void CRepositoryBrowser::Refresh()
{
BeginWaitCursor();
if (m_nExternalOvl >= 0)
SYS_IMAGE_LIST().SetOverlayImage(m_nExternalOvl, OVERLAY_EXTERNAL);
m_RepoTree.DeleteAllItems();
m_RepoList.DeleteAllItems();
m_TreeRoot.m_ShadowTree.clear();
m_TreeRoot.m_sName = "";
m_TreeRoot.m_bFolder = true;
TVINSERTSTRUCT tvinsert = {0};
tvinsert.hParent = TVI_ROOT;
tvinsert.hInsertAfter = TVI_ROOT;
tvinsert.itemex.mask = TVIF_DI_SETITEM | TVIF_PARAM | TVIF_TEXT | TVIF_IMAGE | TVIF_SELECTEDIMAGE | TVIF_STATE;
tvinsert.itemex.pszText = L"/";
tvinsert.itemex.lParam = (LPARAM)&m_TreeRoot;
tvinsert.itemex.iImage = m_nIconFolder;
tvinsert.itemex.iSelectedImage = m_nOpenIconFolder;
m_TreeRoot.m_hTree= m_RepoTree.InsertItem(&tvinsert);
ReadTree(&m_TreeRoot);
m_RepoTree.Expand(m_TreeRoot.m_hTree, TVE_EXPAND);
FillListCtrlForShadowTree(&m_TreeRoot);
m_RepoTree.SelectItem(m_TreeRoot.m_hTree);
EndWaitCursor();
}
DirTree *DirTree_CreateFromFile(geVFile *File)
{
DirTree * Res;
DirTree_Header Header;
long StartPosition;
long EndPosition;
if (geVFile_Tell(File, &StartPosition) == GE_FALSE)
return GE_FALSE;
if (geVFile_Read(File, &Header, sizeof(Header)) == GE_FALSE)
return NULL;
if (Header.Signature != DIRTREE_FILE_SIGNATURE)
return GE_FALSE;
if (ReadTree(File, &Res) == GE_FALSE)
return NULL;
geVFile_Tell(File, &EndPosition);
if (Header.Size != EndPosition - StartPosition)
{
DirTree_Destroy(Res);
return NULL;
}
return Res;
}
void HuffmanProcessor::Decompress(char* input_filename)
{
input = ifstream(input_filename, ios::binary);
root = new Node();
ReadTree(root);
}
static bool ReadTree(LoaderState& State, const XMLObjectVector& vec)
{
XMLObjectVector ret;
bool success = true;
for (auto& obj : vec)
success &= loadObjectTree(State, obj, ret);
if (!ret.empty())
success &= ReadTree(State, ret);
return success;
}
void CRepositoryBrowser::OnTvnItemExpandingRepoTree(NMHDR *pNMHDR, LRESULT *pResult)
{
LPNMTREEVIEW pNMTreeView = reinterpret_cast<LPNMTREEVIEW>(pNMHDR);
*pResult = 0;
CShadowFilesTree* pTree = (CShadowFilesTree*)(m_RepoTree.GetItemData(pNMTreeView->itemNew.hItem));
if (pTree == NULL)
{
ASSERT(FALSE);
return;
}
if (!pTree->m_bLoaded)
{
pTree->m_bLoaded = true;
ReadTree(pTree, pTree->GetFullName());
}
}
bool loadTree(LoaderState& State, const char * sceneName, std::vector<RLIGHT>& Lights)
{
DMLog("loadTree %s\n", sceneName);
XMLActor actor;
XMLObjectVector ret;
XMLLightVector lights;
auto found = TryForEachPath(State.Paths, sceneName, [&](auto& Path) {
return XMLParser::parseScene(Path.c_str(), actor, ret, &lights);
});
if (!found)
{
MLog("loadTree -- Failed to load %s\n", sceneName);
return false;
}
else
DMLog("loadTree -- loaded %s\n", sceneName);
for (auto& srcLight : lights)
{
Lights.emplace_back();
auto& dstLight = Lights.back();
dstLight.Position = srcLight.Position;
dstLight.Color = srcLight.Diffuse;
dstLight.fAttnStart = srcLight.AttStart;
