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Version 2.3.0. Mike Hasson's work on material dependent transport. Also
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.mat file support is here.
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@dukovski
dukovski committed Oct 24, 2016
1 parent 2dfd256 commit 6157bf3
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Showing 7 changed files with 1,170 additions and 31 deletions.
2 changes: 1 addition & 1 deletion comets_simplified/src/edu/bu/segrelab/comets/Comets.java
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ public class Comets implements CometsConstants,
* by each cell just runs through a diffusion routine.
*/
public static boolean DIFFUSION_TEST_MODE = false;
private String versionString = "2.2.3, 2 August 2016";
private String versionString = "2.3.0, 24 October 2016";

// The setup pane
private CometsSimRunner runner;
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2 changes: 1 addition & 1 deletion comets_simplified/src/edu/bu/segrelab/comets/CometsSimRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ else if (c.getParameters().getNumLayers()>1)
c.fireSimulationStateChangeEvent(new SimulationStateChangeEvent(SimulationStateChangeEvent.State.PAUSE));
}
if (c.getParameters().showCycleTime())
// System.out.println("Cycle complete in " + (System.currentTimeMillis() - start)/1000.0 + "s");
System.out.println("Cycle complete in " + (System.currentTimeMillis() - start)/1000.0 + "s");
totalTime += System.currentTimeMillis() - start;
c.updateOnCycle();
}
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3 changes: 1 addition & 2 deletions comets_simplified/src/edu/bu/segrelab/comets/fba/FBACell.java
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Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,6 @@ public synchronized int run(FBAModel[] models)
media = world.getModelMediaAt(x, y, i);
else if (cParams.getNumLayers() > 1)
media = world3D.getModelMediaAt(x, y, z, i);

double[] lb = ((FBAModel)models[i]).getBaseExchLowerBounds();
double[] ub = ((FBAModel)models[i]).getBaseExchUpperBounds();
// String[] exchNames = ((FBAModel)models[i]).getExchangeReactionNames();
Expand Down Expand Up @@ -757,7 +756,7 @@ else if (cParams.getNumLayers() > 1)
if(deltaBiomass[i]<0.0)deltaBiomass[i]=0.0;
// deltaBiomass[i] = (double)(((FBAModel)models[i]).getObjectiveFluxSolution()) * cParams.getTimeStep();
// deltaBiomass[i] = (double)(((FBAModel)models[i]).getObjectiveFluxSolution());
//System.out.println("solution: " + ((FBAModel)models[i]).getObjectiveSolution());
// System.out.println("solution: " + ((FBAModel)models[i]).getObjectiveSolution());

if (cParams.showGraphics())
cellColor = calculateColor();
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264 changes: 255 additions & 9 deletions comets_simplified/src/edu/bu/segrelab/comets/fba/FBACometsLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,15 @@ private enum LoaderState
private boolean useGui;
private Comets c;
private int lineCount;

private boolean substrate = false;
private boolean modelDiffusion = false;
private boolean specific = false;
private boolean friction = false;
private double[][] substrateDiffConsts;
private double[][] modelDiffConsts;
private int[][] substrateLayout;
private double[][] specificMedia;
private double[][] substrateFrictionConsts;
private static final String MODEL_FILE = "model_file",
MODEL_WORLD = "model_world",
GRID_SIZE = "grid_size",
Expand All @@ -87,7 +95,12 @@ private enum LoaderState
BARRIER = "barrier",
MEDIA = "media",
PARAMETERS = "parameters",
DIFFUSION_CONST = "diffusion_constants";
DIFFUSION_CONST = "diffusion_constants",
SUBSTRATE_DIFFUSIVITY = "substrate_diffusivity",
SUBSTRATE_FRICTION = "substrate_friction",
MODEL_DIFFUSIVITY = "model_diffusivity",
SUBSTRATE_LAYOUT = "substrate_layout",
SPECIFIC_MEDIA = "specific_media";
/**
* Returns the recently loaded World2D.
*/
Expand Down Expand Up @@ -202,7 +215,7 @@ public int loadLayoutFile(String filename, Comets c, boolean useGui) throws IOEx
/*
* makes and stores internally: an FBAWorld, an array of FBAModels, an
* ArrayList of FBACells
*/
*/
try
{
BufferedReader reader = new BufferedReader(new FileReader(filename));
Expand Down Expand Up @@ -270,7 +283,6 @@ public int loadLayoutFile(String filename, Comets c, boolean useGui) throws IOEx
if (state == LoaderState.CANCELED)
throw new LayoutFileException("Layout file loading canceled", lineCount);
}

