| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 166 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 122 |
random = new MersenneTwister(getCalculationSeed());
rtab = getReactionTable();
speciesIDs = rtab.getSpeciesIDs();
nreaction = rtab.getNReaction();
rates = rtab.getRates();
// Debug.dump("rates", rates);
lnrates = ArrayUtil.log(rates, -999.);
reactantIndices = rtab.getReactantIndices();
productIndices = rtab.getProductIndices();
reactantStochiometry = rtab.getReactantStochiometry();
productStochiometry = rtab.getProductStochiometry();
vgrid = getVolumeGrid();
nel = vgrid.getNElements();
nspec = rtab.getNSpecies();
specieIDs = rtab.getSpecieIDs();
volumes = vgrid.getElementVolumes();
lnvolumes = ArrayUtil.log(volumes, -999.);
// RO
// ----------------------
// System.out.println("Number of files : " + NspeciesFilef);
// System.out.println("Total numer of species : " + NspeciesIDsOutf);
// ----------------------
// RO
extractOutputScheme(rtab); // see BaseCalc.java
surfaceAreas = vgrid.getExposedAreas();
// WK 6 18 2007
submembranes = vgrid.getSubmembranes();
regionLabels = vgrid.getRegionLabels();
// WK
fdiff = rtab.getDiffusionConstants();
lnfdiff = ArrayUtil.log(fdiff, -999.);
neighbors = vgrid.getPerElementNeighbors();
couplingConstants = vgrid.getPerElementCouplingConstants();
lnCC = ArrayUtil.log(couplingConstants, -999.);
stimTab = getStimulationTable();
stimtargets = vgrid.getAreaIndexes(stimTab.getTargetIDs());
// workspace for the calculation
wkA = new int[nel][nspec];
wkB = new int[nel][nspec];
wkReac = new int[nreaction];
eltregions = vgrid.getRegionIndexes();
double[][] regcon = getRegionConcentrations();
double[][] regsd = getRegionSurfaceDensities();
// apply initial conditions over the grid
for (int i = 0; i < nel; i++) {
double v = volumes[i];
double[] rcs = regcon[eltregions[i]];
for (int j = 0; j < nspec; j++) {
double rnp = v * rcs[j] * PARTICLES_PUVC;
int irnp = (int) rnp;
double drnp = rnp - irnp;
// random allocation to implement the remainder of the
// density (some cells get an extra particle, some dont)
if (random.random() < drnp) {
irnp += 1;
}
wkA[i][j] = irnp;
wkB[i][j] = irnp;
}
double a = surfaceAreas[i];
double[] scs = regsd[eltregions[i]];
if (a > 0 && scs != null) {
for (int j = 0; j < nspec; j++) {
if (Double.isNaN(scs[j])) {
// means not specified by the user;
} else {
wkA[i][j] = 0;
wkB[i][j] = 0;
double rnp = a * scs[j] * PARTICLES_PUASD;
int irnp = (int) rnp;
double drnp = rnp - irnp;
// random allocation to implement the remainder of the
// density (some cells get an extra particle, some dont)
if (random.random() < drnp) {
irnp += 1;
}
wkA[i][j] += irnp;
wkB[i][j] += irnp;
}
}
}
/*
* if (i % 20 == 0) { E.info("elt " + i + " region " + eltregions[i]
* + " n0 " + wkA[i][0]); }
*/
}
if (sdRun.initialStateFile != null) {
double[][] cc = readInitialState(sdRun.initialStateFile, nel, nspec, speciesIDs);
if (cc != null) {
for (int i = 0; i < nel; i++) {
for (int j = 0; j < nspec; j++) {
int np = (int) Math.round(cc[i][j] * volumes[i] / CONC_OF_N);
wkA[i][j] = np;
wkB[i][j] = np;
}
}
}
}
dt = sdRun.fixedStepDt;
lndt = Math.log(dt);
// take logs of integers once only and store;
intlogs = new double[10000];
intlogs[0] = -99;
for (int i = 1; i < intlogs.length; i++) {
intlogs[i] = Math.log(i);
}
// final things we need is something to generate particle numbers
// for steps of given n, p
if (useBinomial())
interpSG = InterpolatingStepGenerator.getBinomialGenerator();
else if (usePoisson()) {
interpSG = InterpolatingStepGenerator.getPoissonGenerator();
} else {
E.error("unknown probability distribution");
}
if (doShared() || doParticle() || doIndependent()) {
if (doShared()) {
E.info("Using SHARED destination allocation");
} else {
E.info("Using PER PARTICLE destination allocation");
}
lnpSharedOut = new double[nel][nspec];
pSharedOut = new double[nel][nspec];
fSharedExit = new double[nel][nspec][];
int maxnn = 0;
for (int iel = 0; iel < nel; iel++) {
for (int k = 0; k < nspec; k++) {
int nn = neighbors[iel].length;
fSharedExit[iel][k] = new double[nn];
if (nn > maxnn) {
maxnn = nn;
}
}
}
E.info("max no of neighbors for a single element is " + maxnn);
for (int iel = 0; iel < nel; iel++) {
for (int k = 0; k < nspec; k++) {
int inbr[] = neighbors[iel];
double lngnbr[] = lnCC[iel];
int nnbr = inbr.length;
// int np0 = wkA[iel][k];
double ptot = 0.;
double[] pcnbr = new double[nnbr];
for (int j = 0; j < nnbr; j++) {
double lnpgo = lnfdiff[k] + lngnbr[j] + lndt - lnvolumes[iel];
// probability is dt * K_diff * contact_area /
// (center_to_center_distance * source_volume)
// gnbr contains the gometry: contact_area / distance
double p = Math.exp(lnpgo);
ptot += p;
pcnbr[j] = ptot;
}
double lnptot = Math.log(ptot);
if (lnptot > -1.) {
// WK 9 11 2007
System.out.println("WK===================================");
System.out.println("In DIFFUSION: probability TOO HIGH!");
System.out.println("Reduce your timestep, and try again...");
System.out.println("WK====================================");
System.exit(0);
/*
* if (nwarn < 4) {
* E.shortWarning("p too large at element " + iel +
* " species " + k + " - capping from " +
* Math.exp(lnptot) + " to " + Math.exp(-1.)); nwarn++;
* } lnptot= -1.;
*/
// WK
}
pSharedOut[iel][k] = ptot;
lnpSharedOut[iel][k] = lnptot;
for (int j = 0; j < nnbr; j++) {
fSharedExit[iel][k][j] = pcnbr[j] / ptot;
}
}
}
}
}
@SuppressWarnings("boxing")
private String getGridConcsText(double time) {
StringBuffer sb = new StringBuffer();
// TODO tag specific to integer quantities;
int nspecout = ispecout.length;
if (nspecout == 0) {
return "";
}
sb.append("gridConcentrations " + nel + " " + nspecout + " " + time + " ");
for (int i = 0; i < nspecout; i++) {
sb.append(specieIDs[ispecout[i]] + " ");
}
sb.append("\n");
for (int i = 0; i < nel; i++) {
for (int j = 0; j < nspecout; j++) {
if (writeConcentration) {
sb.append(stringd((CONC_OF_N * wkA[i][ispecout[j]] / volumes[i])));
} else {
sb.append(stringi(wkA[i][ispecout[j]]));
}
}
sb.append("\n");
}
return sb.toString();
}
private String getGridConcsPlainText_dumb(int filenum, double time) {
StringBuffer sb = new StringBuffer();
sb.append(stringd(time));
for (int j = 0; j < specIndexesOut[filenum].length; j++) {
for (int i = 0; i < nel; i++) {
if (regionsOut[filenum].equals("default") || regionsOut[filenum].equals(regionLabels[eltregions[i]])) {
int npart = wkA[i][specIndexesOut[filenum][j]];
if (writeConcentration) {
sb.append(stringd((CONC_OF_N * npart / volumes[i])));
} else {
sb.append(stringi(npart));
}
}
}
}
sb.append("\n");
return sb.toString();
}
@SuppressWarnings("boxing")
private String getStateText() {
StringBuffer sb = new StringBuffer();
sb.append("nrds " + nel + " " + specieIDs.length + "\n");
for (int i = 0; i < specieIDs.length; i++) {
sb.append(specieIDs[i] + " ");
}
sb.append("\n");
for (int i = 0; i < nel; i++) {
for (int j = 0; j < specieIDs.length; j++) {
sb.append(stringd((CONC_OF_N * wkA[i][j] / volumes[i])));
}
sb.append("\n");
}
return sb.toString();
}
public final int run() {
init();
if (resultWriter != null) { |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 544 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 465 |
resultWriter.writeToFinalSiblingFile(getStateText(), sdRun.stateSavePrefix + Math.round(time) + ".nrds");
stateSaveTime += sdRun.getStateSaveInterval();
}
}
long endTime = System.currentTimeMillis();
E.info("total time " + (endTime - startTime) + "ms");
return 0;
}
// NB the following method is one of the only two that need optimizing
// (the other is nGo in the interpolating step generator)
// things to do (in the c version)
// - use BLAS calls for array operations,
// - remove the two remaining exps
// - unwrap inner conditionals for different reaction types
// - make nGo inlinable
public double advance(double tnow) {
// add in any injections
double[][] stims = stimTab.getStimsForInterval(tnow, dt);
for (int i = 0; i < stims.length; i++) {
double[] astim = stims[i];
for (int j = 0; j < astim.length; j++) {
if (astim[j] > 0.) {
// the stimulus could be spread over a number of elements
// as yet, assume equal probability of entering any of these
// elements (TODO)
// the random < asr ensures we get the right number of
// particles even the average entry per volume is less than
// one
// TODO - allow stim type (deterministic or poisson etc) in
// config;
int nk = stimtargets[i].length;
if (nk > 0) {
double as = astim[j] / nk;
int ias = (int) as;
double asr = as - ((int) as);
for (int k = 0; k < nk; k++) {
int nin = (ias + (random.random() < asr ? 1 : 0));
ninjected += nin;
wkA[stimtargets[i][k]][j] += nin;
}
}
}
}
}
// initialize wkB to the current values.
// It will hold the midstep values for the leapfrog, after diffusion
// but before reactions.
for (int i = 0; i < nel; i++) {
for (int j = 0; j < nspec; j++) {
wkB[i][j] = wkA[i][j];
// if (wkB[i][j] < 0)
// System.out.println("ERROR - NEGATIVE POPULATION at volume_element "
// + i + ", specie " + j);
// E.error("ERROR - NEGATIVE POPULATION at volume_element " + i
// + ", specie " + j);
}
}
// diffusion step;
for (int iel = 0; iel < nel; iel++) {
for (int k = 0; k < nspec; k++) {
if (lnfdiff[k] > -90) {
int np0 = wkA[iel][k];
if (np0 > 0) {
switch(algoID) {
case INDEPENDENT:
// WK 8 28 2007
// parallelDiffusionStep(iel, k);
parallelAndSharedDiffusionStep(iel, k);
// WK
break;
case SHARED:
// WK 9 11 2007
// sharedDiffusionStep(iel, k);
parallelAndSharedDiffusionStep(iel, k);
// WK
break;
case PARTICLE:
particleDiffusionStep(iel, k);
break;
default:
assert false;
}
}
}
}
}
// for the reaction step, the source array is wkB and the
// destination is wkA
for (int i = 0; i < nel; i++) {
for (int j = 0; j < nspec; j++) {
wkA[i][j] = wkB[i][j];
}
}
// reaction step;
for (int iel = 0; iel < nel; iel++) {
double lnvol = lnvolumes[iel];
// start and end quantities for each species in a single
// volume
int[] nstart = wkB[iel];
int[] nend = wkA[iel];
for (int isp = 0; isp < nspecie; isp++) {
nend[isp] = nstart[isp];
}
for (int ireac = 0; ireac < nreaction; ireac++) {
// total number of possible reactions is the number of
// particles in the smallest reactant population
int[] ri = reactantIndices[ireac];
int[] pi = productIndices[ireac];
int[] rs = reactantStochiometry[ireac];
int[] ps = productStochiometry[ireac];
double lnp = lnrates[ireac] + lndt;
int n = nstart[ri[0]];
if (ri[1] >= 0) {
int nk = nstart[ri[1]];
if (nk < n) {
lnp += intlog(n);
n = nk;
} else {
lnp += intlog(nk);
}
lnp -= lnvol;
lnp -= LN_PARTICLES_PUVC;
}
if (lnp > -1.) {
if (nwarn < 5) {
E.shortWarning("p too large at element " + iel + " reaction " + ireac + " capping from "
+ Math.exp(lnp) + " to " + " exp(-1.)");
nwarn++;
}
lnp = -1.;
}
if (n <= 0) {
} else {
int ngo = 0;
if (n == 1) {
// TODO use table to get rid of exp
ngo = (random.random() < Math.exp(lnp) ? 1 : 0);
} else if (n < StepGenerator.NMAX_STOCHASTIC) {
ngo = interpSG.nGo(n, lnp, random.random());
} else {
if (useBinomial()) {
if (n * (Math.exp(lnp)) < NP) {
ngo = StepGenerator.gaussianStep(n, Math.exp(lnp), random.gaussian(), random.random(),
random.poisson(n * (Math.exp(lnp))), NP);
if (ngo < 0) {
ngo = 0;
System.out.println("in advance (reaction), if (n*Math.exp(lnp)) < " + NP
+ "): ngo is NEGATIVE.");
System.out.println("ngo: " + ngo + " n: " + n + " Math.exp(lnp): " + Math.exp(lnp));
}
} else {
ngo = StepGenerator.gaussianStep(n, Math.exp(lnp), random.gaussian(), random.random());
if (ngo < 0) {
ngo = 0;
System.out.println("in advance (reaction), if (n*Math.exp(lnp)) >= " + NP
+ "): ngo is NEGATIVE.");
System.out.println("ngo: " + ngo + " n: " + n + " Math.exp(lnp): " + Math.exp(lnp));
}
}
} else {
ngo = StepGenerator.poissonStep(n, Math.exp(lnp), random.gaussian(), random.random());
if (ngo < 0) {
ngo = 0;
System.out.println("in advance (reaction), if not using binomial: ngo is NEGATIVE.");
System.out.println("ngo: " + ngo + " n: " + n + " Math.exp(lnp): " + Math.exp(lnp));
}
}
}
// WK 7 2 2008: if ngo is negative, exit.