dstLight.fAttnEnd = srcLight.AttEnd;
dstLight.fIntensity = srcLight.Intensity;
dstLight.Name = srcLight.Name;
}
DMLog("loadTree -- actor.isValid = %d\n", actor.isValid);
if (actor.isValid)
{
if (!load(State, actor.eluName.c_str()))
{
MLog("loadTree(%s) -- Failed to load actor thing\n", sceneName);
}
}
ReadTree(State, ret);
return true;
}
bool loadPropTree(LoaderState& State, const char * propName)
{
DMLog("loadPropTree %s\n", propName);
XMLObjectVector ret;
auto found = TryForEachPath(State.Paths, propName, [&](auto& Path) {
return XMLParser::parseProp(Path.c_str(), ret);
});
if (!found)
{
MLog("loadPropTree -- Failed to load %s\n", propName);
return false;
}
ReadTree(State, ret);
return true;
}
void CRepositoryBrowser::FillListCtrlForTreeNode(HTREEITEM treeNode)
{
m_RepoList.DeleteAllItems();
CShadowFilesTree* pTree = (CShadowFilesTree*)(m_RepoTree.GetItemData(treeNode));
if (pTree == NULL)
{
ASSERT(FALSE);
return;
}
CString url = _T("/") + pTree->GetFullName();
GetDlgItem(IDC_REPOBROWSER_URL)->SetWindowText(url);
if (!pTree->m_bLoaded)
{
pTree->m_bLoaded = true;
ReadTree(pTree, pTree->GetFullName());
}
FillListCtrlForShadowTree(pTree);
}
int main(int argc, char **argv)
{
int i, j, k, treeNo, sumLength;
char ch;
TTree **treeSet;
FILE *text_fv;
clock_t totalStart;
double totalSecs, scale, sum;
char *ancestor;
totalStart = clock();
ReadParams(argc, argv);
if (rateHetero == CodonRates && invariableSites) {
fprintf(stderr, "Invariable sites model cannot be used with codon rate heterogeneity.\n");
exit(4);
}
if (writeAncestors && fileFormat == NEXUSFormat) {
fprintf(stderr, "Warning - When writing ancestral sequences, relaxed PHYLIP format is used.\n");
}
if (writeAncestors && maxPartitions > 1) {
fprintf(stderr, "Writing ancestral sequences can only be used for a single partition.\n");
exit(4);
}
if (!userSeed)
randomSeed = CreateSeed();
SetSeed(randomSeed);
if (!quiet)
PrintTitle();
numTrees = OpenTreeFile();
/* if (!treeFile) { */
ReadFileParams();
/*} */
if ((ancestorSeq>0 && !hasAlignment) || ancestorSeq>numSequences) {
fprintf(stderr, "Bad ancestral sequence number: %d (%d sequences loaded)\n", ancestorSeq, numSequences);
exit(4);
}
if (textFile) {
if ( (text_fv=fopen(textFileName, "rt"))==NULL ) {
fprintf(stderr, "Error opening text file for insertion into output: '%s'\n", textFileName);
exit(4);
}
}
ancestor=NULL;
if (hasAlignment) {
AllocateMemory();
ReadFile();
if (numSites<0)
numSites=numAlignmentSites;
if (ancestorSeq>0) {
if (numSites!=numAlignmentSites) {
fprintf(stderr, "Ancestral sequence is of a different length to the simulated sequences (%d)\n", numAlignmentSites);
exit(4);
}
ancestor=sequences[ancestorSeq-1];
}
} else if (numSites<0)
numSites=1000;
SetModel(model);
numTaxa=-1;
scale=1.0;
treeSet = (TTree **)malloc(sizeof(TTree **) * maxPartitions);
if (treeSet==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
