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Fix so it'll build again on libroadrunner-deps #83

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Merged
luciansmith merged 8 commits into from
Aug 29, 2026
Merged

Fix so it'll build again on libroadrunner-deps #83

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25bed1d
Fix so it'll build again on libroadrunner-deps
luciansmith Jan 16, 2026
9e8dbfc
Revert to when it used to work.
luciansmith Jan 17, 2026
2daa7f4
Add name of zlibstatic debug lib.
luciansmith Jan 17, 2026
fb1d981
Merge pull request #86 from sys-bio/develop
luciansmith Mar 13, 2026
0bbf1a6
Merge pull request #90 from sys-bio/fix-escher-style-issues
luciansmith Apr 4, 2026
35f4696
Fix memory leak.
luciansmith Jul 11, 2026
cc0b6ba
Merge branch 'develop' into librrdeps-build
luciansmith Aug 29, 2026
42cfa41
Re-wrap everything Yet Again.
luciansmith Aug 29, 2026
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27 changes: 17 additions & 10 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -48,15 +48,20 @@ endif ()

## Find ZLIB
option(WITH_ZLIB "Link libsbmlnetwork against zlib." ON)
set(LIBZ_LIBRARY "")
if (WITH_ZLIB)
find_package(ZLIB CONFIG REQUIRED)
set(LIBZ_LIBRARY ZLIB::ZLIBSTATIC)
get_target_property(LIBZ_LIBRARY_LOCATION ZLIB::ZLIBSTATIC LOCATION)
message(STATUS "ZLIB Library: ${LIBZ_LIBRARY_LOCATION}")
set(ZLIB_LIBRARY "${LIBZ_LIBRARY_LOCATION}" CACHE FILEPATH "Path to zlib library" FORCE)
set(ZLIB_INCLUDE_DIR "${DEPENDENCIES_INSTALL_PREFIX}/include" CACHE PATH "Path to zlib include directory" FORCE)
set(ZLIB_FOUND TRUE CACHE BOOL "ZLIB found" FORCE)
if (DEFINED LIBZ_LIBRARY)
message(STATUS "ZLIB Library: ${LIBZ_LIBRARY}")
else ()
find_package(ZLIB CONFIG REQUIRED)
set(LIBZ_LIBRARY ZLIB::ZLIBSTATIC)
get_target_property(LIBZ_LIBRARY_LOCATION ZLIB::ZLIBSTATIC LOCATION)
message(STATUS "ZLIB Library: ${LIBZ_LIBRARY_LOCATION}")
set(ZLIB_LIBRARY "${LIBZ_LIBRARY_LOCATION}" CACHE FILEPATH "Path to zlib library" FORCE)
set(ZLIB_INCLUDE_DIR "${DEPENDENCIES_INSTALL_PREFIX}/include" CACHE PATH "Path to zlib include directory" FORCE)
set(ZLIB_FOUND TRUE CACHE BOOL "ZLIB found" FORCE)
endif ()
else ()
set(LIBZ_LIBRARY "")
endif ()

## Find expat
Expand All @@ -81,8 +86,10 @@ else ()
message(STATUS "libSBML Target: ${LIBSBML_LIBRARY}")
endif ()

## Set dependencies include directory
set(DEPENDENCIES_INCLUDE_DIR "${DEPENDENCIES_INSTALL_PREFIX}/include" "${LIBSBML_INSTALL_PREFIX}/include" "${EXPAT_INCLUDE_DIR}")
## Set dependencies include directory if it is not set by a parent project
if (NOT DEFINED DEPENDENCIES_INCLUDE_DIR)
set(DEPENDENCIES_INCLUDE_DIR "${DEPENDENCIES_INSTALL_PREFIX}/include" "${LIBSBML_INSTALL_PREFIX}/include" "${EXPAT_INCLUDE_DIR}")
endif ()

