Attachment #73797 for bug #112773

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                pop++)
            {

                wxString annotatedFileName((wxChar)region->first.c_str());
                GCUnit * uinfo = 
                    AddDataUnit(fileRef,annotatedFileName,pop);
                wxString popName((wxChar)pop->second.getName().c_str());
                GCPopulation * thisPop = &(NoPopulation());
                if(!popName.IsEmpty())
                {



    // converting from wxString to string
    std::string fname((const char*)fileRef.GetName().c_str());
    ConverterIf * converter = NULL;
    MigrateConverter * migrateConverter = NULL;


void
GCDataStore::DebugDump()
{
    wxLogDebug(wxT("******************************************************"));
    wxLogDebug(wxT("GC DataStore: DEBUG DUMP"));
    // data file contents
    dataFileSet::iterator fileIter;
    for(fileIter=m_dataFiles.begin(); fileIter != m_dataFiles.end(); fileIter++)
    {
        GCFile *  p = (*fileIter);
        wxLogDebug(wxT("   *********"));
        wxLogDebug(wxT("   Data file: \"%s\""),p->GetName().c_str());
        wxLogDebug(wxT("                format: %s"),ToWxString(p->GetFileFormat()).c_str());
        wxLogDebug(wxT("           interleaved: %d"),p->GetIsInterleaved());
        wxLogDebug(wxT("              datatype: %s"),ToWxString(p->GetDataType()).c_str());
        const dataUnitSet & units = (*fileIter)->GetUnits();
        dataUnitSet::const_iterator unitIter;
        for(unitIter = units.begin(); unitIter != units.end(); unitIter++)
        {
            GCUnit & uref = *(*unitIter);
            wxLogDebug(wxT("        Unit: \"%s\""),uref.GetName().c_str());
            wxLogDebug(wxT("              reg name: %s"),uref.GetRegion().GetName().c_str());
            wxLogDebug(wxT("              pop name: %s"),uref.GetPopulation().GetName().c_str());
            wxLogDebug(wxT("              num mark: %ld"),uref.GetNMarkers());
            wxLogDebug(wxT("              num tips: %ld"),uref.GetNTips());
            wxLogDebug(wxT("              hap file: %s"),uref.GetHapFileName().c_str());
        }
    }
    regionSet::iterator regionIter;
    for(regionIter=m_regions.begin(); regionIter != m_regions.end(); regionIter++)
    {
        GCRegion * regionP = (*regionIter);
        wxLogDebug(wxT("   *********"));
        wxLogDebug(wxT("   Region: \"%s\""),regionP->GetName().c_str());
        wxLogDebug(wxT("              datatype: %s"),ToWxString(regionP->GetDataType()).c_str());
        wxLogDebug(wxT("              num mark: %ld"),regionP->GetNMarkers());
        wxLogDebug(wxT("                length: %ld"),regionP->GetLength());
        wxLogDebug(wxT("                offset: %ld"),regionP->GetOffset());
        wxLogDebug(wxT("              map file: %s"),regionP->GetMapFileName().c_str());
        /* EWFIX.LATER
        wxLogDebug("          map position: %ld",regionP->GetMapPosition());
        */

    for(popIter=m_populations.begin(); popIter != m_populations.end(); popIter++)
    {
        GCPopulation * popP = (*popIter);
        wxLogDebug(wxT("   *********"));
        wxLogDebug(wxT("      Pop: \"%s\""),popP->GetName().c_str());
    }
}


                GCRegion &      reg = (*uIter)->GetRegion();
                GCPopulation &  pop = (*uIter)->GetPopulation();

                std::string name((const char*)reg.GetName().c_str());
                ModelDS newModel((*iter)->m_lamarcDS->getFirstRegion()->second.getDataModel());
                RegionDS thisRegion(name,newModel);


                if(reg.m_mapFile != NULL)
                {
                    SpaceMap & spaces = reg.m_mapFile->GetSpaceMap();
                    std::string stdRegionName = std::string((const char*)reg.GetName().c_str());
                    if(spaces.find(stdRegionName) != spaces.end())
                    {
                        try

                    thisRegion.setSpacing(*(spacing));
                }

                std::string stdName((const char*)pop.GetName().c_str());
                PopulationDS thisPop(stdName);
                PopMap::iterator pIter = (*uIter)->m_popMapIter;
                thisPop.AddIndividuals((*pIter).second.GetAllIndividuals());

                wxString hapFileName = (*uIter)->GetHapFileName();
                if(!hapFileName.IsEmpty())
                {
                    std::string stdHapFileName((const char*)hapFileName.c_str());
                    HapConverter hapconverter(thisRegion,randomgenerator);
                    vector<IndividualDS> individuals =
                        hapconverter.ReadHapInfo(stdHapFileName);

        }


        ofstream outFile((const char*)fileName.c_str(), ios::out);
        if(!outFile)
        {
            GCError(




    // EWFIX -- this is kinda bogus -- we are reading the
    // file first with an ifstream becuase the wxFileInputStream
    // below produces errors in a way we don't like.
    std::ifstream haplotypefile((const char*)hapFileName.c_str(),std::ios::in);
    if(!haplotypefile)
    {
        throw FileFormatError((const char*)
            wxString::Format(gcstr::hapFileMissing,
                m_hapFileName.c_str()).c_str());
    }

    {
        // ifstream code above should prevent us from getting here
        assert(false);
        throw FileFormatError((const char*)
            wxString::Format(gcstr::hapFileBarf,
                m_hapFileName.c_str()).c_str());
    }

    wxString firstLine = wxTextInputStream(hapFileStream).ReadLine();
    if(firstLine.IsEmpty())
    {
        throw FileFormatError((const char*)
            wxString::Format(gcstr::hapFileEmptyFirstLine,
                m_hapFileName.c_str()).c_str());
    }
    wxStringTokenizer tokens(firstLine);
    if(!tokens.HasMoreTokens())
    {
        throw FileFormatError((const char*)
            wxString::Format(gcstr::hapFileEmptyFirstLine,
                m_hapFileName.c_str()).c_str());
    }
    wxString token = tokens.GetNextToken();
    if(!token.ToLong(&m_nIndividuals))
    {
        throw FileFormatError((const char*)
            wxString::Format(gcstr::hapFileToken1,
                m_hapFileName.c_str(),
                token.c_str()

        token = tokens.GetNextToken();
        if(token != gcstr::adjacent)
        {
            throw FileFormatError((const char*)
                wxString::Format(gcstr::hapFileToken2,
                    m_hapFileName.c_str(),
                    token.c_str()

        m_adjacent = true;
        if(!tokens.HasMoreTokens())
        {
            throw FileFormatError((const char*)
                wxString::Format(gcstr::hapFileToken3Missing,
                    m_hapFileName.c_str()).c_str());
        }
        token = tokens.GetNextToken();
        if(!token.ToLong(&m_nHapsPerIndividual))
        {
            throw FileFormatError((const char*)
                wxString::Format(gcstr::hapFileToken3,
                    m_hapFileName.c_str(),
                    token.c_str()




{
    LamarcDS    lam;
    SpaceConverter converter(lam);
    m_spaceMap = converter.ReadSpacingInfo(std::string((const char*)m_mapFileName.c_str()));
}

GCMapFile::~GCMapFile()

bool
GCMapFile::ContainsRegion(GCRegion & regionRef)
{
    std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
    return (m_spaceMap.find(stdRegionName) != m_spaceMap.end());

}

GCMapFile::FirstPosition(GCRegion & regionRef)
{
    assert(ContainsRegion(regionRef));
    std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
    std::vector<long> spacing = m_spaceMap[stdRegionName];
    return spacing[0];
}

GCMapFile::LastPosition(GCRegion & regionRef)
{
    assert(ContainsRegion(regionRef));
    std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
    std::vector<long> spacing = m_spaceMap[stdRegionName];
    return spacing[spacing.size() - 1];
}

GCMapFile::NumPositions(GCRegion & regionRef)
{
    assert(ContainsRegion(regionRef));
    std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
    std::vector<long> spacing = m_spaceMap[stdRegionName];
    return spacing.size();
}

