Examples with Probe uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe used on opensource projects

Example 41 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class LimmaFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
@Override
protected void generateProbeList() {
    // We need to make a temporary directory, save the data into it, write out the R script
    // and then run it an collect the list of results, then clean up.
    // Make up the list of DataStores in each replicate set
    DataStore[] fromStores = replicateSets[0].dataStores();
    DataStore[] toStores = replicateSets[1].dataStores();
    File tempDir;
    try {
        progressUpdated("Creating temp directory", 0, 1);
        tempDir = TempDirectory.createTempDirectory();
        // System.err.println("Temp dir is "+tempDir.getAbsolutePath());
        progressUpdated("Writing R script", 0, 1);
        // Get the template script
        Template template = new Template(ClassLoader.getSystemResource("uk/ac/babraham/SeqMonk/Filters/LimmaFilter/limma_template.r"));
        // Substitute in the variables we need to change
        template.setValue("WORKING", tempDir.getAbsolutePath().replace("\\", "/"));
        // Say which p value column we're filtering on
        if (multiTest) {
            template.setValue("CORRECTED", "adj.P.Val");
        } else {
            template.setValue("CORRECTED", "P.Value");
        }
        StringBuffer sb = new StringBuffer();
        for (int i = 0; i < fromStores.length; i++) {
            if (i > 0)
                sb.append(",");
            sb.append("\"from\"");
        }
        for (int i = 0; i < toStores.length; i++) {
            sb.append(",");
            sb.append("\"to\"");
        }
        template.setValue("CONDITIONS", sb.toString());
        template.setValue("PVALUE", "" + cutoff);
        // Write the script file
        File scriptFile = new File(tempDir.getAbsoluteFile() + "/script.r");
        PrintWriter pr = new PrintWriter(scriptFile);
        pr.print(template.toString());
        pr.close();
        // Write the count data
        File countFile = new File(tempDir.getAbsoluteFile() + "/counts.txt");
        pr = new PrintWriter(countFile);
        sb = new StringBuffer();
        sb.append("probe");
        for (int i = 0; i < fromStores.length; i++) {
            sb.append("\t");
            sb.append("from");
            sb.append(i);
        }
        for (int i = 0; i < toStores.length; i++) {
            sb.append("\t");
            sb.append("to");
            sb.append(i);
        }
        pr.println(sb.toString());
        progressUpdated("Writing count data", 0, 1);
        Probe[] probes = startingList.getAllProbes();
        float value;
        for (int p = 0; p < probes.length; p++) {
            if (p % 1000 == 0) {
                progressUpdated("Writing count data", p, probes.length);
            }
            sb = new StringBuffer();
            sb.append(p);
            for (int i = 0; i < fromStores.length; i++) {
                sb.append("\t");
                value = fromStores[i].getValueForProbe(probes[p]);
                sb.append(value);
            }
            for (int i = 0; i < toStores.length; i++) {
                sb.append("\t");
                value = toStores[i].getValueForProbe(probes[p]);
                sb.append(value);
            }
            pr.println(sb.toString());
        }
        pr.close();
        progressUpdated("Running R Script", 0, 1);
        RScriptRunner runner = new RScriptRunner(tempDir);
        RProgressListener listener = new RProgressListener(runner);
        runner.addProgressListener(new ProgressRecordDialog("R Session", runner));
        runner.runScript();
        while (true) {
            if (listener.cancelled()) {
                progressCancelled();
                return;
            }
            if (listener.exceptionReceived()) {
                progressExceptionReceived(listener.exception());
                return;
            }
            if (listener.complete())
                break;
            Thread.sleep(500);
        }
        // We can now parse the results and put the hits into a new probe list
        ProbeList newList;
        newList = new ProbeList(startingList, "", "", "FDR");
        File hitsFile = new File(tempDir.getAbsolutePath() + "/hits.txt");
        BufferedReader br = new BufferedReader(new FileReader(hitsFile));
        String line = br.readLine();
        while ((line = br.readLine()) != null) {
            String[] sections = line.split("\t");
            int probeIndex = Integer.parseInt(sections[0]);
            float pValue;
            if (multiTest) {
                pValue = Float.parseFloat(sections[sections.length - 2]);
            } else {
                pValue = Float.parseFloat(sections[sections.length - 3]);
            }
            newList.addProbe(probes[probeIndex], pValue);
        }
        br.close();
        runner.cleanUp();
        // TODO: Show log of R session?
