From 558597672640984d936ea22409a674293192a09c Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 30 Jan 2007 15:35:01 +0000 Subject: [PATCH] Any character non aa or nucleotide is a space --- src/jalview/analysis/AAFrequency.java | 4 ++-- src/jalview/analysis/Conservation.java | 2 +- src/jalview/io/AlignFile.java | 13 ------------- src/jalview/io/BLCFile.java | 7 ------- src/jalview/io/ClustalFile.java | 8 -------- src/jalview/io/FastaFile.java | 15 --------------- src/jalview/io/JPredFile.java | 7 ------- src/jalview/io/MSFfile.java | 8 -------- src/jalview/io/PIRFile.java | 6 ------ src/jalview/io/PfamFile.java | 9 +-------- src/jalview/schemes/ResidueProperties.java | 14 +++++--------- 11 files changed, 9 insertions(+), 84 deletions(-) diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 3d91080..4a68f81 100755 --- 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; float percentage; - int[] values = new int[132]; + int[] values = new int[255]; char [] seq; @@ -83,7 +83,7 @@ public static final void calculate(SequenceI[] sequences, maxCount = 0; maxResidue = ""; nongap = 0; - values = new int[132]; + values = new int[255]; for (j = 0; j < jSize; j++) { diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 99c6e89..b1cc250 100755 --- 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 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -121,20 +121,7 @@ public abstract class AlignFile extends FileParse } } - // Checks whether sequence is valid aa characters - protected boolean isValidProteinSequence(char [] sequence) - { - for (int i = 0; i < sequence.length; i++) - if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1) - { - invalidCharacter = sequence[i]; - return false; - } - - return true; - } - char invalidCharacter; /** * This method must be implemented to parse the contents of the file. diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 04867a2..624e134 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -125,13 +125,6 @@ public class BLCFile extends AlignFile { Sequence newSeq = (Sequence) seqs.elementAt(i); - if (!isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - +" : "+ newSeq.getName() - +" : "+invalidCharacter); - } - newSeq.setSequence(seqstrings[i].toString()); } diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index b43e3ea..90c22f9 100755 --- 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()); newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() ); - if (!isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - + " : " + newSeq.getName() - + " : " + invalidCharacter); - } - - seqs.addElement(newSeq); } else diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index fe5e02f..684f867 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -106,13 +106,6 @@ public class FastaFile extends AlignFile if (!firstLine) { - if (!annotation && !isValidProteinSequence(sb.toString().toCharArray())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - +" : "+seq.getName() - +" : "+invalidCharacter); - } - seq.setSequence(sb.toString()); if (!annotation) @@ -153,14 +146,6 @@ public class FastaFile extends AlignFile else if (!firstLine) { - - if (!isValidProteinSequence(sb.toString().toCharArray())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - +" : "+seq.getName() - +" : "+invalidCharacter); - } - seq.setSequence(sb.toString()); seqs.addElement(seq); } diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index c431cc4..3f308be 100755 --- 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 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -145,14 +145,6 @@ public class MSFfile extends AlignFile // Replace ~ with a sensible gap character seq = seq.replace('~', '-'); - if (!isValidProteinSequence(seq.toCharArray())) - { - throw new IOException(AppletFormatAdapter. - INVALID_CHARACTERS - + " : " + head - + " : " + invalidCharacter); - } - Sequence newSeq = parseId(head); diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 8b05171..a33e118 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -83,12 +83,6 @@ public class PIRFile { sequence.setLength(sequence.length() - 1); newSeq.setSequence(sequence.toString()); - if (!isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - +" : "+ newSeq.getName() - +" : "+invalidCharacter); - } seqs.addElement(newSeq); diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 7cb381d..d84dc70 100755 --- 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()); newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString()); seqs.addElement(newSeq); - - if (!isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - +" : "+ newSeq.getName() - +" : "+invalidCharacter); - } - } + } else { System.err.println("PFAM File reader: Can't find sequence for " + diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 5604ca3..17f6a41 100755 --- 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; -- 1.7.10.2