Lines 15-21 Link Here

(-)lamarc-2.0.2/src/convModel/gc_region.cpp (-1 / +1 lines)
15	{	15	{
16	assert(false);	16	assert(false);
17	}	17	}
18	wxString regionName(regionNameBuffer);	18	wxString regionName((wxChar)regionNameBuffer);
19	return regionName;	19	return regionName;
20	}	20	}
21		21




    static wxArrayString digits;
    if(digits.GetCount() < 1)
    {
        digits.Add(wxT("-"));
        digits.Add(wxT("0"));
        digits.Add(wxT("1"));
        digits.Add(wxT("2"));
        digits.Add(wxT("3"));
        digits.Add(wxT("4"));
        digits.Add(wxT("5"));
        digits.Add(wxT("6"));
        digits.Add(wxT("7"));
        digits.Add(wxT("8"));
        digits.Add(wxT("9"));
    }
    return digits;
}

    static wxArrayString digits;
    if(digits.GetCount() < 1)
    {
        digits.Add(wxT("0"));
        digits.Add(wxT("1"));
        digits.Add(wxT("2"));
        digits.Add(wxT("3"));
        digits.Add(wxT("4"));
        digits.Add(wxT("5"));
        digits.Add(wxT("6"));
        digits.Add(wxT("7"));
        digits.Add(wxT("8"));
        digits.Add(wxT("9"));
    }
    return digits;
}

Lines 32-41 Link Here

(-)lamarc-2.0.2/src/guiconv/gc_export_dialogs.cpp (-2 / +2 lines)
32	wxString regionListString = gcstr::badRegionLength1;	32	wxString regionListString = gcstr::badRegionLength1;
33	for(size_t index = 0; index < m_regionNameList.GetCount(); index++)	33	for(size_t index = 0; index < m_regionNameList.GetCount(); index++)
34	{	34	{
35	regionListString += "\n\t";	35	regionListString += wxT("\n\t");
36	regionListString += m_regionNameList[index];	36	regionListString += m_regionNameList[index];
37	}	37	}
38	regionListString += "\n\n";	38	regionListString += wxT("\n\n");
39	regionListString += gcstr::badRegionLength2;	39	regionListString += gcstr::badRegionLength2;
40		40
41	wxStaticText * message = new wxStaticText(this,-1,regionListString);	41	wxStaticText * message = new wxStaticText(this,-1,regionListString);




{
    // Setting up menu items within Converter Menu
    wxMenu * GCFirstMenu = new wxMenu;
    GCFirstMenu->Append( GC_Quit,           wxT("&Quit"));

    // Setting up menu items within File Menu
    m_fileMenu = new wxMenu;
    m_fileMenu->Append( GC_AddFiles,        wxT("&Add Data File(s)"));
    m_fileMenu->AppendSeparator();
    m_fileMenu->Append( GC_SetAllFormats,   wxT("Set all File &Formats to one kind"));
    m_fileMenu->Append( GC_SetAllDataTypes, wxT("Set all &Data Types to one kind"));
    m_fileMenu->AppendSeparator();
    m_fileMenu->Append( GC_ExportFile,      wxT("E&xport Lamarc File"));
    m_fileMenu->Enable( GC_ExportFile,      false);

    // Setting up menu items within Populations Menu
    m_populationMenu = new wxMenu;
    m_populationMenu->Append( GC_AddPopulation,    wxT("&Add a Population"));
    m_populationMenu->Append( GC_RenamePopulation, wxT("&Rename a Population"));
    m_populationMenu->Enable( GC_RenamePopulation, false);
    m_populationMenu->Append( GC_SetAllOnePopulation,    wxT("Assign All Data Units to &One Population"));
    m_populationMenu->Enable( GC_SetAllOnePopulation, false);
    /* EWFIX.LATER
    m_populationMenu->Append( GC_SetAllDifferentPopulations,  "Assign All Data Units to &Different Populations");
    m_populationMenu->Enable( GC_SetAllDifferentPopulations, false);
    */
    m_populationMenu->Append( GC_RemoveUnusedPopulations,  wxT("Remove &Unused Populations"));
    /* EWFIX.LATER
    m_populationMenu->Enable( GC_RemoveUnusedPopulations, false);
    */

    // Setting up menu items within Regions Menu
    m_regionMenu = new wxMenu;
    m_regionMenu->Append( GC_AddRegion,    wxT("&Add a Region"));
    m_regionMenu->Append( GC_RenameRegion, wxT("&Rename a Region"));
    m_regionMenu->Enable( GC_RenameRegion, false);
    m_regionMenu->Append( GC_SetAllOneRegion,    wxT("Assign All Data Units to &One Region"));
    m_regionMenu->Enable( GC_SetAllOneRegion, false);
    /* EWFIX.LATER
    m_regionMenu->Append( GC_SetAllDifferentRegions,  "Assign All Data Units to &Different Regions");
    m_regionMenu->Enable( GC_SetAllDifferentRegions, false);
    */
    m_regionMenu->Append( GC_RemoveUnusedRegions,  wxT("Remove &Unused Regions"));
    /* EWFIX.LATER
    m_regionMenu->Enable( GC_RemoveUnusedRegions, false);
    */

    // Setting up menu items within Help menu
    wxMenu * GCHelpMenu = new wxMenu;
    GCHelpMenu->Append( GC_About,           wxT("&About..."));
    GCHelpMenu->Append( GC_DescribeErrors,  wxT("&Describe Errors"));

    // Setting up menu items within Debug menu
    wxMenu * GCDebugMenu = new wxMenu;
    GCDebugMenu->Append(GC_DebugDump,       wxT("&Dump..."));


    // Placing top-level items on Menu Bar
    wxMenuBar *GCMenuBar = new wxMenuBar;
// We don't need this menu for WXMAC since it creates it automatically
#ifndef __WXMAC__
    GCMenuBar->Append( GCFirstMenu,     wxT("&Converter") );
#endif
    GCMenuBar->Append( m_fileMenu,      wxT("&File") );
    GCMenuBar->Append( m_populationMenu,wxT("&Populations") );
    GCMenuBar->Append( m_regionMenu,    wxT("&Regions") );
    GCMenuBar->Append( GCHelpMenu,      wxT("&Help") );
#ifndef NDEBUG
    GCMenuBar->Append( GCDebugMenu,     wxT("&Debug") );
#endif

    // Installing Menu Bar

        int numErrors = m_warningStrings.GetCount();
        for(int i=0; i < numErrors; i++)
        {
            errorMessage += wxT("\n\n");
            errorMessage += m_warningStrings[i];
        }
        m_logic.GCWarning(errorMessage);

            eventToSend = S2D_Menu_SetAllOneRegion;
            break;
        default:
            wxLogDebug(wxT("Need to handle menu event %d"),event.GetId());
            assert(false);
            break;
    };

            UpdateUserCues();
            break;
        default:
            wxLogDebug(wxT("Need to handle D2S event %d"),event.GetId());
            assert(false);
            break;
    }

            OnSetRegion(event);
            break;
        default:
            wxLogDebug(wxT("Need to handle S2D event %d"),event.GetId());
            assert(false);
            break;
    }




