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Geneddoc.cpp
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Geneddoc.cpp
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/*
GeneDoc: Multiple Sequence Alignment Editing Utility
Copyright (C) 2000, Karl Nicholas
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
/*
GeneDoc: Multiple Sequence Alignment Editing Utility
Copyright (C) 2000, Karl Nicholas
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
// geneddoc.cpp : implementation of the CGenedocDoc class
//
#include "stdafx.h"
#ifdef _DEBUG
#undef THIS_FILE
static char BASED_CODE THIS_FILE[] = __FILE__;
#endif
/////////////////////////////////////////////////////////////////////////////
// CGenedocDoc
IMPLEMENT_DYNCREATE(CGenedocDoc, CDocument)
BEGIN_MESSAGE_MAP(CGenedocDoc, CDocument)
//{{AFX_MSG_MAP(CGenedocDoc)
ON_COMMAND(IDM_GENESCOREFILE, OnGenescorefile)
ON_COMMAND(IDM_GENESTATFILE, OnGenestatfile)
ON_COMMAND(IDM_CONFIGURE, OnConfigure)
ON_COMMAND(IDM_GENEEDITSEQ, OnGeneeditseq)
ON_COMMAND(IDM_GENESAVEINI, SetIniDefaults)
ON_COMMAND(IDM_GENELOADINI, OnGeneloadini)
ON_COMMAND(IDM_TITLINGF, OnTitlingf)
ON_COMMAND(ID_FILE_SAVE_AS, OnFileSaveAs)
ON_COMMAND(IDM_PHYLODLG, OnPhylodlg)
ON_COMMAND(IDM_PHYLOVIEW, OnPhyloview)
ON_COMMAND(IDM_GENEVIEW, OnGeneview)
ON_COMMAND(IDM_GENESCOREPAIR, OnGenescorepair)
ON_UPDATE_COMMAND_UI(IDM_GENESCOREPAIR, OnUpdateGenescorepair)
ON_COMMAND(IDM_GENESCORETREE, OnGenescoretree)
ON_UPDATE_COMMAND_UI(IDM_GENESCORETREE, OnUpdateGenescoretree)
ON_COMMAND(IDM_SHOWTABLE, OnShowtable)
ON_COMMAND(IDM_GENESCORENUMB, OnGenescorenumb)
ON_UPDATE_COMMAND_UI(IDM_GENESCORENUMB, OnUpdateGenescorenumb)
ON_COMMAND(IDM_GENESCOREINFO, OnGenescoreinfo)
ON_UPDATE_COMMAND_UI(IDM_GENESCOREINFO, OnUpdateGenescoreinfo)
ON_UPDATE_COMMAND_UI(IDM_PHYLOVIEW, OnUpdatePhyloview)
ON_UPDATE_COMMAND_UI(IDM_GENESTATFILE, OnUpdateGenestatfile)
ON_UPDATE_COMMAND_UI(IDM_GENESCOREFILE, OnUpdateGenescorefile)
ON_COMMAND(IDM_EDITGROUPPROP, OnEditgroupprop)
ON_COMMAND(IDM_GENESHADEGROUPS, OnGeneshadegroups)
ON_UPDATE_COMMAND_UI(IDM_GENESHADEGROUPS, OnUpdateGeneshadegroups)
ON_COMMAND(IDM_GENESHADECONTRAST, OnGeneshadecontrast)
ON_COMMAND(IDM_GENESHADEGROUPCONSERVE, OnGeneshadegroupconserve)
ON_UPDATE_COMMAND_UI(IDM_GENESHADECONTRAST, OnUpdateGeneshadecontrast)
ON_UPDATE_COMMAND_UI(IDM_GENESHADEGROUPCONSERVE, OnUpdateGeneshadegroupconserve)
ON_COMMAND(IDM_GENESHADECONTRASTNOGAP, OnGeneshadecontrastnogap)
ON_UPDATE_COMMAND_UI(IDM_GENESHADECONTRASTNOGAP, OnUpdateGeneshadecontrastnogap)
ON_COMMAND(IDM_STCLOADPSDB, OnStcloadpsdb)
ON_UPDATE_COMMAND_UI(IDM_STCLOADPSDB, OnUpdateStcloadpsdb)