// if (ngo < 0)
// {
// System.out.println("in advance: ngo is NEGATIVE. Exiting...");
// System.exit(0);
// }
// WK
// update the new quantities in npn;
int ri0 = ri[0];
int ri1 = ri[1];
int rs0 = rs[0];
int rs1 = rs[1];
int navail = nend[ri0] / rs[0];
// AB changed navail > nend[ri1] / rs1 to navail < nend[ri1]
// / rs1
if (ri1 >= 0 && navail > nend[ri1] / rs1) {
navail = nend[ri1] / rs1;
}
if (ngo > navail) {
// TODO as for diffusion, we've got more particles going
// than there actually are. Should regenerate all
// reactions on theis element
// or use a binomial to share them out
// or use a smaller timestep;
if (nwarn < 10) {
E.shortWarning("reaction " + ireac + " ran out of particles - need " + ngo + " but have "
+ navail);
nwarn++;
}
ngo = navail;
}
// WK 9 25 2007: setting inc/decrements (i.e., ngo*xxx) to
// zero explicitly
// to avoid floating point error
if (ngo == 0) {
int pi0 = pi[0];
int pi1 = pi[1];
nend[ri0] -= 0;
if (ri1 >= 0)
nend[ri1] -= 0;
nend[pi0] += 0;
if (pi1 >= 0)
nend[pi1] += 0;
} else {
// WK
nend[ri0] -= ngo * rs0;
if (ri1 >= 0) {
nend[ri1] -= ngo * rs1;
}
// WK 3/16/2010
if (nend[ri0] < 0) {
System.out.println("nend[ri0] is NEGATIVE!");
}
if (ri1 >= 0 && nend[ri1] < 0) {
System.out.println("nend[ri1] is NEGATIVE!");
}
// WK
int pi0 = pi[0];
int pi1 = pi[1];
nend[pi0] += ngo * ps[0];
if (pi1 >= 0) {
nend[pi1] += ngo * ps[1];
}
}
// TODO this "if (ri[1] >= 0)" business is not great
// it applies for the A+B->C case, where there is a
// second reactant. We could probably do better by
// unrolling the four cases into separate blocks according
// to the reaction type
// - a good case for code generation.
}
}
}
// now wkA contains the actual numbers again;
return dt;
}
// WK 8 28 2007
private final void parallelAndSharedDiffusionStep(int iel, int k) {
int np0 = wkA[iel][k];
int inbr[] = neighbors[iel];
double[] fshare = fSharedExit[iel][k];
int ngo = 0;
int ngo_remaining = 0; // for independent diffusion step ***KTB edit - this is number of molecules not yet diffused
int num_molecules_diffused_so_far = 0;
if (np0 == 1) {
ngo = (random.random() < pSharedOut[iel][k] ? 1 : 0);
} else if (np0 < StepGenerator.NMAX_STOCHASTIC) {
ngo = interpSG.nGo(np0, Math.log(pSharedOut[iel][k]), random.random());
if (ngo < 0) {
System.out.println("in parallelAndSharedDiffusionStep 1st else: ngo is NEGATIVE. Exiting..."); |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 972 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 893 |
}
// WK
wkB[iel][k] -= ngo;
wkB[inbr[j]][k] += ngo;
ngo_remaining-=ngo;
} //end of loop through all but last neighbor
ngo = ngo_remaining;
wkB[iel][k] -= ngo;
wkB[inbr[inbr.length - 1]][k] += ngo;
// WK 3/16/2010
if (wkB[iel][k] < 0) {
System.out.println("In INDEPENDENT DIFFUSION, wkB[iel][k] NEGATIVE!!!");
}
//
}
}
// WK
private final void parallelDiffusionStep(int iel, int k) {
int inbr[] = neighbors[iel];
double lngnbr[] = lnCC[iel];
int nnbr = inbr.length;
int np0 = wkA[iel][k];
for (int j = 0; j < nnbr; j++) {
// use logs here so the operations are all additions
// and the compiler should be able to be clever
double lnpgo = lnfdiff[k] + lngnbr[j] + lndt - lnvolumes[iel];
// probability is dt * K_diff * contact_area /
// (center_to_center_distance * source_volume)
// gnbr contains the gometry: contact_area / distance
if (lnpgo > -1.) {
if (nwarn < 4) {
E.shortWarning("p too large at element " + iel + " transition " + j + " to " + inbr[j]
+ " - capping " + Math.exp(lnpgo) + " coupling is " + lngnbr[j]);
nwarn++;
}
lnpgo = -1.;
}
int ngo = 0;
if (np0 == 1) {
// TODO - use table anyway - avoid exp!
ngo = (random.random() < Math.exp(lnpgo) ? 1 : 0);
} else if (np0 < StepGenerator.NMAX_STOCHASTIC) {
ngo = interpSG.nGo(np0, lnpgo, random.random());
} else {
if (useBinomial()) {
if (np0 * (Math.exp(lnpgo)) >= 10) {
ngo = StepGenerator.gaussianStep(np0, Math.exp(lnpgo), random.gaussian(), random.random());
} else {
ngo = StepGenerator.gaussianStep(np0, Math.exp(lnpgo), random.gaussian(), random.random(),
random.poisson(np0 * (Math.exp(lnpgo))), NP);
}
} else {
ngo = StepGenerator.poissonStep(np0, Math.exp(lnpgo), random.gaussian(), random.random());
}
}
// System.out.println("iel j ngo " + iel + " " + j + " " + ngo + " "
// + np0);
if (ngo > wkB[iel][k]) {
if (nwarn < 10) {
E.shortWarning("ran out of particles - curtailing last transition from " + ngo + " to "
+ wkB[iel][k] + " leaving point " + iel + " species " + k);
} else if (nwarn == 10) {
E.info("Suppressing future warnings");
}
nwarn++;
ngo = wkB[iel][k];
// TODO probably worth flagging if this ever happens
// it means your steps could be too large
// MATH if it does happen, there is a consistent
// bias in that the last exit is the one that
// is curtailed. We should actually restart
// this set of jumps and get new fluxes to all
// neighbours
}
wkB[iel][k] -= ngo;
wkB[inbr[j]][k] += ngo;
}
}
private final void sharedDiffusionStep(int iel, int k) {
int np0 = wkA[iel][k];
int inbr[] = neighbors[iel];
// int nnbr = inbr.length;
double[] fshare = fSharedExit[iel][k];
double lnptot = lnpSharedOut[iel][k];
int ngo = 0;
if (np0 == 1) {
// TODO - use table anyway - avoid exp!
ngo = (random.random() < Math.exp(lnptot) ? 1 : 0);
} else if (np0 < StepGenerator.NMAX_STOCHASTIC) {
ngo = interpSG.nGo(np0, lnptot, random.random());
} else {
if (useBinomial()) {
ngo = StepGenerator.gaussianStep(np0, Math.exp(lnptot), random.gaussian(), random.random());
} else {
ngo = StepGenerator.poissonStep(np0, Math.exp(lnptot), random.gaussian(), random.random());
}
}
wkB[iel][k] -= ngo;
for (int i = 0; i < ngo; i++) {
double r = random.random();
int io = 0;
while (r > fshare[io]) {
io++;
}
wkB[inbr[io]][k] += 1;
}
}
private final void particleDiffusionStep(int iel, int k) {
int np0 = wkA[iel][k];
int inbr[] = neighbors[iel];
// int nnbr = inbr.length;
double[] fshare = fSharedExit[iel][k];
double ptot = pSharedOut[iel][k];
for (int i = 0; i < np0; i++) {
double r = random.random();
if (r < ptot) {
wkB[iel][k] -= 1;
double fr = r / ptot;
int io = 0;
while (fr > fshare[io]) {
io++;
}
wkB[inbr[io]][k] += 1;
}
}
}
public final double intlog(int i) {
double ret = 0.;
if (i <= 0) {
ret = -99.;
} else {
ret = (i < intlogs.length ? intlogs[i] : Math.log(i));
}
return ret;
}
public long getParticleCount() {
long ret = 0;
for (int i = 0; i < nel; i++) {
for (int j = 0; j < nspec; j++) {
ret += wkA[i][j];
}
}
E.info("number injected = " + ninjected);
return ret;
}
protected String getGridConcsHeadings_dumb(int filenum, VolumeGrid vgrid) {
StringBuffer sb = new StringBuffer();
sb.append("time");
for (int j = 0; j < specIndexesOut[filenum].length; j++) {
for (int i = 0; i < nel; i++) {
// WK 6 17 2007
if (regionsOut[filenum].equals("default") || regionsOut[filenum].equals(regionLabels[eltregions[i]])) {
sb.append(" Vol_" + i);
sb.append("_" + regionLabels[eltregions[i]]);
if (vgrid.getGroupID(i) != null) {
sb.append("." + vgrid.getGroupID(i));
} else if (vgrid.getLabel(i) != null) {
String tempLabel = vgrid.getLabel(i);
if (tempLabel.indexOf(".") > 0) {
sb.append("." + tempLabel.substring(0, tempLabel.indexOf(".")));
}
}
if (submembranes[i] == true) {
sb.append("_submembrane");
} else {
sb.append("_cytosol");
}
if (vgrid.getLabel(i) != null) {
String tempLabel = vgrid.getLabel(i);
if (tempLabel.indexOf(".") > 0) {
sb.append("_" + tempLabel.substring(tempLabel.indexOf(".") + 1, tempLabel.length()));
} else {
sb.append("_" + vgrid.getLabel(i));
}
}
// WK
sb.append("_Spc_" + specieIDs[specIndexesOut[filenum][j]]);
}
}
}
sb.append("\n");
return sb.toString();
}
} |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLWriter.java | 183 |
| org/textensor/xml/XMLWriter.java | 158 |
appendObject(sbv, psk + " ", null, listobj);
}
}
sbv.append(psk);
sbv.append("</" + tag + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, String value) {
sbv.append(sk + "<" + name + ">");
appendString(sbv, value);
sbv.append("</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, boolean value) {
sbv.append(sk + "<" + name + ">");
sbv.append(value ? "1" : "0");
sbv.append("</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, int value) {
sbv.append(sk + "<" + name + ">");
sbv.append("" + value);
sbv.append("</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, double value) {
sbv.append(sk + "<" + name + ">");
sbv.append("" + value);
sbv.append("</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, String[] value) {
sbv.append(sk + "<" + name + ">\n");
for (int i = 0; i < value.length; i++) {
sbv.append(sk);
sbv.append(" ");
appendString(sbv, (value[i] != null ? value[i] : ""));
sbv.append("\n");
}
sbv.append(sk + "</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, int[] value) {
sbv.append(sk + "<" + name + ">");
for (int i = 0; i < value.length; i++) {
if (i % 16 == 0)
sbv.append("\n" + sk + " ");
sbv.append(" " + value[i] + " ");
}
sbv.append("\n");
sbv.append(sk + "</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, boolean[] value) {
sbv.append(sk + "<" + name + ">\n" + sk + " ");
for (int i = 0; i < value.length; i++) {
sbv.append(" " + (value[i] ? 1 : 0) + " ");
}
sbv.append("\n");
sbv.append(sk + "</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, double[] value) {
sbv.append(sk + "<" + name + ">");
for (int i = 0; i < value.length; i++) {
if (i % 4 == 0)
sbv.append("\n" + sk + " ");
sbv.append(" " + value[i] + " ");
}
sbv.append("\n");
sbv.append(sk + "</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, int[][] value) {
sbv.append(sk + "<" + name + ">\n");
for (int i = 0; i < value.length; i++) {
sbv.append(sk);
sbv.append(" <row>");
int[] ii = value[i];
for (int k = 0; k < ii.length; k++) {
if (k % 16 == 0)
sbv.append("\n " + sk + " ");
sbv.append(" " + ii[k] + " ");
}
sbv.append("\n");
sbv.append(sk);
sbv.append(" ");
sbv.append("</row>\n");
}
sbv.append(sk + "</" + name + ">\n");
}
private void appendNV(StringBuffer sbv, String sk, String name, double[][] value) {
sbv.append(sk + "<" + name + ">\n");
for (int i = 0; i < value.length; i++) {
sbv.append(sk);
sbv.append(" <row>");
double[] ii = value[i];
for (int k = 0; k < ii.length; k++) {
if (k % 4 == 0)
sbv.append("\n " + sk + " ");
sbv.append(" " + ii[k] + " ");
}
sbv.append("\n");
sbv.append(sk);
sbv.append(" ");
sbv.append("</row>\n");
}
sbv.append(sk + "</" + name + ">\n");
}
private void appendString(StringBuffer sbv, String sssin) { |
| File | Line |
|---|
| org/catacomb/util/FileUtil.java | 78 |
| org/textensor/util/FileUtil.java | 80 |
E.error("Cant read file " + f);
}
}
return sdat;
}
public static boolean writeStringToFile(String sdat, File f) {
String fnm = f.getName();
boolean ok = false;
if (f != null) {
boolean dogz = (fnm.endsWith(".gz"));
try {
OutputStream fos = new FileOutputStream(f);
if (dogz) {
fos = new GZIPOutputStream(fos);
}
OutputStreamWriter osw = new OutputStreamWriter(fos);
osw.write(sdat, 0, sdat.length());
osw.close();
ok = true;
} catch (IOException ex) {
E.error("file writing error, trying to write file " + fnm);
ex.printStackTrace();
}
}
return ok;
}
public static String getRootName(File f) {
String fnm = f.getName();
String root = fnm.substring(0, fnm.lastIndexOf("."));
return root;
}
public static void writeBytes(byte[] ba, File f) {
writeByteArrayToFile(ba, f);
}
public static void writeByteArrayToFile(byte[] ba, File f) {
if (f == null) {
return;
}
try {
OutputStream os = new BufferedOutputStream(new FileOutputStream(f));
os.write(ba);
os.flush();
} catch (Exception e) {
E.error("cant write byte array " + ba + " to " + f);
}
}
public static void copyFile(File fsrc, File fdest) {
if (fsrc.exists()) {
try {
InputStream in = new FileInputStream(fsrc);
OutputStream out = new FileOutputStream(fdest);
// Transfer bytes from in to out
byte[] buf = new byte[1024];
int len;
while ((len = in.read(buf)) > 0) {
out.write(buf, 0, len);
}
in.close();
out.close();
} catch (Exception ex) {
E.error("file copy exception");
}
} else {
E.warning("copy - missing file " + fsrc);
}
}
public static String findPath(File f, String name) {
String ret = null;
for (File fs : f.listFiles()) {
if (fs.getName().equals(name)) {
ret = "";
break;
}
}
if (ret == null) {
for (File fd : f.listFiles()) {
if (fd.isDirectory()) {
String s = findPath(fd, name);
if (s != null) {
if (s.equals("")) {
ret = fd.getName();
} else {
ret = fd.getName() + "/" + s;
}
break;
}
}
}
}
return ret;
}
public static String readFirstLine(File f) {
String ret = null;
if (f != null) {
try {
InputStream ins = new FileInputStream(f);
InputStreamReader insr = new InputStreamReader(ins);
BufferedReader fr = new BufferedReader(insr);
ret = fr.readLine();
fr.close();
} catch (IOException ex) {
E.error("file read error ");
ex.printStackTrace();
}
}
return ret;
}
public static String getRelativeDirectory(File ftgt, File rtFolder) {
File fpar = ftgt.getParentFile();
int ns = 0;
String sret = null;
while (fpar != null && !(fpar.equals(rtFolder))) {
if (sret == null) {
sret = fpar.getName();
} else {
sret = fpar.getName() + "/" + sret;
}
fpar = fpar.getParentFile();
ns += 1;
if (ns > 8) {
E.error("too many steps trying to get relative files ? " + ftgt.getAbsolutePath() + " "
+ rtFolder.getAbsolutePath());
break;
}
}
return sret;
}
// TODO make this smarter (or use GlobFileFilter from jakarta ORO ?)
