-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
-\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
- }\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceFeature
+{
+ public int begin;
+
+ public int end;
+
+ public float score;
+
+ public String type;
+
+ public String description;
+
+ public Hashtable otherDetails;
+
+ public java.util.Vector links;
+
+ // Feature group can be set from a features file
+ // as a group of features between STARTGROUP and ENDGROUP markers
+ public String featureGroup;
+
+ public SequenceFeature()
+ {
+ }
+
+ /**
+ * Constructs a duplicate feature. Note: Uses clone on the otherDetails so
+ * only shallow copies are made of additional properties and method will
+ * silently fail if unclonable objects are found in the hash.
+ *
+ * @param cpy
+ */
+ public SequenceFeature(SequenceFeature cpy)
+ {
+ if (cpy != null)
+ {
+ begin = cpy.begin;
+ end = cpy.end;
+ score = cpy.score;
+ if (cpy.type != null)
+ {
+ type = new String(cpy.type);
+ }
+ if (cpy.description != null)
+ {
+ description = new String(cpy.description);
+ }
+ if (cpy.featureGroup != null)
+ {
+ featureGroup = new String(cpy.featureGroup);
+ }
+ if (cpy.otherDetails != null)
+ {
+ try
+ {
+ otherDetails = (Hashtable) cpy.otherDetails.clone();
+ } catch (Exception e)
+ {
+ // Uncloneable objects in the otherDetails - don't complain
+ }
+ }
+ if (cpy.links != null && cpy.links.size() > 0)
+ {
+ links = new Vector();
+ for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
+ {
+ links.addElement(cpy.links.elementAt(i));
+ }
+ }
+ }
+ }
+
+ public SequenceFeature(String type, String desc, String status,
+ int begin, int end, String featureGroup)
+ {
+ this.type = type;
+ this.description = desc;
+ setValue("status", status);
+ this.begin = begin;
+ this.end = end;
+ this.featureGroup = featureGroup;
+ }
+
+ public SequenceFeature(String type, String desc, int begin, int end,
+ float score, String featureGroup)
+ {
+ this.type = type;
+ this.description = desc;
+ this.begin = begin;
+ this.end = end;
+ this.score = score;
+ this.featureGroup = featureGroup;
+ }
+
+ public boolean equals(SequenceFeature sf)
+ {
+ if (begin != sf.begin || end != sf.end || score != sf.score)
+ {
+ return false;
+ }
+
+ if (!(type + description + featureGroup).equals(sf.type
+ + sf.description + sf.featureGroup))
+ {
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getBegin()
+ {
+ return begin;
+ }
+
+ public void setBegin(int start)
+ {
+ this.begin = start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ public void setEnd(int end)
+ {
+ this.end = end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ public void setType(String type)
+ {
+ this.type = type;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String desc)
+ {
+ description = desc;
+ }
+
+ public String getFeatureGroup()
+ {
+ return featureGroup;
+ }
+
+ public void setFeatureGroup(String featureGroup)
+ {
+ this.featureGroup = featureGroup;
+ }
+
+ public void addLink(String labelLink)
+ {
+ if (links == null)
+ {
+ links = new java.util.Vector();
+ }
+
+ links.insertElementAt(labelLink, 0);
+ }
+
+ public float getScore()
+ {
+ return score;
+ }
+
+ public void setScore(float value)
+ {
+ score = value;
+ }
+
+ /**
+ * Used for getting values which are not in the basic set. eg STRAND, FRAME
+ * for GFF file
+ *
+ * @param key
+ * String
+ */
+ public Object getValue(String key)
+ {
+ if (otherDetails == null)
+ {
+ return null;
+ }
+ else
+ {
+ return otherDetails.get(key);
+ }
+ }
+
+ /**
+ * Used for setting values which are not in the basic set. eg STRAND, FRAME
+ * for GFF file
+ *
+ * @param key
+ * eg STRAND
+ * @param value
+ * eg +
+ */
+ public void setValue(String key, Object value)
+ {
+ if (value != null)
+ {
+ if (otherDetails == null)
+ {
+ otherDetails = new Hashtable();
+ }
+
+ otherDetails.put(key, value);
+ }
+ }
+
+ /*
+ * The following methods are added to maintain the castor Uniprot mapping file
+ * for the moment.
+ */
+ public void setStatus(String status)
+ {
+ setValue("status", status);
+ }
+
+ public String getStatus()
+ {
+ if (otherDetails != null)
+ {
+ String stat = (String) otherDetails.get("status");
+ if (stat != null)
+ return new String(stat);
+ }
+ return null;
+ }
+
+ public void setPosition(int pos)
+ {
+ begin = pos;
+ end = pos;
+ }
+
+ public int getPosition()
+ {
+ return begin;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff