package jalview.datamodel;\r
\r
-import jalview.util.*;\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
\r
public class SequenceFeature {\r
- int start;\r
+ int begin;\r
int end;\r
String type;\r
String description;\r
- Color color;\r
- Sequence sequence;\r
- String id;\r
- double score;\r
- int strand;\r
- double pvalue;\r
- double pid;\r
+ String status;\r
\r
- public SequenceFeature() {\r
+ public SequenceFeature()\r
+ {\r
}\r
\r
- public SequenceFeature(Sequence sequence,String type, int start, int end, String description) {\r
- this.sequence = sequence;\r
+ public SequenceFeature(String type, int start, int end, String description, String status)\r
+ {\r
this.type = type;\r
- this.start = start;\r
+ this.begin = start;\r
this.end = end;\r
this.description = description;\r
-\r
- setColor();\r
- }\r
-\r
-\r
- public String toGFFString() {\r
- String gff = id + "\t" + type + "\tfeature\t" + start + "\t" + end + "\t" + score + "\t" + strand + "\t.";\r
- return gff;\r
- }\r
- public double getScore() {\r
- return score;\r
+ this.status = status;\r
}\r
\r
- public void setScore(double score) {\r
- this.score = score;\r
- }\r
-\r
- public String getId() {\r
- return this.id;\r
- }\r
- public void setId(String id) {\r
- this.id = id;\r
- }\r
- public void setSequence(Sequence seq) {\r
- this.sequence = seq;\r
- }\r
- public void setStart(int start) {\r
- this.start = start;\r
- }\r
- public void setEnd(int end) {\r
- this.end = end;\r
- }\r
- public int getStrand() {\r
- return strand;\r
- }\r
- public void setStrand(int strand) {\r
- this.strand = strand;\r
- }\r
public int getStart() {\r
- return start;\r
+ return begin;\r
}\r
-\r
public int getEnd() {\r
return end;\r
}\r
-\r
public String getType() {\r
return type;\r
}\r
-\r
public String getDescription() {\r
return description;\r
}\r
-\r
- public double getPValue() {\r
- return pvalue;\r
- }\r
- public void setPValue(double value) {\r
- this.pvalue = value;\r
- }\r
- public double getPercentId() {\r
- return pid;\r
- }\r
- public void setPercentId(double pid) {\r
- this.pid = pid;\r
- }\r
- public Color getColor() {\r
- return color;\r
- }\r
-\r
- public void setColor() {\r
- if (type.equals("CHAIN")) {\r
- color = Color.white;\r
- } else if (type.equals("DOMAIN")) {\r
- color = Color.white;\r
- } else if (type.equals("TRANSMEM")) {\r
- color = Color.red.darker();\r
- } else if (type.equals("SIGNAL")) {\r
- color = Color.cyan;\r
- } else if (type.equals("HELIX")) {\r
- color = Color.magenta;\r
- } else if (type.equals("TURN")) {\r
- color = Color.cyan;\r
- } else if (type.equals("SHEET")) {\r
- color = Color.yellow;\r
- } else if (type.equals("STRAND")) {\r
- color = Color.yellow;\r
- } else if (type.equals("CARBOHYD")) {\r
- color = Color.pink;\r
- } else if (type.equals("ACT_SITE")) {\r
- color = Color.red;\r
- } else if (type.equals("TRANSIT")) {\r
- color = Color.orange;\r
- } else if (type.equals("VARIANT")) {\r
- color = Color.orange.darker();\r
- } else if (type.equals("BINDING")) {\r
- color = Color.blue;\r
- } else if (type.equals("DISULFID")) {\r
- color = Color.yellow.darker();\r
- } else if (type.equals("NP_BIND")) {\r
- color = Color.red;\r
- } else if (type.indexOf("BIND") > 0) {\r
- color = Color.red;\r
- } else {\r
- color = Color.lightGray;\r
- }\r
- }\r
- public String print() {\r
- String tmp = new Format("%15s").form(type);\r
- tmp = tmp + new Format("%6d").form(start);\r