## whether to build the dynamic version of the library
set(BUILD_SHARED_LIBS ON CACHE BOOL "Build the dynamic version of the library")
Expand Down
110 changes: 84 additions & 26 deletions src/features/styles/libsbmlnetwork_styles.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -848,10 +848,10 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
UpdateAllCurvesTouchingSpeciesGlyph(document, layoutIndex, sid, sg);

for (unsigned tg = 0; tg < getNumTextGlyphs(document, layoutIndex, sid, sg); ++tg) {
setFontSizeAsDouble(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, 12);
setFontColor(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, "black");
setFontStyle(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, "italic");
setFontWeight(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, "bold");
// setFontSizeAsDouble(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, 12);
// setFontColor(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, "black");
// setFontStyle(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, "italic");
// setFontWeight(document, getGraphicalObject(document, layoutIndex, sid, sg), tg, "bold");
UpdateSpeciesLabelPosition(document, layoutIndex, sid, sg, tg);
}
}
Expand Down Expand Up @@ -1018,16 +1018,64 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
double w = getDimensionWidth(document, layoutIndex, speciesId, speciesGlyphIndex);
double h = getDimensionHeight(document, layoutIndex, speciesId, speciesGlyphIndex);

double tx = getTextPositionX(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex);
double ty = getTextPositionY(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex);
double speciesCX = speciesX + w / 2.0;
double speciesCY = speciesY + h / 2.0;

if (std::abs(speciesX - tx) < 5.0 && std::abs(speciesY - ty) < 5.0) {
setTextPositionX(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, tx + w);
setTextPositionY(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, ty + h);
double reactionCX = -1.0, reactionCY = -1.0;
std::string speciesGlyphId = getId(document, layoutIndex, speciesId, speciesGlyphIndex);
for (unsigned rIdx = 0; rIdx < getNumReactions(document); ++rIdx) {
std::string reactionId = getReactionId(document, rIdx);
for (unsigned rg = 0; rg < getNumReactionGlyphs(document, layoutIndex, reactionId); ++rg) {
for (unsigned sr = 0; sr < getNumSpeciesReferences(document, layoutIndex, reactionId, rg); ++sr) {
if (stringCompare(getSpeciesReferenceSpeciesGlyphId(document, layoutIndex, reactionId, rg, sr), speciesGlyphId)) {
double rx = getPositionX(document, layoutIndex, reactionId, rg);
double ry = getPositionY(document, layoutIndex, reactionId, rg);
reactionCX = rx + getDimensionWidth(document, layoutIndex, reactionId, rg) / 2.0;
reactionCY = ry + getDimensionHeight(document, layoutIndex, reactionId, rg) / 2.0;
goto foundReaction;
}
}
}
}
foundReaction:

const double pad = 8.0;
const double diagThreshold = 0.4;

if (reactionCX < 0.0) {
setTextPositionX(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, speciesX + w + pad * 3.0);
setTextPositionY(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, speciesCY - 7.0);
return;
}

double dx = speciesCX - reactionCX;
double dy = speciesCY - reactionCY;
double absDx = std::abs(dx);
double absDy = std::abs(dy);
double maxD = std::max(absDx, absDy);
bool isDiagonal = (absDx > diagThreshold * maxD) && (absDy > diagThreshold * maxD);

double newTX, newTY;

if (isDiagonal) {
newTX = speciesX + w + pad * 3.0;
newTY = (dy < 0) ? speciesY - 4.0 : speciesY + h + 2.0;

} else if (absDx >= absDy) {
if (dx >= 0) {
newTX = speciesX + w + pad * 3.0;
newTY = speciesCY - 7.0;
} else {
newTX = speciesCX - 20.0;
newTY = speciesY + h + pad;
}
} else {
setTextPositionX(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, tx - 60.0);
setTextPositionY(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, ty + 7.0);
newTX = speciesCX - 20.0;
newTY = (dy < 0) ? speciesY - 20.0 : speciesY + h + pad;
}

setTextPositionX(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, newTX);
setTextPositionY(document, layoutIndex, speciesId, speciesGlyphIndex, textGlyphIndex, newTY);
}