#include "gc_strings.h"
#include "wx/intl.h"

const wxString gcstr::adjacent          =   wxT("adjacent");
const wxString gcstr::allFiles          =   wxT("*");
const wxString gcstr::badRegionLength1  =   wxTRANSLATE("The following regions have suspiciously short lengths:");
const wxString gcstr::badRegionLength2  =   wxTRANSLATE("You may wish to cancel this operation and edit region lengths in the Genomic Region Properties tab");
const wxString gcstr::cancelString      =   wxTRANSLATE("Cancel");

const wxString gcstr::converterTitle    =   wxTRANSLATE("LAMARC File Converter");
const wxString gcstr::dataFileExport    =   wxTRANSLATE("Select data files to write");
const wxString gcstr::dataFilesSelect   =   wxTRANSLATE("Select data files to read");
const wxString gcstr::dna               =   wxT("DNA");
const wxString gcstr::error             =   wxTRANSLATE("ERROR");
const wxString gcstr::errorWrap         =   wxTRANSLATE("Error Type \"%s\" for file \"%s\":\n%s");
const wxString gcstr::errorWrapNoFile   =   wxTRANSLATE("Error Type \"%s\":\n%s");
const wxString gcstr::exportFileDefault =   wxT("infile.lam");
const wxString gcstr::exportFileGlob    =   wxT("Lamarc files (*.lam)|*.lam|All files (*)|*");
const wxString gcstr::exportWarning     =   wxTRANSLATE("Warning: export may not be correct");
const wxString gcstr::fileAlreadyAdded      =   wxTRANSLATE("Cannot add file \"%s\". It is already added.");
const wxString gcstr::fileDoesNotExist      =   wxTRANSLATE("File \"%s\" does not exist or is not readable.");

const wxString gcstr::fileLabelName         =   wxTRANSLATE("File Name");
const wxString gcstr::fileLabelRemove       =   wxTRANSLATE("Remove File");
const wxString gcstr::fileLabelUnlinked     =   wxTRANSLATE("Unlink Microsats");
const wxString gcstr::globAll               =   wxT("*");
const wxString gcstr::hapFileEmptyFirstLine =   wxTRANSLATE("No data found in first line of phase information file \"%s\"");
const wxString gcstr::hapFileBarf       =   wxTRANSLATE("Implementation error reading phase information file \"%s\"");
const wxString gcstr::hapFileMissing    =   wxTRANSLATE("Phase information file \"%s\" missing or un-readable");

const wxString gcstr::hapFileSelectAnother  =   wxTRANSLATE("file not listed here");
const wxString gcstr::hapFileUnSelect   =   wxTRANSLATE("un-select current file");
const wxString gcstr::information       =   wxTRANSLATE("Information");
const wxString gcstr::kallele           =   wxT("Kallele");
const wxString gcstr::mapFileExportFailed   =   wxTRANSLATE("File export failed while reading data for region \"%s\". \n\nThe error was \"%s:%s\n\nPlease check your settings for that region and please report the error.");
const wxString gcstr::mapFileLastPositionTooLate =
    wxTRANSLATE("Map position file \"%s\" has last position of %ld, but region \"%s\" length (%ld) and first position sequenced (%ld) allow last position of %ld or less only");

const wxString gcstr::mapFileSelect     =   wxTRANSLATE("select map position file");
const wxString gcstr::mapFileSelectAnother  =   wxTRANSLATE("file not listed here");
const wxString gcstr::mapFileUnSelect   =   wxTRANSLATE("un-select current file");
const wxString gcstr::microsat          =   wxT("Microsat");
const wxString gcstr::migrate           =   wxT("Migrate");
const wxString gcstr::migrateFileTypeClash =wxTRANSLATE("Setting data type to \"%s\" even though file \"%s\" specifies type \"%s\".");
const wxString gcstr::newName                   =   wxTRANSLATE("New name");
const wxString gcstr::notebookLabelDataTab      =   wxTRANSLATE("Data Files");

const wxString gcstr::notebookLabelRegionTab    =   wxTRANSLATE("Genomic Region Properties");
const wxString gcstr::noWarningsFound   =   wxTRANSLATE("No warning messages were found. You should be able to export a lamarc file now");
const wxString gcstr::parseWarning      =   wxTRANSLATE("Conflict while parsing file");
const wxString gcstr::phylip            =   wxT("Phylip");
const wxString gcstr::plainLong         =   wxT("%ld");
const wxString gcstr::populationExists  =   wxTRANSLATE("Population \"%s\" already exists.");
const wxString gcstr::populationCreate  =   wxTRANSLATE("Create new Population");
const wxString gcstr::populationEnterNewName=   wxTRANSLATE("Enter the name of the new population");

const wxString gcstr::unitLabelNumTips          =   wxTRANSLATE("Sequences");
const wxString gcstr::unitLabelSetPopulation    =   wxTRANSLATE("Population");
const wxString gcstr::unitLabelSetRegion        =   wxTRANSLATE("Genomic Region");
const wxString gcstr::snp                       =   wxT("SNP");
const wxString gcstr::warning                   =   wxTRANSLATE("Warning");
const wxString gcstr::warningMissingPopRegPair  =   wxTRANSLATE("Missing data sample covering (%s,%s) pair");
const wxString gcstr::warningNeedFile           =   wxTRANSLATE("Add one or more files");

const wxString gcstr::warningStringsHeader      =   wxTRANSLATE("You will need to fix the following things before you can create a Lamarc output file:");
const wxString gcstr::warningUnsetPopulation    =   wxTRANSLATE("At least one data unit has no population assigned");
const wxString gcstr::warningUnsetRegion        =   wxTRANSLATE("At least one data unit has no region assigned");
const wxString gcstr::unknown                   =      wxT("???");
const wxString gcstr::unsetPopulation           =   wxTRANSLATE("unset population");
const wxString gcstr::unsetRegion               =   wxTRANSLATE("unset region");


const wxString gcstr::cmdInput                  =   wxT("input");
const wxString gcstr::cmdInputChar              =   wxT("i");
const wxString gcstr::cmdInputDesc              =   wxTRANSLATE("input file");
const wxString gcstr::cmdOutput                 =   wxT("output");
const wxString gcstr::cmdOutputChar             =   wxT("o");
const wxString gcstr::cmdOutputDesc             =   wxTRANSLATE("output file");

