/** Tests the method {@link org.apache.calcite.util.BitSets#closure(java.util.SortedMap)}. */
@Test
public void testClosure() {
final SortedMap<Integer, ImmutableBitSet> empty = Maps.newTreeMap();
assertThat(ImmutableBitSet.closure(empty), equalTo(empty));
// Currently you need an entry for each position, otherwise you get an NPE.
// We should fix that.
final SortedMap<Integer, ImmutableBitSet> map = Maps.newTreeMap();
map.put(0, ImmutableBitSet.of(3));
map.put(1, ImmutableBitSet.of());
map.put(2, ImmutableBitSet.of(7));
map.put(3, ImmutableBitSet.of(4, 12));
map.put(4, ImmutableBitSet.of());
map.put(5, ImmutableBitSet.of());
map.put(6, ImmutableBitSet.of());
map.put(7, ImmutableBitSet.of());
map.put(8, ImmutableBitSet.of());
map.put(9, ImmutableBitSet.of());
map.put(10, ImmutableBitSet.of());
map.put(11, ImmutableBitSet.of());
map.put(12, ImmutableBitSet.of());
final String original = map.toString();
final String expected =
"{0={3, 4, 12}, 1={}, 2={7}, 3={3, 4, 12}, 4={4, 12}, 5={}, 6={}, 7={7}, 8={}, 9={}, 10={}, 11={}, 12={4, 12}}";
assertThat(ImmutableBitSet.closure(map).toString(), equalTo(expected));
assertThat("argument modified", map.toString(), equalTo(original));
// Now a similar map with missing entries. Same result.
final SortedMap<Integer, ImmutableBitSet> map2 = Maps.newTreeMap();
map2.put(0, ImmutableBitSet.of(3));
map2.put(2, ImmutableBitSet.of(7));
map2.put(3, ImmutableBitSet.of(4, 12));
map2.put(9, ImmutableBitSet.of());
final String original2 = map2.toString();
assertThat(ImmutableBitSet.closure(map2).toString(), equalTo(expected));
assertThat("argument modified", map2.toString(), equalTo(original2));
}
/** show some statistics at the end of the collector process */
public void showStatistics() {
// TODO nur fuer mich die folgenden stats...haben in eval
// erstmal! nix verloren
String stat = "";
if (!model.isEvaluating()) {
stat += "\n****************************** START STATS ******************************\n";
stat += "!ALL! DETECTED NOTES AND THEIR LENGTHS IN ms: (just for stats)\n";
stat += midiKeySammlerInsgesamt.toString() + "\n\n";
stat += "AbcNotes-Backup: \n" + notesAsString + "\n";
stat += "YIN/MPM - STATS:\n";
float sum = yin_cnt + mpm_cnt;
stat += "YIN: " + yin_cnt / sum * 100 + "% - MPM: " + mpm_cnt / sum * 100 + "%\n";
stat += "****************************** END STATS ******************************\n\n";
jAM.log(stat, false);
} else evaluator.evaluateCurrentTranscription(evaluationSammler, PITCHDETECTOR, notesAsString);
}
private IntegerCounter internal_check_species_presence_in_sbml_models(
String outputFilename, String modelsContainingDirectory, boolean recursively) {
final SortedMap<String, Integer> countBySpecies = new TreeMap<String, Integer>();
final IntegerCounter analyzedModels = new IntegerCounter();
DotUtilAction<File> action =
new DotUtilAction<File>() {
@Override
public void apply(File element) {
Model model = null;
SBMLDocument document = null;
try {
document = (new SBMLReader()).readSBML(element);
} catch (FileNotFoundException e) {
} catch (XMLStreamException e) {
} catch (Exception e) {
}
if (document != null) {
analyzedModels.increment();
model = document.getModel();
for (Species species : model.getListOfSpecies()) {
String id =
(species.getId()
+ "-("
+ species.getName()
+ ")"
+ "-("
+ species.getCompartment()
+ ")")
.toUpperCase(new Locale("(all)"));
if (countBySpecies.containsKey(id)) {
int value = countBySpecies.get(id);
countBySpecies.remove(id);
countBySpecies.put(id, value + 1);
} else {
countBySpecies.put(id, 1);
}
}
}
}
};
DotFileUtilHandler.mapOnAllFilesInFolder(modelsContainingDirectory, action, recursively);
// now we can generate the output file
Writer writer;
try {
writer =
new FileWriter(
DotFileUtilHandler.dotOutputFolderPathName()
.concat(outputFilename)
.concat(DotFileUtilHandler.getPlainTextFilenameExtensionToken()));
writer.write(countBySpecies.toString());
writer.close();
} catch (IOException e) {
e.printStackTrace();
}
return analyzedModels;
}
public void check_model_presence_in_various_sbml_models_contained_in_BioCyc_folder() {
final SortedMap<String, IntegerCounter> count_by_models = new TreeMap<String, IntegerCounter>();
DotUtilAction<File> action =
new DotUtilAction<File>() {
@Override
public void apply(File element) {
Model model = null;
SBMLDocument document = null;
try {
document = (new SBMLReader()).readSBML(element);
} catch (FileNotFoundException e) {
} catch (XMLStreamException e) {
} catch (Exception e) {
}
if (document != null) {
model = document.getModel();
String model_name = model.getName();
if (model_name == null) {
Assert.fail("Impossible to have a model without a name");
}
if (count_by_models.containsKey(model_name) == false) {
count_by_models.put(model_name, new IntegerCounter());
}
count_by_models.get(model_name).increment();
}
}
};
DotFileUtilHandler.mapOnAllFilesInFolder(
DotFileUtilHandler.getSbmlExampleModelsFolder().concat("BioCyc15.0/"), action, true);
// now we can generate the output file
Writer writer;
try {
writer =
new FileWriter(
DotFileUtilHandler.dotOutputFolderPathName()
.concat("maps-of-models-presence-among-multiple-models-in-ByoCyc-folder")
.concat(DotFileUtilHandler.getPlainTextFilenameExtensionToken()));
writer.write(count_by_models.toString());
writer.close();
} catch (IOException e) {
e.printStackTrace();
}
Assert.assertEquals(92, count_by_models.size());
int exploded_count = 0;
int models_splitted_in_more_than_three_files = 0;
for (Entry<String, IntegerCounter> entry : count_by_models.entrySet()) {
exploded_count = exploded_count + entry.getValue().getCount();
if (entry.getValue().getCount() > 2) {
models_splitted_in_more_than_three_files = models_splitted_in_more_than_three_files + 1;
}
}
Assert.assertEquals(167, exploded_count);
Assert.assertTrue(models_splitted_in_more_than_three_files > 1);
}