.equalsIgnoreCase(COMPLEX))
{
updateSizeForStateAndInfo();
}
}
/**
* Calculates required width according to the given list state and info glyphs of this VNode.
* This method also previously computes the width and height of state and info glyphs
* according to their label.
*
* @param stateORinfoList list that keeps state or info glyphs of this VNode
* @return new width that is adjusted so that all glyphs in stateORinfoList are included.
* */
public int calcReqWidthByStateAndInfos(List stateORinfoList)
{
int wholeSize = 0;
int count = 0;
for (Glyph tmpGlyph: stateORinfoList)
{
String text;
if (tmpGlyph.getState() != null)
{
text = tmpGlyph.getState().getValue();
if (tmpGlyph.getState().getVariable() != null &&
tmpGlyph.getState().getVariable().length() > 0)
{
if(tmpGlyph.getState().getVariable() != null)
text += "@" + tmpGlyph.getState().getVariable();
}
}
else if (tmpGlyph.getLabel() != null)
{
text = tmpGlyph.getLabel().getText();
}
else
{
throw new RuntimeException("Encountered an information glyph with no state " +
"variable (as modification boxes should have) and no label (as molecule type " +
"boxed should have). glyph = " + tmpGlyph);
}
int numOfUpper = 0;
int numOfLower = 0;
for (int i = 0; i < text.length(); i++)
{
if (Character.isLowerCase(text.charAt(i)))
{
numOfLower++;
} else
numOfUpper++;
}
Bbox b = new Bbox();
tmpGlyph.setBbox(b);
//Set width
float requiredSize = numOfLower * LOWERCASE_LETTER_PIXEL_WIDTH + numOfUpper * UPPERCASE_LETTER_PIXEL_WIDTH;
if (requiredSize < MAX_STATE_AND_INFO_WIDTH)
tmpGlyph.getBbox().setW(requiredSize);
else
tmpGlyph.getBbox().setW(STATE_BOUND.width);
//Set height
tmpGlyph.getBbox().setH(MAX_STATE_AND_INFO_HEIGHT);
if (count < MAX_INFO_BOX_NUMBER / 2)
wholeSize += tmpGlyph.getBbox().getW();
count++;
}
return wholeSize;
}
/**
* If glyph attribute of this VNode object includes any "state of information" or "unit of information" glyphs, this method updates the
* size of VNode accordingly.
* */
public void updateSizeForStateAndInfo()
{
// Find all state and info glyphs
for (Glyph glyph : this.glyph.getGlyph())
{
if (glyph.getClazz() == STATE_VARIABLE)
{
stateGlyphs.add(glyph);
}
else if (glyph.getClazz() == UNIT_OF_INFORMATION)
{
infoGlyphs.add(glyph);
}
}
//Calculate "state of information" glyphs' sizes
int wholeWidthOfStates = calcReqWidthByStateAndInfos(stateGlyphs);
int wholeWidthOfInfos = calcReqWidthByStateAndInfos(infoGlyphs);
// Calculate positions
int numOfStates = stateGlyphs.size();
int numOfInfos = infoGlyphs.size();
//set a maximum width to glyph according to state and info boxes
int totNumStateInfo = numOfInfos + numOfStates;
int multiplier = totNumStateInfo <= 2 ? 2 : 3;
float requiredWidth = multiplier * OFFSET_BTW_INFO_GLYPHS + (multiplier-1) * MAX_STATE_AND_INFO_WIDTH;
//Adjust heights so that info box offsets are taken into account in layout.
if(totNumStateInfo > 0 )
this.glyph.getBbox().setH(this.glyph.getBbox().getH()+MAX_STATE_AND_INFO_HEIGHT/2);
if (this.glyph.getBbox().getW() < requiredWidth )
{
this.glyph.getBbox().setW(requiredWidth);
}
}
/**
* Places state and info glyphs of this node
* */
public void placeStateAndInfoGlyphs() {
int numOfStates = stateGlyphs.size();
int numOfInfos = infoGlyphs.size();
//Adjust heights so that info box offsets are taken into account in layout.