Return to bug 112773

Lines 153-162 Link Here

(-)lamarc-2.0.2/src/convModel/gc_datastore.cpp (-30 / +30 lines)
153	pop++)	153	pop++)
154	{	154	{
155		155
156	wxString annotatedFileName(region->first.c_str());	156	wxString annotatedFileName((wxChar)region->first.c_str());
157	GCUnit * uinfo =	157	GCUnit * uinfo =
158	AddDataUnit(fileRef,annotatedFileName,pop);	158	AddDataUnit(fileRef,annotatedFileName,pop);
159	wxString popName(pop->second.getName().c_str());	159	wxString popName((wxChar)pop->second.getName().c_str());
160	GCPopulation * thisPop = &(NoPopulation());	160	GCPopulation * thisPop = &(NoPopulation());
161	if(!popName.IsEmpty())	161	if(!popName.IsEmpty())
162	{	162	{
Lines 193-199 Link Here
193		193
194		194
195	// converting from wxString to string	195	// converting from wxString to string
196	std::string fname(fileRef.GetName().c_str());	196	std::string fname((const char*)fileRef.GetName().c_str());
197	ConverterIf * converter = NULL;	197	ConverterIf * converter = NULL;
198	MigrateConverter * migrateConverter = NULL;	198	MigrateConverter * migrateConverter = NULL;
199		199
Lines 332-373 Link Here
332	void	332	void
333	GCDataStore::DebugDump()	333	GCDataStore::DebugDump()
334	{	334	{
335	wxLogDebug("******************************************************");	335	wxLogDebug(wxT("******************************************************"));
336	wxLogDebug("GC DataStore: DEBUG DUMP");	336	wxLogDebug(wxT("GC DataStore: DEBUG DUMP"));
337	// data file contents	337	// data file contents
338	dataFileSet::iterator fileIter;	338	dataFileSet::iterator fileIter;
339	for(fileIter=m_dataFiles.begin(); fileIter != m_dataFiles.end(); fileIter++)	339	for(fileIter=m_dataFiles.begin(); fileIter != m_dataFiles.end(); fileIter++)
340	{	340	{
341	GCFile * p = (*fileIter);	341	GCFile * p = (*fileIter);
342	wxLogDebug(" *********");	342	wxLogDebug(wxT(" *********"));
343	wxLogDebug(" Data file: \"%s\"",p->GetName().c_str());	343	wxLogDebug(wxT(" Data file: \"%s\""),p->GetName().c_str());
344	wxLogDebug(" format: %s",ToWxString(p->GetFileFormat()).c_str());	344	wxLogDebug(wxT(" format: %s"),ToWxString(p->GetFileFormat()).c_str());
345	wxLogDebug(" interleaved: %d",p->GetIsInterleaved());	345	wxLogDebug(wxT(" interleaved: %d"),p->GetIsInterleaved());
346	wxLogDebug(" datatype: %s",ToWxString(p->GetDataType()).c_str());	346	wxLogDebug(wxT(" datatype: %s"),ToWxString(p->GetDataType()).c_str());
347	const dataUnitSet & units = (*fileIter)->GetUnits();	347	const dataUnitSet & units = (*fileIter)->GetUnits();
348	dataUnitSet::const_iterator unitIter;	348	dataUnitSet::const_iterator unitIter;
349	for(unitIter = units.begin(); unitIter != units.end(); unitIter++)	349	for(unitIter = units.begin(); unitIter != units.end(); unitIter++)
350	{	350	{
351	GCUnit & uref = (unitIter);	351	GCUnit & uref = (unitIter);
352	wxLogDebug(" Unit: \"%s\"",uref.GetName().c_str());	352	wxLogDebug(wxT(" Unit: \"%s\""),uref.GetName().c_str());
353	wxLogDebug(" reg name: %s",uref.GetRegion().GetName().c_str());	353	wxLogDebug(wxT(" reg name: %s"),uref.GetRegion().GetName().c_str());
354	wxLogDebug(" pop name: %s",uref.GetPopulation().GetName().c_str());	354	wxLogDebug(wxT(" pop name: %s"),uref.GetPopulation().GetName().c_str());
355	wxLogDebug(" num mark: %ld",uref.GetNMarkers());	355	wxLogDebug(wxT(" num mark: %ld"),uref.GetNMarkers());
356	wxLogDebug(" num tips: %ld",uref.GetNTips());	356	wxLogDebug(wxT(" num tips: %ld"),uref.GetNTips());
357	wxLogDebug(" hap file: %s",uref.GetHapFileName().c_str());	357	wxLogDebug(wxT(" hap file: %s"),uref.GetHapFileName().c_str());
358	}	358	}
359	}	359	}
360	regionSet::iterator regionIter;	360	regionSet::iterator regionIter;
361	for(regionIter=m_regions.begin(); regionIter != m_regions.end(); regionIter++)	361	for(regionIter=m_regions.begin(); regionIter != m_regions.end(); regionIter++)
362	{	362	{
363	GCRegion * regionP = (*regionIter);	363	GCRegion * regionP = (*regionIter);
364	wxLogDebug(" *********");	364	wxLogDebug(wxT(" *********"));
365	wxLogDebug(" Region: \"%s\"",regionP->GetName().c_str());	365	wxLogDebug(wxT(" Region: \"%s\""),regionP->GetName().c_str());
366	wxLogDebug(" datatype: %s",ToWxString(regionP->GetDataType()).c_str());	366	wxLogDebug(wxT(" datatype: %s"),ToWxString(regionP->GetDataType()).c_str());
367	wxLogDebug(" num mark: %ld",regionP->GetNMarkers());	367	wxLogDebug(wxT(" num mark: %ld"),regionP->GetNMarkers());
368	wxLogDebug(" length: %ld",regionP->GetLength());	368	wxLogDebug(wxT(" length: %ld"),regionP->GetLength());
369	wxLogDebug(" offset: %ld",regionP->GetOffset());	369	wxLogDebug(wxT(" offset: %ld"),regionP->GetOffset());
370	wxLogDebug(" map file: %s",regionP->GetMapFileName().c_str());	370	wxLogDebug(wxT(" map file: %s"),regionP->GetMapFileName().c_str());
371	/* EWFIX.LATER	371	/* EWFIX.LATER
372	wxLogDebug(" map position: %ld",regionP->GetMapPosition());	372	wxLogDebug(" map position: %ld",regionP->GetMapPosition());
373	*/	373	*/
Lines 376-383 Link Here
376	for(popIter=m_populations.begin(); popIter != m_populations.end(); popIter++)	376	for(popIter=m_populations.begin(); popIter != m_populations.end(); popIter++)
377	{	377	{
378	GCPopulation * popP = (*popIter);	378	GCPopulation * popP = (*popIter);
379	wxLogDebug(" *********");	379	wxLogDebug(wxT(" *********"));
380	wxLogDebug(" Pop: \"%s\"",popP->GetName().c_str());	380	wxLogDebug(wxT(" Pop: \"%s\""),popP->GetName().c_str());
381	}	381	}
382	}	382	}
383		383
Lines 401-407 Link Here
401	GCRegion & reg = (*uIter)->GetRegion();	401	GCRegion & reg = (*uIter)->GetRegion();
402	GCPopulation & pop = (*uIter)->GetPopulation();	402	GCPopulation & pop = (*uIter)->GetPopulation();
403		403
404	std::string name(reg.GetName().c_str());	404	std::string name((const char*)reg.GetName().c_str());
405	ModelDS newModel((*iter)->m_lamarcDS->getFirstRegion()->second.getDataModel());	405	ModelDS newModel((*iter)->m_lamarcDS->getFirstRegion()->second.getDataModel());
406	RegionDS thisRegion(name,newModel);	406	RegionDS thisRegion(name,newModel);
407		407
Lines 410-416 Link Here
410	if(reg.m_mapFile != NULL)	410	if(reg.m_mapFile != NULL)
411	{	411	{
412	SpaceMap & spaces = reg.m_mapFile->GetSpaceMap();	412	SpaceMap & spaces = reg.m_mapFile->GetSpaceMap();
413	std::string stdRegionName = std::string(reg.GetName().c_str());	413	std::string stdRegionName = std::string((const char*)reg.GetName().c_str());
414	if(spaces.find(stdRegionName) != spaces.end())	414	if(spaces.find(stdRegionName) != spaces.end())
415	{	415	{
416	try	416	try
Lines 474-480 Link Here
474	thisRegion.setSpacing(*(spacing));	474	thisRegion.setSpacing(*(spacing));
475	}	475	}
476		476
477	std::string stdName(pop.GetName().c_str());	477	std::string stdName((const char*)pop.GetName().c_str());
478	PopulationDS thisPop(stdName);	478	PopulationDS thisPop(stdName);
479	PopMap::iterator pIter = (*uIter)->m_popMapIter;	479	PopMap::iterator pIter = (*uIter)->m_popMapIter;
480	thisPop.AddIndividuals((*pIter).second.GetAllIndividuals());	480	thisPop.AddIndividuals((*pIter).second.GetAllIndividuals());
Lines 483-489 Link Here
483	wxString hapFileName = (*uIter)->GetHapFileName();	483	wxString hapFileName = (*uIter)->GetHapFileName();
484	if(!hapFileName.IsEmpty())	484	if(!hapFileName.IsEmpty())
485	{	485	{
486	std::string stdHapFileName(hapFileName.c_str());	486	std::string stdHapFileName((const char*)hapFileName.c_str());
487	HapConverter hapconverter(thisRegion,randomgenerator);	487	HapConverter hapconverter(thisRegion,randomgenerator);
488	vector<IndividualDS> individuals =	488	vector<IndividualDS> individuals =
489	hapconverter.ReadHapInfo(stdHapFileName);	489	hapconverter.ReadHapInfo(stdHapFileName);
Lines 495-501 Link Here
495	}	495	}
496		496
497		497
498	ofstream outFile(fileName.c_str(), ios::out);	498	ofstream outFile((const char*)fileName.c_str(), ios::out);
499	if(!outFile)	499	if(!outFile)
500	{	500	{
501	GCError(	501	GCError(