        filterFinished(newList);
    } catch (Exception ioe) {
        progressExceptionReceived(ioe);
        return;
    }
// filterFinished(newList);
}

Example 42 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class LogisticRegressionFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
@Override
protected void generateProbeList() {
    // We need to make a temporary directory, save the data into it, write out the R script
    // and then run it an collect the list of results, then clean up.
    // Make up the list of DataStores in each replicate set
    DataStore[] fromStores = replicateSets[0].dataStores();
    DataStore[] toStores = replicateSets[1].dataStores();
    if (minObservations < 3)
        minObservations = 3;
    File tempDir;
    try {
        Probe[] probes = startingList.getAllProbes();
        if (resample) {
            // We need to check that the data stores are quantitated
            for (int i = 0; i < fromStores.length; i++) {
                if (!fromStores[i].isQuantitated()) {
                    progressExceptionReceived(new SeqMonkException("Data Store " + fromStores[i].name() + " wasn't quantitated"));
                    return;
                }
                for (int p = 0; p < probes.length; p++) {
                    float value = fromStores[i].getValueForProbe(probes[p]);
                    if ((!Float.isNaN(value)) && (value < 0 || value > 100)) {
                        progressExceptionReceived(new SeqMonkException("Data Store " + fromStores[i].name() + " had a value outside the range 0-100 (" + value + ")"));
                        return;
                    }
                }
            }
            for (int i = 0; i < toStores.length; i++) {
                if (!toStores[i].isQuantitated()) {
                    progressExceptionReceived(new SeqMonkException("Data Store " + toStores[i].name() + " wasn't quantitated"));
                    return;
                }
                for (int p = 0; p < probes.length; p++) {
                    float value = toStores[i].getValueForProbe(probes[p]);
                    if ((!Float.isNaN(value)) && (value < 0 || value > 100)) {
                        progressExceptionReceived(new SeqMonkException("Data Store " + toStores[i].name() + " had a value outside the range 0-100 (" + value + ")"));
                        return;
                    }
                }
            }
        }
        progressUpdated("Creating temp directory", 0, 1);
        tempDir = TempDirectory.createTempDirectory();
        System.err.println("Temp dir is " + tempDir.getAbsolutePath());
        progressUpdated("Writing R script", 0, 1);
        // Get the template script
        Template template = new Template(ClassLoader.getSystemResource("uk/ac/babraham/SeqMonk/Filters/LogisticRegressionFilter/logistic_regression_template.r"));
        // Write the count data
        // Sort these so we can get probes from the same chromosome together
        Arrays.sort(probes);
        PrintWriter pr = null;
        String lastChr = "";
        // Rather than not testing probes based on their absolute difference
        // we should just post-filter them.  The easiest way to do this will
        // be to not test (as we do now) but explicity pass in the number of
        // tests we should have performed to the multiple testing correction.
