QString PWMatrixSearchPrompter::composeRichDoc() {
Actor* modelProducer = qobject_cast<IntegralBusPort*>(target->getPort(MODEL_PORT))->getProducer(PWMatrixWorkerFactory::WMATRIX_SLOT.getId());
Actor* seqProducer = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()))->getProducer(BaseSlots::DNA_SEQUENCE_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString seqName = tr("For each sequence from <u>%1</u>,").arg(seqProducer ? seqProducer->getLabel() : unsetStr);
QString modelName = tr("with all profiles provided by <u>%1</u>,").arg(modelProducer ? modelProducer->getLabel() : unsetStr);
QString resultName = getRequiredParam(NAME_ATTR);
resultName = getHyperlink(NAME_ATTR, resultName);
QString strandName;
switch (getStrand(getParameter(BaseAttributes::STRAND_ATTRIBUTE().getId()).value<QString>())) {
case 0: strandName = PWMatrixSearchWorker::tr("both strands"); break;
case 1: strandName = PWMatrixSearchWorker::tr("direct strand"); break;
case -1: strandName = PWMatrixSearchWorker::tr("complement strand"); break;
}
strandName = getHyperlink(BaseAttributes::STRAND_ATTRIBUTE().getId(), strandName);
QString doc = tr("%1 search transcription factor binding sites (TFBS) %2."
"<br>Recognize sites with <u>similarity %3%</u>, process <u>%4</u>."
"<br>Output the list of found regions annotated as <u>%5</u>.")
.arg(seqName)
.arg(modelName)
.arg(getHyperlink(SCORE_ATTR, getParameter(SCORE_ATTR).toInt()))
.arg(strandName)
.arg(resultName);
return doc;
}
QString SiteconWritePrompter::composeRichDoc() {
IntegralBusPort *input = qobject_cast<IntegralBusPort*>(target->getPort(SITECON_IN_PORT_ID));
SAFE_POINT(NULL != input, "NULL input port", "");
QString from = getProducersOrUnset(SITECON_IN_PORT_ID, SiteconWorkerFactory::SITECON_SLOT.getId());
QString url = getScreenedURL(input, BaseAttributes::URL_OUT_ATTRIBUTE().getId(), BaseSlots::URL_SLOT().getId());
url = getHyperlink(BaseAttributes::URL_OUT_ATTRIBUTE().getId(), url);
return tr("Save the profile(s) from <u>%1</u> to %2.").arg(from).arg(url);
}
QString CollocationPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
Actor* seqProducer = input->getProducer(SEQ_SLOT);
QString seqName = seqProducer ? tr(" sequence from <u>%1</u>").arg(seqProducer->getLabel()) : "";
QString annName = getProducers(BasePorts::IN_SEQ_PORT_ID(), FEATURE_TABLE_SLOT);
if (!annName.isEmpty()) {
annName = tr(" set of annotations from <u>%1</u>").arg(annName);
}
QString data;
if (seqName.isEmpty() && annName.isEmpty()) {
//return "<font color='red'>"+tr("unset")+"</font>";
} else if (!seqName.isEmpty() && !annName.isEmpty()) {
data = tr("For each %1 and %2,").arg(seqName).arg(annName);
} else {
data = tr("For each %1%2,").arg(seqName).arg(annName);
}
QString annotations;
QStringList names = annotations.split(QRegExp("\\W+"), QString::SkipEmptyParts).toSet().toList();
annotations = names.join(", ");
if (annotations.isEmpty()) {
annotations = getRequiredParam(ANN_ATTR);
}
annotations = getHyperlink(ANN_ATTR, annotations);
int distance = getParameter(LEN_ATTR).toInt();
bool mode = getParameter(FIT_ATTR).toBool();
QString extra;
if (mode) {
extra = tr(" Annotations themselves may not span beyond the region.");
}
QString resultName = getHyperlink(NAME_ATTR, getRequiredParam(NAME_ATTR));
QString doc = tr("%1 look if <u>%2</u> annotations appear collocated within same region of length <u>%3</u>.%4"
"<br>Output the list of found regions annotated as <u>%5</u>.")
