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add cartoon to TagPileupWindow
This commit primarily takes care of adding the read fragment cartoon to clarify parameter selection for users. #71 TagPileupWindow: - create instance of cartoon component and add to the window frame - adjust other components as necessary to maintain balance and function - add method to update cartoon when read aspect or read type are toggled ReadFragmentCartoon: - create graphic component object that can be updated and repainted in response to changes to "aspect" and "read" - add JavaDocs comments PileupParameters - add and reorganize fields to include final static integers that track the encodings for each parameter (like aliases)
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3 files changed

Lines changed: 246 additions & 45 deletions

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‎src/objects/PileupParameters.java‎

Lines changed: 35 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -3,31 +3,42 @@
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import java.io.File;
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import java.io.PrintStream;
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/**
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* Object for storing pileup-related parameter information and constants.
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* @see scripts.Read_Analysis.PileupScripts.PileupExtract
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* @author William KM Lai
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*/
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public class PileupParameters {
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//Directory to save matrix and composite into
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private File OUTPUT = null;
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//Composite values file if output
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private PrintStream COMPOSITE = null;
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//Read aspect
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final static int FIVE = 0;
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final static int THREE = 1;
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final static int MIDPOINT = 2;
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final static int FRAGMENT = 3;
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private int ASPECT = PileupParameters.FIVE;
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//Read type
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final static int READ1 = 0;
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final static int READ2 = 1;
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final static int ALLREADS = 2;
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private int READ = PileupParameters.READ1;
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//Read aspect:
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// 0=5prime end, 1=3prime end, 2=midpoint, 3=fullfragment
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private int ASPECT = 0;
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//Read type:
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// 0=read1, 1=read2, 2=allreads
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private int READ = 0;
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//Strand type
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final static int COMBINED = 1;
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final static int SEPARATE = 0;
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private int STRAND = PileupParameters.SEPARATE;
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//Strand type:
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// 0=separate, 1=combined
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private int STRAND = 0;
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//Transformation/smoothing type
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final static int NO_SMOOTH = 0;
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final static int WINDOW = 1;
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final static int GAUSSIAN = 2;
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private int TRANS = PileupParameters.NO_SMOOTH;
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//Transformation/smoothing type:
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// 0=no_smooth, 1=window, 2=gaussian
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private int TRANS = 0;
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//TRANS=1 parameters: window size (#bins)
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private int SMOOTH = 0;
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//TRANS=2 parameters: stdev window size (#bins) and number of standard devations
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//TRANS=2 parameters: stdev window size (#bins) and number of standard deviations
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private int STDSIZE = 0;
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private int STDNUM = 0;
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private int STDNUM = 0;
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private int SHIFT = 0;
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private int BIN = 1;
@@ -43,7 +54,12 @@ public class PileupParameters {
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private int MIN_INSERT = -9999;
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private int MAX_INSERT = -9999;
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//Directory to save matrix and composite into
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private File OUTPUT = null;
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//Composite values file if output
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private PrintStream COMPOSITE = null;
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public void printAll(){
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System.out.println( "<><><><><><><><><><><><><><><><><><><><>" );
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System.out.println( "private File OUTPUT = " + OUTPUT );