partitionLengths = (int *)malloc(sizeof(int) * maxPartitions);
if (partitionLengths==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
partitionRates = (double *)malloc(sizeof(double) * maxPartitions);
if (partitionRates==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
for (i = 0; i < maxPartitions; i++) {
if ((treeSet[i]=NewTree())==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
}
CreateRates();
treeNo=0;
do {
partitionLengths[0] = -1;
ReadTree(tree_fv, treeSet[0], treeNo+1, 0, NULL, &partitionLengths[0], &partitionRates[0]);
if (treeNo==0) {
numTaxa=treeSet[0]->numTips;
if (!quiet)
fprintf(stderr, "Random number generator seed: %ld\n\n", randomSeed);
if (fileFormat == NEXUSFormat) {
fprintf(stdout, "#NEXUS\n");
fprintf(stdout, "[\nGenerated by %s %s\n\n", PROGRAM_NAME, VERSION_NUMBER);
PrintVerbose(stdout);
fprintf(stdout, "]\n\n");
}
} else if (treeSet[0]->numTips != numTaxa) {
fprintf(stderr, "All trees must have the same number of tips.\n");
exit(4);
}
if (maxPartitions == 1) {
if (partitionLengths[0] != -1) {
fprintf(stderr, "\nWARNING: The treefile contained partion lengths but only one partition\n");
fprintf(stderr, "was specified.\n");
}
partitionLengths[0] = numSites;
}
sumLength = partitionLengths[0];
i = 1;
while (sumLength < numSites && i <= maxPartitions) {
if (!IsTreeAvail(tree_fv)) {
fprintf(stderr, "\nA set of trees number %d had less partition length (%d) than\n", treeNo + 1, sumLength);
fprintf(stderr, "was required to make a sequence of length %d.\n", numSites);
exit(4);
}
ReadTree(tree_fv, treeSet[i], treeNo+1, treeSet[0]->numTips, treeSet[0]->names,
&partitionLengths[i], &partitionRates[i]);
if (treeSet[i]->numTips != numTaxa) {
fprintf(stderr, "All trees must have the same number of tips.\n");
exit(4);
}
sumLength += partitionLengths[i];
i++;
}
if (i > maxPartitions) {
fprintf(stderr, "\nA set of trees number %d had more partitions (%d) than\n", treeNo + 1, i);
fprintf(stderr, "was specified in the user options (%d).\n", maxPartitions);
}
numPartitions = i;
if (sumLength != numSites) {
fprintf(stderr, "The sum of the partition lengths in the treefile does not equal\n");
fprintf(stderr, "the specified number of sites.\n");
exit(4);
}
for (i = 0; i < numPartitions; i++)
CreateSequences(treeSet[i], partitionLengths[i]);
if (numPartitions > 1) {
sum = 0.0;
for (i = 0; i < numPartitions; i++)
sum += partitionRates[i] * partitionLengths[i];
for (i = 0; i < numPartitions; i++)
partitionRates[i] *= numSites / sum;
}
if (treeNo==0 && verbose && !quiet) {
PrintVerbose(stderr);
InitProgressBar(numTrees*numDatasets);
DrawProgressBar();
}
for (i=0; i<numDatasets; i++) {
SetCategories();
k = 0;
for (j = 0; j < numPartitions; j++) {
scale = partitionRates[j];
if (scaleTrees) {
if (!treeSet[j]->rooted) {
fprintf(stderr, "To scale tree length, they must be rooted and ultrametric.\n");
exit(4);
}
scale *= treeScale/treeSet[j]->totalLength;