public static ArrayList<File> matchingFiles(String srcPattern) {
ArrayList<File> ret = new ArrayList<File>();
if (srcPattern.indexOf("*") < 0) {
File fd = new File(srcPattern);
if (fd.exists() && fd.isDirectory()) {
for (File f : fd.listFiles()) {
ret.add(f);
}
}
} else {
int istar = srcPattern.indexOf("*");
String sa = srcPattern.substring(0, istar);
String sb = srcPattern.substring(istar + 1, srcPattern.length());
File ftop = new File(sa);
for (File fg : ftop.listFiles()) {
File fp = new File(fg, sb);
if (fp.exists()) {
ret.add(fp);
}
}
}
return ret;
} |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLTokenizer.java | 220 |
| org/textensor/xml/XMLTokenizer.java | 224 |
int[] ipr = new int[3];
while (ipr[0] != ims || ipr[1] != ims || ipr[2] != iabc) {
itok = ntok(streamTokenizer);
if (streamTokenizer.ttype == StreamTokenizer.TT_WORD) {
svalue += streamTokenizer.sval + " ";
} else if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
svalue += " " + streamTokenizer.nval;
}
if (streamTokenizer.sval != null && streamTokenizer.sval.endsWith("--")) {
ipr[1] = ims;
ipr[2] = ims;
} else {
ipr[0] = ipr[1];
ipr[1] = ipr[2];
ipr[2] = itok;
}
}
streamTokenizer.pushBack();
} else {
E.error("found <!- but not followed by - at " + streamTokenizer.lineno());
}
} else {
E.error("found <! but not followed by - at " + streamTokenizer.lineno());
}
setStringValue(xmlt, svalue);
} else if (sv.startsWith("/")) {
xmlt.setType(XMLToken.CLOSE);
setStringValue(xmlt, sv.substring(1, sv.length()));
} else {
if (sv.endsWith("/")) {
xmlt.setType(XMLToken.OPENCLOSE);
setStringValue(xmlt, sv.substring(0, sv.length() - 1));
} else {
xmlt.setType(XMLToken.OPEN);
setStringValue(xmlt, sv);
}
}
itok = ntok(streamTokenizer);
if (itok == iabc) {
// fine - end of tag;
} else if (streamTokenizer.ttype == StreamTokenizer.TT_WORD) {
String[] attNV = new String[160]; // EFF check eff
int natt = 0;
while (itok != iabc) {
if (streamTokenizer.ttype == StreamTokenizer.TT_WORD) {
if (streamTokenizer.sval.equals("/")) {
xmlt.setType(XMLToken.OPENCLOSE);
} else {
attNV[2 * natt] = streamTokenizer.sval;
itok = ntok(streamTokenizer);
if (itok == ieq) {
itok = ntok(streamTokenizer);
if (itok == iq) {
attNV[2 * natt + 1] = streamTokenizer.sval;
natt++;
} else {
E.shortError("expecting quoted string " + " while reading atributes "
+ "but got " + stok(itok) + " sval=" + streamTokenizer.sval
+ " nval=" + streamTokenizer.nval);
E.info("original string was " + srcString);
}
} else {
E.shortError("at " + streamTokenizer.lineno()
+ " expecting = while reading attributes " + "but got " + stok(itok)
+ " sval=" + streamTokenizer.sval + " nval=" + streamTokenizer.nval);
E.info("original string was " + srcString);
}
}
} else {
E.shortError("at line " + streamTokenizer.lineno()
+ " found non-word while reading attributes " + stok(itok)
+ " item so far = " + this);
E.info("original string was " + srcString);
}
itok = ntok(streamTokenizer);
}
String[] sat = new String[2 * natt];
for (int i = 0; i < 2 * natt; i++) {
sat[i] = attNV[i];
}
xmlt.setAttributes(sat);
} else {
E.error("expecting word " + stok(itok));
}
} else {
// just return the token as a string;
xmlt.setType(XMLToken.STRING);
setStringValue(xmlt, stok(itok));
}
return xmlt;
}
private int ntok(StreamTokenizer st) {
int itok = -1;
try {
itok = st.nextToken();
} catch (IOException e) {
err(" " + e);
itok = -999;
}
/*
* if (count < 20) { E.info("token " + count + " " + itok + " " + st.sval + " " +
* st.nval); count += 1; }
*/
return itok;
}
private String stok(int itok) {
return "" + (char)itok;
}
private void err(String s) {
System.out.println(s);
}
} |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 65 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 111 |
return m;
}
public void setDims(int d1, int d2) {
n1 = d1;
n2 = d2;
}
public void identise() {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
a[i][j] = 0.;
}
a[i][i] = 1.;
}
}
public void randomise() {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
a[i][j] = Math.random();
}
}
}
public void zero() {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
a[i][j] = 0.;
}
}
}
public Matrix identity() {
Matrix m = copy();
m.identise();
return m;
}
public Matrix random() {
Matrix m = copy();
m.randomise();
return m;
}
public void add(double d) {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
a[i][j] += d;
}
}
}
public static Matrix[] average(Matrix[] ma, Matrix[] mb, double f) {
int n = ma.length;
Matrix[] res = new Matrix[n];
for (int i = 0; i < n; i++) {
res[i] = average(ma[i], mb[i], f);
}
return res;
}
public static Matrix average(Matrix ma, Matrix mb, double f) {
double g = 1. - f;
int n = ma.n;
Matrix res = new Matrix(n);
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
res.a[i][j] = f * mb.a[i][j] + g * ma.a[i][j];
}
}
return res;
}
public void add(Matrix m) {
if (m.n != n) {
Sp("incompativle dims in Matrix.mplyBy " + n + " " + m.n);
} else {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
a[i][j] += m.a[i][j];
}
}
}
}
public Matrix sum(Matrix m) {
Matrix mr = copy();
mr.zero();
if (m.n != n) {
Sp("incompativle dims in Matrix.mplyBy " + n + " " + m.n);
} else {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
mr.a[i][j] = a[i][j] + m.a[i][j];
}
}
}
return mr;
}
public void mpyBy(double d) {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
a[i][j] *= d;
}
}
}
public void mpyBy(Matrix m) {
a = (prod(m)).a;
}
public Matrix prod(Matrix m) { |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 298 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 392 |
m.a[i][j] = a[j][i];
}
}
return m;
}
public double det() {
Matrix t = copy();
t.LU();
double d = 1.0 * t.sign;
for (int i = 0; i < n; i++) {
d *= t.a[i][i];
}
return d;
}
public double[][] copyMat() {
double[][] ar = new double[n][n];
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
ar[i][j] = a[i][j];
}
}
return ar;
}
public void LU() {
int i, imax, j, k;
double big, dum, sum, temp;
double vv[] = new double[n];
double TINY = 1.0e-20;
sign = 1;
imax = -1;
for (i = 0; i < n; i++) {
big = 0.0;
for (j = 0; j < n; j++) {
if ((temp = Math.abs(a[i][j])) > big) {
big = temp;
}
}
if (big == 0.0) {
Sp("Singular Matrix in routine LUDCMP");
}
vv[i] = 1.0 / big;
}
for (j = 0; j < n; j++) {
for (i = 0; i < j; i++) {
sum = a[i][j];
for (k = 0; k < i; k++) {
sum -= a[i][k] * a[k][j];
}
a[i][j] = sum;
}
big = 0.0;
for (i = j; i < n; i++) {
sum = a[i][j];
for (k = 0; k < j; k++) {
sum -= a[i][k] * a[k][j];
}
a[i][j] = sum;
if ((dum = vv[i] * Math.abs(sum)) >= big) {
big = dum;
imax = i;
}
}
if (j != imax) {
for (k = 0; k < n; k++) {
dum = a[imax][k];
a[imax][k] = a[j][k];
a[j][k] = dum;
}
sign = -sign;
vv[imax] = vv[j];
}
perm[j] = imax;
if (a[j][j] == 0.0) {
a[j][j] = TINY;
}
if (j != n) {
dum = 1.0 / (a[j][j]);
for (i = j + 1; i < n; i++) {
a[i][j] *= dum;
}
}
}
}
public Matrix inverse() {
Matrix t, r;
t = copy();
r = copy();
t.LU();
double[] c = new double[n];
for (int j = 0; j < n; j++) {
for (int i = 0; i < n; i++) {
c[i] = 0.0;
}
c[j] = 1.0;
t.lubksb(c);
for (int i = 0; i < n; i++) {
r.a[i][j] = c[i];
}
}
return r;
} |
| File | Line |
|---|
| org/catacomb/interlish/reflect/Narrower.java | 104 |
| org/textensor/xml/Narrower.java | 103 |
ArrayList<? extends Object> v = (ArrayList<? extends Object>)ob;
int n = v.size();
sret = new String[n];
int iout = 0;
for (Object sub : v) {
sret[iout++] = (String)sub;
}
} else {
err("ERROR - cant make string array from " + ob);
}
return sret;
}
public static double[] makeDoubleArray(Object ob) {
double[] dret = null;
if (ob instanceof double[]) {
dret = (double[])ob;
} else if (ob instanceof ArrayList) {
ArrayList v = (ArrayList)ob;
int n = v.size();
dret = new double[n];
int iout = 0;
for (Object sub : v) {
dret[iout++] = makeDouble(sub);
}
} else if (ob instanceof String) {
dret = readDoubleArray((String)ob);
} else if (ob != null) {
dret = new double[1];
dret[0] = makeDouble(ob);
}
return dret;
}
public static int[] makeIntArray(Object ob) {
int[] iret = null;
if (ob instanceof int[]) {
iret = (int[])ob;
} else if (ob instanceof ArrayList) {
ArrayList v = (ArrayList)ob;
int n = v.size();
iret = new int[n];
int iout = 0;
for (Object sub : v) {
iret[iout++] = makeInt(sub);
}
// MISSING following needs repeating for other array types
} else if (ob instanceof String) {
String sob = (String)ob;
StringTokenizer st = new StringTokenizer(sob, " ,\n");
int ntok = st.countTokens();
iret = new int[ntok];
for (int i = 0; i < iret.length; i++) {
iret[i] = Integer.parseInt(st.nextToken());
}
} else if (ob != null) {
iret = new int[1];
iret[0] = makeInt(ob);
}
return iret;
}
public static boolean[] makeBooleanArray(Object ob) {
boolean[] bret = null;
if (ob instanceof ArrayList) {
ArrayList v = (ArrayList)ob;
int n = v.size();
bret = new boolean[n];
int iout = 0;
for (Object sub : v) {
bret[iout++] = makeBoolean(sub);
}
} else if (ob != null) {
bret = new boolean[1];
bret[0] = makeBoolean(ob);
}
return bret;
}
public static int makeInt(Object arg) throws NumberFormatException {
int iret = 0;
if (arg instanceof Integer) {
iret = ((Integer)arg).intValue();
} else if (arg instanceof Double) {
iret = (int)(((Double)arg).doubleValue());
} else if (arg instanceof String) {
String s = (String)arg;
if (s.equals("false")) {
iret = 0;
} else if (s.equals("true")) {
iret = 1;
} else {
iret = parseInt((String)arg);
}
} else {
err("cant make an int from " + arg + " " + arg.getClass());
}
return iret;
}
public static int parseInt(String sin) { |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLTokenizer.java | 85 |
| org/textensor/xml/XMLTokenizer.java | 86 |
if (sv.startsWith("xyz")) {
if (cdataHM != null && cdataHM.containsKey(sv)) {
sv = cdataHM.get(sv);
} else {
E.warning("looks like a CDATA key, but not present? " + sv);
}
}
xmlt.setStringValue(sv);
}
public int lineno() {
return streamTokenizer.lineno();
}
public void initializeStreamTokenizer(StreamTokenizer st) {
st.resetSyntax();
st.eolIsSignificant(false);
st.slashStarComments(false);
st.slashSlashComments(false);
st.lowerCaseMode(false);
String slim = "AZaz09";
st.wordChars(slim.charAt(0), slim.charAt(1));
st.wordChars(slim.charAt(2), slim.charAt(3));
st.wordChars(slim.charAt(4), slim.charAt(5));
// st.wordChars(0x00A0, 0x00FF);
String wsc = " \t\n";
for (int i = 0; i < wsc.length(); i++) {
int ic = wsc.charAt(i);
st.whitespaceChars(ic, ic);
}
st.quoteChar(iq);
String swc = "_/.:&;,()\'+-.[]{}$";
for (int i = 0; i < swc.length(); i++) {
int ic = swc.charAt(i);
st.wordChars(ic, ic);
}
}
public XMLToken nextToken() {
XMLToken xmlt = new XMLToken();
int itok = ntok(streamTokenizer);
if (streamTokenizer.ttype == StreamTokenizer.TT_EOF) {
xmlt.setType(XMLToken.NONE);
} else if (itok == iq) {
xmlt.setType(XMLToken.STRING);
// quoted string;
String sss = streamTokenizer.sval;
setStringValue(xmlt, StringEncoder.xmlUnescape(sss));
} else if (streamTokenizer.ttype == StreamTokenizer.TT_WORD) {
xmlt.setType(XMLToken.STRING);
setStringValue(xmlt, StringEncoder.xmlUnescape(streamTokenizer.sval));
} else if (streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
xmlt.setType(XMLToken.NUMBER);
// boolean, int or double, all as doubles;
double d = streamTokenizer.nval;
ntok(streamTokenizer);
if (streamTokenizer.ttype == StreamTokenizer.TT_WORD
&& ((streamTokenizer.sval).startsWith("E-")
|| (streamTokenizer.sval).startsWith("E+") || (streamTokenizer.sval).startsWith("E"))) { // POSERR
// -
// catches
// wrong
// things?