else if (parsed[0].equalsIgnoreCase(MODEL_WORLD))
{
Map<String, Point2D.Double> media = new HashMap<String, Point2D.Double>();
Expand Down Expand Up @@ -363,10 +375,10 @@ else if (worldParsed[0].equalsIgnoreCase(GRID_SIZE))
else if(worldParsed.length == 3)
c.getParameters().setNumLayers(Integer.valueOf(1));

if (Integer.valueOf(worldParsed[3])==1)
{
throw new IOException("In a 3D simulation the number of layers along the 3rd coordinate must be larger than 1.");
}
//if (Integer.valueOf(worldParsed[3])==1)
//{
// throw new IOException("In a 3D simulation the number of layers along the 3rd coordinate must be larger than 1.");
//}
}

/****************** BARRIER *************************/
Expand Down Expand Up @@ -396,6 +408,47 @@ else if (worldParsed[0].equalsIgnoreCase(DIFFUSION_CONST))
List<String> lines = collectLayoutFileBlock(reader);
state = parseMediaDiffusionConstantsBlock(lines, diffConsts);
}
/****************** DIFFUSION CONSTANTS BY SUBSTRATE ********************/

else if (worldParsed[0].equalsIgnoreCase(SUBSTRATE_DIFFUSIVITY))
{
substrate = true;
List<String> lines = collectLayoutFileBlock(reader);
state = parseSubstrateDiffusionConstantsBlock(lines,numMedia);
}
/****************** FRICTION CONSTANTS BY SUBSTRATE ********************/

else if (worldParsed[0].equalsIgnoreCase(SUBSTRATE_FRICTION))
{
friction = true;
List<String> lines = collectLayoutFileBlock(reader);
state = parseSubstrateFrictionConstantsBlock(lines);
}
/****************** DIFFUSION CONSTANTS BY MODEL ********************/

else if (worldParsed[0].equalsIgnoreCase(MODEL_DIFFUSIVITY))
{
modelDiffusion = true;
List<String> lines = collectLayoutFileBlock(reader);
state = parseModelDiffusionConstantsBlock(lines,numMedia);
}

/****************** SUBSTRATE LAYOUT ********************/

else if (worldParsed[0].equalsIgnoreCase(SUBSTRATE_LAYOUT))
{
List<String> lines = collectLayoutFileBlock(reader);
state = parseSubstrateLayoutBlock(lines,c.getParameters().getNumCols(),c.getParameters().getNumRows());
}

/****************** SPECIFIC MEDIA ********************/

else if (worldParsed[0].equalsIgnoreCase(SPECIFIC_MEDIA))
{
specific = true;
List<String> lines = collectLayoutFileBlock(reader);
state = parseSpecificMediaBlock(lines);
}

/****************** MEDIA ***********************/

Expand Down Expand Up @@ -634,7 +687,6 @@ else if (worldParsed[0].equalsIgnoreCase("prevent_media_in"))
}
}
}

/* Set diffusion constants */
double[] diffusionConsts = new double[numMedia];
double defaultDiffConst = pParams.getDefaultDiffusionConstant();
Expand All @@ -649,6 +701,22 @@ else if (worldParsed[0].equalsIgnoreCase("prevent_media_in"))
}
}
world.setDiffusionConstants(diffusionConsts);
if(substrate)
{
world.setSubstrateDiffusion(substrateDiffConsts);
world.setSubstrateLayout(substrateLayout);
}
if(modelDiffusion){
world.setModelDiffusivity(modelDiffConsts);
}
if(specific)
{
world.setSpecificMedia(specificMedia);
}
if(friction)
{
world.setSubstrateFriction(substrateFrictionConsts);
}
System.out.println("Done!");
}
else if(c.getParameters().getNumLayers()>1)
Expand Down Expand Up @@ -1109,6 +1177,184 @@ private LoaderState parseMediaDiffusionConstantsBlock(List<String> lines, Map<In

}

private LoaderState parseSubstrateDiffusionConstantsBlock(List<String> lines, int numMedia) throws LayoutFileException,
NumberFormatException
{
/* the 'diffusion_constants' block is taken from the way of doing it in the Model files, so it looks like this:
*
* diffusion_constants <default>
* <medium number> <diff_const>
* <medium number> <diff_const>
* //
*/
Integer i = 0;
substrateDiffConsts = new double[lines.size()][numMedia];
for (String line : lines)
{
lineCount++;
if (line.length() == 0)
continue;