        int numberOfTestsToCorrectBy = 0;
        PROBE: for (int p = 0; p < probes.length; p++) {
            if (!probes[p].chromosome().name().equals(lastChr)) {
                if (pr != null)
                    pr.close();
                File outFile = new File(tempDir.getAbsoluteFile() + "/data_chr" + probes[p].chromosome().name() + ".txt");
                pr = new PrintWriter(outFile);
                lastChr = probes[p].chromosome().name();
                pr.println("id\tgroup\treplicate\tstate\tcount");
            }
            if (p % 1000 == 0) {
                progressUpdated("Writing data for chr" + lastChr, p, probes.length);
            }
            int[] fromMethCounts = new int[fromStores.length];
            int[] fromUnmethCounts = new int[fromStores.length];
            int[] toMethCounts = new int[toStores.length];
            int[] toUnmethCounts = new int[toStores.length];
            for (int i = 0; i < fromStores.length; i++) {
                long[] reads = fromStores[i].getReadsForProbe(probes[p]);
                int totalCount = 0;
                int methCount = 0;
                if (resample) {
                    float value = fromStores[i].getValueForProbe(probes[p]);
                    if (Float.isNaN(value)) {
                        continue PROBE;
                    }
                    totalCount = reads.length;
                    methCount = Math.round((totalCount * value) / 100f);
                } else {
                    for (int r = 0; r < reads.length; r++) {
                        totalCount++;
                        if (SequenceRead.strand(reads[r]) == Location.FORWARD) {
                            ++methCount;
                        }
                    }
                }
                fromMethCounts[i] = methCount;
                fromUnmethCounts[i] = totalCount - methCount;
            }
            for (int i = 0; i < toStores.length; i++) {
                long[] reads = toStores[i].getReadsForProbe(probes[p]);
                int totalCount = 0;
                int methCount = 0;
                if (resample) {
                    float value = toStores[i].getValueForProbe(probes[p]);
                    if (Float.isNaN(value)) {
                        continue PROBE;
                    }
                    totalCount = reads.length;
                    methCount = Math.round((totalCount * value) / 100f);
                } else {
                    for (int r = 0; r < reads.length; r++) {
                        totalCount++;
                        if (SequenceRead.strand(reads[r]) == Location.FORWARD) {
                            ++methCount;
                        }
                    }
                }
                toMethCounts[i] = methCount;
                toUnmethCounts[i] = totalCount - methCount;
            }
            // Check to see we meet the requirements for the min amount of information
            // and the min diff.
            int totalFromMeth = 0;
            int totalFrom = 0;
            int totalToMeth = 0;
            int totalTo = 0;
            int validFrom = 0;
            for (int i = 0; i < fromStores.length; i++) {
                totalFromMeth += fromMethCounts[i];
                totalFrom += fromMethCounts[i];
                totalFrom += fromUnmethCounts[i];
                if (fromMethCounts[i] + fromUnmethCounts[i] >= minObservations) {
                    ++validFrom;
                }
            }
            int validTo = 0;
            for (int i = 0; i < toStores.length; i++) {
                totalToMeth += toMethCounts[i];
                totalTo += toMethCounts[i];
                totalTo += toUnmethCounts[i];
                if (toMethCounts[i] + toUnmethCounts[i] >= minObservations) {
                    ++validTo;
                }
            }
            // have enough data in all stores to go ahead and do the test.
            if (validFrom < fromStores.length || validTo < toStores.length) {
                // We don't have enough data to measure this one
                continue;
            }
            // At this point we have to count this probe as valid for the
            // purposes of multiple testing correction
            ++numberOfTestsToCorrectBy;
            float[] fromPercentages = new float[validFrom];
            float[] toPercentages = new float[validTo];
            int lastFromIndex = 0;
            int lastToIndex = 0;
            for (int i = 0; i < fromMethCounts.length; i++) {
                if (fromMethCounts[i] + fromUnmethCounts[i] == 0)
                    continue;
                fromPercentages[lastFromIndex] = fromMethCounts[i] * 100f / (fromMethCounts[i] + fromUnmethCounts[i]);
                ++lastFromIndex;
            }
            for (int i = 0; i < toMethCounts.length; i++) {
                if (toMethCounts[i] + toUnmethCounts[i] == 0)
                    continue;
                toPercentages[lastToIndex] = toMethCounts[i] * 100f / (toMethCounts[i] + toUnmethCounts[i]);
                ++lastToIndex;
            }
            for (int i = 0; i < fromMethCounts.length; i++) {
                pr.println(p + "\tfrom\tfrom" + i + "\tmeth\t" + fromMethCounts[i]);
                pr.println(p + "\tfrom\tfrom" + i + "\tunmeth\t" + fromUnmethCounts[i]);
            }
            for (int i = 0; i < toMethCounts.length; i++) {
                pr.println(p + "\tto\tto" + i + "\tmeth\t" + toMethCounts[i]);
                pr.println(p + "\tto\tto" + i + "\tunmeth\t" + toUnmethCounts[i]);
            }
        }
        pr.close();
        // Sanity check to make sure we have something to work with.