String s = streamTokenizer.sval.substring(1, streamTokenizer.sval.length());
int ppp = Integer.parseInt(s);
// err ("st.sval " + st.sval);
// err ("read exponent: " + ppp);
d *= Math.pow(10., ppp);
} else {
streamTokenizer.pushBack();
}
xmlt.setDValue(d);
} else if (itok == iabo) {
itok = ntok(streamTokenizer);
String sv = streamTokenizer.sval;
if (itok == iqm) {
// should be the first line of a file - read on until
// the next question mark, just keeping the text in sinfo
// for now;
xmlt.setType(XMLToken.INTRO);
String svalue = "";
itok = -1;
while (itok != iqm) {
itok = ntok(streamTokenizer);
if (streamTokenizer.sval != null)
svalue += streamTokenizer.sval + " ";
}
setStringValue(xmlt, svalue);
} else if (itok == iexc) {
itok = ntok(streamTokenizer);
String sval = streamTokenizer.sval;
String svalue = "";
if (sval != null && sval.startsWith("[CDATA[")) {
E.error("shouldn't get CDATA in xml tokenizer");
} else if (sval != null && sval.startsWith("--")) { |
| File | Line |
|---|
| org/catacomb/druid/swing/RolloverEffect.java | 12 |
| org/catacomb/graph/gui/RolloverEffect.java | 12 |
public class RolloverEffect extends MouseAdapter {
JComponent button;
int inormal;
int iactive;
Border normalBorder;
Border activeBorder;
public final static int NONE = 0;
public final static int ETCHED_DOWN = 1;
public final static int ETCHED_UP = 2;
public final static int RAISED = 2;
Color bgColor;
int pL;
int pR;
int pT;
int pB;
private boolean hasPadding;
public RolloverEffect(JComponent buttonIn) {
this(buttonIn, ETCHED_DOWN, ETCHED_UP);
}
public RolloverEffect(JComponent buttonIn, int norm, int active) {
hasPadding = false;
bgColor = buttonIn.getBackground();
inormal = norm;
iactive = active;
button = buttonIn;
makeBorders();
if (button instanceof AbstractButton) {
((AbstractButton)button).setBorderPainted(true);
} else if (button instanceof JMenu) {
((JMenu)button).setBorderPainted(true);
} else if (button instanceof JCheckBox) {
((JCheckBox)button).setBorderPainted(true);
} else if (button instanceof JPanel) {
// ((JPanel)button).setBorderPainted(true);
}
mouseExited(null);
}
public void setPadding(int p) {
setPadding(p, p, p, p);
}
public void setPadding(int pl, int pr, int pt, int pb) {
pL = pl;
pR = pr;
pT = pt;
pB = pb;
hasPadding = true;
makeBorders();
mouseExited(null);
}
public void setBg(Color c) {
bgColor = c;
makeBorders();
mouseExited(null);
}
public void makeBorders() {
normalBorder = makeBorder(inormal);
activeBorder = makeBorder(iactive);
}
public void mouseEntered(MouseEvent me) {
button.setBorder(activeBorder);
}
public void mouseExited(MouseEvent me) {
button.setBorder(normalBorder);
}
private Border makeBorder(int type) {
Color c = bgColor;
Color cbr = myBrighter(c);
Color cdk = myDarker(c);
Border ret = null;
if (type == ETCHED_DOWN) {
// ret = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
ret = BorderFactory.createEtchedBorder(cbr, cdk);
} else if (type == ETCHED_UP) {
// ret = BorderFactory.createEtchedBorder(EtchedBorder.RAISED);
ret = BorderFactory.createEtchedBorder(cdk, cbr);
} else {
ret = BorderFactory.createEmptyBorder(2, 2, 2, 2);
}
if (hasPadding) {
Border bdr = BorderFactory.createEmptyBorder(pT, pL, pB, pR);
ret = BorderFactory.createCompoundBorder(ret, bdr);
}
return ret;
}
public static Color myBrighter(Color c) {
return linMod(c, 35);
}
public static Color myDarker(Color c) {
return linMod(c, -35);
}
public static Color linMod(Color c, int d) {
int r = c.getRed();
int g = c.getGreen();
int b = c.getBlue();
r += d;
g += d;
b += d;
r = (r > 0 ? (r < 255 ? r : 255) : 0);
g = (g > 0 ? (g < 255 ? g : 255) : 0);
b = (b > 0 ? (b < 255 ? b : 255) : 0);
return new Color(r, g, b);
}
} |
| File | Line |
|---|
| org/catacomb/interlish/reflect/Narrower.java | 223 |
| org/textensor/xml/Narrower.java | 221 |
int iret = 0;
if (s.startsWith("0x")) {
s = s.substring(2, s.length());
iret = Integer.parseInt(s, 16);
} else {
iret = Integer.parseInt(s, 10);
}
return iret;
}
public static double makeDouble(Object arg) {
double dret = 0;
if (arg instanceof Double) {
dret = ((Double)arg).doubleValue();
} else if (arg instanceof String) {
dret = parseDouble((String)arg);
} else {
err(" cant make a double from " + arg + " " + arg.getClass());
(new Exception()).printStackTrace();
}
return dret;
}
public static boolean makeBoolean(Object arg) {
boolean bret = false;
if (arg instanceof Double) {
bret = ((((Double)arg).doubleValue()) > 0.5);
} else if (arg instanceof String) {
String sob = ((String)arg).trim();
bret = (sob.equals("1") || sob.equals("true"));
} else {
err(" instantiator cant make a boolean from " + arg);
}
return bret;
}
public static double[][] makeDDArray(Object ob) {
double[][] dret = null;
if (ob == null) {
dret = new double[0][0];
} else if (ob instanceof Double || ob instanceof String) {
dret = new double[1][1];
dret[0][0] = makeDouble(ob);
} else if (ob instanceof ArrayList) {
ArrayList v = (ArrayList)ob;
dret = new double[v.size()][];
int iout = 0;
for (Object sub : v) {
dret[iout++] = makeDoubleArray(sub);
}
} else {
err("cant make DD array from " + ob);
}
return dret;
}
public static int[][] makeIIArray(Object ob) {
int[][] iret = null;
if (ob == null) {
iret = new int[0][0];
} else if (ob instanceof Double || ob instanceof String) {
iret = new int[1][1];
iret[0][0] = makeInt(ob);
} else if (ob instanceof ArrayList) {
ArrayList v = (ArrayList)ob;
iret = new int[v.size()][];
int iout = 0;
for (Object sub : v) {
iret[iout++] = makeIntArray(sub);
}
} else {
err("cant make II array from " + ob);
}
return iret;
}
public static ArrayList<Object> makeArrayList(Object arg) {
ArrayList<Object> vret = new ArrayList<Object>();
if (arg instanceof ArrayList<?>) {
vret.addAll((ArrayList<?>)arg);
} else {
vret.add(arg);
}
return vret;
}
public static double[] readDoubleArray(String sin) { |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLWriter.java | 103 |
| org/textensor/xml/XMLWriter.java | 76 |
}
String tag = "error";
if (knownAs != null) {
tag = knownAs;
} else {
tag = ob.getClass().getName();
if (conciseTags) {
int ilast = tag.lastIndexOf(".");
if (ilast >= 0) {
tag = tag.substring(ilast + 1, tag.length());
}
}
}
sbv.append(psk);
sbv.append("<" + tag + ">\n");
/*
* if (writeClass) { sbv.append("<"+tag + " class=\"" +
* ob.getClass().getName() + "\">\n"); } else { sbv.append("<"+tag +
* ">\n"); }
*/
String sk = psk + " ";
Field[] flds = ob.getClass().getFields();
for (int i = 0; i < flds.length; i++) {
String fieldName = flds[i].getName();
Object ret = null;
try {
ret = flds[i].get(ob);
} catch (Exception e) {
err("WARNING - failed to get field " + fieldName + " in " + ob);
}
if (Modifier.isFinal(flds[i].getModifiers()))
ret = null;
if (ret instanceof Double) {
appendNV(sbv, sk, fieldName, ((Double)ret).doubleValue());
} else if (ret instanceof Integer) {
appendNV(sbv, sk, fieldName, ((Integer)ret).intValue());
} else if (ret instanceof Boolean) {
appendNV(sbv, sk, fieldName, ((Boolean)ret).booleanValue());
} else if (ret instanceof String) {
appendNV(sbv, sk, fieldName, (String)ret);
} else if (ret instanceof double[]) {
appendNV(sbv, sk, fieldName, (double[])ret);
} else if (ret instanceof int[]) {
appendNV(sbv, sk, fieldName, (int[])ret);
} else if (ret instanceof boolean[]) {
appendNV(sbv, sk, fieldName, (boolean[])ret);
} else if (ret instanceof String[]) {
appendNV(sbv, sk, fieldName, (String[])ret);
} else if (ret instanceof double[][]) {
appendNV(sbv, sk, fieldName, (double[][])ret);
} else if (ret instanceof int[][]) {
appendNV(sbv, sk, fieldName, (int[][])ret);
} else if (ret != null) {
appendObject(sbv, sk, fieldName, ret); |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 486 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 593 |
for (int j = 0; j < n; j++) {
sa[i] += (" " + a[i][j]);
}
}
Sp(" n1: " + n1 + " n2: " + n2);
for (int i = 0; i < sa.length; i++) {
Sp("" + i + " " + sa[i]);
}
}
public double maxAbsElt() {
double d = 0.0;
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
if (Math.abs(a[i][j]) > d) {
d = Math.abs(a[i][j]);
}
}
}
return d;
}
public Matrix power(int p) {
Matrix mr = identity();
int pg = 0;
int pl = 1;
Matrix mp = copy();
while (pg < p) {
if ((p & pl) > 0) {
pg += pl;
mr = mr.prod(mp);
}
pl *= 2;
mp = mp.prod(mp);
}
if (pg != p) {
Sp("got Matrix power wrong: " + p + " " + pg + " " + pl);
}
return mr;
}
public Matrix crudeExpOf(double t) {
Matrix m = copy();
m.mpyBy(t);
double eps = 1.0e-8;
double d = m.maxAbsElt();
int p = 0;
double f = 1;
for (p = 0; d * f > eps; f *= 0.5, p++) {
;
}
m.mpyBy(f);
m.add(m.identity());
for (; p > 0; p--) {
m.mpyBy(m);
}
return m;
}
public Matrix expOf(double t) {
Matrix m = copy();
m.mpyBy(t);
double eps = 1.0e-12;
double d = m.maxAbsElt();
int p = 0;
double f = 1;
for (p = 0; d * f > eps; f *= 0.5, p++) {
;
}
m.mpyBy(f);
// now we want to calculate (I + m)^p
// without doing the obvious
for (; p > 0; p--) {
Matrix u = m.copy();
u.mpyBy(u);
m.add(m);
m.add(u);
}
m.add(m.identity());
return m;
}
public int randomIndexFromColumn(int c) {
return randomIndexFromColumn(c, Math.random());
}
public final int randomIndexFromColumn(int c, double rin) { |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLToken.java | 8 |
| org/textensor/xml/XMLToken.java | 5 |
public class XMLToken {
final static int NONE = 0;
final static int OPEN = 1;
final static int CLOSE = 2;
final static int NUMBER = 3;
final static int STRING = 4;
final static int OPENCLOSE = 5;
final static int INTRO = 6;
final static int COMMENT = 7;
String[] types = {"NONE", "OPEN", "CLOSE", "NUMBER", "STRING",
"OPENCLOSE", "INTRO", "COMMENT"
};
int type;
String svalue;
double dvalue;
int natt;
String[] attNV;
public XMLToken() {
type = NONE;
}
/*
public String toString() {
String sr = ("XMLToken type=" + type + " sv=" + svalue + " dv=" + dvalue +
" natt=" + natt);
for (int i = 0; i < natt; i++) {
sr += " att[" + i + "]:" + attNV[i] + "\n";
}
return sr;
}
*/
public boolean isOpen() {
return (type == OPEN || type == OPENCLOSE);
}
public boolean isClose() {
return (type == OPENCLOSE || type == CLOSE);
}
public boolean isNumber() {
return (type == NUMBER);
}
public boolean isString() {
return (type == STRING);
}
public boolean isNone() {
return (type == NONE);
}
public boolean isIntro() {
return (type == INTRO);
}
public boolean isComment() {
return (type == COMMENT);
}
public String toString() {
String s = types[type] + " " ;
if (type == OPEN ||
type == STRING ||
type == INTRO ||
type == COMMENT ||
type == CLOSE ||
type == OPENCLOSE) {
s += svalue;
if (type == OPEN || type==OPENCLOSE) {
if (natt > 0) {
for (int i = 0; i < natt; i++) {
s += "\n " + attNV[2*i] + "=" + attNV[2*i+1];
}
}
}
} else if (type == NUMBER) {
s += " " + dvalue;
}
return s;
}
public void setType(int itype) {
type = itype;
}
public void setStringValue(String s) {
svalue = s;
}
public void setDValue(double d) {
dvalue = d;
}
public void setAttributes(String[] sa) {
attNV = sa;
natt = sa.length / 2;
}
public boolean hasAttribute(String sat) {
boolean bret = false;
for (int i = 0; i < natt; i++) {
if (attNV[2*i].equals(sat)) bret = true;
}
return bret;
}
public Attribute[] getAttributes() { |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 230 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 325 |
}
public double[] rvprod(double[] v) {
double[] r = new double[n];
if (v.length != n) {
Sp("incompatible dimensions in lvprod");
} else {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
r[i] += a[i][j] * v[j];
}
}
}
return r;
}
public void multiplyInto(double[] v) {
for (int i = 0; i < n; i++) {
ws[i] = 0.;
for (int j = 0; j < n; j++) {
ws[i] += a[i][j] * v[j];
}
}
for (int i = 0; i < n; i++) {
v[i] = ws[i];
}
}
public void rect2rvprod(double[] v, double[] r1, double[] r2) {
for (int i = 0; i < n1; i++) {
ws[i] = 0.0;
for (int j = 0; j < n1; j++) {
ws[i] += a[i][j] * v[j];
}
}
for (int i = 0; i < n2 - n1; i++) {
r2[i] = 0.0;
for (int j = 0; j < n1; j++) {
r2[i] += a[i + n1][j] * v[j];
}
}
for (int i = 0; i < n1; i++) {
r1[i] = ws[i];
}
}
public double rvprodOneElt(double[] v, int elt) {
double r = 0.0;
for (int j = 0; j < n; j++) {
r += a[elt][j] * v[j];
}
return r;
}
public Matrix transpose() {
Matrix m = copy(); |
| File | Line |
|---|
| org/catacomb/interlish/reflect/ReflectionConstructor.java | 142 |
| org/textensor/xml/ReflectionInstantiator.java | 114 |
for (int i = 0; i < npkg; i++) {
E.info("tried package " + pkgs[i]);
}
if (scl.endsWith("ing")) {
(new Exception()).printStackTrace();
}
} else {
int imod = c.getModifiers();
if (Modifier.isAbstract(imod)) {
E.error("cant instantiatie " + c + ": it is an abstract class");
} else {
try {
oret = c.newInstance();
} catch (Exception e) {
E.error(" " + e + " instantiating " + c);
e.printStackTrace();
}
}
}
if (oret != null) {
checkAddPackage(oret);
}
return oret;
}
public Object getField(Object ob, String fnm) {
Object ret = null;
boolean hasField = false;
// EFF improve
Field[] flds = ob.getClass().getFields();
for (int i = 0; i < flds.length; i++) {
if (flds[i].getName().equals(fnm)) {
hasField = true;
break;
}
}
if (hasField) {
try {
Field f = ob.getClass().getField(fnm);
Class fcl = f.getType();
if (fcl.equals(String[].class)) {
ret = new String[0];
} else if (fcl.isArray()) {
ret = new ArrayList(); // ADHOC - wrap ArrayList?
