Id parsing moved to Sequence

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c24dc02..8e821a2 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,11 +33,11 @@ public class Sequence implements SequenceI
 {\r
     SequenceI datasetSequence;\r
     String name;\r
+    String shortName;\r
     String sequence;\r
     String description;\r
     int start;\r
     int end;\r
-    String displayId;\r
     Color color = Color.white;\r
     String pdbId;\r
     String vamsasId;\r
@@ -58,6 +58,8 @@ public class Sequence implements SequenceI
     public Sequence(String name, String sequence, int start, int end)\r
     {\r
       this.name = name;\r
+      parseId();\r
+\r
       this.sequence = sequence;\r
       this.start = start;\r
       this.end = end;\r
@@ -65,6 +67,57 @@ public class Sequence implements SequenceI
       checkValidRange();\r
     }\r
 \r
+    void parseId()\r
+    {\r
+        // Read in any DB refs first\r
+         StringTokenizer st = new StringTokenizer(name, "|");\r
+         if(st.countTokens()<1)\r
+         {\r
+           shortName = name;\r
+           return;\r
+         }\r
+\r
+         while (st.countTokens() > 1)\r
+         {\r
+           String a = st.nextToken();\r
+           String b = st.nextToken();\r
+           addDBRef(new DBRefEntry(a, "0", b));\r
+         }\r
+\r
+         if (st.hasMoreTokens())\r
+           shortName = st.nextToken();\r
+\r
+         // Remove /start-end from sequence\r
+         if (shortName.indexOf("/") > 0)\r
+         {\r
+           st = new StringTokenizer(shortName, "/");\r
+           String limits = null;\r
+           try\r
+           {\r
+             if (st.countTokens() == 2)\r
+             {\r
+               shortName = st.nextToken();\r
+\r
+               limits = st.nextToken();\r
+\r
+               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
+           }\r
+           catch (NumberFormatException ex)\r
+           {\r
+             // Problem parsing sequence limits. Just add it back to the\r
+             // Id so we dont lose this info\r
+             shortName += "/" + limits;\r
+           }\r
+         }\r
+    }\r
+\r
     void checkValidRange()\r
     {\r
       if (end < 1)\r
@@ -97,7 +150,7 @@ 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
@@ -175,7 +228,7 @@ public class Sequence implements SequenceI
         }\r
       }\r
 \r
-      result.append(name);\r
+      result.append(shortName);\r
 \r
       if (jvsuffix)\r
       {\r
@@ -192,7 +245,8 @@ public class Sequence implements SequenceI
      */\r
     public void setName(String name)\r
     {\r
-        this.name = name;\r
+      this.name = name;\r
+      this.parseId();\r
     }\r
 \r
     /**\r
@@ -202,7 +256,7 @@ public class Sequence implements SequenceI
      */\r
     public String getName()\r
     {\r
-        return this.name;\r
+       return this.name;\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1377de2..6055230 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -795,7 +795,7 @@ public class PopupMenu extends JPopupMenu
      */\r
     void sequenceName_actionPerformed(ActionEvent e)\r
     {\r
-        String id = sequence.getName();\r
+        String id = sequence.getDisplayId(false, false);\r
         String s = (String) JOptionPane.showInternalInputDialog(ap,\r
                 "Edit sequence name",\r
                 "Edit sequence name (" + sequence.getName() + ")",\r

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 842f2fc..1ec2805 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -171,58 +171,20 @@ public abstract class AlignFile extends FileParse
      */\r
     Sequence parseId(String id)\r
     {\r
+      Sequence seq = null;\r
       id = id.trim();\r
-      Sequence seq = new Sequence("","");\r
       int space = id.indexOf(" ");\r
       if(space>-1)\r
       {\r
+        seq = new Sequence(id.substring(0, space),"");\r
         seq.setDescription(id.substring(space+1));\r
-        id = id.substring(0, space);\r
       }\r
-\r
-      // Read in any DB refs first\r
-      StringTokenizer st;\r
-      st = new StringTokenizer(id, "|");\r
-\r
-      while (st.countTokens()>1)\r
+      else\r
       {\r
-        String a = st.nextToken();\r
-        String b = st.nextToken();\r
-        seq.addDBRef( new DBRefEntry( a, "0", b));\r
+        seq = new Sequence(id, "");\r
       }\r
 \r
-      if(st.hasMoreTokens())\r
-        id = st.nextToken();\r
-\r
-\r
-      // Remove /start-end from sequence\r
-      if (id.indexOf("/") > 0)\r
-      {\r
-        st = new StringTokenizer(id, "/");\r
-        String limits=null;\r
-        try{\r
-          if (st.countTokens() == 2)\r
-          {\r
-            id = st.nextToken();\r
-\r
-            limits = st.nextToken();\r
 \r
-            st = new StringTokenizer(limits, "-");\r
-\r
-            if (st.countTokens() == 2)\r
-            {\r
-              seq.setStart(Integer.valueOf(st.nextToken()).intValue());\r
-              seq.setEnd(Integer.valueOf(st.nextToken()).intValue());\r
-            }\r
-          }\r
-        }catch(NumberFormatException ex)\r
-        {\r
-            // Problem parsing sequence limits. Just add it back to the\r
-          // Id so we dont lose this info\r
-          id += "/" + limits;\r
-        }\r
-      }\r
-      seq.setName(id);\r
       return seq;\r
     }\r
 \r
@@ -235,25 +197,7 @@ public abstract class AlignFile extends FileParse
      */\r
     String printId(SequenceI seq)\r
     {\r
-      StringBuffer result = new StringBuffer();\r
-      if(dbPrefix && seq.getDBRef()!=null)\r
-      {\r
-        Vector dbrefs = seq.getDBRef();\r
-        for(int i=0; i<dbrefs.size(); i++)\r
-        {\r
-          DBRefEntry entry = (DBRefEntry)dbrefs.elementAt(i);\r
-          result.append(entry.getSource()+"|"+entry.getAccessionId()+"|");\r
-        }\r
-      }\r
-\r
-      result.append(seq.getName());\r
-\r
-      if(jvSuffix)\r
-      {\r
-        result.append("/"+seq.getStart()+"-"+seq.getEnd());\r
-      }\r
-\r
-      return result.toString();\r
+      return seq.getDisplayId(dbPrefix, jvSuffix);\r
     }\r
 \r
 }\r