/*
FILE:     STable.C
*/
/*
VERSION:  6.302
*/
/*
DATE:     4/26/2005
*/
/*
  Comments and Questions to: sw-help@rcsb.rutgers.edu
*/
/*
COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR
IMPLIED.  RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE
SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER
PROPRIETARY RIGHT.

The user of this software shall indemnify, hold harmless and defend
Rutgers, its governors, trustees, officers, employees, students,
agents and the authors against any and all claims, suits,
losses, liabilities, damages, costs, fees, and expenses including
reasonable attorneys' fees resulting from or arising out of the
use of this software.  This indemnification shall include, but is
not limited to, any and all claims alleging products liability.
*/
/*
               PDB SOFTWARE LICENSE AGREEMENT

BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING 
THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE  
SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS 
BECOMING A PARTY TO THIS AGREEMENT.  IF LICENSEE DOES NOT 
AGREE TO ALL OF THE TERMS OF THIS AGREEMENT
THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE.

1. LICENSE AGREEMENT

This is a license between you ("Licensee") and the Protein Data Bank (PDB) 
at Rutgers, The State University of New Jersey (hereafter referred to 
as "RUTGERS").   The software is owned by RUTGERS and protected by 
copyright laws, and some elements are protected by laws governing 
trademarks, trade dress and trade secrets, and may be protected by 
patent laws. 

2. LICENSE GRANT

RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free 
perpetual license to install, use, modify, prepare derivative works, 
incorporate into other computer software, and distribute in binary 
and source code format, or any derivative work thereof, together with 
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the version originally obtained from RUTGERS.  

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The above license grant is conditioned on the following: (i) you must 
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The SOFTWARE is protected by copyright and other intellectual 
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of the applicable content owner and is protected by applicable law.  
The license granted under this Agreement gives Licensee no rights to such
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7. DISCLAIMER OF WARRANTY.  THE SOFTWARE IS PROVIDED FREE OF 
CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF 
ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT 
IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE 
OR NON-INFRINGING.  THE ENTIRE RISK AS TO THE QUALITY AND 
PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE.  SHOULD THE 
SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT 
LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR.  
THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF 
THIS AGREEMENT.  NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER 
EXCEPT UNDER THIS DISCLAIMER.

8. LIMITATION OF LIABILITY.  TO THE MAXIMUM EXTENT PERMITTED BY
APPLICABLE LAW,  IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY 
INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 
OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, 
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STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL 
OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE
POSSIBILITY THEREOF. 
*/
/* 
  PURPOSE:    Class for string table
*/
#include <iostream.h>
#include <iomanip.h>
#include <strings.h>

#include "ReVarPCifArray.h"
#include "STable.h"

void STable::Rename(const char * label) {

  if (label) {
    _tableName.Clear();
    _tableName.Copy(label);

  }
}

void STable::Clear() {
  _tableName.Clear();
  _numColumns = 0;
  _numRows = 0;
  _colAlloc = 0;
  _theData = NULL;
}

void STable::Delete() {
  int i;

  _columnNames.Clear();
  if (_theData) {
    for (i = 0; i < _numColumns; i++) {
      if (_theData[i])
	{ 
	  _theData[i]->Clear();
	  delete _theData[i];
	}
    }
    delete[] _theData; 
  }
  Clear();
}


int STable::AddColumn(const char * newColumnName) {
  CifString *cName;
  int i;

  if (!newColumnName) return -1; // Column name null

  for (i = 0; i < _numColumns; i++)
    if (!strcmp(_columnNames[i].Text(), newColumnName)) break;

  if (i != _numColumns) return -1; // Column already in table

  cName = new CifString(newColumnName);
  _columnNames.Add(*cName);

  if (_numColumns >= _colAlloc) {
    _colAlloc += ALLOC_INCR;

    // Added 5/21/97
#ifdef OLD_REALLOC
    cerr << "WARNING...OLD_REALLOC SET" << endl;
    _theData = (ReVarCifArray<CifString> **) realloc(_theData, (_colAlloc)*sizeof(ReVarCifArray<CifString> *));
#else
    ReVarCifArray<CifString> ** t = new ReVarCifArray<CifString> *[_colAlloc];
    memset(t, 0, _colAlloc*sizeof(ReVarCifArray<CifString> *));
    t = (ReVarCifArray<CifString> **) memcpy(t, _theData, (_colAlloc-ALLOC_INCR)*sizeof(ReVarCifArray<CifString> *));
    delete[] _theData;
    _theData = t;
#endif