} else {
ret = f.get(ob);
}
if (ret == null) {
Class<?> cl = f.getType();
ret = cl.newInstance();
}
} catch (Exception e) {
E.error("cant get field " + fnm + " on " + ob + " " + "excception= " + e);
}
}
/*
* if (!hasField && ob instanceof FieldValueProvider) { ret =
* ((FieldValueProvider)ob).getFieldValue(fnm); if (ret != null) {
* hasField = true; } }
*/
if (!hasField) {
if (ob instanceof ArrayList) {
// we're OK - the object will just be added;
} else {
// System.out.println("error - cant get field " + fnm + " on " +
// ob);
/*
* Field[] af = ob.getClass().getFields(); for (int i = 0; i <
* af.length; i++) { System.out.println("fld " + i + " " + af[i]); }
*/
}
}
return ret;
}
public Object getChildObject(Object parent, String name, Attribute[] attain) { |
| File | Line |
|---|
| org/catacomb/util/FileUtil.java | 12 |
| org/textensor/util/FileUtil.java | 13 |
public abstract class FileUtil {
public static byte[] readHeader(File f, int n) {
byte[] ret = null;
try {
FileInputStream ins = new FileInputStream(f);
ret = new byte[n];
int nread = ins.read(ret);
if (nread != n) {
E.error("readNBytes wanted " + n + " but got " + nread);
}
ins.close();
} catch (Exception ex) {
E.error("readNBytes problem " + ex);
}
return ret;
}
public static byte[] readBytes(File f) {
byte[] ret = null;
try {
FileInputStream fis = new FileInputStream(f);
BufferedInputStream bis = new BufferedInputStream(fis);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
byte[] bb = new byte[4096];
int nread = bis.read(bb);
while (nread > 0) {
baos.write(bb, 0, nread);
nread = bis.read(bb);
}
ret = baos.toByteArray();
} catch (Exception ex) {
E.error("readNBytes problem " + ex);
}
return ret;
}
public static String readStringFromFile(File f) {
String sdat = "null";
if (f != null) {
try {
boolean dogz = (f.getName().endsWith(".gz"));
InputStream ins = new FileInputStream(f);
if (dogz) {
ins = new GZIPInputStream(ins);
}
InputStreamReader insr = new InputStreamReader(ins);
BufferedReader fr = new BufferedReader(insr);
StringBuffer sb = new StringBuffer();
while (fr.ready()) {
sb.append(fr.readLine());
sb.append("\n");
}
fr.close();
sdat = sb.toString();
} catch (IOException ex) {
E.error("Cant read file " + f); |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/morph/CuboidVolumeElement.java | 13 |
| org/textensor/stochdiff/numeric/morph/CurvedVolumeElement.java | 26 |
public void setAlongArea(double d) {
alongArea = d;
}
public double getAlongArea() {
return alongArea;
}
public void setSideArea(double d) {
sideArea = d;
}
public double getSideArea() {
return sideArea;
}
public void setTopArea(double d) {
topArea = d;
}
public double getTopArea() {
return topArea;
}
public String getAsText() {
StringBuffer sb = new StringBuffer();
// export boundary if have it, ow just the center point;
if (boundary != null) {
for (Position p : boundary) {
sb.append(String.format(" (%.5g %.5g %.5g) ", p.getX(), p.getY(), p.getZ()));
}
} else {
sb.append(String.format(" (%.5g %.5g %.5g) ", cx, cy, cz));
}
return sb.toString();
}
@SuppressWarnings("boxing")
public String getAsPlainText() {
StringBuffer sb = new StringBuffer();
// export boundary if have it, ow just the center point;
if (boundary != null) {
for (Position p : boundary) {
sb.append(String.format(" %.5g %.5g %.5g", p.getX(), p.getY(), p.getZ()));
}
} else {
sb.append(String.format(" %.5g %.5g %.5g", cx, cy, cz));
}
sb.append(String.format(" %.5g %.5g", volume, deltaZ));
return sb.toString();
}
@SuppressWarnings("boxing")
public String getHeadings() {
StringBuffer sb = new StringBuffer();
// export boundary if have it, ow just the center point;
if (boundary != null) {
for (int i = 0; i < boundary.length; i++) {
sb.append(" x" + i + " y" + i + " z" + i);
}
} else {
sb.append(" cx cy cz");
}
sb.append(" volume deltaZ");
return sb.toString();
} |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLTokenizer.java | 25 |
| org/textensor/xml/XMLTokenizer.java | 27 |
static {
String sord = "\"=<>?!-";
iq = sord.charAt(0);
ieq = sord.charAt(1);
iabo = sord.charAt(2);
iabc = sord.charAt(3);
iqm = sord.charAt(4);
iexc = sord.charAt(5);
ims = sord.charAt(6);
}
HashMap<String, String> cdataHM;
String srcString;
public XMLTokenizer(String s) {
// EFF remove this - just for debugging;
srcString = extractCDATAs(s);
streamTokenizer = new StreamTokenizer(new StringReader(srcString));
initializeStreamTokenizer(streamTokenizer);
}
private String extractCDATAs(String src) {
StringBuffer sret = new StringBuffer();
int icur = 0;
int iscd = src.indexOf("<![CDATA[");
while (iscd >= icur) {
sret.append(src.substring(icur, iscd));
int iecd = src.indexOf("]]>", iscd + 9);
if (iecd >= 0) {
String cdata = src.substring(iscd + 9, iecd);
if (cdataHM == null) {
cdataHM = new HashMap<String, String>();
}
String rpl = "xyz" + cdataHM.size();
cdataHM.put(rpl, cdata);
sret.append(rpl);
} else {
iecd = iscd + 6;
E.error("no closure of cdata beginning character " + iscd + "? ");
}
icur = iecd + 3;
iscd = src.indexOf("<![CDATA[", icur);
}
if (icur < src.length()) {
sret.append(src.substring(icur, src.length()));
}
return sret.toString();
}
private void setStringValue(XMLToken xmlt, String svin) { |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLReader.java | 112 |
| org/textensor/xml/XMLReader.java | 105 |
}
return xmlt;
}
public void readFieldIntoParent(XMLTokenizer tkz, Object parent, XMLToken start) {
// read the child object that is known to the parent as item.name
// if the parent is a vector, the object is added as a new element;
// if the parent is a string, the xml is just apended;
// otherwise the field is set.
if (!start.isOpen()) {
nerror++;
err("ERROR - read object start item was not an open tag " + start);
return;
}
Object child = null;
if (parent instanceof String || parent instanceof StringBuffer) {
child = new StringBuffer();
((StringBuffer)child).append(start.getOpenTagString());
} else {
// attributes may contain the class - the instantiator processes
// all the attributes here
Attribute[] atts = start.getAttributes();
child = instantiator.getChildObject(parent, start.getName(), atts);
if (child != null) {
instantiator.applyAttributes(child, atts);
}
if (child == null) {
child = new ArrayList();
} else if (child instanceof String) {
// in this case, set its length to 0. Subseqnet parts of the
// string will get appended to the current value, so want to
// keep track of the fact that it is a string, without keeping
// the default that may have come from above;
child = new StringBuffer();
} else if (child.getClass().isArray()) {
// make it an array list for the time being, then
// give the lsit to teh instantiator to make into theright sort of
// array;
child = new ArrayList();
}
if (start.isClose()) {
// the tag was both an open and a close tag, so now that we've
// processed the attributes, we're done;
} else {
// read on and fill in fields until we get a closing tag which
// matches the start tag
// the fields will be inserted in target;
XMLToken next = readToken(tkz);
while (true) {
if (next.isNone()) {
// should mean EOF, but could also be an error
// return whatever;
break;
} else if (next.isOpen()) {
// open tags could mean anything - elementary field, array,
// or object, but in any case, pass them back to this method;
readFieldIntoParent(tkz, child, next);
} else if (next.isClose()) {
if (next.closes(start)) {
// fine - close item
if (parent instanceof String || parent instanceof StringBuffer) {
((StringBuffer)child).append(next.getCloseTagString());
}
} else {
nerror++;
E.shortError(" non-matching close item \n" + "start Item was: \n"
+ start.toString() + "\n" + "but close was: \n" + next.toString() + "\n" + |
| File | Line |
|---|
| org/catacomb/druid/gui/edit/DruCheckboxListPanel.java | 32 |
| org/catacomb/druid/gui/edit/DruToggleListPanel.java | 27 |
public DruCheckboxListPanel(int nr) {
super();
nrow = nr;
dList = new DCheckboxList();
addSingleDComponent(dList);
dList.setItems(new Object[0]);
dList.setLabelActor(this);
}
public void setItems(String[] sa) {
dList.setItems(sa);
if (listWatcher != null) {
listWatcher.listChanged(this);
}
}
public void setItems(ArrayList<? extends Object> obal) {
Object[] obar = obal.toArray(new Object[obal.size()]);
dList.setItems(obar);
if (listWatcher != null) {
listWatcher.listChanged(this);
}
}
public void setSelected(String[] sa) {
dList.setSelected(sa);
}
public void setSelected(int[] ia) {
dList.setSelected(ia);
}
public void selectAll() {
dList.selectAll();
}
public ArrayList<Object> getAllItems() {
return dList.getAllItems();
}
public ArrayList<Object> getSelectedItems() {
return dList.getCheckedItems();
}
public void setBg(Color c) {
dList.setBackground(c);
super.setBg(c);
}
public void updateDisplay() {
// EFF
dList.repaint();
}
public Object getSelectedItem() {
return dList.getSelectedValue();
}
public String getSelectedName() {
return "" + getSelectedItem();
}
public void labelAction(String s, boolean b) {
if (s.equals("selected")) {
valueChange(getSelectedName());
} else if (s.equals("toggle")) { |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 850 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 770 |
System.out.println("in parallelAndSharedDiffusionStep 1st else: ngo is NEGATIVE. Exiting...");
System.exit(0);
}
} else {
if (useBinomial()) {
// WK 7 2 2008: if n*p < 10, then use poission to get ngo;
// otherwise, use gaussian.
// RO 7 3 2008: changed from 10 to 20 because observed negative
// ngo
if (np0 * pSharedOut[iel][k] < NP) {
// RO
ngo = StepGenerator.gaussianStep(np0, pSharedOut[iel][k], random.gaussian(), random.random(),
random.poisson(np0 * pSharedOut[iel][k]), NP);
if (ngo < 0) {
ngo = 0;
System.out.println("in parallelAndSharedDiffusionStep, if (np0*pSharedOut[iel][k] < " + NP
+ "): ngo is NEGATIVE.");
System.out.println("ngo: " + ngo + " np0: " + np0 + " pSharedOut[iel][k]: "
+ pSharedOut[iel][k]);
}
} else {
ngo = StepGenerator.gaussianStep(np0, pSharedOut[iel][k], random.gaussian(), random.random());
if (ngo < 0) {
ngo = 0;
System.out.println("in parallelAndSharedDiffusionStep, if (np0*pSharedOut[iel][k] >= " + NP
+ "): ngo is NEGATIVE.");
System.out.println("ngo: " + ngo + " np0: " + np0 + " pSharedOut[iel][k]: "
+ pSharedOut[iel][k]);
}
// WK
}
} else {
ngo = StepGenerator.poissonStep(np0, pSharedOut[iel][k], random.gaussian(), random.random());
if (ngo < 0) {
ngo = 0;
System.out.println("in parallelAndSharedDiffusionStep, if not using Binomial: ngo is NEGATIVE.");
System.out.println("ngo: " + ngo + " np0: " + np0 + " pSharedOut[iel][k]: " + pSharedOut[iel][k]);
}
}
}
// WK 7 2 2008: if ngo is negative, exit.
if (ngo < 0) { |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 429 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 539 |
}
public double[] lubksb(double[] b) {
int ip;
int ii = -1;
double sum;
for (int i = 0; i < n; i++) {
ip = perm[i];
sum = b[ip];
b[ip] = b[i];
if (ii >= 0) {
for (int j = ii; j < i; j++) {
sum -= a[i][j] * b[j];
}
} else if (sum != 0.0) {
ii = i;
}
b[i] = sum;
}
for (int i = n - 1; i >= 0; i--) {
sum = b[i];
for (int j = i + 1; j < n; j++) {
sum -= a[i][j] * b[j];
}
b[i] = sum / a[i][i];
}
return b;
}
public void round(double d) {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
if (Math.abs(a[i][j]) < d) {
a[i][j] = 0.0;
}
}
}
}
public void round() {
round(1.0e-15);
}
public void print() {
String[] sa = new String[n]; |
| File | Line |
|---|
| org/catacomb/numeric/math/Random.java | 22 |
| org/textensor/stochdiff/numeric/math/NRRandom.java | 24 |
public static double random() {
jran = (jran * ia + ic) % im;
double ran = (1. * jran) / im;
return ran;
}
public static int getSeed() {
return jran;
}
public static void setSeed(int jr) {
jran = jr;
}
public static double nextRandom() {
return random();
}
public static double uniformRV() {
return random();
}
public static int weightedSample(double[] rw) {
int n = rw.length;
double a = random();
int inew = 0;
while ((a -= rw[inew]) > 0 && inew < n-1) {
inew++;
}
return inew;
}
public static double gaussianRV() {
return grv();
}
public static double grv() {
double r, ran1, ran2, fac, g1;
r = -1;
ran1 = 0.0;
ran2 = 0.0;
while (r <= 0.0 || r >= 1.0) {
jran = (jran * ia + ic) % im;
ran1 = (2. * jran) / im - 1;
jran = (jran * ia + ic) % im;
ran2 = (2. * jran) / im - 1;
r = ran1 * ran1 + ran2 * ran2;
}
fac = Math.sqrt(-2. * Math.log(r) / r);
g1 = ran1 * fac;
// g2 = ran2 * fac;
return g1;
} |
| File | Line |
|---|
| org/catacomb/druid/swing/DFloatSlider.java | 288 |
| org/catacomb/druid/swing/DSlider.java | 241 |
}
private void drawUpButton(Graphics g, int icx, int icy, int hw, int hh) {
Color c = getBackground();
g.setColor(c.darker());
g.drawLine(icx - hw - 1, icy + hh + 1, icx + hw + 1, icy + hh + 1);
g.drawLine(icx - hw, icy + hh, icx + hw, icy + hh);
g.drawLine(icx + hw + 1, icy - hh - 1, icx + hw + 1, icy + hh + 1);
g.drawLine(icx + hw, icy - hh, icx + hw, icy + hh);
g.setColor(c.brighter());
g.drawLine(icx - hw - 1, icy - hh - 1, icx + hw + 1, icy - hh - 1);
g.drawLine(icx - hw, icy - hh, icx + hw, icy - hh);
g.drawLine(icx - hw - 1, icy - hh - 1, icx - hw - 1, icy + hh + 1);
g.drawLine(icx - hw, icy - hh, icx - hw, icy + hh);
}
public void nudgeLeft() { |
| File | Line |
|---|
| org/catacomb/interlish/reflect/Narrower.java | 58 |
| org/textensor/xml/Narrower.java | 53 |
