package jalview.datamodel; import jalview.util.*; import jalview.jbgui.*; import jalview.schemes.*; import java.awt.*; public class SequenceFeature { int start; int end; String type; String description; Color color; Sequence sequence; String id; double score; int strand; double pvalue; double pid; public SequenceFeature() { } public SequenceFeature(Sequence sequence,String type, int start, int end, String description) { this.sequence = sequence; this.type = type; this.start = start; this.end = end; this.description = description; setColor(); } public String toGFFString() { String gff = id + "\t" + type + "\tfeature\t" + start + "\t" + end + "\t" + score + "\t" + strand + "\t."; return gff; } public double getScore() { return score; } public void setScore(double score) { this.score = score; } public String getId() { return this.id; } public void setId(String id) { this.id = id; } public void setSequence(Sequence seq) { this.sequence = seq; } public void setStart(int start) { this.start = start; } public void setEnd(int end) { this.end = end; } public int getStrand() { return strand; } public void setStrand(int strand) { this.strand = strand; } public int getStart() { return start; } public int getEnd() { return end; } public String getType() { return type; } public String getDescription() { return description; } public double getPValue() { return pvalue; } public void setPValue(double value) { this.pvalue = value; } public double getPercentId() { return pid; } public void setPercentId(double pid) { this.pid = pid; } public Color getColor() { return color; } public void setColor() { if (type.equals("CHAIN")) { color = Color.white; } else if (type.equals("DOMAIN")) { color = Color.white; } else if (type.equals("TRANSMEM")) { color = Color.red.darker(); } else if (type.equals("SIGNAL")) { color = Color.cyan; } else if (type.equals("HELIX")) { color = Color.magenta; } else if (type.equals("TURN")) { color = Color.cyan; } else if (type.equals("SHEET")) { color = Color.yellow; } else if (type.equals("STRAND")) { color = Color.yellow; } else if (type.equals("CARBOHYD")) { color = Color.pink; } else if (type.equals("ACT_SITE")) { color = Color.red; } else if (type.equals("TRANSIT")) { color = Color.orange; } else if (type.equals("VARIANT")) { color = Color.orange.darker(); } else if (type.equals("BINDING")) { color = Color.blue; } else if (type.equals("DISULFID")) { color = Color.yellow.darker(); } else if (type.equals("NP_BIND")) { color = Color.red; } else if (type.indexOf("BIND") > 0) { color = Color.red; } else { color = Color.lightGray; } } public String print() { String tmp = new Format("%15s").form(type); tmp = tmp + new Format("%6d").form(start); tmp = tmp + new Format("%6d").form(end); tmp = tmp + " " + description; return tmp; } public void draw(Graphics g, int fstart, int fend, int x1, int y1, int width, int height) { g.setColor(new Color((float)(Math.random()),(float)(Math.random()),(float)(Math.random()))); // int xstart = sequence.findIndex(start); //int xend = sequence.findIndex(end); int xstart = start; int xend = end; long tstart = System.currentTimeMillis(); if (!(xend < fstart && xstart > fend)) { if (xstart > fstart) { x1 = x1 + (xstart-fstart)*width; fstart = xstart; } if (xend < fend) { fend = xend; } for (int i = fstart; i <= fend; i++) { String s = sequence.sequence.substring(i,i+1); if (!(s.equals(".") || s.equals("-") || s.equals(" "))) { g.fillRect(x1+(i-fstart)*width,y1,width,height); } else { g.drawString("-",x1+(i-fstart)*width,y1+height); } } } long tend = System.currentTimeMillis(); System.out.println("Time = " + (tend-tstart) + "ms"); } public static void main(String[] args) { SequenceFeature sf = new SequenceFeature(); System.out.println("Feature " + sf); } public static int CHAIN = 0; public static int DOMAIN = 1; public static int TRANSMEM = 2; public static int SIGNAL = 3; public static int HELIX = 4; public static int TURN = 5; public static int SHEET = 6; public static int CARBOHYD = 7; public static int ACT_SITE = 8; public static int TRANSIT = 9; public static int VARIANT = 10; public static int BINDING = 11; }