Lines 131-147 Link Here

(-)lamarc-2.0.2/src/guiconv/gc_data.cpp (-21 / +21 lines)
131	static wxArrayString digits;	131	static wxArrayString digits;
132	if(digits.GetCount() < 1)	132	if(digits.GetCount() < 1)
133	{	133	{
134	digits.Add("-");	134	digits.Add(wxT("-"));
135	digits.Add("0");	135	digits.Add(wxT("0"));
136	digits.Add("1");	136	digits.Add(wxT("1"));
137	digits.Add("2");	137	digits.Add(wxT("2"));
138	digits.Add("3");	138	digits.Add(wxT("3"));
139	digits.Add("4");	139	digits.Add(wxT("4"));
140	digits.Add("5");	140	digits.Add(wxT("5"));
141	digits.Add("6");	141	digits.Add(wxT("6"));
142	digits.Add("7");	142	digits.Add(wxT("7"));
143	digits.Add("8");	143	digits.Add(wxT("8"));
144	digits.Add("9");	144	digits.Add(wxT("9"));
145	}	145	}
146	return digits;	146	return digits;
147	}	147	}
Lines 152-167 Link Here
152	static wxArrayString digits;	152	static wxArrayString digits;
153	if(digits.GetCount() < 1)	153	if(digits.GetCount() < 1)
154	{	154	{
155	digits.Add("0");	155	digits.Add(wxT("0"));
156	digits.Add("1");	156	digits.Add(wxT("1"));
157	digits.Add("2");	157	digits.Add(wxT("2"));
158	digits.Add("3");	158	digits.Add(wxT("3"));
159	digits.Add("4");	159	digits.Add(wxT("4"));
160	digits.Add("5");	160	digits.Add(wxT("5"));
161	digits.Add("6");	161	digits.Add(wxT("6"));
162	digits.Add("7");	162	digits.Add(wxT("7"));
163	digits.Add("8");	163	digits.Add(wxT("8"));
164	digits.Add("9");	164	digits.Add(wxT("9"));
165	}	165	}
166	return digits;	166	return digits;
167	}	167	}

Lines 35-106 Link Here

(-)lamarc-2.0.2/src/guiconv/gc_frame.cpp (-26 / +26 lines)
35	{	35	{
36	// Setting up menu items within Converter Menu	36	// Setting up menu items within Converter Menu
37	wxMenu * GCFirstMenu = new wxMenu;	37	wxMenu * GCFirstMenu = new wxMenu;
38	GCFirstMenu->Append( GC_Quit, "&Quit" );	38	GCFirstMenu->Append( GC_Quit, wxT("&Quit"));
39		39
40	// Setting up menu items within File Menu	40	// Setting up menu items within File Menu
41	m_fileMenu = new wxMenu;	41	m_fileMenu = new wxMenu;
42	m_fileMenu->Append( GC_AddFiles, "&Add Data File(s)");	42	m_fileMenu->Append( GC_AddFiles, wxT("&Add Data File(s)"));
43	m_fileMenu->AppendSeparator();	43	m_fileMenu->AppendSeparator();
44	m_fileMenu->Append( GC_SetAllFormats, "Set all File &Formats to one kind");	44	m_fileMenu->Append( GC_SetAllFormats, wxT("Set all File &Formats to one kind"));
45	m_fileMenu->Append( GC_SetAllDataTypes, "Set all &Data Types to one kind");	45	m_fileMenu->Append( GC_SetAllDataTypes, wxT("Set all &Data Types to one kind"));
46	m_fileMenu->AppendSeparator();	46	m_fileMenu->AppendSeparator();
47	m_fileMenu->Append( GC_ExportFile, "E&xport Lamarc File");	47	m_fileMenu->Append( GC_ExportFile, wxT("E&xport Lamarc File"));
48	m_fileMenu->Enable( GC_ExportFile, false);	48	m_fileMenu->Enable( GC_ExportFile, false);
49		49
50	// Setting up menu items within Populations Menu	50	// Setting up menu items within Populations Menu
51	m_populationMenu = new wxMenu;	51	m_populationMenu = new wxMenu;
52	m_populationMenu->Append( GC_AddPopulation, "&Add a Population");	52	m_populationMenu->Append( GC_AddPopulation, wxT("&Add a Population"));
53	m_populationMenu->Append( GC_RenamePopulation, "&Rename a Population");	53	m_populationMenu->Append( GC_RenamePopulation, wxT("&Rename a Population"));
54	m_populationMenu->Enable( GC_RenamePopulation, false);	54	m_populationMenu->Enable( GC_RenamePopulation, false);
55	m_populationMenu->Append( GC_SetAllOnePopulation, "Assign All Data Units to &One Population");	55	m_populationMenu->Append( GC_SetAllOnePopulation, wxT("Assign All Data Units to &One Population"));
56	m_populationMenu->Enable( GC_SetAllOnePopulation, false);	56	m_populationMenu->Enable( GC_SetAllOnePopulation, false);
57	/* EWFIX.LATER	57	/* EWFIX.LATER
58	m_populationMenu->Append( GC_SetAllDifferentPopulations, "Assign All Data Units to &Different Populations");	58	m_populationMenu->Append( GC_SetAllDifferentPopulations, "Assign All Data Units to &Different Populations");
59	m_populationMenu->Enable( GC_SetAllDifferentPopulations, false);	59	m_populationMenu->Enable( GC_SetAllDifferentPopulations, false);
60	*/	60	*/
61	m_populationMenu->Append( GC_RemoveUnusedPopulations, "Remove &Unused Populations");	61	m_populationMenu->Append( GC_RemoveUnusedPopulations, wxT("Remove &Unused Populations"));
62	/* EWFIX.LATER	62	/* EWFIX.LATER
63	m_populationMenu->Enable( GC_RemoveUnusedPopulations, false);	63	m_populationMenu->Enable( GC_RemoveUnusedPopulations, false);
64	*/	64	*/
65		65
66	// Setting up menu items within Regions Menu	66	// Setting up menu items within Regions Menu
67	m_regionMenu = new wxMenu;	67	m_regionMenu = new wxMenu;
68	m_regionMenu->Append( GC_AddRegion, "&Add a Region");	68	m_regionMenu->Append( GC_AddRegion, wxT("&Add a Region"));
69	m_regionMenu->Append( GC_RenameRegion, "&Rename a Region");	69	m_regionMenu->Append( GC_RenameRegion, wxT("&Rename a Region"));
70	m_regionMenu->Enable( GC_RenameRegion, false);	70	m_regionMenu->Enable( GC_RenameRegion, false);
71	m_regionMenu->Append( GC_SetAllOneRegion, "Assign All Data Units to &One Region");	71	m_regionMenu->Append( GC_SetAllOneRegion, wxT("Assign All Data Units to &One Region"));
72	m_regionMenu->Enable( GC_SetAllOneRegion, false);	72	m_regionMenu->Enable( GC_SetAllOneRegion, false);
73	/* EWFIX.LATER	73	/* EWFIX.LATER
74	m_regionMenu->Append( GC_SetAllDifferentRegions, "Assign All Data Units to &Different Regions");	74	m_regionMenu->Append( GC_SetAllDifferentRegions, "Assign All Data Units to &Different Regions");
75	m_regionMenu->Enable( GC_SetAllDifferentRegions, false);	75	m_regionMenu->Enable( GC_SetAllDifferentRegions, false);
76	*/	76	*/
77	m_regionMenu->Append( GC_RemoveUnusedRegions, "Remove &Unused Regions");	77	m_regionMenu->Append( GC_RemoveUnusedRegions, wxT("Remove &Unused Regions"));
78	/* EWFIX.LATER	78	/* EWFIX.LATER
79	m_regionMenu->Enable( GC_RemoveUnusedRegions, false);	79	m_regionMenu->Enable( GC_RemoveUnusedRegions, false);
80	*/	80	*/
81		81
82	// Setting up menu items within Help menu	82	// Setting up menu items within Help menu
83	wxMenu * GCHelpMenu = new wxMenu;	83	wxMenu * GCHelpMenu = new wxMenu;
84	GCHelpMenu->Append( GC_About, "&About..." );	84	GCHelpMenu->Append( GC_About, wxT("&About..."));
85	GCHelpMenu->Append( GC_DescribeErrors, "&Describe Errors");	85	GCHelpMenu->Append( GC_DescribeErrors, wxT("&Describe Errors"));
86		86
87	// Setting up menu items within Debug menu	87	// Setting up menu items within Debug menu
88	wxMenu * GCDebugMenu = new wxMenu;	88	wxMenu * GCDebugMenu = new wxMenu;
89	GCDebugMenu->Append(GC_DebugDump, "&Dump..." );	89	GCDebugMenu->Append(GC_DebugDump, wxT("&Dump..."));
90		90
91		91
92	// Placing top-level items on Menu Bar	92	// Placing top-level items on Menu Bar
93	wxMenuBar *GCMenuBar = new wxMenuBar;	93	wxMenuBar *GCMenuBar = new wxMenuBar;
94	// We don't need this menu for WXMAC since it creates it automatically	94	// We don't need this menu for WXMAC since it creates it automatically
95	#ifndef __WXMAC__	95	#ifndef __WXMAC__
96	GCMenuBar->Append( GCFirstMenu, "&Converter" );	96	GCMenuBar->Append( GCFirstMenu, wxT("&Converter") );
97	#endif	97	#endif
98	GCMenuBar->Append( m_fileMenu, "&File" );	98	GCMenuBar->Append( m_fileMenu, wxT("&File") );
99	GCMenuBar->Append( m_populationMenu,"&Populations" );	99	GCMenuBar->Append( m_populationMenu,wxT("&Populations") );
100	GCMenuBar->Append( m_regionMenu, "&Regions" );	100	GCMenuBar->Append( m_regionMenu, wxT("&Regions") );
101	GCMenuBar->Append( GCHelpMenu, "&Help" );	101	GCMenuBar->Append( GCHelpMenu, wxT("&Help") );
102	#ifndef NDEBUG	102	#ifndef NDEBUG
103	GCMenuBar->Append( GCDebugMenu, "&Debug" );	103	GCMenuBar->Append( GCDebugMenu, wxT("&Debug") );
104	#endif	104	#endif
105		105
106	// Installing Menu Bar	106	// Installing Menu Bar
Lines 332-338 Link Here
332	int numErrors = m_warningStrings.GetCount();	332	int numErrors = m_warningStrings.GetCount();
333	for(int i=0; i < numErrors; i++)	333	for(int i=0; i < numErrors; i++)
334	{	334	{
335	errorMessage += "\n\n";	335	errorMessage += wxT("\n\n");
336	errorMessage += m_warningStrings[i];	336	errorMessage += m_warningStrings[i];
337	}	337	}
338	m_logic.GCWarning(errorMessage);	338	m_logic.GCWarning(errorMessage);
Lines 584-590 Link Here
584	eventToSend = S2D_Menu_SetAllOneRegion;	584	eventToSend = S2D_Menu_SetAllOneRegion;
585	break;	585	break;
586	default:	586	default:
587	wxLogDebug("Need to handle menu event %d",event.GetId());	587	wxLogDebug(wxT("Need to handle menu event %d"),event.GetId());
588	assert(false);	588	assert(false);
589	break;	589	break;
590	};	590	};
Lines 601-607 Link Here
601	UpdateUserCues();	601	UpdateUserCues();
602	break;	602	break;
603	default:	603	default:
604	wxLogDebug("Need to handle D2S event %d",event.GetId());	604	wxLogDebug(wxT("Need to handle D2S event %d"),event.GetId());
605	assert(false);	605	assert(false);
606	break;	606	break;
607	}	607	}
Lines 717-723 Link Here
717	OnSetRegion(event);	717	OnSetRegion(event);
718	break;	718	break;
719	default:	719	default:
720	wxLogDebug("Need to handle S2D event %d",event.GetId());	720	wxLogDebug(wxT("Need to handle S2D event %d"),event.GetId());
721	assert(false);	721	assert(false);
722	break;	722	break;
723	}	723	}

