Any character non aa or nucleotide is a space

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 3d91080..4a68f81 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -73,7 +73,7 @@ public static final void calculate(SequenceI[] sequences,
   char c;\r
   float percentage;\r
 \r
-  int[] values = new int[132];\r
+  int[] values = new int[255];\r
 \r
   char [] seq;\r
 \r
@@ -83,7 +83,7 @@ public static final void calculate(SequenceI[] sequences,
     maxCount = 0;\r
     maxResidue = "";\r
     nongap = 0;\r
-    values = new int[132];\r
+    values = new int[255];\r
 \r
     for (j = 0; j < jSize; j++)\r
     {\r

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 99c6e89..b1cc250 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -157,7 +157,7 @@ public class Conservation
 
       for (int i = start; i <= end; i++)
         {
-            values = new int[132];
+            values = new int[255];
 
             for (j = 0; j < jSize; j++)
             {

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a800f06..3fa4ac2 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -121,20 +121,7 @@ public abstract class AlignFile extends FileParse
         }\r
     }\r
 \r
-    // Checks whether sequence is valid aa characters\r
-    protected boolean isValidProteinSequence(char [] sequence)\r
-    {\r
-        for (int i = 0; i < sequence.length; i++)\r
-            if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)\r
-            {\r
-                invalidCharacter = sequence[i];\r
-                return false;\r
-            }\r
-\r
-        return true;\r
-    }\r
 \r
-    char invalidCharacter;\r
 \r
     /**\r
      * This method must be implemented to parse the contents of the file.\r

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 04867a2..624e134 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -125,13 +125,6 @@ public class BLCFile extends AlignFile
             {\r
               Sequence newSeq = (Sequence) seqs.elementAt(i);\r
 \r
-              if (!isValidProteinSequence(newSeq.getSequence()))\r
-              {\r
-                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                               +" : "+ newSeq.getName()\r
-                               +" : "+invalidCharacter);\r
-              }\r
-\r
               newSeq.setSequence(seqstrings[i].toString());\r
             }\r
 \r

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index b43e3ea..90c22f9 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -126,14 +126,6 @@ public class ClustalFile
           Sequence newSeq = parseId(headers.elementAt(i).toString());\r
           newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );\r
 \r
-          if (!isValidProteinSequence(newSeq.getSequence()))\r
-          {\r
-              throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                    + " : " + newSeq.getName()\r
-                                    + " : " + invalidCharacter);\r
-          }\r
-\r
-\r
           seqs.addElement(newSeq);\r
         }\r
         else\r

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index fe5e02f..684f867 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -106,13 +106,6 @@ public class FastaFile extends AlignFile
 \r
                     if (!firstLine)\r
                     {\r
-                      if (!annotation && !isValidProteinSequence(sb.toString().toCharArray()))\r
-                      {\r
-                        throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                              +" : "+seq.getName()\r
-                                              +" : "+invalidCharacter);\r
-                      }\r
-\r
                        seq.setSequence(sb.toString());\r
 \r
                        if (!annotation)\r
@@ -153,14 +146,6 @@ public class FastaFile extends AlignFile
 \r
         else if (!firstLine)\r
         {\r
-\r
-            if (!isValidProteinSequence(sb.toString().toCharArray()))\r
-            {\r
-                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                      +" : "+seq.getName()\r
-                                      +" : "+invalidCharacter);\r
-            }\r
-\r
             seq.setSequence(sb.toString());\r
             seqs.addElement(seq);\r
         }\r

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index c431cc4..3f308be 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -270,13 +270,6 @@ public class JPredFile extends AlignFile
                     seq_entries.elementAt(i).toString(), 1,
                     seq_entries.elementAt(i).toString().length());
 
-            if (!Symscores.containsKey(ids.elementAt(i)) &&
-                    !isValidProteinSequence(newSeq.getSequence()))
-            {
-                throw new IOException("JPredConcise: "
-                                      +AppletFormatAdapter.INVALID_CHARACTERS +" : "
-                                      +ids.elementAt(i).toString() + ")");
-            }
 
             if (maxLength != seq_entries.elementAt(i).toString().length())
             {

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 61b3528..f21a106 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -145,14 +145,6 @@ public class MSFfile extends AlignFile
 \r
                 // Replace ~ with a sensible gap character\r
                 seq = seq.replace('~', '-');\r
-                if (!isValidProteinSequence(seq.toCharArray()))\r
-                {\r
-                    throw new IOException(AppletFormatAdapter.\r
-                                          INVALID_CHARACTERS\r
-                                          + " : " + head\r
-                                          + " : " + invalidCharacter);\r
-                }\r
-\r
 \r
                 Sequence newSeq = parseId(head);\r
 \r

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 8b05171..a33e118 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -83,12 +83,6 @@ public class PIRFile
         {\r
           sequence.setLength(sequence.length() - 1);\r
           newSeq.setSequence(sequence.toString());\r
-          if (!isValidProteinSequence(newSeq.getSequence()))\r
-          {\r
-            throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                  +" : "+ newSeq.getName()\r
-                                  +" : "+invalidCharacter);\r
-          }\r
 \r
           seqs.addElement(newSeq);\r
 \r

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 7cb381d..d84dc70 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -109,14 +109,7 @@ public class PfamFile
         Sequence newSeq = parseId(headers.elementAt(i).toString());\r
         newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());\r
         seqs.addElement(newSeq);\r
-\r
-        if (!isValidProteinSequence(newSeq.getSequence()))\r
-        {\r
-          throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
-                                +" : "+ newSeq.getName()\r
-                                +" : "+invalidCharacter);\r
-        }\r
-      }\r
+     }\r
       else\r
       {\r
         System.err.println("PFAM File reader: Can't find sequence for " +\r

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 5604ca3..17f6a41 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -35,9 +35,9 @@ public class ResidueProperties
 
   static
   {
-    aaIndex = new int[132];
-    for(int i=0; i<132; i++)
-      aaIndex[i] = -1;
+    aaIndex = new int[255];
+    for(int i=0; i<255; i++)
+      aaIndex[i] = 23;
 
     aaIndex['A'] = 0;
     aaIndex['R'] = 1;
@@ -87,16 +87,12 @@ public class ResidueProperties
     aaIndex['z'] = 21;
     aaIndex['x'] = 22;
     aaIndex['u'] = 22;
-    aaIndex['-'] = 23;
-    aaIndex['*'] = 23;
-    aaIndex['.'] = 23;
-    aaIndex[' '] = 23;
   }
 
   static
   {
-    nucleotideIndex = new int[132];
-    for (int i = 0; i < 132; i++)
+    nucleotideIndex = new int[255];
+    for (int i = 0; i < 255; i++)
       nucleotideIndex[i] = -1;
 
     nucleotideIndex['A'] = 0;