X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=094e060662c3f88331227235eab017b45c58c23b;hb=cfbeda226e2ac27f6d02572b1c9589a3e2f1c747;hp=cba91dfa22f7639d03753d4b6d63b91a01eb7ec5;hpb=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index cba91df..094e060 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,197 +1,267 @@
-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++) {
-        char c = sequence.sequence.charAt(i);
-        if (!jalview.util.Comparison.isGap((c)))
-          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;
-
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+/**
+ * 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;
+            type = new String(cpy.type);
+            description = new String(cpy.description);
+            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.setElementAt(cpy.links.elementAt(i), 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)
+        return otherDetails.get("status").toString();
+      else
+        return null;
+    }
+
+    public void setPosition(int pos)
+    {
+      begin = pos;
+      end = pos;
+    }
+
+    public int getPosition()
+    {
+      return begin;
+    }
+
+}