        if (numberOfTestsToCorrectBy == 0) {
            progressExceptionReceived(new IllegalStateException("No probes had enough data to test."));
        }
        // Now we can complete the template
        // Substitute in the variables we need to change
        template.setValue("WORKING", tempDir.getAbsolutePath().replace("\\", "/"));
        template.setValue("CORRECTCOUNT", "" + numberOfTestsToCorrectBy);
        template.setValue("PVALUE", "" + pValueCutoff);
        if (multiTest) {
            template.setValue("MULTITEST", "TRUE");
        } else {
            template.setValue("MULTITEST", "FALSE");
        }
        // Write the script file
        File scriptFile = new File(tempDir.getAbsoluteFile() + "/script.r");
        pr = new PrintWriter(scriptFile);
        pr.print(template.toString());
        pr.close();
        progressUpdated("Running R Script", 0, 1);
        RScriptRunner runner = new RScriptRunner(tempDir);
        RProgressListener listener = new RProgressListener(runner);
        runner.addProgressListener(new ProgressRecordDialog("R Session", runner));
        runner.runScript();
        while (true) {
            if (listener.cancelled()) {
                progressCancelled();
                pr.close();
                return;
            }
            if (listener.exceptionReceived()) {
                progressExceptionReceived(new SeqMonkException("R Script failed"));
                pr.close();
                return;
            }
            if (listener.complete())
                break;
            Thread.sleep(500);
        }
        // We can now parse the results and put the hits into a new probe list
        ProbeList newList;
        if (multiTest) {
            newList = new ProbeList(startingList, "", "", "FDR");
        } else {
            newList = new ProbeList(startingList, "", "", "p-value");
        }
        File hitsFile = new File(tempDir.getAbsolutePath() + "/hits.txt");
        BufferedReader br = new BufferedReader(new FileReader(hitsFile));
        String line = br.readLine();
        while ((line = br.readLine()) != null) {
            String[] sections = line.split("\t");
            String[] indexSections = sections[0].split("\\.");
            int probeIndex = Integer.parseInt(indexSections[indexSections.length - 1]);
            float pValue = Float.parseFloat(sections[sections.length - 1]);
            newList.addProbe(probes[probeIndex], pValue);
        }
        br.close();
        runner.cleanUp();
        filterFinished(newList);
    } catch (Exception ioe) {
        progressExceptionReceived(ioe);
        return;
    }
}

Example 43 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class ManualCorrelationFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
@Override
protected void generateProbeList() {
    // System.out.println("Data store size="+stores.length+" lower="+lowerLimit+" upper="+upperLimit+" type="+limitType+" chosen="+chosenNumber);
    profiles = new double[optionsPanel.graphs.length][];
    for (int g = 0; g < optionsPanel.graphs.length; g++) {
        profiles[g] = optionsPanel.graphs[g].profile();
    }
    Probe[] probes = startingList.getAllProbes();
    ProbeList parentList = null;
    ProbeList[] newLists = new ProbeList[profiles.length];
    if (newLists.length > 1) {
        parentList = new ProbeList(startingList, "Filtered Probes", "", null);
        for (int p = 0; p < newLists.length; p++) {
            newLists[p] = new ProbeList(parentList, listName() + " " + (p + 1), listDescription(), "R-value");
        }
    } else {
        // We won't have a parent list
        newLists[0] = new ProbeList(startingList, listName(), listDescription(), "R-value");
    }
    double[] currentProfile = new double[stores.length];
    for (int p = 0; p < probes.length; p++) {
        progressUpdated(p, probes.length);
        if (cancel) {
            cancel = false;
            progressCancelled();
            return;
        }
        try {
            for (int s = 0; s < stores.length; s++) {
                currentProfile[s] = stores[s].getValueForProbe(probes[p]);
            }
            float bestR = 0;
            int bestRIndex = -1;
            for (int pr = 0; pr < profiles.length; pr++) {
                float r = PearsonCorrelation.calculateCorrelation(profiles[pr], currentProfile);
                if (correlationCutoff > 0) {
                    if (r >= correlationCutoff && r > bestR) {
                        bestR = r;
                        bestRIndex = pr;
                    }
                } else {
                    if (r <= correlationCutoff && r < bestR) {
                        bestR = r;
                        bestRIndex = pr;
                    }
                }
            }
            if (bestRIndex >= 0) {
                newLists[bestRIndex].addProbe(probes[p], bestR);
                if (parentList != null) {
                    parentList.addProbe(probes[p], null);
                }
            }
        } catch (SeqMonkException ex) {
            continue;
        }
    }
    // If we only have one cluster then we just return that list
    if (newLists.length == 1) {
        filterFinished(newLists[0]);
    } else {
        filterFinished(parentList);
    }
}

Example 44 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class DESeqFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
@Override
protected void generateProbeList() {
    // We need to make a temporary directory, save the data into it, write out the R script
    // and then run it an collect the list of results, then clean up.
