X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;fp=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=c2a6a9cdd1b294dade726b95237af449d429f182;hb=daf64249356f9a156423bd56ab0336d9da2e5325;hp=9cc7b4a35ff054f5a6a3a48728216f0eaa197105;hpb=4f9c22055c3cdbfc9c4375dcb74755a89ec32b62;p=jalview.git diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java index 9cc7b4a..c2a6a9c 100644 --- a/src/jalview/datamodel/SeqCigar.java +++ b/src/jalview/datamodel/SeqCigar.java @@ -113,8 +113,9 @@ public class SeqCigar extends CigarSimple @Override public String getSequenceString(char GapChar) { - return (length == 0) ? "" : (String) getSequenceAndDeletions( - refseq.getSequenceAsString(start, end), GapChar)[0]; + return (length == 0) ? "" + : (String) getSequenceAndDeletions( + refseq.getSequenceAsString(start, end), GapChar)[0]; } /** @@ -134,14 +135,13 @@ public class SeqCigar extends CigarSimple refseq.getSequenceAsString(start, end), GapChar); if (edit_result == null) { - throw new Error( - MessageManager - .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions")); + throw new Error(MessageManager.getString( + "error.implementation_error_unexpected_null_from_get_sequence_and_deletions")); } int bounds[] = (int[]) edit_result[1]; seq = new Sequence(refseq.getName(), (String) edit_result[0], - refseq.getStart() + start + bounds[0], refseq.getStart() - + start + ((bounds[2] == 0) ? -1 : bounds[2])); + refseq.getStart() + start + bounds[0], refseq.getStart() + start + + ((bounds[2] == 0) ? -1 : bounds[2])); seq.setDescription(refseq.getDescription()); int sstart = seq.getStart(), send = seq.getEnd(); // seq.checkValidRange(); probably not needed @@ -184,15 +184,14 @@ public class SeqCigar extends CigarSimple boolean hasgaps = false; if (seq == null) { - throw new Error( - MessageManager - .getString("error.implementation_error_set_seq_null")); + throw new Error(MessageManager + .getString("error.implementation_error_set_seq_null")); } if (_s < 0) { - throw new Error(MessageManager.formatMessage( - "error.implementation_error_s", new String[] { Integer - .valueOf(_s).toString() })); + throw new Error(MessageManager + .formatMessage("error.implementation_error_s", new String[] + { Integer.valueOf(_s).toString() })); } String seq_string = seq.getSequenceAsString(); if (_e == 0 || _e < _s || _e > seq_string.length()) @@ -258,9 +257,8 @@ public class SeqCigar extends CigarSimple // Check offsets if (end > ds.getLength()) { - throw new Error( - MessageManager - .getString("error.implementation_error_seqcigar_possible")); + throw new Error(MessageManager + .getString("error.implementation_error_seqcigar_possible")); // end = ds.getLength(); } @@ -289,9 +287,8 @@ public class SeqCigar extends CigarSimple } if (operation.length != range.length) { - throw new Error( - MessageManager - .getString("error.implementation_bug_cigar_operation_list_range_list")); + throw new Error(MessageManager.getString( + "error.implementation_bug_cigar_operation_list_range_list")); } if (operation != null) @@ -301,9 +298,8 @@ public class SeqCigar extends CigarSimple if (_setSeq(seq, false, 0, 0)) { - throw new Error( - MessageManager - .getString("error.not_yet_implemented_cigar_object_from_cigar_string")); + throw new Error(MessageManager.getString( + "error.not_yet_implemented_cigar_object_from_cigar_string")); } for (int i = this.length, j = 0; j < operation.length; i++, j++) { @@ -311,8 +307,8 @@ public class SeqCigar extends CigarSimple if (op != M && op != I && op != D) { throw new Error(MessageManager.formatMessage( - "error.implementation_bug_cigar_operation", new String[] { - Integer.valueOf(j).toString(), + "error.implementation_bug_cigar_operation", new String[] + { Integer.valueOf(j).toString(), Integer.valueOf(op).toString(), Integer.valueOf(M).toString(), Integer.valueOf(I).toString(), @@ -330,9 +326,8 @@ public class SeqCigar extends CigarSimple this.length = 0; if (_setSeq(seq, false, 0, 0)) { - throw new Error( - MessageManager - .getString("error.not_yet_implemented_cigar_object_from_cigar_string")); + throw new Error(MessageManager.getString( + "error.not_yet_implemented_cigar_object_from_cigar_string")); } } } @@ -378,8 +373,9 @@ public class SeqCigar extends CigarSimple while (p <= endpos) { - boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq - .getCharAt(p)) : true; + boolean isGap = (p < res) + ? jalview.util.Comparison.isGap(seq.getCharAt(p)) + : true; if ((startpos <= p) && (p <= endpos)) { if (isGap) @@ -439,9 +435,8 @@ public class SeqCigar extends CigarSimple super(); if (seq == null) { - throw new Error( - MessageManager - .getString("error.implementation_error_for_new_cigar")); + throw new Error(MessageManager + .getString("error.implementation_error_for_new_cigar")); } _setSeq(seq, false, 0, 0); // there is still work to do @@ -463,9 +458,8 @@ public class SeqCigar extends CigarSimple super(); if (seq == null) { - throw new Error( - MessageManager - .getString("error.implementation_error_for_new_cigar")); + throw new Error(MessageManager + .getString("error.implementation_error_for_new_cigar")); } _setSeq(seq, false, start, end + 1); // there is still work to do @@ -513,8 +507,8 @@ public class SeqCigar extends CigarSimple Object[] gs_regions = new Object[alseqs.length]; for (int i = 0; i < alseqs.length; i++) { - alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString( - alseqs[i].start, alseqs[i].end); + alseqs_string[i] = alseqs[i].getRefSeq() + .getSequenceAsString(alseqs[i].start, alseqs[i].end); gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. // endcol}, hidden regions {{start, end, col}}) @@ -522,7 +516,8 @@ public class SeqCigar extends CigarSimple { throw new Error(MessageManager.formatMessage( "error.implementation_error_cigar_seq_no_operations", - new String[] { Integer.valueOf(i).toString() })); + new String[] + { Integer.valueOf(i).toString() })); } g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the // visible @@ -587,8 +582,9 @@ public class SeqCigar extends CigarSimple int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]); SequenceI ref = alseqs[i].getRefSeq(); seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(), - ref.getStart() + alseqs[i].start + bounds[0], ref.getStart() - + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2])); + ref.getStart() + alseqs[i].start + bounds[0], + ref.getStart() + alseqs[i].start + + (bounds[2] == 0 ? -1 : bounds[2])); seqs[i].setDatasetSequence(ref); seqs[i].setDescription(ref.getDescription()); } @@ -598,8 +594,8 @@ public class SeqCigar extends CigarSimple { // int start=shifts.shift(segments[i]-1)+1; // int end=shifts.shift(segments[i]+segments[i+1]-1)-1; - hidden.hideColumns(segments[i + 1], segments[i + 1] - + segments[i + 2] - 1); + hidden.hideColumns(segments[i + 1], + segments[i + 1] + segments[i + 2] - 1); } } return seqs;