  }

  _theData[_numColumns] = new ReVarCifArray<CifString>;
  _numColumns = _columnNames.Length();
  if (cName!=NULL) delete cName;
  return _numColumns - 1;
}


int STable::RenameColumn(const char * oldColumnName,const char * newColumnName) {
  int i;

  if (!oldColumnName) return -1; // old column name null
  if (!newColumnName) return -1; // new column name null

  for (i = 0; i < _numColumns; i++)
    if (!strcmp(_columnNames[i].Text(), newColumnName)) break;

  if (i != _numColumns) return -1; // Column already in table
  
  for (i = 0; i < _numColumns; i++)
    if (!strcmp(_columnNames[i].Text(), oldColumnName)) break;
  
  if (i == _numColumns) return -1; // Column not found in table

  _columnNames[i].Copy(newColumnName);
  return i;
}


int STable::InsertColumn(const char * newColumnName, int destination) {
  CifString **cName;
  int i;

  if (!newColumnName) return -1; // Column name null

  for (i = 0; i < _numColumns; i++)
    if (!strcmp(_columnNames[i].Text(), newColumnName)) break;

  if (i != _numColumns) return -1; // Column already in table

  if ((destination < 0) || (destination > _numColumns)) return -1;
  if (destination == _numColumns) {
    return AddColumn(newColumnName);
  }

  if (_numColumns >= _colAlloc) {
    _colAlloc += ALLOC_INCR;

    // Added 5/21/97
#ifdef OLD_REALLOC
    cerr << "WARNING...OLD_REALLOC SET" << endl;
    _theData = (ReVarCifArray<CifString> **) realloc(_theData, (_colAlloc)*sizeof(ReVarCifArray<CifString> *));
#else
    ReVarCifArray<CifString> ** t = new ReVarCifArray<CifString> *[_colAlloc];
    memset(t, 0, _colAlloc*sizeof(ReVarCifArray<CifString> *));
    t = (ReVarCifArray<CifString> **) memcpy(t, _theData, (_colAlloc-ALLOC_INCR)*sizeof(ReVarCifArray<CifString> *));
    delete _theData;
    _theData = t;
#endif

  }

  memmove((void *) &_theData[destination+1], (void *) &_theData[destination],
       (_numColumns - destination) * sizeof(ReVarCifArray<CifString> *));

  _theData[destination] = new ReVarCifArray<CifString>;

  cName = new CifString *;
  *cName = new CifString(newColumnName);
  _columnNames.InsertNAt(destination, *cName);
  _numColumns = _columnNames.Length();
  delete *cName;
  delete cName;
  return destination;
}


int STable::InsertColumn(ReVarCifArray<CifString> & theCol,
                          const char * newColumnName, int destination) {
  InsertColumn(newColumnName, destination);
  FillColumn(theCol, destination);
  return destination;
}


int STable::FillColumn(ReVarCifArray<CifString> & theCol, int colIndex) {

 if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS; // out of range
 if (theCol.Length() < 1) return ADD_UPDATE_NULL;
 if (_theData[colIndex]) {
   if (theCol.Length() < _theData[colIndex]->Length()) {
     _theData[colIndex]->DeleteAt(0, theCol.Length());
     _theData[colIndex]->InsertNAt(0, theCol.Data(), theCol.Length());
   } else {
     _theData[colIndex]->DeleteAt(0, _theData[colIndex]->Length());
     _theData[colIndex]->InsertNAt(0, theCol.Data(), theCol.Length());
   }
  } else {
   _theData[colIndex] = new ReVarCifArray<CifString>();
   *_theData[colIndex] = theCol;
 }
 if (_theData[colIndex]->Length() > _numRows)
   _numRows = _theData[colIndex]->Length();

 return NO_TABLE_ERROR;
}


ReVarCifArray<CifString> * STable::GetColumn(int colIndex) {
  ReVarCifArray<CifString> * ret;

  if ((colIndex < 0) || (colIndex >= _numColumns)) return NULL; // out of range

  ret = new ReVarCifArray<CifString>();
  if (_theData[colIndex]) *ret = *_theData[colIndex];
  return ret;
}


int STable::AppendToColumn(ReVarCifArray<CifString> & theCol, CifString & colName) {
  int colIndex = GetColumnIndex(colName.Text());
  return AppendToColumn(theCol, colIndex);
}

int STable::AppendToColumn(ReVarCifArray<CifString> & theCol, int colIndex) {
  if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS;
  if (!theCol.Length()) return ADD_UPDATE_NULL;