String[] diffConstParsed = line.split("\\s+");
if (diffConstParsed.length != numMedia)
throw new LayoutFileException("Each line of the 'diffusion_constants' block should have two tokens.\n The first should be the index of the medium component, followed by its (non-default) diffusion constant.", lineCount);

else
{
for(int j = 0;j<numMedia;j++)
{
substrateDiffConsts[i][j] = Double.parseDouble(diffConstParsed[j]);
}
i++;
}
}
return LoaderState.OK;

}

private LoaderState parseSubstrateFrictionConstantsBlock(List<String> lines) throws LayoutFileException,
NumberFormatException
{
/* the 'diffusion_constants' block is taken from the way of doing it in the Model files, so it looks like this:
*
* diffusion_constants <default>
* <medium number> <diff_const>
* <medium number> <diff_const>
* //
*/
Integer i = 0;
substrateFrictionConsts = new double[lines.size()][models.length];
for (String line : lines)
{
lineCount++;
if (line.length() == 0)
continue;

String[] diffConstParsed = line.split("\\s+");
if (diffConstParsed.length != models.length)
throw new LayoutFileException("Each line of the 'diffusion_constants' block should have two tokens.\n The first should be the index of the medium component, followed by its (non-default) diffusion constant.", lineCount);

else
{
for(int j = 0;j<models.length;j++)
{
substrateFrictionConsts[i][j] = Double.parseDouble(diffConstParsed[j]);
}
i++;
}
}
return LoaderState.OK;

}
private LoaderState parseModelDiffusionConstantsBlock(List<String> lines, int numMedia) throws LayoutFileException,
NumberFormatException
{
/* the 'diffusion_constants' block is taken from the way of doing it in the Model files, so it looks like this:
*
* diffusion_constants <default>
* <medium number> <diff_const>
* <medium number> <diff_const>
* //
*/
Integer i = 0;
modelDiffConsts = new double[lines.size()][numMedia];
for (String line : lines)
{
lineCount++;
if (line.length() == 0)
continue;

String[] diffConstParsed = line.split("\\s+");
if (diffConstParsed.length != numMedia)
throw new LayoutFileException("Each line of the 'diffusion_constants' block should have two tokens.\n The first should be the index of the medium component, followed by its (non-default) diffusion constant.", lineCount);

else
{
for(int j = 0;j<numMedia;j++)
{
modelDiffConsts[i][j] = Double.parseDouble(diffConstParsed[j]);
}
i++;
}
}
return LoaderState.OK;

}

private LoaderState parseSubstrateLayoutBlock(List<String> lines,int cols,int rows) throws LayoutFileException,
NumberFormatException
{
/* the 'diffusion_constants' block is taken from the way of doing it in the Model files, so it looks like this:
*
* diffusion_constants <default>
* <medium number> <diff_const>
* <medium number> <diff_const>
* //
*/
if (lines.size() != rows)
throw new LayoutFileException("Each line of the 'diffusion_constants' block should have two tokens.\n The first should be the index of the medium component, followed by its (non-default) diffusion constant.", lineCount);
else
{
Integer i = 0;
substrateLayout = new int[cols][rows];
for (String line : lines)
{
lineCount++;
if (line.length() == 0)
continue;

String[] layoutParsed = line.split("\\s+");
if (layoutParsed.length != cols)
throw new LayoutFileException("Each line of the 'diffusion_constants' block should have two tokens.\n The first should be the index of the medium component, followed by its (non-default) diffusion constant.", lineCount);

else
{
for(int j = 0;j<cols;j++)
{
substrateLayout[j][i] = Integer.parseInt(layoutParsed[j]);
}
i++;
}
}
}
return LoaderState.OK;

}

private LoaderState parseSpecificMediaBlock(List<String> lines) throws LayoutFileException,
NumberFormatException
{
/* the 'diffusion_constants' block is taken from the way of doing it in the Model files, so it looks like this:
*
* diffusion_constants <default>
* <medium number> <diff_const>
* <medium number> <diff_const>
* //
*/
Integer i = 0;
specificMedia = new double[4][lines.size()];
for (String line : lines)
{
lineCount++;
if (line.length() == 0)
continue;

String[] sMediaParsed = line.split("\\s+");
if (sMediaParsed.length != 4)
throw new LayoutFileException("Each line of the 'specific_media' block should have two tokens.\n The first should be the index of the medium component, followed by its (non-default) diffusion constant.", lineCount);

else
{
for(int j = 0;j<4;j++)
{
specificMedia[j][i] = Double.parseDouble(sMediaParsed[j]);
}
i++;
}
}
return LoaderState.OK;
}

private LoaderState parseInitialPopBlock(String[] header, List<String> lines) throws LayoutFileException,
NumberFormatException
{
Expand Down
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