.arg(data) //sequence from Read Fasta 1
.arg(annotations)
.arg(getHyperlink(LEN_ATTR, distance))
.arg(extra)
.arg(resultName);
return doc;
}
QString ConservationPlotPrompter::composeRichDoc() {
QString res = "";
Actor* annProducer = qobject_cast<IntegralBusPort*>(target->getPort(IN_PORT_DESCR))->getProducer(ANNOT_SLOT_ID);
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString annUrl = annProducer ? annProducer->getLabel() : unsetStr;
QString file = getHyperlink(OUTPUT_FILE, getURL(OUTPUT_FILE));
QString assembly = getHyperlink(ASSEMBLY_VER, getURL(ASSEMBLY_VER));
res.append(tr("Uses annotations from <u>%1</u> as peak regions for conservation plot.").arg(annUrl));
res.append(tr(" Conservations scores from <u>%1</u>.").arg(assembly));
res.append(tr(" Outputs the result to <u>%1</u>").arg(file));
res.append(".");
return res;
}
/*******************************
* FilterSequencePrompter
*******************************/
QString PassFilterPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort("in-data"));
Actor* producer = input->getProducer(BaseSlots::TEXT_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr("<u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
QString passVals = getRequiredParam(BaseSlots::TEXT_SLOT().getId());
passVals = getHyperlink(BaseSlots::TEXT_SLOT().getId(), passVals);
QString res = tr("Filters input data from %1 by value(s) %2.").arg(producerName).arg(passVals);
return res;
}
/******************************
* RepeatPrompter
******************************/
QString RepeatPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
Actor* producer = input->getProducer(BaseSlots::DNA_SEQUENCE_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr(" from <u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
// TODO extend ?
QString resultName = getRequiredParam(NAME_ATTR);
QString inverted = getParameter(INVERT_ATTR).toBool() ? tr("inverted") : tr("direct");
QString doc = tr("For each sequence%1, find <u>%2</u> repeats."
"<br>Detect <u>%3% identical</u> repeats <u>not shorter than %4 bps</u>."
"<br>Output the list of found regions annotated as <u>%5</u>.")
.arg(producerName) //sequence from Read Fasta 1
.arg(getHyperlink(INVERT_ATTR, inverted))
.arg(getHyperlink(IDENTITY_ATTR, getParameter(IDENTITY_ATTR).toInt()))
.arg(getHyperlink(LEN_ATTR, getParameter(LEN_ATTR).toInt()))
.arg(getHyperlink(NAME_ATTR, resultName));
return doc;
}
QString GenomeAlignerPrompter::composeRichDoc() {
QString res = "";
Actor* readsProducer = qobject_cast<IntegralBusPort*>(target->getPort(IN_PORT_DESCR))->getProducer(READS_URL_SLOT_ID);
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString readsUrl = readsProducer ? readsProducer->getLabel() : unsetStr;
QString genome = getHyperlink(REFERENCE_GENOME, getURL(REFERENCE_GENOME));
res.append(tr("Aligns reads from <u>%1</u> ").arg(readsUrl));
res.append(tr(" to reference genome <u>%1</u>.").arg(genome));
return res;
}
BOOL AP_Win32Dialog_InsertHyperlink::_onInitDialog(HWND hWnd, WPARAM /*wParam*/, LPARAM /*lParam*/)
{
const XAP_StringSet* pSS = m_pApp->getStringSet();
// Update the caption
setDialogTitle(pSS->getValue(AP_STRING_ID_DLG_InsertHyperlink_Title));
/* Localise controls*/
_DSX(INSERTHYPERLINK_BTN_OK, DLG_OK);
_DSX(INSERTHYPERLINK_BTN_CANCEL, DLG_Cancel);
_DS(INSERTHYPERLINK_LBL_MSG, DLG_InsertHyperlink_Msg);
// initial data
resetContent(AP_RID_DIALOG_INSERTHYPERLINK_LBX_LINK);
UT_uint32 count = getExistingBookmarksCount();
for( UT_uint32 i = 0; i < count; i++)
{
addItemToList( AP_RID_DIALOG_INSERTHYPERLINK_LBX_LINK,
getNthExistingBookmark( i ) );
}
SetFocus(GetDlgItem(hWnd,AP_RID_DIALOG_INSERTHYPERLINK_EBX_LINK));
const gchar * hyperlink = getHyperlink();
if(hyperlink)
{
if(hyperlink[0]=='#') //ignore the anchor for internal bookmarks
{
setControlText(AP_RID_DIALOG_INSERTHYPERLINK_EBX_LINK, hyperlink+1);
}
else
{
setControlText(AP_RID_DIALOG_INSERTHYPERLINK_EBX_LINK, hyperlink);
}
selectControlText(AP_RID_DIALOG_INSERTHYPERLINK_EBX_LINK, 0, -1);
}
centerDialog();
return 0; // 0 because we called set focus
}
QString GetFileListPrompter::composeRichDoc() {
QString url = getHyperlink(URL_ATTR, getURL(URL_ATTR));
return tr("Gets paths of files: <u>%1</u>.")