ret = new SColor((String)arg);
}
return ret;
}
public static void err(String s) {
E.error(s);
}
public static double parseDouble(String s) {
double dret = 0.;
int ii = s.indexOf("e");
if (ii < 0)
ii = s.indexOf("E");
if (ii < 0) {
dret = (new Double(s)).doubleValue();
} else {
String sa = s.substring(0, ii - 1);
String sp = s.substring(ii + 1, s.length());
int ppp = Integer.parseInt(sp);
dret = (new Double(sa)).doubleValue();
dret *= Math.pow(10., ppp);
}
return dret;
}
public static String[] makeStringArray(Object ob) {
String[] sret = null;
if (ob instanceof String[]) {
sret = (String[])ob;
} else if (ob instanceof String) {
sret = new String[1];
sret[0] = (String)ob;
} else if (ob instanceof ArrayList<?>) {
ArrayList<? extends Object> v = (ArrayList<? extends Object>)ob; |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 601 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 715 |
for (int i = 0; i < n2; i++) {
c[i] = a[i][ic];
}
return c;
}
public int randomIndexFromOffsetColumn(int c, int off) {
double r = Math.random();
int ir;
for (ir = off; (r -= a[ir][c]) > 0; ir++) {
;
}
return ir;
}
public double[] ev1vec(int np) {
// find the vector with eigenvalue 1., assuming it exists... or
// equivalently the null space of M-I, which is assumed to have
// dimension 1;
// actually just take a large power of the Matrix ***
Matrix q = copy();
for (int i = 0; i < np; i++) {
q = q.prod(q);
}
double[] s = new double[n];
for (int i = 0; i < n; i++) {
s[i] = 1. / n;
}
s = q.rvprod(s);
double t = 0.0;
for (int i = 0; i < n; i++) {
t += s[i];
}
for (int i = 0; i < n; i++) {
s[i] /= t;
}
if (Math.abs(t - 1.) > 0.01) {
Sp("WARNING - ev1vec in class Matrix chnaged size " + t);
}
return s;
} |
| File | Line |
|---|
| org/catacomb/druid/swing/DFloatSlider.java | 384 |
| org/catacomb/druid/swing/DSlider.java | 326 |
export();
repaint();
}
}
// map listeners to rfsXXX methods;
public void mouseDragged(MouseEvent e) {
int x = e.getX();
int y = e.getY();
rsfMouseDrag(x, y);
}
public void mouseMoved(MouseEvent e) {
}
public void mousePressed(MouseEvent e) {
int x = e.getX();
int y = e.getY();
long when = e.getWhen();
int modif = e.getModifiers();
int button = 0;
if (modif == InputEvent.BUTTON1_MASK) {
button = 1;
} else if (modif == InputEvent.BUTTON2_MASK) {
button = 2;
} else if (modif == InputEvent.BUTTON3_MASK) {
button = 3;
}
rsfMouseDown(x, y, when, button);
}
public void mouseReleased(MouseEvent e) {
int x = e.getX();
int y = e.getY();
rsfMouseUp(x, y);
}
public void mouseEntered(MouseEvent e) {
requestFocus();
}
public void mouseExited(MouseEvent e) {
}
public void mouseClicked(MouseEvent e) {
requestFocus();
}
public double getTotalRange() { |
| File | Line |
|---|
| org/catacomb/interlish/reflect/Narrower.java | 24 |
| org/textensor/xml/Narrower.java | 22 |
if (fcln.endsWith("int")) {
ret = new Integer(makeInt(arg));
} else if (fcln.endsWith("boolean")) {
ret = new Boolean(makeBoolean(arg));
} else if (fcln.endsWith("double")) {
ret = new Double(makeDouble(arg));
} else if (fcln.startsWith("java.lang.String")) {
ret = arg;
} else if (fcln.startsWith("[D")) {
ret = makeDoubleArray(arg);
} else if (fcln.startsWith("[I")) {
ret = makeIntArray(arg);
} else if (fcln.startsWith("[Ljava.lang.String")) {
ret = makeStringArray(arg);
} else if (fcln.startsWith("[Z")) {
ret = makeBooleanArray(arg);
} else if (fcln.startsWith("[[D")) {
ret = makeDDArray(arg);
} else if (fcln.startsWith("[[I")) {
ret = makeIIArray(arg);
} else if (fcln.endsWith("ArrayList")) {
ret = makeArrayList(arg);
} else if (fcln.endsWith("SColor")) { |
| File | Line |
|---|
| org/catacomb/druid/blocks/ScrollingCheckboxList.java | 61 |
| org/catacomb/druid/blocks/ScrollingList.java | 59 |
if (renderer != null) {
// TODO move renderer defs to XML;
if (renderer.equals("quantity")) {
drup.setCellRenderer(new DruListQuantityRenderer());
} else if (renderer.equals("progress")) {
drup.setCellRenderer(new DruListProgressRenderer());
} else if (renderer.equals("color")) {
drup.setCellRenderer(new DruListColorRenderer());
} else {
E.error("unrecognized renderer " + renderer);
}
}
if (multiple) {
drup.setMultiple();
}
if (clickAction != null) {
if (clickAction.equals("toggle")) {
drup.setToggleAction();
} else {
E.warning("unrecognized action " + clickAction);
}
}
if (order != null) {
if (order.equals("reverse")) {
drup.setOrder(DruListPanel.REVERSE_ORDER);
} else {
E.warning("unknown list order " + order + " (only know reverse)");
}
}
if (clickAreas != null) {
for (ListClickArea lca : clickAreas) {
drup.addClickAction(lca.makeActor());
}
}
}
} |
| File | Line |
|---|
| org/catacomb/druid/swing/DChoice.java | 306 |
| org/catacomb/druid/swing/DValueHistory.java | 138 |
}
public void setLabelActor(LabelActor bl) {
lact = bl;
}
public void deliverAction(String s, boolean b) {
if (lact != null) {
lact.labelAction(s, b);
}
}
// icon methods to draw the button;
public void paintIcon(Component c, Graphics g, int x, int y) {
JComponent component = (JComponent)c;
int iconWidth = getIconWidth();
g.translate(x, y);
g.setColor(component.isEnabled() ? Color.gray : Color.blue);
g.drawLine(2, 0, iconWidth - 1, 0);
g.drawLine(3, 1, 1 + (iconWidth - 3), 1);
g.drawLine(5, 3, 3 + (iconWidth - 7), 3);
g.drawLine(6, 4, 4 + (iconWidth - 9), 4);
g.translate(-x, -y);
}
public int getIconWidth() {
return 12;
}
public int getIconHeight() {
return 5;
}
public void setUpdatable(Updatable u) { |
| File | Line |
|---|
| org/textensor/vis/SceneGraphBuilder.java | 257 |
| org/textensor/vis/SceneGraphBuilder.java | 341 |
int nvert = 2 * nside * nstrip;
int[] svc = new int[nstrip];
for (int i = 0; i < nstrip; i++) {
svc[i] = 2 * nside;
}
float[] datv = new float[3 * nvert];
float[] datn = new float[3 * nvert];
double dtheta = 2. * Math.PI / (nside-1);
double[][] csas = new double[nside][2];
double[][] csbs = new double[nside][2];
for (int i = 0; i < nside; i++) {
double tha = i * dtheta;
double thb = (i + 0.5) * dtheta;
csas[i][0] = Math.cos(tha);
csas[i][1] = Math.sin(tha);
csbs[i][0] = Math.cos(thb);
csbs[i][1] = Math.sin(thb);
} |
| File | Line |
|---|
| org/catacomb/dataview/FrameController.java | 191 |
| org/catacomb/dataview/gui/FramePlayerController.java | 147 |
framePlayer.start();
}
}
public void stop() {
if (framePlayer != null) {
framePlayer.stop();
}
}
public void faster() {
speed *= 1.3;
}
public void slower() {
speed /= 1.3;
}
public boolean canAdvance() {
return (indexes != null && shownFrame < indexes.length-1);
}
public void advance() {
showFrame(shownFrame + 1);
}
public double getSpeed() {
return speed;
}
public void record() {
E.missing();
/*
File f = FileChooser.getWriteFile();
if (f != null) {
makeAnimatedGif(f);
}
*/
}
public void miniRecord() {
E.missing();
/*
File f = FileChooser.getWriteFile();
if (f != null) {
makeMiniAnimatedGif(f, 160, 100);
}
*/
}
public void makeMovie(File f) {
makeAnimatedGif(f);
}
public void makeThumbnailMovie(File f) {
makeMiniAnimatedGif(f, 160, 160);
}
public void makeAnimatedGif(File f) {
stop();
rewind();
AnimatedGifEncoder enc = new AnimatedGifEncoder();
enc.start(f);
enc.setDelay(160); // ms
int ifr = 0;
E.info("animated gif - frame " + ifr); |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLToken.java | 140 |
| org/textensor/xml/XMLToken.java | 137 |
nvpa[i] = new NamedString(attNV[2*i], attNV[2*i+1]);
}
return nvpa;
}
public String getAttribute(String sat) {
String sret = null;
for (int i = 0; i < natt; i++) {
if (attNV[2*i].equals(sat)) sret = attNV[2*i+1];
}
return sret;
}
public String getName() {
return svalue;
}
public String getOpenTagString() {
return ("<" + svalue + ">");
}
public String getCloseTagString() {
return ("</" + svalue + ">");
}
public boolean closes(XMLToken start) {
return (svalue.equals(start.getName()) && isClose());
}
public int getNumAttributes() {
return natt;
}
public String getAttributeName(int i) {
return attNV[2*i];
}
public String getAttributeValue(int i) {
return attNV[2*i+1];
}
} |
| File | Line |
|---|
| org/catacomb/druid/swing/DFloatSlider.java | 236 |
| org/catacomb/druid/swing/DSlider.java | 172 |
g.drawString(label, 40, 20);
}
}
private void paintArrows(Graphics g) {
int w = getWidth();
int h = getHeight();
Color cbg = bgColor;
Color cbr = cbg.brighter();
Color cdk = cbg.darker();
int hh = h / 2;
g.setColor(cbr);
g.drawLine(4, hh, 15, 4);
g.drawLine(w - 15, h - 4, w - 15, 4);
// g.drawLine(w-15, 4, w-10, hh);
g.setColor(cdk);
g.drawLine(15, 4, 15, h - 4);
// g.drawLine(15, h-4, 10, hh);
g.drawLine(4, hh, 15, h - 4);
g.drawLine(w - 15, h - 4, w - 4, hh);
g.drawLine(w - 15, 4, w - 4, hh);
}
private void paintKnob(Graphics g) {
int width = getWidth();
int height = getHeight();
int hh = height / 2; |
| File | Line |
|---|
| org/catacomb/interlish/reflect/ReflectionConstructor.java | 321 |
| org/textensor/xml/ReflectionInstantiator.java | 274 |
}
if (child == null) {
E.warning("ReflectionInstantiator failed to get field " + name + " on " + parent + " "
+ (parent != null ? parent.getClass().toString() : ""));
}
/*
* POSERR did this do anything useful? if (child instanceof IDd &&
* ((IDd)child).getID() == null) { // setAttributeField(child, "id",
* name); // System.out.println("autoset id to " + name); }
*/
return child;
}
public void applyAttributes(Object target, Attribute[] atta) {
for (int i = 0; i < atta.length; i++) {
Attribute att = atta[i];
setAttributeField(target, att.getName(), att.getValue());
}
}
public boolean setAttributeField(Object target, String name, String arg) {
boolean bret = false;
if (name.equals("class") || name.equals("package") || name.equals("provides")
|| name.equals("archive-hash")) {
// already done; ADHOC
} else {
bret = setField(target, name, arg);
}
return bret;
}
// ADHOC suppressing warnings
@SuppressWarnings( { "unchecked" })
public boolean setField(Object ob, String sfin, Object argin) { |
| File | Line |
|---|
| org/catacomb/interlish/reflect/ReflectionConstructor.java | 462 |
| org/textensor/xml/ReflectionInstantiator.java | 394 |
f.set(ob, d);
} else if (ftyp == Double.TYPE && arg instanceof Double) {
f.set(ob, arg);
} else if (ftyp == Boolean.TYPE && arg instanceof Boolean) {
f.set(ob, arg);
} else if (ftyp == Integer.TYPE && arg instanceof Integer) {
f.set(ob, arg);
} else if (f.getType().isArray() && arg instanceof ArrayList) {
setArrayField(ob, f, (ArrayList)arg);
} else {
Object onarg = Narrower.narrow(ftyp.getName(), arg);
if (onarg != null) {
f.set(ob, onarg);
} else {
f.set(ob, arg);
}
}
ok = true;
} catch (Exception e) {
ok = false;
E.error(" cant set field " + sf + " in " + ob + " from typed " + |
| File | Line |
|---|
| org/catacomb/interlish/reflect/Narrower.java | 328 |
| org/catacomb/serial/DataIO.java | 12 |
public static double[] readDoubleArray(String sin) {
String s = sin;
if (s.startsWith("{")) {
s = s.substring(1, s.indexOf("}"));
}
s = s.trim();
String[] sa = s.split("[ ,\t\n\r]+");
/*
E.info("after splitting " + s);
for (int i = 0; i < sa.length; i++) {
E.info("item " + i + " " + sa[i]);
}
*/
int nt = sa.length;
double[] value = new double[nt];
try {
for (int i = 0; i < nt; i++) {
value[i] = (new Double(sa[i])).doubleValue();
}
} catch (Exception ex) {
E.error("float reading cant extract " + nt + " doubles from " + s);
for (int i = 0; i < nt; i++) {
E.info("string " + i + "=xxx" + sa[i] + "xxx");
}
}
return value;
}
} |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 84 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 42 |
Column mconc;
ReactionTable rtab;
public VolumeGrid vgrid;
StimulationTable stimTab;
double dt;
public int nel;
int nspec;
public String[] specieIDs;
double[] volumes;
double[] lnvolumes;
double[] fdiff;
double[] lnfdiff;
double[] surfaceAreas;
// WK 6 18 2007
public boolean[] submembranes;
public String[] regionLabels;
public int[] eltregions;
// WK
int[][] neighbors;
double[][] couplingConstants;
double[][] lnCC;
int[][] wkA;
int[][] wkB;
int[] wkReac;
int[][] nparticle;
int nreaction;
public int nspecie;
String[] speciesIDs;
double[] diffusionConstants;
int[][] reactantIndices;
int[][] productIndices;
int[][] reactantStochiometry;
int[][] productStochiometry;
double[] rates;
double[] lnrates;
int[][] stimtargets;
double[] intlogs;
double lndt;
int ninjected = 0;
InterpolatingStepGenerator interpSG;
MersenneTwister random;
int nwarn;
int nngowarn = 0; //added in v2.1.1 by BHK to keep track of a different type of warning |
| File | Line |
|---|
| org/textensor/stochdiff/disc/DiscSplitter.java | 96 |
| org/textensor/stochdiff/disc/LineBoxer.java | 103 |
CurvedVolumeSlice vg = null;
if (tpn.subAreaPeer == tp) {
// nothing to do for now - put line in when we
// do the first child of tpn
// E.info("skipping pt with peer " + tpn);
} else if (tp.subAreaPeer != null && tp.subAreaPeer == tp.parent) {
// E.info("first pt after branch " + tpn);
TreePoint par = tp.parent;
E.info("starting a sub-branch at " + tp + " - " + tpn + " " + pGrid);
vg = baseGrid(tp, tpn, lbl);
pGrid.subPlaneConnect(tp, tpn, vg, par.partBranchOffset);
par.partBranchOffset += 2 * tpn.r;
} else {
// normal case: make a new one or add a slice and connect
// it up with the centres aligned
if (pGrid == null) {
vg = baseGrid(tp, tpn, lbl);
} else {
// TODO - probably not what we want
// too much mumerical diffusion if boxes can have gradually changing
// sizes? restrict to a few dicrete multiples?