if(numOfStates > 0 || numOfInfos > 0)
this.glyph.getBbox().setH(this.glyph.getBbox().getH()-MAX_STATE_AND_INFO_HEIGHT/2);
float parent_y_up = this.glyph.getBbox().getY()-INFO_BOUND.height/2;
float parent_y_bot = this.glyph.getBbox().getY()+this.glyph.getBbox().getH()-INFO_BOUND.height/2;;
float parent_x_up = this.glyph.getBbox().getX();
float parentWidth = this.glyph.getBbox().getW();
String parentID = this.glyph.getId();
int maxNumberOfStates = stateGlyphs.size();
int maxNumberOfInfos = infoGlyphs.size();
if (maxNumberOfInfos + maxNumberOfStates > 4)
{
if(maxNumberOfInfos < 2 || maxNumberOfStates < 2)
{
int minimum = Math.min(maxNumberOfInfos,maxNumberOfStates);
if (maxNumberOfInfos - minimum == 0)
{
maxNumberOfInfos = minimum;
maxNumberOfStates = maxNumberOfStates - maxNumberOfInfos;
}
else
{
maxNumberOfStates = minimum;
maxNumberOfInfos = maxNumberOfInfos - maxNumberOfStates;
}
}
}
//else normal placement
//Some variables for placement of state and info boxes
int totalNumberOfStateAndInfos = maxNumberOfInfos+maxNumberOfStates;
Glyph tmpglyph = null;
int infoIndex = 0;
int stateIndex = 0;
int topUsedWidth = 0;
int bottomUsedWidth = 0;
int additionalStateInfoOffset = 0;
boolean placeTopFlag = true;
//Place state and info glyphs
for (int i = 0; i < totalNumberOfStateAndInfos; i++)
{
//Adjust offsets between state and info boxes
int offsetMultiplier = i % 4 <= 1 ? 1 : 2;
if (maxNumberOfInfos - i > 0 && infoGlyphs.size() > 0)
tmpglyph = infoGlyphs.get(infoIndex++);
else if (stateGlyphs.size() > 0)
tmpglyph = stateGlyphs.get(stateIndex++);
//Top placement
if (placeTopFlag)
{
if( totalNumberOfStateAndInfos <= 2 )
{
tmpglyph.getBbox().setX(parent_x_up+parentWidth/2-tmpglyph.getBbox().getW()/2);
tmpglyph.getBbox().setY(parent_y_up - additionalStateInfoOffset);
//set dummy id
tmpglyph.setId(parentID + ".info." + (i+1) );
}
else
{
//set dummy id
tmpglyph.setId(parentID + ".info." + (i+1) );
tmpglyph.getBbox().setX(parent_x_up + offsetMultiplier * OFFSET_BTW_INFO_GLYPHS + topUsedWidth);
tmpglyph.getBbox().setY(parent_y_up - additionalStateInfoOffset);
}
topUsedWidth += tmpglyph.getBbox().getW();
}
//bottom placement
else
{
if(( i % 2 == 1 ) && ( totalNumberOfStateAndInfos == 2 || totalNumberOfStateAndInfos == 3 ))
{
tmpglyph.getBbox().setX(parent_x_up+parentWidth/2-tmpglyph.getBbox().getW()/2);
tmpglyph.getBbox().setY(parent_y_bot + additionalStateInfoOffset);
//set dummy id
tmpglyph.setId(parentID + ".state." + (i+1) );
}
else
{
//set dummy id
tmpglyph.setId(parentID + ".state." + (i+1) );
tmpglyph.getBbox().setX(parent_x_up+ offsetMultiplier *OFFSET_BTW_INFO_GLYPHS + bottomUsedWidth);
tmpglyph.getBbox().setY(parent_y_bot + additionalStateInfoOffset);
}
bottomUsedWidth += tmpglyph.getBbox().getW();
}
// Alternate between placing top and bottom
placeTopFlag = !placeTopFlag;
//More than 4 state and info glyps are placed with an offset on top of previously placed state and info boxes
//This can be easily filtered out on the application side where the resultant graphs of this layout is used.
if ( ( i + 1 ) % 4 == 0 )
additionalStateInfoOffset += NON_SUPPORTED_GLYPH_OFFSET;
}
}
/**
* Inner Class for glyph bounds
* */
public class Bound
{
public float width;
public float height;
public Bound(float width, float height)
{
this.width = width;
this.height = height;
}
public float getWidth()
{
return width;
}
public void setWidth(float width)
{
this.width = width;
}
public float getHeight()
{
return height;
}
public void setHeight(float height)
{
this.height = height;
}
}
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