From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 4 Nov 2005 10:56:54 +0000 (+0000)
Subject: Id parsing moved to Sequence
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=820ae6f18432291d846be13bb776de9767b7a8ec;p=jalview.git

Id parsing moved to Sequence
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c24dc02..8e821a2 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,11 +33,11 @@ public class Sequence implements SequenceI
 {
     SequenceI datasetSequence;
     String name;
+    String shortName;
     String sequence;
     String description;
     int start;
     int end;
-    String displayId;
     Color color = Color.white;
     String pdbId;
     String vamsasId;
@@ -58,6 +58,8 @@ public class Sequence implements SequenceI
     public Sequence(String name, String sequence, int start, int end)
     {
       this.name = name;
+      parseId();
+
       this.sequence = sequence;
       this.start = start;
       this.end = end;
@@ -65,6 +67,57 @@ public class Sequence implements SequenceI
       checkValidRange();
     }
 
+    void parseId()
+    {
+        // Read in any DB refs first
+         StringTokenizer st = new StringTokenizer(name, "|");
+         if(st.countTokens()<1)
+         {
+           shortName = name;
+           return;
+         }
+
+         while (st.countTokens() > 1)
+         {
+           String a = st.nextToken();
+           String b = st.nextToken();
+           addDBRef(new DBRefEntry(a, "0", b));
+         }
+
+         if (st.hasMoreTokens())
+           shortName = st.nextToken();
+
+         // Remove /start-end from sequence
+         if (shortName.indexOf("/") > 0)
+         {
+           st = new StringTokenizer(shortName, "/");
+           String limits = null;
+           try
+           {
+             if (st.countTokens() == 2)
+             {
+               shortName = st.nextToken();
+
+               limits = st.nextToken();
+
+               st = new StringTokenizer(limits, "-");
+
+               if (st.countTokens() == 2)
+               {
+                 setStart(Integer.valueOf(st.nextToken()).intValue());
+                 setEnd(Integer.valueOf(st.nextToken()).intValue());
+               }
+             }
+           }
+           catch (NumberFormatException ex)
+           {
+             // Problem parsing sequence limits. Just add it back to the
+             // Id so we dont lose this info
+             shortName += "/" + limits;
+           }
+         }
+    }
+
     void checkValidRange()
     {
       if (end < 1)
@@ -97,7 +150,7 @@ public class Sequence implements SequenceI
      */
     public Sequence(String name, String sequence)
     {
-        this(name, sequence, 1, sequence.length());
+        this(name, sequence, 1, -1);
     }
 
     /**
@@ -175,7 +228,7 @@ public class Sequence implements SequenceI
         }
       }
 
-      result.append(name);
+      result.append(shortName);
 
       if (jvsuffix)
       {
@@ -192,7 +245,8 @@ public class Sequence implements SequenceI
      */
     public void setName(String name)
     {
-        this.name = name;
+      this.name = name;
+      this.parseId();
     }
 
     /**
@@ -202,7 +256,7 @@ public class Sequence implements SequenceI
      */
     public String getName()
     {
-        return this.name;
+       return this.name;
     }
 
     /**
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1377de2..6055230 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -795,7 +795,7 @@ public class PopupMenu extends JPopupMenu
      */
     void sequenceName_actionPerformed(ActionEvent e)
     {
-        String id = sequence.getName();
+        String id = sequence.getDisplayId(false, false);
         String s = (String) JOptionPane.showInternalInputDialog(ap,
                 "Edit sequence name",
                 "Edit sequence name (" + sequence.getName() + ")",
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 842f2fc..1ec2805 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -171,58 +171,20 @@ public abstract class AlignFile extends FileParse
      */
     Sequence parseId(String id)
     {
+      Sequence seq = null;
       id = id.trim();
-      Sequence seq = new Sequence("","");
       int space = id.indexOf(" ");
       if(space>-1)
       {
+        seq = new Sequence(id.substring(0, space),"");
         seq.setDescription(id.substring(space+1));
-        id = id.substring(0, space);
       }
-
-      // Read in any DB refs first
-      StringTokenizer st;
-      st = new StringTokenizer(id, "|");
-
-      while (st.countTokens()>1)
+      else
       {
-        String a = st.nextToken();
-        String b = st.nextToken();
-        seq.addDBRef( new DBRefEntry( a, "0", b));
+        seq = new Sequence(id, "");
       }
 
-      if(st.hasMoreTokens())
-        id = st.nextToken();
-
-
-      // Remove /start-end from sequence
-      if (id.indexOf("/") > 0)
-      {
-        st = new StringTokenizer(id, "/");
-        String limits=null;
-        try{
-          if (st.countTokens() == 2)
-          {
-            id = st.nextToken();
-
-            limits = st.nextToken();
 
-            st = new StringTokenizer(limits, "-");
-
-            if (st.countTokens() == 2)
-            {
-              seq.setStart(Integer.valueOf(st.nextToken()).intValue());
-              seq.setEnd(Integer.valueOf(st.nextToken()).intValue());
-            }
-          }
-        }catch(NumberFormatException ex)
-        {
-            // Problem parsing sequence limits. Just add it back to the
-          // Id so we dont lose this info
-          id += "/" + limits;
-        }
-      }
-      seq.setName(id);
       return seq;
     }
 
@@ -235,25 +197,7 @@ public abstract class AlignFile extends FileParse
      */
     String printId(SequenceI seq)
     {
-      StringBuffer result = new StringBuffer();
-      if(dbPrefix && seq.getDBRef()!=null)
-      {
-        Vector dbrefs = seq.getDBRef();
-        for(int i=0; i<dbrefs.size(); i++)
-        {
-          DBRefEntry entry = (DBRefEntry)dbrefs.elementAt(i);
-          result.append(entry.getSource()+"|"+entry.getAccessionId()+"|");
-        }
-      }
-
-      result.append(seq.getName());
-
-      if(jvSuffix)
-      {
-        result.append("/"+seq.getStart()+"-"+seq.getEnd());
-      }
-
-      return result.toString();
+      return seq.getDisplayId(dbPrefix, jvSuffix);
     }
 
 }