vg = baseGrid(tp, tpn, lbl);
pGrid.planeConnect(vg);
}
}
lbl = null; // only use it once
if (vg != null) {
gridAL.add(vg);
recAdd(vg, tpn);
} else {
// skipped the point that is the start of a new segment
// of different radius
recAdd(pGrid, tpn);
}
}
}
}
public CurvedVolumeSlice baseGrid(TreePoint tpa, TreePoint tpb, String lbl) { |
| File | Line |
|---|
| org/catacomb/graph/gui/Geom.java | 16 |
| org/catacomb/graph/gui/Iconizer.java | 226 |
public final static boolean pointIsInside(double[] xb, double[] yb, double x, double y) {
int n = xb.length;
int iwn = 0;
for (int i = 0; i < n; i++) {
int idir = 0;
int p = (i + 1) % n;
if (yb[i] <= y && yb[p] > y) {
idir = 1;
}
if (yb[i] > y && yb[p] <= y) {
idir = -1;
}
if (idir != 0) {
double f = (y - yb[i]) / (yb[p] - yb[i]);
double xc = f * xb[p] + (1. - f) * xb[i];
int isid = (xc > x ? 1 : -1);
iwn += isid * idir;
}
}
return (iwn != 0);
} |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/DeterministicGridCalc.java | 338 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 441 |
while (time < endtime) {
// RO 5 13 2010: follows template in SteppedStochaticGridCalc
if (time >= writeTime) {
if (resultWriter != null) {
resultWriter.writeString(getGridConcsText(time));
}
writeTime += sdRun.outputInterval;
}
for (int i = 0; i < fnmsOut.length; i++) {
if (time >= writeTimeArray[i]) {
resultWriter.writeToSiblingFile(getGridConcsPlainText_dumb(i, time), "-" +fnmsOut[i] + "-conc.txt");
writeTimeArray[i] += Double.valueOf(dtsOut[i]);
}
}
time += advance(time);
if (time > tlog) {
E.info("time " + time + " dt=" + dt);
tlog += Math.max(50 * sdRun.outputInterval, 5);
}
if (time >= stateSaveTime) {
resultWriter.writeToSiblingFile(getStateText(), sdRun.stateSavePrefix + "-" + Math.round(time) + ".nrds"); |
| File | Line |
|---|
| org/catacomb/interlish/reflect/Narrower.java | 330 |
| org/catacomb/serial/DataIO.java | 14 |
| org/textensor/xml/Narrower.java | 326 |
if (s.startsWith("{")) {
s = s.substring(1, s.indexOf("}"));
}
s = s.trim();
String[] sa = s.split("[ ,\t\n\r]+");
/*
E.info("after splitting " + s);
for (int i = 0; i < sa.length; i++) {
E.info("item " + i + " " + sa[i]);
}
*/
int nt = sa.length;
double[] value = new double[nt];
try {
for (int i = 0; i < nt; i++) {
value[i] = (new Double(sa[i])).doubleValue();
}
} catch (Exception ex) {
E.error("float reading cant extract " + nt + " doubles from " + s);
for (int i = 0; i < nt; i++) {
E.info("string " + i + "=xxx" + sa[i] + "xxx");
}
}
return value;
}
} |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/DeterministicGridCalc.java | 338 |
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 520 |
while (time < endtime) {
// RO 5 13 2010: follows template in SteppedStochaticGridCalc
if (time >= writeTime) {
if (resultWriter != null) {
resultWriter.writeString(getGridConcsText(time));
}
writeTime += sdRun.outputInterval;
}
for (int i = 0; i < fnmsOut.length; i++) {
if (time >= writeTimeArray[i]) {
resultWriter.writeToSiblingFile(getGridConcsPlainText_dumb(i, time), "-" +fnmsOut[i] + "-conc.txt");
writeTimeArray[i] += Double.valueOf(dtsOut[i]);
}
}
time += advance(time);
if (time > tlog) {
E.info("time " + time + " dt=" + dt);
tlog += Math.max(50 * sdRun.outputInterval, 5);
}
if (time >= stateSaveTime) {
resultWriter.writeToSiblingFile(getStateText(), sdRun.stateSavePrefix + "-" + Math.round(time) + ".nrds"); |
| File | Line |
|---|
| org/catacomb/graph/gui/Painter.java | 1340 |
| org/catacomb/graph/gui/Painter.java | 1354 |
public void drawUpper3DIntMarks(float[][] ca, int n, int w, int h, double zp, double zd) {
for (int i = 0; i < n; i++) {
double z = zProj(ca[i][0], ca[i][1], ca[i][2]);
double f = ca[i][4];
if (z < (f * zd + (1.-f) * zp)) {
int x = powx(xProj(ca[i][0], ca[i][1], ca[i][2]));
int y = powy(yProj(ca[i][0], ca[i][1], ca[i][2]));
g.fillRect(x, y, w, h); |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 520 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 441 |
while (time < endtime) {
if (time >= writeTime) {
if (resultWriter != null) {
resultWriter.writeString(getGridConcsText(time));
}
writeTime += sdRun.outputInterval;
}
for (int i = 0; i < fnmsOut.length; i++) {
if (time >= writeTimeArray[i]) {
resultWriter.writeToSiblingFile(getGridConcsPlainText_dumb(i, time), "-" + fnmsOut[i] + "-conc.txt");
writeTimeArray[i] += Double.valueOf(dtsOut[i]);
}
}
time += advance(time);
if (time > tlog) {
E.info("time " + time + " dt=" + dt);
tlog += Math.max(50 * sdRun.outputInterval, 5);
}
if (time >= stateSaveTime) {
resultWriter.writeToFinalSiblingFile(getStateText(), sdRun.stateSavePrefix + Math.round(time) + ".nrds"); |
| File | Line |
|---|
| org/catacomb/interlish/reflect/ReflectionConstructor.java | 87 |
| org/textensor/xml/ReflectionInstantiator.java | 52 |
}
public void checkAddPackage(Object oret) {
String scl = oret.getClass().getName();
if (scl.startsWith("java")) {
return;
}
int ild = scl.lastIndexOf(".");
String pkg = scl.substring(0, ild);
if (pkg.equals(wkpkg)) {
// just same as before;
} else {
boolean got = false;
for (int i = 0; i < npkg; i++) {
if (pkgs[i].equals(pkg)) {
got = true;
break;
}
}
if (!got) {
pkgs[npkg++] = pkg;
// System.out.println("Reflection instantiator added search package
// " + pkg);
}
}
}
public Object newInstance(String scl) {
Object oret = null;
Class<?> c = null; |
| File | Line |
|---|
| org/catacomb/numeric/mesh/Discretizer.java | 337 |
| org/textensor/stochdiff/disc/SegmentSlicer.java | 315 |
} else {
// chop up the carrot;
double delf = fdist / (nadd+1);
double ffa = (rb - ra) / dab; // dr/dx
double xa = ra / ffa;
double xb = rb / ffa;
// xa and xb are the end positions measured from where
// the carrot comes to a point.
double x = xa;
// the integral of sqrt(r) dx is
// 2/3 * dx / (rb-ra) * (rb^3/2 - ra^3/2)
// so need dx such that this is delf (= total_int / nseg)
for (int i = 0; i < nadd+1; i++) {
double ttt = (delf * ffa * 3./2. +
Math.pow(ffa * x, 3./2.));
double dx = Math.pow(ttt, (2./3.)) / ffa - x;
x += dx;
if (i < nadd) {
dpos[i] = (x - xa) / dab;
}
}
if (Math.abs(xb - x) > 1.e-5) { |
| File | Line |
|---|
| org/catacomb/interlish/reflect/ReflectionConstructor.java | 393 |
| org/textensor/xml/ReflectionInstantiator.java | 330 |
return true;
}
if (arg.equals(ob)) {
E.error("ReflectionInstantiator setField: " + "the child is the same as the parent " + ob);
return true;
}
int icolon = sf.indexOf(":");
if (icolon >= 0) {
sf = sf.substring(0, icolon) + "_" + sf.substring(icolon + 1, sf.length());
}
boolean ok = false;
Class c = ob.getClass();
Field f = null;
try {
f = c.getField(sf);
} catch (NoSuchFieldException e) {
}
if (f == null) {
if (ob instanceof ArrayList) {
((ArrayList)ob).add(arg);
ok = true;
} else if (arg instanceof String && ob instanceof AttributeAddableTo) { |
| File | Line |
|---|
| org/catacomb/report/E.java | 255 |
| org/textensor/report/E.java | 170 |
}
public static String getShortSource() {
StackTraceElement[] stea = (new Exception()).getStackTrace();
String ss = (" at " + stea[2].toString());
if (ss.equals(lastShortSource)) {
ss = "";
} else {
lastShortSource = ss;
}
return ss;
}
public static void delay() {
pause(200);
}
public static void pause(int n) {
try {
Thread.sleep(n);
} catch (Exception ex) {
}
}
public static void newLine() {
System.out.println("...");
}
public static void cacheAction(String s) {
cachedAction = s;
}
public static void reportCached() { |
| File | Line |
|---|
| org/textensor/vis/SceneGraphBuilder.java | 367 |
| org/textensor/vis/SceneGraphBuilder.java | 382 |
for (int ic = 0; ic < ncap; ic++) {
double[][] incs = (ic % 2 == 0 ? csbs : csas);
double[][] outcs = (ic % 2 == 0 ? csas : csbs);
double t0 = ic * (0.5 * Math.PI / (ncap + 0.1));
double t1 = (ic + 1) * (0.5 * Math.PI / (ncap + 0.1));
double s0 = Math.sin(t0);
double c0 = Math.cos(t0);
double s1 = Math.sin(t1);
double c1 = Math.cos(t1);
vnStrip(datv, datn, koff, nside, c1 * ra, c0 * ra, -1 * s1 * ra, -1 * s0 * ra, -s1, c1, -s0, c0, incs, outcs); |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLWriter.java | 14 |
| org/textensor/xml/XMLWriter.java | 10 |
public class XMLWriter {
boolean conciseTags;
boolean quoteStrings;
public XMLWriter() {
conciseTags = false;
quoteStrings = true;
}
public void setConciseTags(boolean b) {
conciseTags = b;
}
public void setQuoteStrings(boolean b) {
quoteStrings = b;
}
public static void err(String s) {
System.out.println(s);
}
public static XMLWriter newInstance() {
return new XMLWriter();
}
public static String serialize(Object ob) {
return getSerialization(ob);
}
public static String getSerialization(Object ob) {
return newInstance().writeObject(ob);
}
public String writeObject(Object obj) {
StringBuffer sb = new StringBuffer();
appendObject(sb, "", null, obj); |
| File | Line |
|---|
| org/catacomb/graph/gui/Painter.java | 1329 |
| org/catacomb/graph/gui/Painter.java | 1342 |
double z = zProj(ca[i][0], ca[i][1], ca[i][2]);
double f = ca[i][4];
if (z < (f * zd + (1.-f) * zp)) {
int x = powx(xProj(ca[i][0], ca[i][1], ca[i][2]));
int y = powy(yProj(ca[i][0], ca[i][1], ca[i][2]));
g.fillRect(x, y, 1, 1); |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/DeterministicGridCalc.java | 195 |
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 379 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 335 |
}
}
}
}
}
@SuppressWarnings("boxing")
// RO 5 13 2010: Commented out in favor of new version above.
// private String getGridConcsText(double time) {
// StringBuffer sb = new StringBuffer();
// sb.append("gridConcentrations " + nel + " " + nspec + " " + time + " ");
// for (int i = 0; i < nspec; i++) {
// sb.append(specieIDs[i] + " ");
// }
// sb.append("\n");
//
// for (int i = 0; i < nel; i++) {
// // sb.append("");
// for (int j = 0; j < nspec; j++) {
// sb.append(String.format(" %g5 ", wkB[i][j]));
// }
// sb.append("\n");
// }
// return sb.toString();
// }
// RO
private String getGridConcsText(double time) {
StringBuffer sb = new StringBuffer();
// TODO tag specific to integer quantities;
int nspecout = ispecout.length;
if (nspecout == 0) {
return "";
}
sb.append("gridConcentrations " + nel + " " + nspecout + " " + time + " ");
for (int i = 0; i < nspecout; i++) {
sb.append(specieIDs[ispecout[i]] + " ");
}
sb.append("\n");
for (int i = 0; i < nel; i++) {
for (int j = 0; j < nspecout; j++) {
// rcc May 2010: this was wrong, was it just saving species j,
// not species ispecout[j]
// sb.append(stringd(wkA[i][j]));
if (writeConcentration) {
sb.append(stringd(wkA[i][ispecout[j]])); |
| File | Line |
|---|
| org/catacomb/serial/om/OmFileReader.java | 16 |
| org/catacomb/serial/om/OmFileWriter.java | 16 |
public OmFileReader(File f) {
file = f;
}
public File getFile() {
return file;
}
public File getResourceDir() {
/*
String fnm = FileUtil.getRootName(file);
String resnm = fnm + "_resources";
File fparent = file.getParentFile();
File fres = new File(fparent, resnm);
if (fres.exists()) {
// OK;
} else {
fres.mkdir();
}
return fres;
*/
return file.getParentFile();
}
public void writeResource(Object oext, String resnm) {
File fres = new File(getResourceDir(), resnm);
Archivist.storeXMLOnly(oext, fres);
}
public Object readResource(String resnm) {
Object ret = null;
File f = new File(getResourceDir(), resnm);
if (f.exists()) {
String ftxt = FileUtil.readStringFromFile(f);
ret = Deserializer.deserialize(ftxt);
} else {
E.error("no such resource file " + f);
}
return ret;
}
} |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLChecker.java | 9 |
| org/textensor/xml/XMLChecker.java | 8 |
public class XMLChecker {
public static void checkXML(String s, boolean bshow) {
long starttime = System.currentTimeMillis();
XMLTokenizer tkz = new XMLTokenizer(s);
int nerror = 0;
int nread = 0;
while (true) {
XMLToken xmlt = tkz.nextToken();
if (bshow) {
System.out.println("item " + nread + " " + xmlt);
}
nread++;
if (xmlt.isNone()) {
break;
}
}
long endtime = System.currentTimeMillis();
System.out.println(" Total tags: " + nread + "\n total errors: " + nerror +
"\n tokenizing took " + (int)(endtime - starttime) + " ms");
}
public static String deGarbage(String sin) { |
| File | Line |
|---|
| org/catacomb/dataview/FrameController.java | 138 |
| org/catacomb/dataview/gui/FramePlayerController.java | 95 |
}
public void sliderMoved() {
int ival = frameSlider.getValue();
showFrame(ival);
}
public void rewind() {
stop();
showFrame(0);
}
public void pause() {
if (isPaused) {
dePause();
start();
} else {
rePause();
stop();
}
}
public void dePause() {
isPaused = false;
pauseButton.setLabelText(" pause ");
}
private void rePause() {
isPaused = true;
pauseButton.setLabelText("resume");
}
public void play() {
stop();
rewind();
start();
dePause();
}
private void start() {
if (indexes != null) {
framePlayer = null; // new FramePlayer(this); |
| File | Line |
|---|
| org/catacomb/graph/gui/Painter.java | 1329 |
| org/catacomb/graph/gui/Painter.java | 1356 |
double z = zProj(ca[i][0], ca[i][1], ca[i][2]);
double f = ca[i][4];
if (z < (f * zd + (1.-f) * zp)) {
int x = powx(xProj(ca[i][0], ca[i][1], ca[i][2]));
int y = powy(yProj(ca[i][0], ca[i][1], ca[i][2]));
g.fillRect(x, y, 1, 1); |
| File | Line |
|---|
| org/catacomb/interlish/reflect/ReflectionConstructor.java | 243 |
| org/textensor/xml/ReflectionInstantiator.java | 214 |
Object child = null;
if (parent != null) {
checkAddPackage(parent); // EFF inefficient
}
// Three possibilities:
// 1 there is an attribute called class;
// 2 the parent has a field called name;
// 3 the name is a class name;
if (atta == null) {
atta = new Attribute[0];
}
// process special attributes and instantiate child if class is known