Lines 21-30 Link Here

(-)lamarc-2.0.2/src/convModel/gc_hapfile.cpp (-9 / +9 lines)
21	// EWFIX -- this is kinda bogus -- we are reading the	21	// EWFIX -- this is kinda bogus -- we are reading the
22	// file first with an ifstream becuase the wxFileInputStream	22	// file first with an ifstream becuase the wxFileInputStream
23	// below produces errors in a way we don't like.	23	// below produces errors in a way we don't like.
24	std::ifstream haplotypefile(hapFileName.c_str(),std::ios::in);	24	std::ifstream haplotypefile((const char*)hapFileName.c_str(),std::ios::in);
25	if(!haplotypefile)	25	if(!haplotypefile)
26	{	26	{
27	throw FileFormatError(	27	throw FileFormatError((const char*)
28	wxString::Format(gcstr::hapFileMissing,	28	wxString::Format(gcstr::hapFileMissing,
29	m_hapFileName.c_str()).c_str());	29	m_hapFileName.c_str()).c_str());
30	}	30	}
Lines 34-40 Link Here
34	{	34	{
35	// ifstream code above should prevent us from getting here	35	// ifstream code above should prevent us from getting here
36	assert(false);	36	assert(false);
37	throw FileFormatError(	37	throw FileFormatError((const char*)
38	wxString::Format(gcstr::hapFileBarf,	38	wxString::Format(gcstr::hapFileBarf,
39	m_hapFileName.c_str()).c_str());	39	m_hapFileName.c_str()).c_str());
40	}	40	}
Lines 42-62 Link Here
42	wxString firstLine = wxTextInputStream(hapFileStream).ReadLine();	42	wxString firstLine = wxTextInputStream(hapFileStream).ReadLine();
43	if(firstLine.IsEmpty())	43	if(firstLine.IsEmpty())
44	{	44	{
45	throw FileFormatError(	45	throw FileFormatError((const char*)
46	wxString::Format(gcstr::hapFileEmptyFirstLine,	46	wxString::Format(gcstr::hapFileEmptyFirstLine,
47	m_hapFileName.c_str()).c_str());	47	m_hapFileName.c_str()).c_str());
48	}	48	}
49	wxStringTokenizer tokens(firstLine);	49	wxStringTokenizer tokens(firstLine);
50	if(!tokens.HasMoreTokens())	50	if(!tokens.HasMoreTokens())
51	{	51	{
52	throw FileFormatError(	52	throw FileFormatError((const char*)
53	wxString::Format(gcstr::hapFileEmptyFirstLine,	53	wxString::Format(gcstr::hapFileEmptyFirstLine,
54	m_hapFileName.c_str()).c_str());	54	m_hapFileName.c_str()).c_str());
55	}	55	}
56	wxString token = tokens.GetNextToken();	56	wxString token = tokens.GetNextToken();
57	if(!token.ToLong(&m_nIndividuals))	57	if(!token.ToLong(&m_nIndividuals))
58	{	58	{
59	throw FileFormatError(	59	throw FileFormatError((const char*)
60	wxString::Format(gcstr::hapFileToken1,	60	wxString::Format(gcstr::hapFileToken1,
61	m_hapFileName.c_str(),	61	m_hapFileName.c_str(),
62	token.c_str()	62	token.c_str()
Lines 67-73 Link Here
67	token = tokens.GetNextToken();	67	token = tokens.GetNextToken();
68	if(token != gcstr::adjacent)	68	if(token != gcstr::adjacent)
69	{	69	{
70	throw FileFormatError(	70	throw FileFormatError((const char*)
71	wxString::Format(gcstr::hapFileToken2,	71	wxString::Format(gcstr::hapFileToken2,
72	m_hapFileName.c_str(),	72	m_hapFileName.c_str(),
73	token.c_str()	73	token.c_str()
Lines 76-89 Link Here
76	m_adjacent = true;	76	m_adjacent = true;
77	if(!tokens.HasMoreTokens())	77	if(!tokens.HasMoreTokens())
78	{	78	{
79	throw FileFormatError(	79	throw FileFormatError((const char*)
80	wxString::Format(gcstr::hapFileToken3Missing,	80	wxString::Format(gcstr::hapFileToken3Missing,
81	m_hapFileName.c_str()).c_str());	81	m_hapFileName.c_str()).c_str());
82	}	82	}
83	token = tokens.GetNextToken();	83	token = tokens.GetNextToken();
84	if(!token.ToLong(&m_nHapsPerIndividual))	84	if(!token.ToLong(&m_nHapsPerIndividual))
85	{	85	{
86	throw FileFormatError(	86	throw FileFormatError((const char*)
87	wxString::Format(gcstr::hapFileToken3,	87	wxString::Format(gcstr::hapFileToken3,
88	m_hapFileName.c_str(),	88	m_hapFileName.c_str(),
89	token.c_str()	89	token.c_str()

