+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
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 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
-\r
- public SequenceFeature() {\r
- }\r
-\r
- public SequenceFeature(Sequence sequence,String type, int start, int end, String description) {\r
- this.sequence = sequence;\r
- this.type = type;\r
- this.start = 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
- }\r
+import java.util.Hashtable;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceFeature\r
+{\r
+ public int begin;\r
+ public int end;\r
+ public float score;\r
+ public String type;\r
+ public String description;\r
+ Hashtable otherDetails;\r
+ public java.util.Vector links;\r
+\r
+ // Feature group can be set from a features file\r
+ // as a group of features between STARTGROUP and ENDGROUP markers\r
+ public String featureGroup;\r
+\r
+ public SequenceFeature()\r
+ {}\r
+\r
+ public SequenceFeature(String type,\r
+ String desc,\r
+ String status,\r
+ int begin, int end,\r
+ String featureGroup)\r
+ {\r
+ this.type = type;\r
+ this.description = desc;\r
+ if(status!=null)\r
+ setValue("status", status);\r
+\r
+ this.begin = begin;\r
+ this.end = end;\r
+ this.featureGroup = featureGroup;\r
+ }\r
\r
- public void setScore(double score) {\r
+ public SequenceFeature(String type,\r
+ String desc,\r
+ int begin, int end,\r
+ float score,\r
+ String featureGroup)\r
+ {\r
+ this.type = type;\r
+ this.description = desc;\r
+ this.begin = begin;\r
+ this.end = end;\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.featureGroup = featureGroup;\r
+ }\r
+\r
+ public boolean equals(SequenceFeature sf)\r
+ {\r
+ if(begin != sf.begin\r
+ || end != sf.end)\r
+ return false;\r
+\r
+\r
+ if(!(type+description).equals\r
+ (sf.type+sf.description))\r
+ return false;\r
+\r
+ return true;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getBegin()\r
+ {\r
+ return begin;\r
+ }\r
+\r
+ public void setBegin(int start)\r
+ {\r
+ this.begin = start;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return end;\r
+ }\r
+\r
+ public void setEnd(int end)\r
+ {\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
- }\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
+ }\r
\r
-}\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getType()\r
+ {\r
+ return type;\r
+ }\r
+\r
+ public void setType(String type)\r
+ {\r
+ this.type = type;\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription()\r
+ {\r
+ return description;\r
+ }\r
+\r
+ public void setDescription(String desc)\r
+ {\r
+ description = desc;\r
+ }\r
+\r
+ public String getFeatureGroup()\r
+ {\r
+ return featureGroup;\r
+ }\r
+\r
+ public void setFeatureGroup(String featureGroup)\r
+ {\r
+ this.featureGroup = featureGroup;\r
+ }\r
+\r
+ public void addLink(String labelLink)\r
+ {\r
+ if(links==null)\r
+ links = new java.util.Vector();\r
+\r
+ links.insertElementAt(labelLink,0);\r
+ }\r
+\r
+ public float getScore()\r
+ {\r
+ return score;\r
+ }\r
+\r
+ public void setScore(float value)\r
+ {\r
+ score = value;\r
+ }\r
+\r
+ /**\r
+ * Used for getting values which are not in the\r
+ * basic set. eg STRAND, FRAME for GFF file\r
+ * @param key String\r
+ */\r
+ public Object getValue(String key)\r
+ {\r
+ if(otherDetails==null)\r
+ return null;\r
+ else\r
+ return otherDetails.get(key);\r
+ }\r
+\r
+ /**\r
+ * Used for setting values which are not in the\r
+ * basic set. eg STRAND, FRAME for GFF file\r
+ * @param key eg STRAND\r
+ * @param value eg +\r
+ */\r
+ public void setValue(String key, Object value)\r
+ {\r
+ if(otherDetails == null)\r
+ otherDetails = new Hashtable();\r
+\r
+ otherDetails.put(key, value);\r
+ }\r
+\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff