Todo notes for feature issue: 0011711

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 34c1cd9..80dfda5 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,10 +18,6 @@
 */\r
 package jalview.datamodel;\r
 \r
-import MCview.*;\r
-\r
-import jalview.analysis.*;\r
-\r
 import java.awt.*;\r
 \r
 import java.util.*;\r
@@ -35,17 +31,20 @@ 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
+    public Vector sequenceFeatures;\r
 \r
     /**\r
      * Creates a new Sequence object.\r
@@ -57,12 +56,55 @@ public class Sequence implements SequenceI
      */\r
     public Sequence(String name, String sequence, int start, int end)\r
     {\r
-        this.name = name;\r
-        this.sequence = sequence;\r
-        this.start = start;\r
-        this.end = end;\r
+      this.name = name;\r
+      this.sequence = sequence;\r
+      this.start = start;\r
+      this.end = end;\r
+\r
+      parseId();\r
+\r
+      checkValidRange();\r
+    }\r
+\r
+    static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
+                        "[/][0-9]{1,}[-][0-9]{1,}$");\r
+    static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
+                        "[0-9]{1,}$");\r
+\r
+    void parseId()\r
+    {\r
+        // Does sequence have the /start-end signiature?\r
+         if(limitrx.search(name))\r
+         {\r
+            name = limitrx.left();\r
+            endrx.search(limitrx.stringMatched());\r
+            setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));\r
+            setEnd(   Integer.parseInt( endrx.stringMatched() ));\r
+         }\r
+    }\r
+\r
+    void checkValidRange()\r
+    {\r
+      if (end < 1)\r
+      {\r
+        int endRes = 0;\r
+        char ch;\r
+        for (int j = 0; j < sequence.length(); j++)\r
+        {\r
+          ch = sequence.charAt(j);\r
+          if (!jalview.util.Comparison.isGap( (ch)))\r
+          {\r
+            endRes++;\r
+          }\r
+        }\r
+        if (endRes > 0)\r
+        {\r
+          endRes += start - 1;\r
+        }\r
+\r
+        this.end = endRes;\r
+      }\r
 \r
-        setDisplayId();\r
     }\r
 \r
     /**\r
@@ -73,7 +115,7 @@ 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
@@ -96,6 +138,14 @@ 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
@@ -106,14 +156,22 @@ 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
@@ -121,9 +179,9 @@ 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
@@ -131,17 +189,15 @@ 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
@@ -151,8 +207,8 @@ 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
@@ -162,7 +218,7 @@ public class Sequence implements SequenceI
      */\r
     public String getName()\r
     {\r
-        return this.name;\r
+       return this.name;\r
     }\r
 \r
     /**\r
@@ -173,7 +229,6 @@ public class Sequence implements SequenceI
     public void setStart(int start)\r
     {\r
         this.start = start;\r
-        setDisplayId();\r
     }\r
 \r
     /**\r
@@ -194,7 +249,6 @@ public class Sequence implements SequenceI
     public void setEnd(int end)\r
     {\r
         this.end = end;\r
-        setDisplayId();\r
     }\r
 \r
     /**\r
@@ -225,6 +279,7 @@ public class Sequence implements SequenceI
     public void setSequence(String seq)\r
     {\r
         this.sequence = seq;\r
+        checkValidRange();\r
     }\r
 \r
     /**\r
@@ -315,9 +370,7 @@ 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
@@ -350,9 +403,7 @@ 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
@@ -485,4 +536,42 @@ 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