0000090: MEGA7 - MantisBT

(0000028)
gstecher (administrator)
1969-12-31 17:33

Has this bug been fixed? I can\'t seem to reproduce the problem.

(0000030)
Nikita Vikhrev (reporter)
1969-12-31 17:33

This happens only when reading a long sequence. The problem is in TFormatConvertToMega.convert_from_fasta because of a memory allocation deficiency of Delphi. Here is my version of the fix.

//==================================================================
procedure TFormatConvertToMega.convert_from_fasta;
//==================================================================
Var
  NextPos : integer;
  NewStr, AStr, CurKey : String;
  i,CurSize, SeqStart : integer;

  procedure SetSeqDataHash;
  var
    CurSeq: string;
    CurPos,j,k: integer;
  begin
    if (CurKey = \'\') or (CurSize = 0) then
      exit;
    SetLength(CurSeq, CurSize);
    CurPos := 0;
    for j := SeqStart to BStrList.Count-1 do
    begin
      for k := 1 to Length(BStrList[j]) do
        CurSeq[k+CurPos] := BStrList[j][k];
      inc(CurPos, Length(BStrList[j]));
    end;
    SeqDataHash.Values[CurKey] := CurSeq;
  end;

begin
  CurKey := \'\';
  CurSize := 0;
  for i := 0 to AStrList.Count-1 do
  begin
    AStr := Trim(AStrList[i]);
    if Astr <> \'\' then
    begin
      if AStr[1] = \'>\' then // Retrieves Name of Sequence
      begin
        SetSeqDataHash;

        // Check for >P1; type formatting and delete to ;
        if Pos(\';\', AStr) > 0 then
        begin
          // We have a semicolon but is it
        end;
        NextPos := Pos(\' \', AStr);
        Delete (AStr, NextPos, (Length(AStr) - NextPos + 1));
        Delete (Astr, 1, 1);
        CurKey := AStr;
        NewStr := \'#\';
        BStrList.Add( NewStr+Astr );

        CurSize := 0;
        SeqStart := BStrList.Count;
      end
      else
      begin // Retrieves Sequence Data
        BStrList.Add( Astr );
        CurSize := CurSize +Length(Astr);
{
        if (SeqDataHash.IndexOfName(CurKey) = -1) then
          SeqDataHash.Values[CurKey] := Astr
        else
          SeqDataHash.Values[CurKey] := SeqDataHash.Values[CurKey] + Astr;
}
      end;
    end;
  end;
  SetSeqDataHash;
end;

edited on: 10-14 20:00

(0000034)
gstecher (administrator)
1969-12-31 17:33

I fixed this bug already and noticed the same memory problem. Thanks for the suggestion.

Issue History
Date Modified	Username	Field	Change
2016-03-08 20:01	guest	New Issue

Notes
(0000028) gstecher (administrator) 1969-12-31 17:33	Has this bug been fixed? I can\'t seem to reproduce the problem.

(0000030) Nikita Vikhrev (reporter) 1969-12-31 17:33	This happens only when reading a long sequence. The problem is in TFormatConvertToMega.convert_from_fasta because of a memory allocation deficiency of Delphi. Here is my version of the fix. //================================================================== procedure TFormatConvertToMega.convert_from_fasta; //================================================================== Var NextPos : integer; NewStr, AStr, CurKey : String; i,CurSize, SeqStart : integer; procedure SetSeqDataHash; var CurSeq: string; CurPos,j,k: integer; begin if (CurKey = \'\') or (CurSize = 0) then exit; SetLength(CurSeq, CurSize); CurPos := 0; for j := SeqStart to BStrList.Count-1 do begin for k := 1 to Length(BStrList[j]) do CurSeq[k+CurPos] := BStrList[j][k]; inc(CurPos, Length(BStrList[j])); end; SeqDataHash.Values[CurKey] := CurSeq; end; begin CurKey := \'\'; CurSize := 0; for i := 0 to AStrList.Count-1 do begin AStr := Trim(AStrList[i]); if Astr <> \'\' then begin if AStr[1] = \'>\' then // Retrieves Name of Sequence begin SetSeqDataHash; // Check for >P1; type formatting and delete to ; if Pos(\';\', AStr) > 0 then begin // We have a semicolon but is it end; NextPos := Pos(\' \', AStr); Delete (AStr, NextPos, (Length(AStr) - NextPos + 1)); Delete (Astr, 1, 1); CurKey := AStr; NewStr := \'#\'; BStrList.Add( NewStr+Astr ); CurSize := 0; SeqStart := BStrList.Count; end else begin // Retrieves Sequence Data BStrList.Add( Astr ); CurSize := CurSize +Length(Astr); { if (SeqDataHash.IndexOfName(CurKey) = -1) then SeqDataHash.Values[CurKey] := Astr else SeqDataHash.Values[CurKey] := SeqDataHash.Values[CurKey] + Astr; } end; end; end; SetSeqDataHash; end; edited on: 10-14 20:00

(0000034) gstecher (administrator) 1969-12-31 17:33	I fixed this bug already and noticed the same memory problem. Thanks for the suggestion.

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