} else if (scaleBranches)
scale *= branchScale;
EvolveSequences(treeSet[j], k, partitionLengths[j], scale, ancestor);
k += partitionLengths[j];
}
if (writeAncestors)
WriteAncestralSequences(stdout, treeSet[0]);
else
WriteSequences(stdout, (numTrees > 1 ? treeNo+1 : -1), (numDatasets > 1 ? i+1 : -1), treeSet, partitionLengths);
if (writeRates) {
WriteRates(stderr);
}
if (textFile) {
while (!feof(text_fv)) {
ch = fgetc(text_fv);
if (!feof(text_fv))
fputc(ch, stdout);
}
fputc('\n', stdout);
rewind(text_fv);
}
if (verbose && !quiet)
ProgressBar();
}
for (i = 0; i < numPartitions; i++)
DisposeTree(treeSet[i]);
treeNo++;
} while (IsTreeAvail(tree_fv));
/* for (i = 0; i < maxPartitions; i++)
FreeTree(treeSet[i]); */
if (treeFile)
fclose(tree_fv);
if (textFile)
fclose(text_fv);
totalSecs = (double)(clock() - totalStart) / CLOCKS_PER_SEC;
if (!quiet) {
fprintf(stderr, "Time taken: %G seconds\n", totalSecs);
if (verboseMemory)
fprintf(stderr, "Total memory used: %ld\n", totalMem);
}
return 0;
}
static geBoolean ReadTree(geVFile *File, DirTree **TreePtr)
{
int Terminator;
int Length;
DirTree * Tree;
if (geVFile_Read(File, &Terminator, sizeof(Terminator)) == GE_FALSE)
return GE_FALSE;
if (Terminator == DIRTREE_LIST_TERMINATED)
{
*TreePtr = NULL;
return GE_TRUE;
}
Tree = geRam_Allocate(sizeof(*Tree));
if (!Tree)
return GE_FALSE;
memset(Tree, 0, sizeof(*Tree));
// Read the name
if (geVFile_Read(File, &Length, sizeof(Length)) == GE_FALSE)
goto fail;
assert(Length > 0);
Tree->Name = geRam_Allocate(Length);
if (!Tree->Name)
{
geRam_Free(Tree);
return GE_FALSE;
}
if (geVFile_Read(File, Tree->Name, Length) == GE_FALSE)
goto fail;
//printf("Reading '%s'\n", Tree->Name);
// Read out the attribute information
if (geVFile_Read(File, &Tree->Time, sizeof(Tree->Time)) == GE_FALSE)
goto fail;
if (geVFile_Read(File, &Tree->AttributeFlags, sizeof(Tree->AttributeFlags)) == GE_FALSE)
goto fail;
if (geVFile_Read(File, &Tree->Size, sizeof(Tree->Size)) == GE_FALSE)
goto fail;
if (geVFile_Read(File, &Tree->Offset, sizeof(Tree->Offset)) == GE_FALSE)
goto fail;
if (geVFile_Read(File, &Tree->Hints.HintDataLength, sizeof(Tree->Hints.HintDataLength)) == GE_FALSE)
goto fail;
if (Tree->Hints.HintDataLength != 0)
{
Tree->Hints.HintData = geRam_Allocate(Tree->Hints.HintDataLength);
if (!Tree->Hints.HintData)
goto fail;
//bug fix. someone got copy happy and forgot to remove the & from Tree->Hints.HintData
if (geVFile_Read(File, Tree->Hints.HintData, Tree->Hints.HintDataLength) == GE_FALSE)
goto fail;
}
//printf("Reading children of '%s'\n", Tree->Name);
// Read the children
if (ReadTree(File, &Tree->Children) == GE_FALSE)
goto fail;
//printf("Reading siblings of '%s'\n", Tree->Name);
// Read the Siblings
if (ReadTree(File, &Tree->Siblings) == GE_FALSE)
goto fail;
//DirTree_Dump(Tree);
*TreePtr = Tree;
return GE_TRUE;
fail:
DirTree_Destroy(Tree);
return GE_FALSE;
}
