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 df7345a..dce2e51 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,7 +33,6 @@ public class Sequence implements SequenceI
 {\r
     SequenceI datasetSequence;\r
     String name;\r
-    String shortName;\r
     String sequence;\r
     String description;\r
     int start;\r
@@ -69,57 +68,26 @@ public class Sequence implements SequenceI
 \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
+         if (name.indexOf("/") > 0)\r
          {\r
-           st = new StringTokenizer(shortName, "/");\r
-           String limits = null;\r
+           String limits = name.substring(name.lastIndexOf("/")+1);\r
            try\r
            {\r
-             if (st.countTokens() == 2)\r
-             {\r
-\r
-               shortName = st.nextToken();\r
-\r
-               limits = st.nextToken();\r
-\r
-               st = new StringTokenizer(limits, "-");\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
 \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
-             // 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
     }\r
@@ -230,20 +198,9 @@ public class Sequence implements SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getDisplayId(boolean dbref, boolean jvsuffix)\r
+    public String getDisplayId(boolean jvsuffix)\r
     {\r
-      StringBuffer result = new StringBuffer();\r
-      if (dbref && dbrefs != null)\r
-      {\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(shortName);\r
-\r
+      StringBuffer result = new StringBuffer(name);\r
       if (jvsuffix)\r
       {\r
         result.append("/" + start + "-" + end);\r
@@ -455,9 +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
@@ -628,9 +583,4 @@ public class Sequence implements SequenceI
       return datasetSequence;\r
     }\r
 \r
-    public String getShortName()\r
-    {\r
-      return shortName;\r
-    }\r
-\r
 }\r