  _theData[colIndex]->InsertNAt(_theData[colIndex]->Length(), theCol.Data(), theCol.Length());
  if (_theData[colIndex]->Length() > _numRows)
    _numRows = _theData[colIndex]->Length();
  return NO_TABLE_ERROR;
}

int STable::AddElementToColumn(CifString & theElement, int colIndex) {
  if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS;
  if (!(theElement.Text())) return ADD_UPDATE_NULL;

  _theData[colIndex]->InsertNAt(_theData[colIndex]->Length(), &theElement, 1);
  if (_theData[colIndex]->Length() > _numRows)
    _numRows = _theData[colIndex]->Length();
  return NO_TABLE_ERROR;
}

int STable::ClearColumn(int colIndex) {
  unsigned int i;
  if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS;

  for (i = 0; i < _theData[colIndex]->Length(); i++) {
    (*_theData[colIndex])[i].Clear();
  }
  return NO_TABLE_ERROR;
}

int STable::DeleteColumn(int colIndex) {
  if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS;

  _columnNames.DeleteAt(colIndex, 1);
  _theData[colIndex]->Clear();
  delete _theData[colIndex];
  _theData[colIndex] = NULL;

  memmove((void *) &_theData[colIndex], (void *) &_theData[colIndex+1],
       (_numColumns - colIndex) * sizeof(ReVarCifArray<CifString> *));

  _numColumns = _columnNames.Length();
  return NO_TABLE_ERROR;
}
 
 
ReVarCifArray<CifString> * STable::GetSubColumn(int colIndex, int from,
                                                                  int to) {
  int i;
  CifString temp;

  if ((colIndex < 0) || (colIndex >= _numColumns)) return NULL;
  if (to < from) return NULL;
  if ((from < 0) || (from >= (int)(_theData[colIndex]->Length()))) return NULL;
  if (to >= (int)(_theData[colIndex]->Length())) to = _theData[colIndex]->Length() - 1;

  ReVarCifArray<CifString> * ret = new ReVarCifArray<CifString>;

  for (i = from; i <= to; i++) {
    temp = (*_theData[colIndex])[i];
    ret->Add(temp);
    temp.Clear();
  }

  return ret;
}

ReVarCifArray<CifString> * STable::GetSubColumnByIndex(int colIndex, ReVarPCifArray<int> *rowIndex) {
  int i;
  CifString temp;

  if ((colIndex < 0) || (colIndex >= _numColumns)) return NULL;

  ReVarCifArray<CifString> * ret = new ReVarCifArray<CifString>;

  for (i = 0; i <  (int)(rowIndex->Length()); i++) {
    if ((i < 0) || (i >= (int)(_theData[colIndex]->Length()))) continue;
    temp = (*_theData[colIndex])[(*rowIndex)[i]];
    ret->Add(temp);
    temp.Clear();
  }

  return ret;
}


int STable::AddRow() {
  int i, j, target = _numRows + 1;
  CifString empty("");

  for (i = 0; i < _numColumns; i++) {
    for (j = _theData[i]->Length(); j < target; j++) {
      _theData[i]->Add(empty);
    }
  }
  return _numRows++;
}


int STable::InsertRow(int rowIndex) {
  int i, j;
  CifString empty("");

  if ((((int)(_numRows)) < rowIndex) || (rowIndex < 0)) return ROW_OUT_OF_BOUNDS;
  if (((int)(_numRows)) == rowIndex)
    return AddRow();

  for (i = 0; i < _numColumns; i++) {
    if ((int)(_theData[i]->Length()) >  rowIndex) {
      _theData[i]->InsertNAt(rowIndex, &empty, 1);
    }
    else {
      for (j = _theData[i]->Length(); j <= rowIndex; j++) {
        _theData[i]->Add(empty);
      }
    }
  }
  return _numRows++;
}