Lines 7-13 Link Here

(-)lamarc-2.0.2/src/convModel/gc_mapfile.cpp (-5 / +5 lines)
7	{	7	{
8	LamarcDS lam;	8	LamarcDS lam;
9	SpaceConverter converter(lam);	9	SpaceConverter converter(lam);
10	m_spaceMap = converter.ReadSpacingInfo(std::string(m_mapFileName.c_str()));	10	m_spaceMap = converter.ReadSpacingInfo(std::string((const char*)m_mapFileName.c_str()));
11	}	11	}
12		12
13	GCMapFile::~GCMapFile()	13	GCMapFile::~GCMapFile()
Lines 17-23 Link Here
17	bool	17	bool
18	GCMapFile::ContainsRegion(GCRegion & regionRef)	18	GCMapFile::ContainsRegion(GCRegion & regionRef)
19	{	19	{
20	std::string stdRegionName = std::string(regionRef.GetName().c_str());	20	std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
21	return (m_spaceMap.find(stdRegionName) != m_spaceMap.end());	21	return (m_spaceMap.find(stdRegionName) != m_spaceMap.end());
22		22
23	}	23	}
Lines 26-32 Link Here
26	GCMapFile::FirstPosition(GCRegion & regionRef)	26	GCMapFile::FirstPosition(GCRegion & regionRef)
27	{	27	{
28	assert(ContainsRegion(regionRef));	28	assert(ContainsRegion(regionRef));
29	std::string stdRegionName = std::string(regionRef.GetName().c_str());	29	std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
30	std::vector<long> spacing = m_spaceMap[stdRegionName];	30	std::vector<long> spacing = m_spaceMap[stdRegionName];
31	return spacing[0];	31	return spacing[0];
32	}	32	}
Lines 35-41 Link Here
35	GCMapFile::LastPosition(GCRegion & regionRef)	35	GCMapFile::LastPosition(GCRegion & regionRef)
36	{	36	{
37	assert(ContainsRegion(regionRef));	37	assert(ContainsRegion(regionRef));
38	std::string stdRegionName = std::string(regionRef.GetName().c_str());	38	std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
39	std::vector<long> spacing = m_spaceMap[stdRegionName];	39	std::vector<long> spacing = m_spaceMap[stdRegionName];
40	return spacing[spacing.size() - 1];	40	return spacing[spacing.size() - 1];
41	}	41	}
Lines 51-57 Link Here
51	GCMapFile::NumPositions(GCRegion & regionRef)	51	GCMapFile::NumPositions(GCRegion & regionRef)
52	{	52	{
53	assert(ContainsRegion(regionRef));	53	assert(ContainsRegion(regionRef));
54	std::string stdRegionName = std::string(regionRef.GetName().c_str());	54	std::string stdRegionName = std::string((const char*)regionRef.GetName().c_str());
55	std::vector<long> spacing = m_spaceMap[stdRegionName];	55	std::vector<long> spacing = m_spaceMap[stdRegionName];
56	return spacing.size();	56	return spacing.size();
57	}	57	}

