Remove getsfarray

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1adff25..dd39f9f 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -26,36 +26,61 @@ package jalview.datamodel;
  */\r
 public class SequenceFeature\r
 {\r
-    int position;\r
-    int begin;\r
-    int end;\r
-    String type;\r
-    String description;\r
-    String status;\r
+    public int begin;\r
+    public int end;\r
+    public float score;\r
+    public String type;\r
+    public String description;\r
+    public String status;\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, String desc, String status, int begin, int end)\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
       this.status = status;\r
-      this.position = begin;\r
       this.begin = begin;\r
       this.end = end;\r
+      this.featureGroup = featureGroup;\r
     }\r
-\r
-    public int getPosition()\r
+    public SequenceFeature(String type,\r
+                           String desc,\r
+                           int begin, int end,\r
+                           float score,\r
+                           String featureGroup)\r
     {\r
-      return position;\r
+      this.type = type;\r
+      this.description = desc;\r
+      this.status = status;\r
+      this.begin = begin;\r
+      this.end = end;\r
+      this.score = score;\r
+      this.featureGroup = featureGroup;\r
     }\r
 \r
-    public void setPosition(int pos)\r
+    public boolean equals(SequenceFeature sf)\r
     {\r
-      position = pos;\r
-      begin = pos;\r
-      end = pos;\r
+      if(begin != sf.begin\r
+      || end != sf.end)\r
+     return false;\r
+\r
+\r
+      if(!(type+description+status).equals\r
+         (sf.type+sf.description+sf.status))\r
+        return false;\r
+\r
+      return true;\r
     }\r
 \r
 \r
@@ -134,4 +159,31 @@ public class SequenceFeature
       this.status = status;\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