int STable::InsertRow(ReVarCifArray<CifString> & theRow, int rowIndex) {
  int ret = InsertRow(rowIndex);
  if (ret < TABLE_WARNING) return ret;
  ret = FillRow(theRow, rowIndex);
  if (ret < TABLE_WARNING) return ret;
  return rowIndex;
}

int STable::FillRow(ReVarCifArray<CifString> & theRow, int rowIndex) {
  int i, j, len;
  CifString empty("");

  if (((int)(_numRows) < rowIndex) || (rowIndex < 0)) return ROW_OUT_OF_BOUNDS;
  len = theRow.Length();
  if (_numColumns < len) len = _numColumns;

  for (i = 0; i < len; i++) {
    if ((int)(_theData[i]->Length()) <= rowIndex) {
      for (j = _theData[i]->Length(); j <= rowIndex; j++) {
        _theData[i]->Add(empty);
      }
    }
    (*_theData[i])[rowIndex] = theRow[i];
  }

  return NO_TABLE_ERROR;
}

int STable::FillRowAt(ReVarCifArray<CifString> & theRow, int rowIndex) {
  int ret = InsertRow(rowIndex);
  if (ret < TABLE_WARNING) return ret;
  ret = FillRow(theRow, rowIndex);
  if (ret < TABLE_WARNING) return ret;
  return _numRows;
}


int STable::AppendToRow(ReVarCifArray<CifString> & theRow, int rowIndex) {
  int i, j, start, finish;
  CifString empty("");

  if (((int)(_numRows) < rowIndex) || (rowIndex < 0)) return ROW_OUT_OF_BOUNDS;
  if (theRow.Length() == 0) return ADD_UPDATE_NULL;

  for (i = _numColumns - 1; i >= 0; i--) {
    if (rowIndex < (int)(_theData[i]->Length())) {
      if (strcmp(empty.Text(), (*_theData[i])[rowIndex].Text()) ) {
        i++; break;
      }   
    } else {
      for (j = _theData[i]->Length(); j <= rowIndex; j++) {
        _theData[i]->Add(empty);
      }
    }
  }

  start = i;
  finish = start + theRow.Length() - 1;
  if (finish >= _numColumns) finish = _numColumns - 1;

  for (i = start; i <= finish; i++) {
    (*_theData[i])[rowIndex] = theRow[i - start];
  }
  return NO_TABLE_ERROR;
}


int STable::AddElementToRow(CifString & theElement, int rowIndex) {
  int i, j;
  CifString empty("");

  if (((int)(_numRows) < rowIndex) || (rowIndex < 0)) return ROW_OUT_OF_BOUNDS;

  for (i = 0; i < _numColumns; i++) {
    if (rowIndex < (int)(_theData[i]->Length())) {
      if (!strcmp(empty.Text(), (*_theData[i])[rowIndex].Text()) ) {
        break;
      }   
    } else break;
  }

  if (i == _numColumns) return ROW_OUT_OF_BOUNDS; // Full row

  if (rowIndex >= (int)(_theData[i]->Length())) {
      for (j = _theData[i]->Length(); j <= rowIndex; j++) {
        _theData[i]->Add(empty);
      }
  }    

  (*_theData[i])[rowIndex] = theElement;
  return NO_TABLE_ERROR;
}


int STable::ClearRow(int rowIndex) {
  int i;

  if ((rowIndex < 0) || (rowIndex >= (int)(_numRows))) return ROW_OUT_OF_BOUNDS;
  for (i = 0; i < _numColumns; i++) {
    if (rowIndex < (int)(_theData[i]->Length())) {
      (*_theData[i])[rowIndex].Clear();
    }
  }
  return NO_TABLE_ERROR;
}


int STable::DeleteRow(int rowIndex) {
  int i;

  if ((rowIndex < 0) || (rowIndex >= (int)(_numRows))) return ROW_OUT_OF_BOUNDS;
  for (i = 0; i < _numColumns; i++) {
    if (rowIndex < (int)(_theData[i]->Length())) {
      _theData[i]->DeleteAt(rowIndex, 1);
    }
  }
  return _numRows--;
}


int STable::UpdateCell(CifString & theElement, int colIndex, int rowIndex) {
  int i;
  CifString empty("");

  if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS;
  if ((rowIndex < 0) || (rowIndex > (int)(_numRows))) return ROW_OUT_OF_BOUNDS;

  if (rowIndex == (int)(_numRows)) AddRow();

  if (rowIndex >= (int)(_theData[colIndex]->Length())) {
    for (i = _theData[colIndex]->Length(); i <= rowIndex; i++) {
      _theData[colIndex]->Add(empty);
    }
  }
  
