FeaturesGroup added to constructor

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 5bf4e88..f8444a0 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -26,48 +26,78 @@ package jalview.datamodel;
  */\r
 public class SequenceFeature\r
 {\r
-    int begin;\r
-    int end;\r
-    String type;\r
-    String description;\r
-    String status;\r
+    public int position;\r
+    public int begin;\r
+    public int end;\r
+    public String type;\r
+    public String description;\r
+    public String status;\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
-    /**\r
-     * Creates a new SequenceFeature object.\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
+      this.status = status;\r
+      this.position = begin;\r
+      this.begin = begin;\r
+      this.end = end;\r
+      this.featureGroup = featureGroup;\r
     }\r
 \r
-    /**\r
-     * Creates a new SequenceFeature object.\r
-     *\r
-     * @param type DOCUMENT ME!\r
-     * @param start DOCUMENT ME!\r
-     * @param end DOCUMENT ME!\r
-     * @param description DOCUMENT ME!\r
-     * @param status DOCUMENT ME!\r
-     */\r
-    public SequenceFeature(String type, int start, int end, String description,\r
-        String status)\r
+    public boolean equals(SequenceFeature sf)\r
     {\r
-        this.type = type;\r
-        this.begin = start;\r
-        this.end = end;\r
-        this.description = description;\r
-        this.status = status;\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
+    public int getPosition()\r
+    {\r
+      return position;\r
+    }\r
+\r
+    public void setPosition(int pos)\r
+    {\r
+      position = pos;\r
+      begin = pos;\r
+      end = pos;\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public int getStart()\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
@@ -78,6 +108,11 @@ public class SequenceFeature
         return end;\r
     }\r
 \r
+    public void setEnd(int end)\r
+    {\r
+      this.end = end;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -88,6 +123,11 @@ public class SequenceFeature
         return type;\r
     }\r
 \r
+    public void setType(String type)\r
+    {\r
+      this.type = type;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -98,6 +138,11 @@ public class SequenceFeature
         return description;\r
     }\r
 \r
+    public void setDescription(String desc)\r
+    {\r
+      description = desc;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -108,42 +153,20 @@ public class SequenceFeature
         return status;\r
     }\r
 \r
-    /*\r
-          <xs:enumeration value="active site" />\r
-         <xs:enumeration value="binding site" />\r
-         <xs:enumeration value="calcium-binding region" />\r
-         <xs:enumeration value="chain" />\r
-         <xs:enumeration value="cross-link" />\r
-         <xs:enumeration value="disulfide bond" />\r
-         <xs:enumeration value="DNA-binding region" />\r
-         <xs:enumeration value="domain" />\r
-         <xs:enumeration value="glycosylation site" />\r
-         <xs:enumeration value="helix" />\r
-         <xs:enumeration value="initiator methionine" />\r
-         <xs:enumeration value="lipid moiety-binding region" />\r
-         <xs:enumeration value="metal ion-binding site" />\r
-         <xs:enumeration value="modified residue" />\r
-         <xs:enumeration value="mutagenesis site" />\r
-         <xs:enumeration value="non-consecutive residues" />\r
-         <xs:enumeration value="non-terminal residue" />\r
-         <xs:enumeration value="nucleotide phosphate-binding region" />\r
-         <xs:enumeration value="peptide" />\r
-         <xs:enumeration value="propeptide" />\r
-         <xs:enumeration value="repeat" />\r
-         <xs:enumeration value="selenocysteine" />\r
-         <xs:enumeration value="sequence conflict" />\r
-         <xs:enumeration value="sequence variant" />\r
-         <xs:enumeration value="signal peptide" />\r
-         <xs:enumeration value="similar" />\r
-         <xs:enumeration value="site" />\r
-         <xs:enumeration value="splice variant" />\r
-         <xs:enumeration value="strand" />\r
-         <xs:enumeration value="thioether bond" />\r
-         <xs:enumeration value="thiolester bond" />\r
-         <xs:enumeration value="transit peptide" />\r
-         <xs:enumeration value="transmembrane region" />\r
-         <xs:enumeration value="turn" />\r
-         <xs:enumeration value="unsure residue" />\r
-         <xs:enumeration value="zinc finger region" />\r
-     */\r
+    public void setStatus(String status)\r
+    {\r
+      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
+\r
 }\r