- tmp = tmp + new Format("%6d").form(end);\r
- tmp = tmp + " " + description;\r
- return tmp;\r
- }\r
- public void draw(Graphics g, int fstart, int fend, int x1, int y1, int width, int height) {\r
- g.setColor(new Color((float)(Math.random()),(float)(Math.random()),(float)(Math.random())));\r
-\r
- // int xstart = sequence.findIndex(start);\r
- //int xend = sequence.findIndex(end);\r
- int xstart = start;\r
- int xend = end;\r
- long tstart = System.currentTimeMillis();\r
- if (!(xend < fstart && xstart > fend)) {\r
-\r
- if (xstart > fstart) {\r
- x1 = x1 + (xstart-fstart)*width;\r
- fstart = xstart;\r
- }\r
-\r
- if (xend < fend) {\r
- fend = xend;\r
- }\r
-\r
- for (int i = fstart; i <= fend; i++) {\r
- char c = sequence.sequence.charAt(i);\r
- if (!jalview.util.Comparison.isGap((c)))\r
- g.fillRect(x1+(i-fstart)*width,y1,width,height);\r
- else\r
- g.drawString("-",x1+(i-fstart)*width,y1+height);\r
-\r
- }\r
-\r
- }\r
- long tend = System.currentTimeMillis();\r
- System.out.println("Time = " + (tend-tstart) + "ms");\r
-\r
- }\r
-\r
- public static void main(String[] args) {\r
- SequenceFeature sf = new SequenceFeature();\r
-\r
- System.out.println("Feature " + sf);\r
- }\r
- public static int CHAIN = 0;\r
- public static int DOMAIN = 1;\r
- public static int TRANSMEM = 2;\r
- public static int SIGNAL = 3;\r
- public static int HELIX = 4;\r
- public static int TURN = 5;\r
- public static int SHEET = 6;\r
- public static int CARBOHYD = 7;\r
- public static int ACT_SITE = 8;\r
- public static int TRANSIT = 9;\r
- public static int VARIANT = 10;\r
- public static int BINDING = 11;\r
+ public String getStatus()\r
+ {return status;}\r
+\r
+\r
+/*\r
+ <xs:enumeration value="active site" />\r
+<xs:enumeration value="binding site" />\r
+<xs:enumeration value="calcium-binding region" />\r
+<xs:enumeration value="chain" />\r
+<xs:enumeration value="cross-link" />\r
+<xs:enumeration value="disulfide bond" />\r
+<xs:enumeration value="DNA-binding region" />\r
+<xs:enumeration value="domain" />\r
+<xs:enumeration value="glycosylation site" />\r
+<xs:enumeration value="helix" />\r
+<xs:enumeration value="initiator methionine" />\r
+<xs:enumeration value="lipid moiety-binding region" />\r
+<xs:enumeration value="metal ion-binding site" />\r
+<xs:enumeration value="modified residue" />\r
+<xs:enumeration value="mutagenesis site" />\r
+<xs:enumeration value="non-consecutive residues" />\r
+<xs:enumeration value="non-terminal residue" />\r
+<xs:enumeration value="nucleotide phosphate-binding region" />\r
+<xs:enumeration value="peptide" />\r
+<xs:enumeration value="propeptide" />\r
+<xs:enumeration value="repeat" />\r
+<xs:enumeration value="selenocysteine" />\r
+<xs:enumeration value="sequence conflict" />\r
+<xs:enumeration value="sequence variant" />\r
+<xs:enumeration value="signal peptide" />\r
+<xs:enumeration value="similar" />\r
+<xs:enumeration value="site" />\r
+<xs:enumeration value="splice variant" />\r
+<xs:enumeration value="strand" />\r
+<xs:enumeration value="thioether bond" />\r
+<xs:enumeration value="thiolester bond" />\r
+<xs:enumeration value="transit peptide" />\r
+<xs:enumeration value="transmembrane region" />\r
+<xs:enumeration value="turn" />\r
+<xs:enumeration value="unsure residue" />\r
+<xs:enumeration value="zinc finger region" />\r
+*/\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff