X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=cd2650626b0834e4a57dd3c5f8947460fc09165b;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=251297883a0d4111ecc5844b039084af15557bba;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2512978..cd26506 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,197 +1,324 @@
-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;
-
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+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 Vector<String> 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<String>();
+        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 Vector<String>();
+    }
+
+    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;
+  }
+
+  public int getStrand()
+  {
+    String str;
+    if (otherDetails == null
+            || (str = otherDetails.get("STRAND").toString()) == null)
+    {
+      return 0;
+    }
+    if (str.equals("-"))
+    {
+      return -1;
+    }
+    if (str.equals("+"))
+    {
+      return 1;
+    }
+    return 0;
+  }
+
+}