ON_COMMAND(IDM_STCLOADUSERFILE, OnStcloaduserfile)
ON_COMMAND(IDM_STCLEARALL, OnStclearall)
ON_COMMAND(IDM_STCLOADEMBL, OnStcloadembl)
ON_UPDATE_COMMAND_UI(IDM_STCLOADEMBL, OnUpdateStcloadembl)
ON_COMMAND(IDM_GENEAUTOSHADE2, OnGeneautoshade2)
ON_UPDATE_COMMAND_UI(IDM_GENEAUTOSHADE2, OnUpdateGeneautoshade2)
ON_COMMAND(IDM_GENEAUTOSHADE3, OnGeneautoshade3)
ON_UPDATE_COMMAND_UI(IDM_GENEAUTOSHADE3, OnUpdateGeneautoshade3)
ON_COMMAND(IDM_GENEAUTOSHADE4, OnGeneautoshade4)
ON_UPDATE_COMMAND_UI(IDM_GENEAUTOSHADE4, OnUpdateGeneautoshade4)
ON_COMMAND(IDM_GENECLEARSHADE, OnGeneclearshade)
ON_UPDATE_COMMAND_UI(IDM_GENECLEARSHADE, OnUpdateGeneclearshade)
ON_COMMAND(IDM_GENEGROUPENABLE, OnGenegroupenable)
ON_UPDATE_COMMAND_UI(IDM_GENEGROUPENABLE, OnUpdateGenegroupenable)
ON_COMMAND(IDM_GENEMODECONSERVED, OnGenemodeconserved)
ON_UPDATE_COMMAND_UI(IDM_GENEMODECONSERVED, OnUpdateGenemodeconserved)
ON_COMMAND(IDM_GENEMODEPROPERTY, OnGenemodeproperty)
ON_UPDATE_COMMAND_UI(IDM_GENEMODEPROPERTY, OnUpdateGenemodeproperty)
ON_COMMAND(IDM_GENEMODEQUANTIFY, OnGenemodequantify)
ON_UPDATE_COMMAND_UI(IDM_GENEMODEQUANTIFY, OnUpdateGenemodequantify)
ON_COMMAND(IDM_GENEMODESTRUCTURE, OnGenemodestructure)
ON_UPDATE_COMMAND_UI(IDM_GENEMODESTRUCTURE, OnUpdateGenemodestructure)
ON_COMMAND(IDM_GENERESIDUEMODEDIFF, OnGeneresiduemodediff)
ON_UPDATE_COMMAND_UI(IDM_GENERESIDUEMODEDIFF, OnUpdateGeneresiduemodediff)
ON_COMMAND(IDM_GENEDSTATVIEW, OnGenedstatview)
ON_UPDATE_COMMAND_UI(IDM_GENEDSTATVIEW, OnUpdateGenedstatview)
ON_COMMAND(IDM_GROUPSHADEPCR, OnGroupshadepcr)
ON_UPDATE_COMMAND_UI(IDM_GROUPSHADEPCR, OnUpdateGroupshadepcr)
ON_COMMAND(IDM_GROUPSHADEPCRSIM, OnGroupshadepcrsim)
ON_UPDATE_COMMAND_UI(IDM_GROUPSHADEPCRSIM, OnUpdateGroupshadepcrsim)
ON_COMMAND(IDM_FILEIMPORT, OnFileimport)
ON_COMMAND(IDM_FILEEXPORT, OnFileexport)
ON_COMMAND(IDM_CLEARGAPCOLS, OnCleargapcols)
ON_COMMAND(IDM_PLOTSTATDSTAT, OnPlotstatdstat)
ON_COMMAND(IDM_PLOTFAVSUBS, OnPlotfavsubs)
ON_COMMAND(IDM_PLOTGROUP, OnPlotgroup)
ON_COMMAND(IDM_PLOTGROUPFAV, OnPlotgroupfav)
ON_COMMAND(IDM_GENEMODEPHYSIOCHEM, OnGenemodephysiochem)
ON_COMMAND(IDM_GENESHADEGROUPPHYSCHEM, OnGeneshadegroupphyschem)
ON_UPDATE_COMMAND_UI(IDM_GENESHADEGROUPPHYSCHEM, OnUpdateGeneshadegroupphyschem)
ON_UPDATE_COMMAND_UI(IDM_GENEMODEPHYSIOCHEM, OnUpdateGenemodephysiochem)
ON_COMMAND(IDM_GENEGROUPSGCONX, OnGenegroupsgconx)
ON_UPDATE_COMMAND_UI(IDM_GENEGROUPSGCONX, OnUpdateGenegroupsgconx)
ON_COMMAND(IDM_GENEMODESEARCH, OnGenemodesearch)
ON_UPDATE_COMMAND_UI(IDM_GENEMODESEARCH, OnUpdateGenemodesearch)
ON_COMMAND(IDM_GENESHADEGROUPDNA, OnGeneshadegroupdna)
ON_UPDATE_COMMAND_UI(IDM_GENESHADEGROUPDNA, OnUpdateGeneshadegroupdna)
