Don't parse input id, leave it as it is

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 824a33b..dce2e51 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,8 +18,6 @@
 */\r
 package jalview.datamodel;\r
 \r
-import jalview.analysis.*;\r
-\r
 import java.awt.*;\r
 \r
 import java.util.*;\r
@@ -33,14 +31,17 @@ import java.util.*;
  */\r
 public class Sequence implements SequenceI\r
 {\r
-    protected String name;\r
-    protected String sequence;\r
-    protected String description;\r
-    protected int start;\r
-    protected int end;\r
-    protected String displayId;\r
-    protected Color color = Color.white;\r
-    String pdbId;\r
+    SequenceI datasetSequence;\r
+    String name;\r
+    String sequence;\r
+    String description;\r
+    int start;\r
+    int end;\r
+    Color color = Color.white;\r
+    Vector pdbIds;\r
+    String vamsasId;\r
+    Vector dbrefs;\r
+\r
 \r
     /** DOCUMENT ME!! */\r
     public Vector sequenceFeatures = new Vector();\r
@@ -60,6 +61,39 @@ public class Sequence implements SequenceI
       this.start = start;\r
       this.end = end;\r
 \r
+      parseId();\r
+\r
+      checkValidRange();\r
+    }\r
+\r
+    void parseId()\r
+    {\r
+         // Remove /start-end from sequence\r
+         if (name.indexOf("/") > 0)\r
+         {\r
+           String limits = name.substring(name.lastIndexOf("/")+1);\r
+           try\r
+           {\r
+               StringTokenizer st = new StringTokenizer(limits, "-");\r
+\r
+               if (st.countTokens() == 2)\r
+               {\r
+                 setStart(Integer.valueOf(st.nextToken()).intValue());\r
+                 setEnd(Integer.valueOf(st.nextToken()).intValue());\r
+               }\r
+\r
+             // If we're still in this loop, parsing of start and end was ok\r
+             // Therefore remove it from the sequence name\r
+             name = name.substring(0, name.lastIndexOf("/"));\r
+           }\r
+           catch (NumberFormatException ex)\r
+           {      }\r
+         }\r
+\r
+    }\r
+\r
+    void checkValidRange()\r
+    {\r
       if (end < 1)\r
       {\r
         int endRes = 0;\r
@@ -80,7 +114,6 @@ public class Sequence implements SequenceI
         this.end = endRes;\r
       }\r
 \r
-        setDisplayId();\r
     }\r
 \r
     /**\r
@@ -91,7 +124,7 @@ public class Sequence implements SequenceI
      */\r
     public Sequence(String name, String sequence)\r
     {\r
-        this(name, sequence, 1, sequence.length());\r
+        this(name, sequence, 1, -1);\r
     }\r
 \r
     /**\r
@@ -114,6 +147,14 @@ public class Sequence implements SequenceI
         sequenceFeatures = v;\r
     }\r
 \r
+    public void addSequenceFeature(SequenceFeature sf)\r
+    {\r
+      if(sequenceFeatures==null)\r
+        sequenceFeatures = new Vector();\r
+\r
+      sequenceFeatures.addElement(sf);\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -124,14 +165,22 @@ public class Sequence implements SequenceI
         return sequenceFeatures;\r
     }\r
 \r
+    public void addPDBId(PDBEntry entry)\r
+    {\r
+      if(pdbIds == null)\r
+        pdbIds = new Vector();\r
+\r
+      pdbIds.addElement(entry);\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
      * @param id DOCUMENT ME!\r
      */\r
-    public void setPDBId(String id)\r
+    public void setPDBId(Vector id)\r
     {\r
-        pdbId = id;\r
+        pdbIds = id;\r
     }\r
 \r
     /**\r
@@ -139,9 +188,9 @@ public class Sequence implements SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getPDBId()\r
+    public Vector getPDBId()\r
     {\r
-        return pdbId;\r
+        return pdbIds;\r
     }\r
 \r
     /**\r
@@ -149,17 +198,15 @@ public class Sequence implements SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getDisplayId()\r
+    public String getDisplayId(boolean jvsuffix)\r
     {\r
-        return displayId;\r
-    }\r
+      StringBuffer result = new StringBuffer(name);\r
+      if (jvsuffix)\r
+      {\r
+        result.append("/" + start + "-" + end);\r
+      }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void setDisplayId()\r
-    {\r
-        displayId = name + "/" + start + "-" + end;\r
+      return result.toString();\r
     }\r
 \r
     /**\r
@@ -169,8 +216,8 @@ public class Sequence implements SequenceI
      */\r
     public void setName(String name)\r
     {\r
-        this.name = name;\r
-        setDisplayId();\r
+      this.name = name;\r
+      this.parseId();\r
     }\r
 \r
     /**\r
@@ -180,7 +227,7 @@ public class Sequence implements SequenceI
      */\r
     public String getName()\r
     {\r
-        return this.name;\r
+       return this.name;\r
     }\r
 \r
     /**\r
@@ -191,7 +238,6 @@ public class Sequence implements SequenceI
     public void setStart(int start)\r
     {\r
         this.start = start;\r
-        setDisplayId();\r
     }\r
 \r
     /**\r
@@ -212,7 +258,6 @@ public class Sequence implements SequenceI
     public void setEnd(int end)\r
     {\r
         this.end = end;\r
-        setDisplayId();\r
     }\r
 \r
     /**\r
@@ -243,6 +288,7 @@ public class Sequence implements SequenceI
     public void setSequence(String seq)\r
     {\r
         this.sequence = seq;\r
+        checkValidRange();\r
     }\r
 \r
     /**\r
@@ -333,9 +379,7 @@ public class Sequence implements SequenceI
 \r
         while ((i < sequence.length()) && (j <= end) && (j <= pos))\r
         {\r
-            char c = sequence.charAt(i);\r
-\r
-            if (!jalview.util.Comparison.isGap((c)))\r
+            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))\r
             {\r
                 j++;\r
             }\r
@@ -368,9 +412,7 @@ public class Sequence implements SequenceI
 \r
         while ((j < i) && (j < sequence.length()))\r
         {\r
-            char c = sequence.charAt(j);\r
-\r
-            if (!jalview.util.Comparison.isGap((c)))\r
+            if (!jalview.util.Comparison.isGap((sequence.charAt(j))))\r
             {\r
                 pos++;\r
             }\r
@@ -503,4 +545,42 @@ public class Sequence implements SequenceI
     {\r
         return color;\r
     }\r
+\r
+    public String getVamsasId()\r
+    {\r
+      return vamsasId;\r
+    }\r
+\r
+    public void setVamsasId(String id)\r
+    {\r
+      vamsasId = id;\r
+    }\r
+\r
+    public void setDBRef(Vector dbref)\r
+    {\r
+      dbrefs = dbref;\r
+    }\r
+    public Vector getDBRef()\r
+    {\r
+      return dbrefs;\r
+    }\r
+\r
+    public void addDBRef(DBRefEntry entry)\r
+    {\r
+      if(dbrefs == null)\r
+        dbrefs = new Vector();\r
+\r
+      dbrefs.addElement(entry);\r
+    }\r
+\r
+    public void setDatasetSequence(SequenceI seq)\r
+    {\r
+      datasetSequence = seq;\r
+    }\r
+\r
+    public SequenceI getDatasetSequence()\r
+    {\r
+      return datasetSequence;\r
+    }\r
+\r
 }\r