.arg(url);
}
QString SiteconReadPrompter::composeRichDoc() {
return tr("Read model(s) from <u>%1</u>.").arg(getHyperlink(BaseAttributes::URL_IN_ATTRIBUTE().getId(), getURL(BaseAttributes::URL_IN_ATTRIBUTE().getId())));
}
/*****************************
* ORFPrompter
*****************************/
QString ORFPrompter::composeRichDoc() {
IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
Actor* producer = input->getProducer(BaseSlots::DNA_SEQUENCE_SLOT().getId());
QString unsetStr = "<font color='red'>"+tr("unset")+"</font>";
QString producerName = tr(" from <u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
ORFAlgorithmSettings cfg;
cfg.strand = getStrand(getParameter(BaseAttributes::STRAND_ATTRIBUTE().getId()).value<QString>());
cfg.minLen = getParameter(LEN_ATTR).toInt();
cfg.mustFit = getParameter(FIT_ATTR).toBool();
cfg.mustInit = getParameter(INIT_ATTR).toBool();
cfg.allowAltStart = getParameter(ALT_ATTR).toBool();
cfg.includeStopCodon = getParameter(ISC_ATTR).toBool();
QString extra;
if (!cfg.mustInit) {
QString anyLink = getHyperlink(INIT_ATTR, tr("starting with any codon"));
extra += tr(", allow ORFs %1 other than terminator").arg(anyLink);
} else if (cfg.allowAltStart) {
QString altLink = getHyperlink(ALT_ATTR, tr("alternative start codons"));
extra += tr(", take into account %1").arg(altLink);
}
if (cfg.mustFit) {
QString mustFitLink = getHyperlink(FIT_ATTR, tr("ignore non-terminated"));
extra += tr(", %1 ORFs").arg(mustFitLink);
}
QString strandName;
switch (cfg.strand) {
case ORFAlgorithmStrand_Both:
strandName = ORFWorker::tr("both strands");
break;
case ORFAlgorithmStrand_Direct:
strandName = ORFWorker::tr("direct strand");
break;
case ORFAlgorithmStrand_Complement:
strandName = ORFWorker::tr("complement strand");
break;
}
strandName = getHyperlink(BaseAttributes::STRAND_ATTRIBUTE().getId(), strandName);
QString resultName = getHyperlink(NAME_ATTR, getRequiredParam(NAME_ATTR));
QString transId = getParameter(ID_ATTR).toString();
QString ttName = AppContext::getDNATranslationRegistry()->
lookupTranslation(AppContext::getDNAAlphabetRegistry()->findById(BaseDNAAlphabetIds::NUCL_DNA_DEFAULT()), DNATranslationType_NUCL_2_AMINO, transId)->getTranslationName();
ttName = getHyperlink(ID_ATTR, ttName);
QString doc = tr("For each nucleotide sequence%1, find ORFs in <u>%2</u> using the <u>%3</u>."
"<br>Detect only ORFs <u>not shorter than %4 bps</u>%5."
"<br>Output the list of found regions annotated as <u>%6</u>.")
.arg(producerName) //sequence from Read Fasta 1
.arg(strandName) //both strands
.arg(ttName) //Standard Genetic Code
.arg(getHyperlink(LEN_ATTR, cfg.minLen)) //100
.arg(extra) // take into account alternative start codons.
.arg(resultName);
return doc;
}
void AP_UnixDialog_InsertHyperlink::_constructWindowContents ( GtkWidget * vbox2 )
{
const XAP_StringSet * pSS = m_pApp->getStringSet();
GtkWidget *label1;
GtkWidget *label2;
std::string s;
pSS->getValueUTF8(AP_STRING_ID_DLG_InsertHyperlink_Msg,s);
label1 = gtk_label_new (s.c_str());
gtk_widget_show (label1);
gtk_box_pack_start (GTK_BOX (vbox2), label1, FALSE, FALSE, 3);
m_entry = gtk_entry_new();
gtk_box_pack_start (GTK_BOX (vbox2), m_entry, FALSE, FALSE, 0);
gtk_widget_show(m_entry);
const gchar * hyperlink = getHyperlink();
if (hyperlink && *hyperlink)
{
if (*hyperlink == '#')
{
gtk_entry_set_text ( GTK_ENTRY(m_entry), hyperlink + 1) ;
}
else
{
gtk_entry_set_text ( GTK_ENTRY(m_entry), hyperlink ) ;
}
}
// the bookmark list
m_swindow = gtk_scrolled_window_new(NULL, NULL);
gtk_scrolled_window_set_policy (GTK_SCROLLED_WINDOW (m_swindow),GTK_POLICY_AUTOMATIC, GTK_POLICY_AUTOMATIC);
gtk_widget_show(m_swindow);
gtk_box_pack_start (GTK_BOX (vbox2), m_swindow, TRUE, TRUE, 0);
GtkListStore * store = gtk_list_store_new(1, G_TYPE_STRING);
GtkTreeView * treeview;
m_clist = gtk_tree_view_new_with_model(GTK_TREE_MODEL(store));
treeview = GTK_TREE_VIEW(m_clist);
gtk_tree_view_set_headers_visible(treeview, FALSE);
gtk_tree_selection_set_mode(gtk_tree_view_get_selection(treeview),
GTK_SELECTION_BROWSE);
GtkCellRenderer *renderer = GTK_CELL_RENDERER(gtk_cell_renderer_text_new());
GtkTreeViewColumn *col;
col = gtk_tree_view_column_new_with_attributes("",
renderer, "text", 0, NULL);
gtk_tree_view_append_column(GTK_TREE_VIEW(treeview), col);
//gtk_box_pack_start (GTK_BOX (vbox2), m_blist, FALSE, FALSE, 0);
m_pBookmarks.clear();
for (int i = 0; i < static_cast<int>(getExistingBookmarksCount()); i++) {
m_pBookmarks.push_back(getNthExistingBookmark(i));
}
std::sort(m_pBookmarks.begin(), m_pBookmarks.end());
for (int i = 0; i < static_cast<int>(getExistingBookmarksCount()); i++) {
GtkTreeIter iter;
gtk_list_store_append(store, &iter);
gtk_list_store_set(store, &iter, 0, m_pBookmarks[i].c_str(), -1);
}
gtk_scrolled_window_add_with_viewport(GTK_SCROLLED_WINDOW(m_swindow),m_clist);
pSS->getValueUTF8(AP_STRING_ID_DLG_InsertHyperlink_TitleLabel, s);
label2 = gtk_label_new(s.c_str());
gtk_widget_show(label2);
gtk_box_pack_start(GTK_BOX(vbox2), label2, TRUE, TRUE, 3);
m_titleEntry = gtk_entry_new();
gtk_box_pack_start(GTK_BOX(vbox2), m_titleEntry, FALSE, FALSE, 0);
gtk_widget_show(m_titleEntry);
const gchar * hyperlinkTitle = getHyperlinkTitle();
if (hyperlinkTitle && *hyperlinkTitle)
{
gtk_entry_set_text(GTK_ENTRY(m_titleEntry), hyperlinkTitle);
}
}