bool AreSubstratesDirectionsReversed(SBMLDocument* document, int layoutIndex, const std::string& reactionId, unsigned reactionGlyphIndex) {
Expand Down Expand Up @@ -1128,42 +1176,52 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
++numSegments;
double sX = getSpeciesReferenceCurveSegmentStartPointX(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double sY = getSpeciesReferenceCurveSegmentStartPointY(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c1X= getSpeciesReferenceCurveSegmentBasePoint1X(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c1Y= getSpeciesReferenceCurveSegmentBasePoint1Y(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double eX = getSpeciesReferenceCurveSegmentEndPointX (document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double eY = getSpeciesReferenceCurveSegmentEndPointY (document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c2X= getSpeciesReferenceCurveSegmentBasePoint2X(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c2Y= getSpeciesReferenceCurveSegmentBasePoint2Y(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
if ((std::abs(sX - c1X) < 1e-6 && std::abs(sY - c1Y) > 1e-6) ||
(std::abs(eX - c2X) < 1e-6 && std::abs(eY - c2Y) > 1e-6)) {

double dx = std::abs(eX - sX);
double dy = std::abs(eY - sY);

if (dx < 1e-6 && dy < 1e-6) {
--numSegments;
continue;
}

if (dy >= dx) {
++count;
}
}
}
return (numSegments > 0) && (count >= 0.3 * numSegments);
return (numSegments > 0) && (count >= 0.5 * numSegments);
}

bool IsHorizontalReaction(SBMLDocument* document, int layoutIndex, const std::string& reactionId, unsigned reactionGlyphIndex) {
bool IsHorizontalReaction(SBMLDocument* document, int layoutIndex,
const std::string& reactionId, unsigned reactionGlyphIndex) {
int count = 0, numSegments = 0;
for (unsigned sr = 0; sr < getNumSpeciesReferences(document, layoutIndex, reactionId, reactionGlyphIndex); ++sr) {
int nSeg = getNumSpeciesReferenceCurveSegments(document, layoutIndex, reactionId, reactionGlyphIndex, sr);
for (int k = 0; k < nSeg; ++k) {
++numSegments;
double sX = getSpeciesReferenceCurveSegmentStartPointX(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double sY = getSpeciesReferenceCurveSegmentStartPointY(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c1X= getSpeciesReferenceCurveSegmentBasePoint1X(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c1Y= getSpeciesReferenceCurveSegmentBasePoint1Y(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double eX = getSpeciesReferenceCurveSegmentEndPointX (document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double eY = getSpeciesReferenceCurveSegmentEndPointY (document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c2X= getSpeciesReferenceCurveSegmentBasePoint2X(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
double c2Y= getSpeciesReferenceCurveSegmentBasePoint2Y(document, layoutIndex, reactionId, reactionGlyphIndex, sr, k);
if ((std::abs(sY - c1Y) < 1e-6 && std::abs(sX - c1X) > 1e-6) ||
(std::abs(eY - c2Y) < 1e-6 && std::abs(eX - c2X) > 1e-6)) {

double dx = std::abs(eX - sX);
double dy = std::abs(eY - sY);

// Treat degenerate (zero-length) segments as neutral — skip them
if (dx < 1e-6 && dy < 1e-6) {
--numSegments;
continue;
}

if (dx >= dy) {
++count;
}
}
}
return (numSegments > 0) && (count >= 0.3 * numSegments);
return (numSegments > 0) && (count >= 0.5 * numSegments);
}

void UpdateReactionLabelPosition(SBMLDocument* document, int layoutIndex, const std::string& reactionId, unsigned reactionGlyphIndex, unsigned textGlyphIndex) {
Expand Down
3 changes: 2 additions & 1 deletion src/libsbmlnetwork_sbmldocument.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,11 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
SBMLDocument* document = readSBMLFromFile(sbml.c_str());
if (document && document->isSetModel())
return document;
delete document;
document = readSBMLFromString(sbml.c_str());
if (document && document->isSetModel())
return document;

delete document;
return NULL;
}

Expand Down
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