ON_COMMAND(IDM_PLOTFRAG, OnPlotfrag)
ON_COMMAND(IDM_GENEMODESIMILARITY, OnGenemodesimilarity)
ON_UPDATE_COMMAND_UI(IDM_GENEMODESIMILARITY, OnUpdateGenemodesimilarity)
ON_COMMAND(IDM_STCLOADPDB, OnStcloadpdb)
ON_UPDATE_COMMAND_UI(IDM_STCLOADPDB, OnUpdateStcloadpdb)
ON_COMMAND(IDM_SUMMARYVIEW, OnSummaryview)
ON_UPDATE_COMMAND_UI(IDM_SUMMARYVIEW, OnUpdateSummaryview)
ON_COMMAND(IDM_GENEMODELOGODDS, OnGenemodelogodds)
ON_UPDATE_COMMAND_UI(IDM_GENEMODELOGODDS, OnUpdateGenemodelogodds)
ON_COMMAND(IDM_LOGODDSVIEW, OnLogoddsview)
ON_UPDATE_COMMAND_UI(IDM_LOGODDSVIEW, OnUpdateLogoddsview)
ON_COMMAND(ID_FILE_SAVE, OnFileSave)
ON_COMMAND(IDM_COPYCONS, OnCopycons)
ON_UPDATE_COMMAND_UI(IDM_COPYCONS, OnUpdateCopycons)
ON_COMMAND(IDM_SHOWMANSHADE, OnShowmanshade)
ON_UPDATE_COMMAND_UI(IDM_SHOWMANSHADE, OnUpdateShowman)
ON_COMMAND(IDM_SHOWCOMMENTS, OnShowcomments)
ON_UPDATE_COMMAND_UI(IDM_SHOWCOMMENTS, OnUpdateShowcom)
ON_COMMAND(IDM_CLEARCOMMENTS, OnClearcomments)
ON_COMMAND(IDM_CLEARMANSHADE, OnClearmanshade)
ON_COMMAND(IDM_SELECTARRSEQ, OnSelectarrseq)
ON_COMMAND(IDM_GENESCORELO, OnGenescorelo)
ON_UPDATE_COMMAND_UI(IDM_GENESCORELO, OnUpdateGenescorelo)
ON_COMMAND(IDM_RESCOREALL, OnRescoreall)
ON_COMMAND(IDM_COMPLIMENTSEL, OnComplimentsel)
ON_COMMAND(IDM_GENEREPORTVIEW, OnGenereportview)
ON_COMMAND(IDM_REGAPDNA, OnRegapdna)
ON_COMMAND(IDM_SRCHREPVIEW, OnSrchrepview)
ON_COMMAND(IDM_GENEGELVIEW, OnGenegelview)
ON_UPDATE_COMMAND_UI(IDM_GENEGELVIEW, OnUpdateGenegelview)
ON_COMMAND(IDM_ALIGN, OnAlign)
ON_COMMAND(IDM_MANSHADEREP, OnManshaderep)
ON_UPDATE_COMMAND_UI(IDM_MANSHADEREP, OnUpdateManshaderep)
ON_COMMAND(IDM_SHADING_REP, OnShadingRep)
ON_COMMAND(IDM_CONFIGREPORT, OnConfigreport)
ON_COMMAND(IDM_CONSPROSITE, OnConsprosite)
ON_UPDATE_COMMAND_UI(IDM_CONSPROSITE, OnUpdateConsprosite)
//}}AFX_MSG_MAP
END_MESSAGE_MAP()
/////////////////////////////////////////////////////////////////////////////
// CGenedocDoc construction/destruction
ScoreTableStruct ScoreInit[] = {
{ "Blosum 35", Blosum35, "DE,NQ,ST,KR,FYW,LIVM,","Blosum 35 in 1/4 bits, Entropy = 0.2111, Expected = -0.1550", 0},
{ "Blosum 45", Blosum45, "DE,NH,ST,QKR,FYW,LIVM,", "Blosum 45 in 1/3 bits, Entropy = 0.3795, Expected = -0.2789", 0},
{ "Blosum 62", Blosum62, "DN,EQ,ST,KR,FYW,LIVM,", "Blosum 62 in 1/3 bits, Entropy = 0.6979, Expected = -0.5209", 0 },
{ "Blosum 80", Blosum80, "DN,EQ,ST,KR,FY,LIVM,", "Blosum 80 in 1/3 bits, Entropy = 0.9868, Expected = -0.7442", 0 },
{ "Blosum 100", Blosum100, "DN,EQ,ST,KR,FY,LM,IV,","Blosum 100 in 1/3 bits, Entropy = 1.4516, Expected = -1.0948", 0 },