‎src/objects/ReadFragmentCartoon.java‎

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package objects;
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import java.awt.Color;
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import java.awt.Dimension;
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import java.awt.Graphics;
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import java.awt.Polygon;
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import java.util.ArrayList;
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import javax.swing.JPanel;
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/**
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* Component that displays a graphic of a sequenced DNA fragment with annotated
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* Read1, Read2, and dynamically updating encoding reference points marked by
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* arrows.
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*
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* @author Olivia Lang
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*
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*/
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public class ReadFragmentCartoon extends JPanel {
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int readHeight = 20;
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int readWidth = 100;
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public int cartoonHeight = 80;
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public int arrowHeight = 15;
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public int arrowWidth = 6;
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int fragmentLength = 480;
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int fragmentThickness = 3;
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int edgePad = 20;
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int verticalPad;
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public ArrayList<Polygon> arrows = new ArrayList<Polygon>(6);
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@Override
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protected void paintComponent(Graphics g) {
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super.paintComponent(g);
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// Determine distance from top of graphic
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verticalPad = (cartoonHeight - 2*(readHeight) - fragmentThickness - arrowHeight) / 2 + arrowHeight;
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// Draw Read 1
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g.setColor(Color.CYAN);
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g.fillRect(edgePad, verticalPad, readWidth, readHeight);
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// Draw Read 2
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g.setColor(Color.ORANGE);
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g.fillRect(edgePad+fragmentLength - readWidth, verticalPad + readHeight + fragmentThickness, readWidth, readHeight);
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// Draw Fragment
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g.setColor(Color.BLACK);
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g.fillRect(edgePad, verticalPad + readHeight, fragmentLength, fragmentThickness);
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// Label Reads
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g.drawString("Read1", edgePad, verticalPad + readHeight - 1);
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g.drawString("Read2", edgePad + fragmentLength - 37, verticalPad + 2*readHeight + fragmentThickness - 1);
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// Draw arrows
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for (int p=0; p<arrows.size(); p++) {
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g.fillPolygon(arrows.get(p));
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}
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}
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/**
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* Update graphic to reflect changes in aspect and read encodings.
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*
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* @param aspect
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* @param read
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*/
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public void redrawArrows(int aspect, int read) {
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verticalPad = (cartoonHeight - (2 * readHeight) - fragmentThickness - arrowHeight) / 2 + arrowHeight;
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arrows = new ArrayList<Polygon>(2);
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int topY = verticalPad - arrowHeight;
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if (aspect == PileupParameters.FRAGMENT) { // handle fragment
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// arrows.add(bigArrow());
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for (int i = 0; i < fragmentLength; i += 6) {
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arrows.add(arrow(edgePad + i, topY));
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}
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} else if (aspect == PileupParameters.MIDPOINT) { // handle midpoint
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arrows.add(arrow(edgePad + fragmentLength / 2, topY));
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} else if (aspect == PileupParameters.THREE) { // handle 3 prime ends
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if (read == PileupParameters.READ1 || read == PileupParameters.ALLREADS) {
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arrows.add(arrow(edgePad + readWidth, topY));
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}
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if (read == PileupParameters.READ2 || read == PileupParameters.ALLREADS) {
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arrows.add(arrow(edgePad + fragmentLength - readWidth, topY));
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}
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} else if (aspect == PileupParameters.FIVE) { // handle 5 prime ends
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if (read == PileupParameters.READ1 || read == PileupParameters.ALLREADS) {
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arrows.add(arrow(edgePad, topY));
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}
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if (read == PileupParameters.READ2 || read == PileupParameters.ALLREADS) {
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arrows.add(arrow(edgePad + fragmentLength, topY));
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}
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}
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repaint();
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}
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/**
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* Unused legacy code for how Full Fragment was initially represented: a
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* rightward-pointing arrow across length of DNA fragment.
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* @return
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*/
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public Polygon bigArrow() {
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int arrowThickness = 5;
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int arrowHead = 20;
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int arrowflank = (arrowHeight - arrowThickness)/2;
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int xPoly[] = {edgePad, edgePad+fragmentLength-arrowHead, edgePad+fragmentLength-arrowHead,
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edgePad+fragmentLength, edgePad +fragmentLength -arrowHead, edgePad+fragmentLength-arrowHead, edgePad};
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int yPoly[] = {verticalPad-arrowflank, verticalPad-arrowflank, verticalPad, verticalPad-arrowHeight/2,
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verticalPad-arrowHeight, verticalPad-arrowHeight+arrowflank, verticalPad-arrowHeight+arrowflank};
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return(new Polygon(xPoly,yPoly,xPoly.length));
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}
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/**
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* Draw downward-pointing arrow at (x,y) coordinate (upper-center) for marking
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* where on the DNA fragment coverage is tallied on this graphic. Arrow size is
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* arrowHeight tall (15px) and flank*2 (6px) wide.
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*
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* (x,y)
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* ||
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* ||
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* ||
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* ||
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* \ /
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* \/
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*
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* @param x
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* @param y
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* @return
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*/
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public Polygon arrow(int x,int y) {
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// arrowhead flank size
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int flank = arrowWidth/2;
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// arrow thickness
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int thick = 2;
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// arrowhead height
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int head = 5;
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x = x-thick/2;
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int xPoly[] = {x, x, x-flank, x+thick/2, x+thick+flank, x+thick, x+thick};
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int yPoly[] = {y, y+arrowHeight-head, y+arrowHeight-head, y+arrowHeight, y+arrowHeight-head, y+arrowHeight-head, y};
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return(new Polygon(xPoly,yPoly,xPoly.length));
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}
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@Override
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public Dimension getPreferredSize() {
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return new Dimension(800,cartoonHeight);
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}
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}

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