Lines 2-9 Link Here

(-)lamarc-2.0.2/src/guiconv/gc_strings.cpp (-17 / +17 lines)
2	#include "gc_strings.h"	2	#include "gc_strings.h"
3	#include "wx/intl.h"	3	#include "wx/intl.h"
4		4
5	const wxString gcstr::adjacent = "adjacent";	5	const wxString gcstr::adjacent = wxT("adjacent");
6	const wxString gcstr::allFiles = "*";	6	const wxString gcstr::allFiles = wxT("*");
7	const wxString gcstr::badRegionLength1 = wxTRANSLATE("The following regions have suspiciously short lengths:");	7	const wxString gcstr::badRegionLength1 = wxTRANSLATE("The following regions have suspiciously short lengths:");
8	const wxString gcstr::badRegionLength2 = wxTRANSLATE("You may wish to cancel this operation and edit region lengths in the Genomic Region Properties tab");	8	const wxString gcstr::badRegionLength2 = wxTRANSLATE("You may wish to cancel this operation and edit region lengths in the Genomic Region Properties tab");
9	const wxString gcstr::cancelString = wxTRANSLATE("Cancel");	9	const wxString gcstr::cancelString = wxTRANSLATE("Cancel");
Lines 15-26 Link Here
15	const wxString gcstr::converterTitle = wxTRANSLATE("LAMARC File Converter");	15	const wxString gcstr::converterTitle = wxTRANSLATE("LAMARC File Converter");
16	const wxString gcstr::dataFileExport = wxTRANSLATE("Select data files to write");	16	const wxString gcstr::dataFileExport = wxTRANSLATE("Select data files to write");
17	const wxString gcstr::dataFilesSelect = wxTRANSLATE("Select data files to read");	17	const wxString gcstr::dataFilesSelect = wxTRANSLATE("Select data files to read");
18	const wxString gcstr::dna = "DNA";	18	const wxString gcstr::dna = wxT("DNA");
19	const wxString gcstr::error = wxTRANSLATE("ERROR");	19	const wxString gcstr::error = wxTRANSLATE("ERROR");
20	const wxString gcstr::errorWrap = wxTRANSLATE("Error Type \"%s\" for file \"%s\":\n%s");	20	const wxString gcstr::errorWrap = wxTRANSLATE("Error Type \"%s\" for file \"%s\":\n%s");
21	const wxString gcstr::errorWrapNoFile = wxTRANSLATE("Error Type \"%s\":\n%s");	21	const wxString gcstr::errorWrapNoFile = wxTRANSLATE("Error Type \"%s\":\n%s");
22	const wxString gcstr::exportFileDefault = "infile.lam";	22	const wxString gcstr::exportFileDefault = wxT("infile.lam");
23	const wxString gcstr::exportFileGlob = "Lamarc files (.lam)\|.lam\|All files ()\|";	23	const wxString gcstr::exportFileGlob = wxT("Lamarc files (.lam)\|.lam\|All files ()\|");
24	const wxString gcstr::exportWarning = wxTRANSLATE("Warning: export may not be correct");	24	const wxString gcstr::exportWarning = wxTRANSLATE("Warning: export may not be correct");
25	const wxString gcstr::fileAlreadyAdded = wxTRANSLATE("Cannot add file \"%s\". It is already added.");	25	const wxString gcstr::fileAlreadyAdded = wxTRANSLATE("Cannot add file \"%s\". It is already added.");
26	const wxString gcstr::fileDoesNotExist = wxTRANSLATE("File \"%s\" does not exist or is not readable.");	26	const wxString gcstr::fileDoesNotExist = wxTRANSLATE("File \"%s\" does not exist or is not readable.");
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30	const wxString gcstr::fileLabelName = wxTRANSLATE("File Name");	30	const wxString gcstr::fileLabelName = wxTRANSLATE("File Name");
31	const wxString gcstr::fileLabelRemove = wxTRANSLATE("Remove File");	31	const wxString gcstr::fileLabelRemove = wxTRANSLATE("Remove File");
32	const wxString gcstr::fileLabelUnlinked = wxTRANSLATE("Unlink Microsats");	32	const wxString gcstr::fileLabelUnlinked = wxTRANSLATE("Unlink Microsats");
33	const wxString gcstr::globAll = "*";	33	const wxString gcstr::globAll = wxT("*");
34	const wxString gcstr::hapFileEmptyFirstLine = wxTRANSLATE("No data found in first line of phase information file \"%s\"");	34	const wxString gcstr::hapFileEmptyFirstLine = wxTRANSLATE("No data found in first line of phase information file \"%s\"");
35	const wxString gcstr::hapFileBarf = wxTRANSLATE("Implementation error reading phase information file \"%s\"");	35	const wxString gcstr::hapFileBarf = wxTRANSLATE("Implementation error reading phase information file \"%s\"");
36	const wxString gcstr::hapFileMissing = wxTRANSLATE("Phase information file \"%s\" missing or un-readable");	36	const wxString gcstr::hapFileMissing = wxTRANSLATE("Phase information file \"%s\" missing or un-readable");
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42	const wxString gcstr::hapFileSelectAnother = wxTRANSLATE("file not listed here");	42	const wxString gcstr::hapFileSelectAnother = wxTRANSLATE("file not listed here");
43	const wxString gcstr::hapFileUnSelect = wxTRANSLATE("un-select current file");	43	const wxString gcstr::hapFileUnSelect = wxTRANSLATE("un-select current file");
44	const wxString gcstr::information = wxTRANSLATE("Information");	44	const wxString gcstr::information = wxTRANSLATE("Information");
45	const wxString gcstr::kallele = "Kallele";	45	const wxString gcstr::kallele = wxT("Kallele");
46	const wxString gcstr::mapFileExportFailed = wxTRANSLATE("File export failed while reading data for region \"%s\". \n\nThe error was \"%s:%s\n\nPlease check your settings for that region and please report the error.");	46	const wxString gcstr::mapFileExportFailed = wxTRANSLATE("File export failed while reading data for region \"%s\". \n\nThe error was \"%s:%s\n\nPlease check your settings for that region and please report the error.");
47	const wxString gcstr::mapFileLastPositionTooLate =	47	const wxString gcstr::mapFileLastPositionTooLate =
48	wxTRANSLATE("Map position file \"%s\" has last position of %ld, but region \"%s\" length (%ld) and first position sequenced (%ld) allow last position of %ld or less only");	48	wxTRANSLATE("Map position file \"%s\" has last position of %ld, but region \"%s\" length (%ld) and first position sequenced (%ld) allow last position of %ld or less only");
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54	const wxString gcstr::mapFileSelect = wxTRANSLATE("select map position file");	54	const wxString gcstr::mapFileSelect = wxTRANSLATE("select map position file");
55	const wxString gcstr::mapFileSelectAnother = wxTRANSLATE("file not listed here");	55	const wxString gcstr::mapFileSelectAnother = wxTRANSLATE("file not listed here");
56	const wxString gcstr::mapFileUnSelect = wxTRANSLATE("un-select current file");	56	const wxString gcstr::mapFileUnSelect = wxTRANSLATE("un-select current file");
57	const wxString gcstr::microsat = "Microsat";	57	const wxString gcstr::microsat = wxT("Microsat");
58	const wxString gcstr::migrate = "Migrate";	58	const wxString gcstr::migrate = wxT("Migrate");
59	const wxString gcstr::migrateFileTypeClash =wxTRANSLATE("Setting data type to \"%s\" even though file \"%s\" specifies type \"%s\".");	59	const wxString gcstr::migrateFileTypeClash =wxTRANSLATE("Setting data type to \"%s\" even though file \"%s\" specifies type \"%s\".");
60	const wxString gcstr::newName = wxTRANSLATE("New name");	60	const wxString gcstr::newName = wxTRANSLATE("New name");
61	const wxString gcstr::notebookLabelDataTab = wxTRANSLATE("Data Files");	61	const wxString gcstr::notebookLabelDataTab = wxTRANSLATE("Data Files");
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63	const wxString gcstr::notebookLabelRegionTab = wxTRANSLATE("Genomic Region Properties");	63	const wxString gcstr::notebookLabelRegionTab = wxTRANSLATE("Genomic Region Properties");
64	const wxString gcstr::noWarningsFound = wxTRANSLATE("No warning messages were found. You should be able to export a lamarc file now");	64	const wxString gcstr::noWarningsFound = wxTRANSLATE("No warning messages were found. You should be able to export a lamarc file now");
65	const wxString gcstr::parseWarning = wxTRANSLATE("Conflict while parsing file");	65	const wxString gcstr::parseWarning = wxTRANSLATE("Conflict while parsing file");
66	const wxString gcstr::phylip = "Phylip";	66	const wxString gcstr::phylip = wxT("Phylip");
67	const wxString gcstr::plainLong = "%ld";	67	const wxString gcstr::plainLong = wxT("%ld");
68	const wxString gcstr::populationExists = wxTRANSLATE("Population \"%s\" already exists.");	68	const wxString gcstr::populationExists = wxTRANSLATE("Population \"%s\" already exists.");
69	const wxString gcstr::populationCreate = wxTRANSLATE("Create new Population");	69	const wxString gcstr::populationCreate = wxTRANSLATE("Create new Population");
70	const wxString gcstr::populationEnterNewName= wxTRANSLATE("Enter the name of the new population");	70	const wxString gcstr::populationEnterNewName= wxTRANSLATE("Enter the name of the new population");
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103	const wxString gcstr::unitLabelNumTips = wxTRANSLATE("Sequences");	103	const wxString gcstr::unitLabelNumTips = wxTRANSLATE("Sequences");
104	const wxString gcstr::unitLabelSetPopulation = wxTRANSLATE("Population");	104	const wxString gcstr::unitLabelSetPopulation = wxTRANSLATE("Population");
105	const wxString gcstr::unitLabelSetRegion = wxTRANSLATE("Genomic Region");	105	const wxString gcstr::unitLabelSetRegion = wxTRANSLATE("Genomic Region");
106	const wxString gcstr::snp = "SNP";	106	const wxString gcstr::snp = wxT("SNP");
107	const wxString gcstr::warning = wxTRANSLATE("Warning");	107	const wxString gcstr::warning = wxTRANSLATE("Warning");
108	const wxString gcstr::warningMissingPopRegPair = wxTRANSLATE("Missing data sample covering (%s,%s) pair");	108	const wxString gcstr::warningMissingPopRegPair = wxTRANSLATE("Missing data sample covering (%s,%s) pair");
109	const wxString gcstr::warningNeedFile = wxTRANSLATE("Add one or more files");	109	const wxString gcstr::warningNeedFile = wxTRANSLATE("Add one or more files");
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112	const wxString gcstr::warningStringsHeader = wxTRANSLATE("You will need to fix the following things before you can create a Lamarc output file:");	112	const wxString gcstr::warningStringsHeader = wxTRANSLATE("You will need to fix the following things before you can create a Lamarc output file:");
113	const wxString gcstr::warningUnsetPopulation = wxTRANSLATE("At least one data unit has no population assigned");	113	const wxString gcstr::warningUnsetPopulation = wxTRANSLATE("At least one data unit has no population assigned");
114	const wxString gcstr::warningUnsetRegion = wxTRANSLATE("At least one data unit has no region assigned");	114	const wxString gcstr::warningUnsetRegion = wxTRANSLATE("At least one data unit has no region assigned");
115	const wxString gcstr::unknown = "???";	115	const wxString gcstr::unknown = wxT("???");
116	const wxString gcstr::unsetPopulation = wxTRANSLATE("unset population");	116	const wxString gcstr::unsetPopulation = wxTRANSLATE("unset population");
117	const wxString gcstr::unsetRegion = wxTRANSLATE("unset region");	117	const wxString gcstr::unsetRegion = wxTRANSLATE("unset region");
118		118
119		119
120	const wxString gcstr::cmdInput = "input";	120	const wxString gcstr::cmdInput = wxT("input");
121	const wxString gcstr::cmdInputChar = "i";	121	const wxString gcstr::cmdInputChar = wxT("i");
122	const wxString gcstr::cmdInputDesc = wxTRANSLATE("input file");	122	const wxString gcstr::cmdInputDesc = wxTRANSLATE("input file");
123	const wxString gcstr::cmdOutput = "output";	123	const wxString gcstr::cmdOutput = wxT("output");
124	const wxString gcstr::cmdOutputChar = "o";	124	const wxString gcstr::cmdOutputChar = wxT("o");
125	const wxString gcstr::cmdOutputDesc = wxTRANSLATE("output file");	125	const wxString gcstr::cmdOutputDesc = wxTRANSLATE("output file");