{ "Dayhoff PAM 120", Pam120, "DEN,HQ,SAT,KR,FY,LIVM,", "Dayhoff PAM 120 in 1/2 bit units. Entropy = 0.98", 0 },
{ "Dayhoff PAM 160", Pam160, "DEN,HQ,SAT,KR,FY,LIVM,","Dayhoff PAM 160 similarity matrix. Entropy = 0.70", 0 },
{ "Dayhoff PAM 200", Pam200, "DEQ,HN,SAT,KR,FY,LIVM,","Dayhoff PAM 200 similarity matrix. Entropy = 0.51", 0 },
{ "Dayhoff PAM 250", Pam250, "DENQH,SAT,KR,FY,LIVM,","Dayhoff PAM 250 in 1/3 bit units. Entropy = 0.36", 0 },
{ "Nucleic Acid PAM 20", dp20, "", "Nucleic Acid PAM 20 similarity matrix. Entropy = 1.05", 1 },
{ "Nucleic Acid PAM 30", dp30, "", "Nucleic Acid PAM 30 similarity matrix. Entropy = 0.80", 1 },
{ "Nucleic Acid PAM 47", dp47, "","Nucleic Acid PAM 47 similarity matrix. Entropy = 0.50", 1 },
{ "Nucleic Acid PAM 50", dp50, "", "Nucleic Acid PAM 50 similarity matrix. Entropy = 0.47", 1 },
{ "Nucleic Acid PAM 65", dp65, "", "Nucleic Acid PAM 65 similarity matrix. Entropy = 0.32", 1 },
{ "Nucleic Acid PAM 85", dp85, "", "Nucleic Acid PAM 85 similarity matrix. Entropy = 0.19", 1 },
{ "Nucleic Acid PAM 110", dp110, "", "Nucleic Acid PAM 110 similarity matrix. Entropy = 0.10", 1 },
{ "DNA PAM 20", dp20b, "", "DNA PAM 20, 1 transversion / 3 transitions, Entropy = 1.09", 1 },
{ "DNA PAM 50", dp50b, "", "DNA PAM 50, 1 transversion / 3 transitions, Entropy = 0.54", 1 },
{ "DNA PAM 85", dp85b, "", "DNA PAM 85, 1 transversion / 3 transitions, Entropy = 0.26", 1 },
{ "Identity Matrix", IDMat, "", "Identity Matrix: Identities = 10, Mismatches = -5", 1 },
};
CGenedocDoc::CGenedocDoc()
{
int i;
// TODO: add one-time construction code here
pGSFiller = NULL;
m_pTextView = NULL;
m_pTreeView = NULL;
m_pSummaryView = NULL;
m_pDStatView = NULL;
m_pGelView = NULL;
m_pPGBase = NULL;
m_TreeDebugOutput = 0;
m_SummaryMessaged = 0;
m_pFS.FindStr = "";
m_pFS.FindFrom = 0;
m_pFS.MisMatch = 0;
m_pFS.InsDel = 0;
m_pFS.rgbText = RGB(0,0,0);
m_pFS.rgbBack = RGB(0,255,0);
m_pFS.PrevSeq = -1;
// Array init
ScoreTableStruct *tSTS;
int ts = sizeof (ScoreInit) / sizeof(ScoreTableStruct);
for ( i = 0; i < sizeof (ScoreInit) / sizeof(ScoreTableStruct) ; ++i ) {
tSTS = new ScoreTableStruct;
if ( tSTS == 0 ) {
AfxMessageBox( "Geneddoc:new:fail:1" );
return;
}
tSTS->Name = ScoreInit[i].Name;
tSTS->TableFunction = ScoreInit[i].TableFunction;
tSTS->ScoreType = ScoreInit[i].ScoreType;
m_UserVars.m_ScoreTableArray.Add( tSTS );
}
// Add the Base DisplayVars entry ..
// CDisplayVars *DisplayVars = new CDisplayVars;
// m_UserVars.m_DisplayVars.AddTail( DisplayVars );
// Load User Defaults
GetIniDefaults();
((CGenedocApp *)AfxGetApp())->SetLandscape( m_UserVars.m_Orientation );
// Load up score table // CptrArray
((ScoreTableStruct *)m_UserVars.m_ScoreTableArray.
GetAt(m_UserVars.m_CurrentScoreTable))->TableFunction( ScoreArray, &NewGap, &GapLen, &CurrentZeroDistance );
}
CGenedocDoc::~CGenedocDoc()
{
if ( pGSFiller != NULL ) {
delete pGSFiller;
}
ClearUserVars( &m_UserVars );
ScoreTableStruct *tSTS;
int count = m_UserVars.m_ScoreTableArray.GetSize();
for ( int i = 0; i < count; ++i ) {
tSTS = (ScoreTableStruct *)m_UserVars.m_ScoreTableArray[i];
delete tSTS;
}
// dUserVars->m_ScoreTableArray.RemoveAll();
if ( m_pPGBase != NULL ) {
delete m_pPGBase;
}
}
void
CGenedocDoc::SetShadeGroupDefault(CPtrArray *ShadePairArray, int NewScoreTable)
{
int i;
ShadePairStruct *tSPS;
char DecodeBuff[64];
int count = ShadePairArray->GetSize();
for ( i = 0; i < count; ++i ) {
tSPS = (ShadePairStruct *)(*ShadePairArray)[i];
delete tSPS;
}
ShadePairArray->RemoveAll();
const char *tStr = ScoreInit[NewScoreTable].DefStrings;
int RowCount = 0;
// Fill in array with new values.
const char *pc = tStr;
while ( 1 ) {
if ((*pc == ' ') || (*pc == 0)) {
break;
}
char *pc2 = DecodeBuff;
while ( *pc != ',' && (*pc != 0) ) {
*pc2++ = *pc++;
}
// little paranoia code here
if ( *pc == 0 ) break;
// Point to next group
pc++;
// Copy This Group
*pc2 = 0;
tSPS = new ShadePairStruct;
if ( tSPS == 0 ) {
AfxMessageBox( "Geneddoc:new:fail:2" );
return;
}
tSPS->RowNum = RowCount + 1;
strcpy ( tSPS->Group, DecodeBuff );
ShadePairArray->Add(tSPS);
RowCount++;
}
}
const char *
CGenedocDoc::GetScoreTableDescr(int ScoreTable)
{
ASSERT ( ScoreTable < (sizeof(ScoreInit) / sizeof(ScoreTableStruct)));
return ScoreInit[ScoreTable].TableDefs;
}
void
CGenedocDoc::SetShadePairArray(CPtrArray *nShadePairArray, CPtrArray *oShadePairArray)
{
ShadePairStruct *tSPS;
ShadePairStruct *tSPSn;
int count = nShadePairArray->GetSize();
int i;
for ( i = 0; i < count; ++i ) {
tSPS = (ShadePairStruct *)(*nShadePairArray)[i];
delete tSPS;
}
nShadePairArray->RemoveAll();
count = oShadePairArray->GetSize();
for (i = 0; i < count; ++i ) {
tSPS = new ShadePairStruct;
if ( tSPS == 0 ) {
AfxMessageBox( "Geneddoc:new:fail:3" );
return;
}
tSPSn = (ShadePairStruct *)oShadePairArray->GetAt(i);
tSPS->RowNum = tSPSn->RowNum;
strcpy ( tSPS->Group, tSPSn->Group );
nShadePairArray->Add( tSPS );
}
}
CString CGenedocDoc::ConvertPathname( const char *nExt )
{
char *pName;
CString PathName = GetPathName();
int NameLen = PathName.GetLength();
pName = PathName.GetBuffer(NameLen);
int tLen = NameLen - 1;
int i;
for ( i = 0; i < 4; ++i ) {
if ( pName[tLen] == '.' ) {
break;
}
tLen--;
}
if ( pName[tLen] == '.' ) {
i = 0;
while ( (tLen < NameLen) && (i < 4) ) {
pName[tLen] = nExt[i];
i++;
tLen++;
}
PathName.ReleaseBuffer();
} else {
PathName.ReleaseBuffer();
PathName += nExt;
}
return PathName;
}
void
CGenedocDoc::CheckOrientation()
{
int nLS = ((CGenedocApp *)AfxGetApp())->GetLandscape();
if ( nLS != m_UserVars.m_Orientation ) {
m_UserVars.m_Orientation = nLS;
SetModifiedFlag();
}
}
void
CGenedocDoc::SetFilePath(const char *pszPathName)
{
m_PathName = pszPathName;
int NameLen = m_PathName.GetLength();
char *pName = m_PathName.GetBuffer(NameLen);
while ( NameLen != -1 ) {
if ( pName[NameLen] == '\\' ) break;
if ( pName[NameLen] == ':' ) break;
NameLen -= 1;
}
NameLen++;
m_PathName.ReleaseBuffer(NameLen);
}
void
CGenedocDoc::GetProjectType()
{
int tType = 0, rc;
if ( pGSFiller != NULL ) {
if ( !pGSFiller->SegHeaderList.IsEmpty() ) {
CString *cStr = (CString *)pGSFiller->SegHeaderList.GetTail();
// Looking for Master Checksum location ...
if ( (rc = cStr->Find("Type: ")) != -1 ) {
const char *rStr = (const char *)*cStr;
rStr += rc + strlen ( "Type: " );
if ( *rStr == 'N' ) {
tType = 1;
}
}
}
}
m_UserVars.m_ProjectType = tType + 1;
}
BOOL
CGenedocDoc::OnOpenDocument(const char *pszPathName)
{
if (IsModified())
TRACE0("Warning: OnOpenDocument replaces an unsaved document\n");
BeginWaitCursor();
DeleteContents();
if ( pGSFiller != NULL ) {
delete pGSFiller;
pGSFiller = NULL;
}
if ( !GetMSFFile( pszPathName ) ) {
EndWaitCursor();
return FALSE;
}
// Save the File Path
SetFilePath(pszPathName);
// Read the user defaults from the comment list
GetUserDefaults( );
// Set printer orientation for this file.
((CGenedocApp *)AfxGetApp())->SetLandscape( m_UserVars.m_Orientation );
// Set Gap Char Correctly
ChangeGapChar();
// Set correct scoring table.
((ScoreTableStruct *)m_UserVars.m_ScoreTableArray[m_UserVars.m_CurrentScoreTable])
->TableFunction(ScoreArray, &NewGap, &GapLen, &CurrentZeroDistance );
if ( m_UserVars.m_ProjectType == 0 ) {
GetProjectType();
if ( m_UserVars.m_ProjectType > 1 && m_UserVars.m_CurrentScoreTable < 9 ) {
for ( int i = 0; i < 3; ++i ) {
SetPropertyDefault(
m_UserVars.m_Vars.GetProperty().GetArray(i),
i, m_UserVars.m_ProjectType
);
}
m_UserVars.m_CurrentScoreTable = 13;
// Load up score table // CptrArray
((ScoreTableStruct *)m_UserVars.m_ScoreTableArray.
GetAt(m_UserVars.m_CurrentScoreTable))->TableFunction( ScoreArray, &NewGap, &GapLen, &CurrentZeroDistance );
SetShadeGroupDefault( &m_UserVars.m_ShadePairArray, m_UserVars.m_CurrentScoreTable );
}
}
// Assume 0 = clear, already cleared.
AutoShade( m_UserVars.m_Vars.GetLastShadeLevel() );
SetModifiedFlag(FALSE); // start off with unmodified
if ( !ParseTree( m_UserVars.m_ParseString, 0) ) {
SetModifiedFlag();
ResetTree();
}
EndWaitCursor();
return TRUE;
}
BOOL
CGenedocDoc::OnNewDocument()
{
GetProjectType();
/* if ( ((CGenedocApp*)AfxGetApp())->m_ReallyNewFlag ) {
CProjTypeDialog tDlg;
tDlg.m_ProjectType = m_UserVars.m_ProjectType - 1;
tDlg.DoModal();
m_UserVars.m_ProjectType = tDlg.m_ProjectType + 1;
AfxMessageBox("Use File or Sequence Edit/Import Function to retrieve Data Files" );
}
*/
return TRUE;
}
void CGenedocDoc::OnFileSave()
{
// TODO: Add your command handler code here
if ( pGSFiller == NULL ) {
AfxMessageBox("Empty Project: Cannot Save!");
return;
}
CDocument::OnFileSave();
}
void CGenedocDoc::OnFileSaveAs()
{
// TODO: Add your command handler code here
if ( pGSFiller == NULL ) {
AfxMessageBox("Empty Project: Cannot Save!");
return;
}
OnTitlingf();
CDocument::OnFileSaveAs();
}
BOOL
CGenedocDoc::OnSaveDocument(const char *pszPathName)
{
// Get printer orientation for this file.
m_UserVars.m_Orientation = ((CGenedocApp *)AfxGetApp())->GetLandscape();
if (
(strlen ( m_UserVars.m_TitleProgram ) == 0 )
|| (strlen ( m_UserVars.m_TitleScoreMatrix ) == 0 )
|| (strlen ( m_UserVars.m_TitleOpenGap ) == 0 )
|| (strlen ( m_UserVars.m_TitleExtendGap ) == 0 )
) {
OnTitlingf();
}
BeginWaitCursor();
// Write new user defaults to the comment list
SetUserDefaults();
WriteMSFFile( pszPathName );
EndWaitCursor();
SetModifiedFlag(FALSE); // start off with unmodified
return TRUE;
}
/////////////////////////////////////////////////////////////////////////////
// CGenedocDoc serialization
void CGenedocDoc::Serialize(CArchive& ar)
{
if (ar.IsStoring())
{
// TODO: add storing code here
}
else
{
// TODO: add loading code here
}
}
/////////////////////////////////////////////////////////////////////////////
// CGenedocDoc diagnostics
#ifdef _DEBUG
void CGenedocDoc::AssertValid() const
{
CDocument::AssertValid();
}
void CGenedocDoc::Dump(CDumpContext& dc) const
{
CDocument::Dump(dc);
}
#endif //_DEBUG
/////////////////////////////////////////////////////////////////////////////
// CGenedocDoc commands
// Working Spot
void
CGenedocDoc::CopyGSFiller( CGSFiller *npGSFiller )
{
pGSFiller = npGSFiller;
SetModifiedFlag(); // start off with unmodified
UpdateAllViews(NULL);
}
void
CGenedocDoc::ClearShade()
{
if ( pGSFiller == NULL ) {
return;
}
CGeneSegment *tCGSeg;
int i = 0;
HANDLE tSegHandle;
m_UserVars.m_Vars.SetLastShadeLevel( SHADELEVEL0 );
int RowCount = pGSFiller->SegDataList.GetCount(); // Subtract 1 for comment rows
ShadeSegStc* pSegArr = new ShadeSegStc[RowCount]; // Gonna need access to comment row
if ( pSegArr == 0 ) {
AfxMessageBox( "Geneddoc:new:fail:" );
return;
}
POSITION tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
tSegHandle = tCGSeg->GetTextHandle();
pSegArr[i].pGeneStor = (GeneStor *) GlobalLock( tSegHandle );
pSegArr[i].pCGSeg = tCGSeg;
if ( pSegArr[i].pGeneStor == NULL ) {
AfxMessageBox("ClearShade:GlobalLock:Fail");
delete pSegArr;
return;
}
i++;
}
DWORD OuterCount = tCGSeg->GetTextLength();
for ( DWORD tCount = 0L; tCount < OuterCount; ++tCount ) {
// Inner Loop
for ( i = 0; i < RowCount; ++i ) {
if ( pSegArr[i].pCGSeg->GetStyle() != LINESEQUENCE ) {
(pSegArr[i].pGeneStor)[tCount].CharDisplay = ' ';
(pSegArr[i].pGeneStor)[tCount].BackColor = m_UserVars.m_BackColor0;
(pSegArr[i].pGeneStor)[tCount].TextColor = m_UserVars.m_ForeColor0;
(pSegArr[i].pGeneStor)[tCount].CharScore = 0;
continue;
}
// Lets Clear out old shades here.
(pSegArr[i].pGeneStor)[tCount].BackColor = m_UserVars.m_BackColor0;
(pSegArr[i].pGeneStor)[tCount].TextColor = m_UserVars.m_ForeColor0;
// (pSegArr[i].pGeneStor)[tCount].CharScore = 0;
// Lets Clear out old Displays
char tChar = (pSegArr[i].pGeneStor)[tCount].CharGene;
if ( m_UserVars.m_ResidueUpper == 1 ) {
(pSegArr[i].pGeneStor)[tCount].CharDisplay = toupper(tChar);
} else if ( m_UserVars.m_ResidueUpper == 2 ) {
(pSegArr[i].pGeneStor)[tCount].CharDisplay = tolower(tChar);
} else {
(pSegArr[i].pGeneStor)[tCount].CharDisplay = tChar;
}
if ( m_UserVars.m_TransTilde ) {
if ( tChar == '~' ) (pSegArr[i].pGeneStor)[tCount].CharDisplay = ' ';
}
}
}
if ( m_UserVars.m_Vars.GetResidueMode() == 1 ) {
AutoShadeDifference( &pSegArr[2], RowCount - 3, 0, &m_UserVars.m_Vars, NULL );
}
tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
tSegHandle = tCGSeg->GetTextHandle();
GlobalUnlock( tSegHandle );
}
delete pSegArr;
}
void
CGenedocDoc::ClearScore()
{
if ( pGSFiller == NULL ) {
return;
}
CGeneSegment *tCGSeg;
GeneStor *pGeneStor;
HANDLE tSegHandle;
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetHead();
tSegHandle = tCGSeg->GetTextHandle();
pGeneStor = (GeneStor *) GlobalLock( tSegHandle );
if ( pGeneStor == NULL ) {
AfxMessageBox("ClearScore:GlobalLock:Fail");
return;
}
DWORD OuterCount = tCGSeg->GetTextLength();
for ( DWORD tCount = 0L; tCount < OuterCount; ++tCount ) {
if ( pGeneStor[tCount].CharScore != 0 ) {
pGeneStor[tCount].CharScore = 0;
pGeneStor[tCount].CharDisplay = ' ';
// Reset the colors
pGeneStor[tCount].BackColor = m_UserVars.m_BackColor0;
pGeneStor[tCount].TextColor = m_UserVars.m_ForeColor0;
}
}
GlobalUnlock( tSegHandle );
}
void
CGenedocDoc::ChangeGapChar()
{
if ( pGSFiller == NULL ) {
return;
}
CGeneSegment *tCGSeg;
char tGapChar = m_UserVars.m_GapInd ? '.' : '-';
POSITION tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
tCGSeg->ChangeGapChar(tGapChar );
}
}
void
CGenedocDoc::InsertFillerRange(DWORD StartRange, DWORD EndRange)
{
if ( pGSFiller == NULL ) {
return;
}
CGeneSegment *tCGSeg;
int MaxExpanded = 0;
BeginWaitCursor();
POSITION tPos;
int OnlyExp = 0;
// if ( InsSelected ) {
tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
if ( tCGSeg->GetArrangeFlag() ) {
OnlyExp = 1;
break;
}
}
// }
//
tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
if ( OnlyExp ) if ( !tCGSeg->GetArrangeFlag() ) {
tCGSeg->m_Expanded = 0;
continue;
}
tCGSeg->InsertFillerRange( StartRange, EndRange );
if ( tCGSeg->m_Expanded > MaxExpanded ) {
MaxExpanded = tCGSeg->m_Expanded;
}
}
//
if ( MaxExpanded ) {
// Here we gots increase sizes of strings.
POSITION tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
if ( tCGSeg->m_Expanded != MaxExpanded ) {
tCGSeg->AppendFiller( MaxExpanded - tCGSeg->m_Expanded );
}
}
}
EndWaitCursor();
// Reset the screen
AutoShade( -1, 1 );
}
void
CGenedocDoc::DeleteFillerRange(DWORD StartRange, DWORD EndRange, int DelData )
{
if ( pGSFiller == NULL ) {
return;
}
CGeneSegment *tCGSeg;
int isok;
BeginWaitCursor();
POSITION tPos;
int OnlyExp = 0;
// if ( DelSelected ) {
tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
if ( tCGSeg->GetArrangeFlag() ) {
OnlyExp = 1;
break;
}
}
// }
tPos = pGSFiller->SegDataList.GetHeadPosition();
if ( DelData ) {
isok = 1;
} else {
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
if ( OnlyExp ) if ( !tCGSeg->GetArrangeFlag() ) {
continue;
}
isok = tCGSeg->TestDeleteFillerRange( StartRange, EndRange );
if ( !isok ) break;
}
if ( !isok ) {
AfxMessageBox( "Residues detected in Selected Range" );
return;
}
}
tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
if ( OnlyExp ) if ( !tCGSeg->GetArrangeFlag() ) {
continue;
}
tCGSeg->DeleteFillerRange( StartRange, EndRange, DelData );
}
// Here we gots increase sizes of strings.
ReSizeRows();
EndWaitCursor();
// Reset the screen
AutoShade( -1, 1 );
}
void CGenedocDoc::OnCleargapcols()
{
// TODO: Add your command handler code here
if ( pGSFiller == NULL ) {
return;
}
CGeneSegment *tCGSeg;
int isok;
BeginWaitCursor();
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetHead();
DWORD dwLen = tCGSeg->GetTextLength();
for ( DWORD dwCount = 0; dwCount < dwLen; ++dwCount ) {
POSITION tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
isok = tCGSeg->TestDeleteFillerRange( dwCount, dwCount );
if ( !isok ) break;
}
if ( isok ) {
tPos = pGSFiller->SegDataList.GetHeadPosition();
while (tPos != NULL ) {
tCGSeg = (CGeneSegment *)pGSFiller->SegDataList.GetNext(tPos);
tCGSeg->DeleteFillerRange( dwCount, dwCount );
}
dwLen--;
dwCount--;
}
}
//
EndWaitCursor();
// Reset the screen
AutoShade( -1, 1 );
}
int
CGenedocDoc::GetNumColors(CDisplayVars *DisplayVars)
{
if ( DisplayVars->GetModeConserved() == SHADEPROPERTY ) {
if ( DisplayVars->GetLastShadeLevel() >= SHADELEVEL2 ) {
return
DisplayVars->GetProperty()
.GetArray(DisplayVars->GetLastShadeLevel() - SHADELEVEL2)
->GetSize() + 1;
} else {
return 1;
}
} else {
return 4;
}
}
void
CGenedocDoc::GetLevelColors( CDisplayVars *DisplayVars, int Level, COLORREF * TextColor, COLORREF *BkColor )
{