// (case 1);
String classname = null;
for (int i = 0; i < atta.length; i++) {
Attribute att = atta[i];
String attName = att.getName();
String attValue = att.getValue();
if (attName.equals("package")) {
StringTokenizer stok = new StringTokenizer(attValue, ", ");
while (stok.hasMoreTokens()) {
addSearchPackage(stok.nextToken());
}
} else if (attName.equals("archive-hash")) { |
| File | Line |
|---|
| org/catacomb/druid/swing/dnd/RegionDropTarget.java | 62 |
| org/catacomb/druid/swing/dnd/TextFieldDropTarget.java | 48 |
textCanvas.paintImmediately(dragBounds);
} else {
dragBounds = new Rectangle();
}
Point p = dtde.getLocation();
Object obj = DragAndDrop.getDnD();
if (obj instanceof ImageDragSource) {
ImageDragSource ids = (ImageDragSource)obj;
BufferedImage bim = ids.getDragImage();
Point poff = ids.getDragImageOffset();
int bw = bim.getWidth();
int bh = bim.getHeight();
if (bim == null) {
E.warning("no drag image?");
} else {
// And remember where we are about to draw the new ghost image
dragBounds.setRect(p.x - poff.x, p.y - poff.y, bw, bh);
Graphics g = textCanvas.getGraphics(); |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/DeterministicGridCalc.java | 267 |
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 426 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 382 |
sb.append(stringd((PARTICLES_PUVC * wkv * volumes[i])));
}
}
}
}
sb.append("\n");
return sb.toString();
}
@SuppressWarnings("boxing")
private String getStateText() {
StringBuffer sb = new StringBuffer();
sb.append("nrds " + nel + " " + specieIDs.length + "\n");
for (int i = 0; i < specieIDs.length; i++) {
sb.append(specieIDs[i] + " ");
}
sb.append("\n");
for (int i = 0; i < nel; i++) {
for (int j = 0; j < specieIDs.length; j++) {
sb.append(stringd(wkA[i][j])); |
| File | Line |
|---|
| org/catacomb/dataview/AxisPainter.java | 159 |
| org/catacomb/graph/gui/YAxisCanvas.java | 79 |
int ii = intervals[iiind];
dy = Math.pow(10.0, powten) * ii;
int i0 = (int)(ylow / dy);
int i1 = (int)(yhigh / dy);
for (int i = i0; i <= i1; i++) {
double yy = i * dy;
String lab = "0";
if (i == 0) {
// OK;
} else if (dy >= 0.999 && dy < 1.e4) {
lab = String.valueOf((int)(yy));
} else {
lab = String.valueOf((float)(yy));
}
int iy = height - bm - (int)((height - bm) * (yy - ylow) / (yhigh - ylow)); |
| File | Line |
|---|
| org/catacomb/graph/gui/Painter.java | 1173 |
| org/catacomb/graph/gui/Painter.java | 1192 |
| org/catacomb/graph/gui/Painter.java | 1209 |
final void drawOutline(double xa, double ya, double ra,
double xb, double yb, double rb) {
double vy = xb - xa;
double vx = -(yb - ya);
double vl = Math.sqrt(vx * vx + vy * vy);
if (vl <= 0.0) vl = 1.e-6; // ***
vx /= vl;
vy /= vl;
drawLine(xa - ra * vx, ya - ra * vy, xb - rb * vx, yb - rb * vy);
drawLine(xa + ra * vx, ya + ra * vy, xb + rb * vx, yb + rb * vy); |
| File | Line |
|---|
| org/catacomb/dataview/gui/CCVizController.java | 78 |
| org/catacomb/dataview/gui/DViewController.java | 140 |
}
public void requestClose() {
exit();
}
public void reload() {
E.info("time to reload...");
}
public void requestExit() {
exit();
}
public void exit() {
System.exit(0);
}
public void syncOptions() {
String[] sa = new String[0];
if (dataHandler != null) {
sa = dataHandler.getViewOptions();
}
viewMenu.setOptions(sa);
}
public void setViewStyle(String s) {
if (dataHandler != null) {
dataHandler.setViewStyle(s);
}
basicController.repaint(); |
| File | Line |
|---|
| org/catacomb/druid/swing/RolloverEffect.java | 155 |
| org/catacomb/graph/gui/RolloverEffect.java | 155 |
| org/catacomb/util/ColorUtil.java | 71 |
public static Color linMod(Color c, int d) {
int r = c.getRed();
int g = c.getGreen();
int b = c.getBlue();
r += d;
g += d;
b += d;
r = (r > 0 ? (r < 255 ? r : 255) : 0);
g = (g > 0 ? (g < 255 ? g : 255) : 0);
b = (b > 0 ? (b < 255 ? b : 255) : 0);
return new Color(r, g, b);
} |
| File | Line |
|---|
| org/catacomb/dataview/AxisPainter.java | 105 |
| org/catacomb/graph/gui/XAxisCanvas.java | 74 |
int i1 = (int)(xr[1] / dx);
for (int i = i0; i <= i1; i++) {
double xx = i * dx;
String lab = "0";
if (i == 0) {
// OK;
} else if (dx >= 0.999 && dx < 1.e4) {
lab = String.valueOf((int)(xx));
} else {
lab = String.valueOf((float)(xx));
}
int off = lab.length();
off = 1 - 4 * off;
if (i * dx < 0.0) {
off -= 4;
}
int ix = (int)(lm + (width - lm) * (xx - xr[0]) / (xr[1] - xr[0])); |
| File | Line |
|---|
| org/textensor/stochdiff/disc/DiscBoxer.java | 104 |
| org/textensor/stochdiff/disc/DiscSplitter.java | 107 |
| org/textensor/stochdiff/disc/LineBoxer.java | 114 |
vg = baseGrid(tp, tpn, lbl);
pGrid.subPlaneConnect(tp, tpn, vg, par.partBranchOffset);
par.partBranchOffset += 2 * tpn.r;
} else {
// normal case: make a new one or add a slice and connect
// it up with the centres aligned
if (pGrid == null) {
vg = baseGrid(tp, tpn, lbl);
} else {
// TODO - probably not what we want
// too much mumerical diffusion if boxes can have gradually changing
// sizes? restrict to a few dicrete multiples?
vg = baseGrid(tp, tpn, lbl);
pGrid.planeConnect(vg);
}
}
lbl = null; // only use it once
if (vg != null) {
gridAL.add(vg);
recAdd(vg, tpn);
} else {
// skipped the point that is the start of a new segment
// of different radius
recAdd(pGrid, tpn);
}
}
}
}
public VolumeSlice baseGrid(TreePoint tpa, TreePoint tpb, String lbl) { |
| File | Line |
|---|
| org/catacomb/numeric/math/Matrix.java | 29 |
| org/textensor/stochdiff/numeric/math/Matrix.java | 75 |
}
public double[] flatten() {
double[] d = new double[n1 * n2];
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
d[n * i + j] = a[i][j];
}
}
return d;
}
public void Sp(String s) {
System.out.println(s);
}
public final int dim() {
return n;
}
public Matrix copy() {
Matrix m = new Matrix(n); |
| File | Line |
|---|
| org/catacomb/druid/swing/DFloatSlider.java | 188 |
| org/catacomb/druid/swing/DSlider.java | 136 |
}
}
/*
private void ensureRangeCovers() {
if (linmin > linvalue) {
linmin = linvalue;
}
if (linmax < linvalue) {
linmax = linvalue;
}
}
*/
public Dimension getMinimumSize() {
return new Dimension(80, 20);
}
public Dimension getPreferredSize() {
return new Dimension(140, 22);
}
public void paintComponent(Graphics g) {
realPaint(g);
}
public void realPaint(Graphics g) {
int w = getWidth();
int h = getHeight();
if (bgColor == null) {
bgColor = getBackground();
}
g.setColor(bgColor);
g.fillRect(0, 0, w, h);
paintArrows(g);
paintKnob(g);
if (label != null) { |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLChecker.java | 44 |
| org/textensor/xml/XMLChecker.java | 42 |
if (s.startsWith("<")) {
// fine;
} else {
int iob = s.indexOf("<");
if (iob > 0) {
String junk = s.substring(0, iob);
if (junk.trim().length() > 0) {
System.out.println("WARNING - garbage at start of xml file - first < is at " +
iob + " preceded by ---" + junk + "---");
}
s = s.substring(iob, s.length());
} else {
E.error(" - xml file contains no xml " + s);
s = null;
}
}
return s;
}
} |
| File | Line |
|---|
| org/catacomb/druid/gui/edit/DruCheckboxMenuItem.java | 76 |
| org/catacomb/druid/gui/edit/DruMenuItem.java | 65 |
}
public void setEnableOnSelection(String depends) {
enableOn = depends;
}
public void setSelectionSource(SelectionSource source) {
selectionSource = source;
}
public void sync() {
// E.info("dmi syncing enable=" + enableOn);
if (selectionSource != null && enableOn != null) {
String s = selectionSource.getSelectionType();
if (enableOn.indexOf(s) >= 0) {
dItem.setEnabled(true);
} else {
dItem.setEnabled(false);
}
}
}
public void setInfo(String s) {
info = s;
}
public void setInfoReceiver(InfoReceiver irec) {
infoReceiver = irec;
}
} |
| File | Line |
|---|
| org/catacomb/druid/swing/DTreeDragSource.java | 86 |
| org/catacomb/druid/swing/dnd/RegionDragSource.java | 77 |
source.startDrag(dge, Cursor.getPredefinedCursor(Cursor.HAND_CURSOR), dragImg, imgOffset, transferable, this);
}
/*
* Drag Event Handlers
*/
public void dragEnter(DragSourceDragEvent dsde) {
}
public void dragExit(DragSourceEvent dse) {
}
public void dragOver(DragSourceDragEvent dsde) {
}
public void dropActionChanged(DragSourceDragEvent dsde) {
System.out.println("Action: " + dsde.getDropAction());
System.out.println("Target Action: " + dsde.getTargetActions());
System.out.println("User Action: " + dsde.getUserAction());
}
public void dragDropEnd(DragSourceDropEvent dsde) { |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/DeterministicGridCalc.java | 244 |
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 406 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 362 |
sb.append(stringd(wkA[i][ispecout[j]] * volumes[i] * PARTICLES_PUVC));
}
}
sb.append("\n");
}
return sb.toString();
}
private String getGridConcsPlainText_dumb(int filenum, double time) {
StringBuffer sb = new StringBuffer();
// TODO tag specific to integer quantities;
sb.append(stringd(time));
for (int j = 0; j < specIndexesOut[filenum].length; j++) {
for (int i = 0; i < nel; i++) {
// WK 6 17 2007
if (regionsOut[filenum].equals("default") || regionsOut[filenum].equals(regionLabels[eltregions[i]])) { |
| File | Line |
|---|
| org/catacomb/druid/blocks/Choice.java | 91 |
| org/catacomb/druid/blocks/RadioButtons.java | 51 |
sopts = new String[sa.length];
slabs = new String[sa.length];
for (int i = 0; i < sa.length; i++) {
String s = sa[i].trim();
sopts[i] = s;
slabs[i] = s;
}
if (labels != null) {
String[] sb = labels.split(",");
for (int i = 0; i < sa.length && i < sopts.length; i++) {
slabs[i] = sb[i].trim();
}
} |
| File | Line |
|---|
| org/catacomb/druid/blocks/List.java | 52 |
| org/catacomb/druid/blocks/ScrollingList.java | 55 |
DruListPanel drup = (DruListPanel)dp;
drup.setAction(action);
if (renderer != null) {
// TODO move renderer defs to XML;
if (renderer.equals("quantity")) {
drup.setCellRenderer(new DruListQuantityRenderer());
} else if (renderer.equals("progress")) {
drup.setCellRenderer(new DruListProgressRenderer());
} else if (renderer.equals("color")) {
drup.setCellRenderer(new DruListColorRenderer());
} else {
E.error("unrecognized renderer " + renderer);
}
}
if (multiple) {
drup.setMultiple();
}
if (order != null) { |
| File | Line |
|---|
| org/textensor/stochdiff/numeric/grid/SteppedStochaticGridCalc.java | 901 |
| org/textensor/stochdiff/numeric/tmp/Tmp1A.java | 824 |
}
// WK
// if (ngo < (# of neighbors)*SHARED_DIFF_PARTICLES) then do
// shared_diffusion
// else then do independent_diffusion
if (ngo <= (inbr.length) * SHARED_DIFF_PARTICLES) // SHARED diffusion
{
wkB[iel][k] -= ngo;
for (int i = 0; i < ngo; i++) {
double r = random.random();
int io = 0;
while (r > fshare[io]) {
io++;
}
wkB[inbr[io]][k] += 1;
}
} else // MULTINOMIAL diffusion
{
ngo_remaining = ngo; //**KTB ngo_remaining is number of particles not yet diffused. initially this is ngo
//KTB 09-23-2011, use multi-nomial instead of separate binomials to calculate lnpgo, from ngo_remaining
// WK 9 11 2007
double prev = 0;
for (int j = 0; j < inbr.length - 1; j++) {
//double lnpgo = Math.log(fSharedExit[iel][k][j] - prev); (KTB) old method - INDEPENDENT
//BHK and KTB implemented the multinomial using tables instead of gaussianStep for small N, and use symmetry of binomial 09/23/11
double pgoTmp = (fSharedExit[iel][k][j] - prev)/(fSharedExit[iel][k][inbr.length-1]-prev); |
| File | Line |
|---|
| org/catacomb/act/FunctionSignature.java | 34 |
| org/catacomb/act/MethodSignature.java | 90 |
}
public int getTypeCode() {
return type;
}
public static String getTypeInfo(int itc) {
String ret = "";
if (itc == RECEIVE) {
ret = "Handlers: functions that are called when an event occurs in a connected component.";
} else if (itc == SEND) {
ret = "Senders: these send an event to any connected components. The handler \n" +
"on the receiving component will be called.";
} else if (itc == SETTER) {
ret = "Setters: these set a value for use later, but have no other effect: \n" +
"the value is available to connected components if they ask for it";
} else if (itc == GETTER) {
ret = "Getters: give access to quantities in connected components.";
}
return ret;
}
public void setInfo(String s) {
info = s;
}
public String getName() {
return functionName;
}
public String toJavaScriptStub() { |
| File | Line |
|---|
| org/catacomb/graph/gui/DataDisplay.java | 216 |
| org/catacomb/graph/gui/MovieDisplay.java | 119 |
pwCanvas.requestRepaint();
}
public void setXRange(double low, double high) {
pwCanvas.setXRange(low, high);
}
public double[] getXRange() {
return pwCanvas.getXRange();
}
public double[] getYRange() {
return pwCanvas.getYRange();
}
public void setFixedAspectRatio(double ar) {
pwCanvas.setFixedAspectRatio(ar);
}
public void viewChanged() {
if (pwCanvas != null) {
pwCanvas.repaint();
}
}
public void reframe() {
pwCanvas.reframe();
}
public static void main(String[] argv) { |
| File | Line |
|---|
| org/catacomb/graph/gui/Painter.java | 993 |
| org/catacomb/graph/gui/Painter.java | 1027 |
for (int i = 0; i < nel; i++) {
double[] xb = mesh[i][0];
double[] yb = mesh[i][1];
double fc = (dat[i] - ctMin) / dc;
if (fc < 0.) {
fc = 0.;
}
int ic = (int)(255 * fc);
if (ic > 255) {
ic = 255;
}
if (ic < 0) {
ic = 0;
}
fillPolygon(xb, yb, xb.length, colorTable[ic]);
}
} |
| File | Line |
|---|
| org/catacomb/serial/xml/XMLReader.java | 233 |
| org/textensor/xml/XMLReader.java | 226 |
StringBuffer sbo = (StringBuffer)child;
String ssf = sbo.toString();
if (ssf.endsWith(">") || next.svalue.startsWith("<") || ssf.length() == 0) {
sbo.append(next.svalue);
} else {
sbo.append(" ");
sbo.append(next.svalue);
}
} else {
if (child instanceof String && ((String)child).length() > 0) {
child = child + " " + next.svalue; |