  (*_theData[colIndex])[rowIndex] = theElement;
  return NO_TABLE_ERROR;
}

void STable::PrintTable() {
  int i, j;

  cout << endl << "Table " << _tableName.Text() <<  "  Columns: " << _numColumns << "  Rows: " << _numRows << endl << endl;

  for (i = 0; i < _numColumns; i++) {
    cout << setw(10) << _columnNames[i].Text() << " ";
  }
  cout << endl;

  for (j = 0; j < (int)(_numRows); j++) {

    for (i = 0; i < _numColumns; i++) {

      if ((int)(_theData[i]->Length()) > j)

        cout << setw(10) << (*(_theData[i]))[j].Text() << " ";

      else

        cout << setw(10) << " " << " ";
    }
    
    cout << endl;
  }

}

    
ReVarCifArray<CifString> * STable::GetRow(int rowIndex) {
  return GetSubRow(rowIndex, 0, _numColumns - 1);
}

ReVarCifArray<CifString> * STable::GetSubRow(int rowIndex, int from,
                                                                  int to) {
  int i;
  CifString temp;

  if ((rowIndex < 0) || (rowIndex >= (int)(_numRows))) return NULL;
  if (to < from) return NULL;
  if ((from < 0) || (from >= _numColumns)) return NULL;
  if (to >= _numColumns) to = _numColumns - 1;

  ReVarCifArray<CifString> * ret = new ReVarCifArray<CifString>;

  for (i = from; i <= to; i++) {
    if (rowIndex < (int)(_theData[i]->Length())) {
      temp = (*_theData[i])[rowIndex];
      ret->Add(temp);
    } else {
      temp.Clear();
      ret->Add(temp);
    }
  }

  return ret;
}


int STable::GetCell(CifString & theCell, int colIndex, int rowIndex) {
  if ((colIndex < 0) || (colIndex >= _numColumns)) return COLUMN_OUT_OF_BOUNDS;
  if ((rowIndex < 0) || (rowIndex >= (int)(_theData[colIndex]->Length()))) return ROW_OUT_OF_BOUNDS;
  theCell.Copy( (*_theData[colIndex])[rowIndex] );
  return NO_TABLE_ERROR;
}

int STable::GetColumnIndex(const char * columnName) {
  int i;
  CifString cs(columnName);

  for (i = 0; i < _numColumns; i++) {
    if (_columnNames[i] == cs) break;
  }
  if (i == _numColumns) return COLUMN_NAME_NOT_FOUND;
  else return i;
}

ReVarCifArray<CifString> * STable::GetColumnNames() {
  ReVarCifArray<CifString> * ret;

  ret = new ReVarCifArray<CifString>();
  ret->InsertNAt(0, _columnNames.Data(), _columnNames.Length());
  return ret;
}

ReVarCifArray<CifString> * STable::GetItemNames() {
  ReVarCifArray<CifString> * ret;
  CifString cs;
  ret = new ReVarCifArray<CifString>();
  ret->InsertNAt(0, _columnNames.Data(), _columnNames.Length());
  for (int i=0; i < (int)(_columnNames.Length()); i++) {
    cs.Clear(); cs+="_"; cs+=_tableName; cs+="."; cs+=(*ret)[i];
    (*ret)[i].Copy(cs);
  }
  return ret;
}


void STable::Copy(STable *st) {
  int i;
  _tableName.Copy(st->_tableName);
  _numColumns = st->_numColumns;
  _numRows = st->_numRows;
  _columnNames = CifArray<CifString> (st->_columnNames);
  _colAlloc = st->_colAlloc;
  _theData = (ReVarCifArray<CifString> **) new ReVarCifArray<CifString> *[_colAlloc];
  for (i = 0; i < _numColumns; i++) {
    _theData[i] = new ReVarCifArray<CifString>(*st->_theData[i]);
  }
}