    // Make up the list of DataStores in each replicate set
    DataStore[][] storeGroups = new DataStore[replicateSets.length][];
    for (int r = 0; r < replicateSets.length; r++) {
        storeGroups[r] = replicateSets[r].dataStores();
    }
    File tempDir;
    try {
        progressUpdated("Creating temp directory", 0, 1);
        tempDir = TempDirectory.createTempDirectory();
        // System.err.println("Temp dir is "+tempDir.getAbsolutePath());
        progressUpdated("Writing R script", 0, 1);
        // Get the template script
        Template template = new Template(ClassLoader.getSystemResource("uk/ac/babraham/SeqMonk/Filters/DESeqFilter/deseq_template.r"));
        // Substitute in the variables we need to change
        template.setValue("WORKING", tempDir.getAbsolutePath().replace("\\", "/"));
        // Say which p value column we're filtering on
        if (multiTest) {
            template.setValue("CORRECTED", "padj");
        } else {
            template.setValue("CORRECTED", "pvalue");
        }
        if (independentFiltering) {
            template.setValue("INDEPENDENT", "TRUE");
        } else {
            template.setValue("INDEPENDENT", "FALSE");
        }
        StringBuffer sb = new StringBuffer();
        for (int s = 0; s < storeGroups.length; s++) {
            for (int i = 0; i < storeGroups[s].length; i++) {
                if (!(s == 0 && i == 0)) {
                    sb.append(",");
                }
                sb.append("\"group" + s + "\"");
            }
        }
        template.setValue("CONDITIONS", sb.toString());
        template.setValue("PVALUE", "" + cutoff);
        // Write the script file
        File scriptFile = new File(tempDir.getAbsoluteFile() + "/script.r");
        PrintWriter pr = new PrintWriter(scriptFile);
        pr.print(template.toString());
        pr.close();
        // Write the count data
        File countFile = new File(tempDir.getAbsoluteFile() + "/counts.txt");
        pr = new PrintWriter(countFile);
        sb = new StringBuffer();
        sb.append("probe");
        for (int s = 0; s < storeGroups.length; s++) {
            for (int i = 0; i < storeGroups[s].length; i++) {
                sb.append("\t");
                sb.append("group");
                sb.append(s);
                sb.append("_");
                sb.append(i);
            }
        }
        pr.println(sb.toString());
        progressUpdated("Writing count data", 0, 1);
        Probe[] probes = startingList.getAllProbes();
        float value;
        for (int p = 0; p < probes.length; p++) {
            if (p % 1000 == 0) {
                progressUpdated("Writing count data", p, probes.length);
            }
            sb = new StringBuffer();
            sb.append(p);
            for (int s = 0; s < storeGroups.length; s++) {
                for (int i = 0; i < storeGroups[s].length; i++) {
                    sb.append("\t");
                    value = storeGroups[s][i].getValueForProbe(probes[p]);
                    if (value != (int) value) {
                        progressExceptionReceived(new IllegalArgumentException("Inputs to the DESeq filter MUST be raw, incorrected counts, not things like " + value));
                        pr.close();
                        return;
                    }
                    sb.append(value);
                }
            }
            pr.println(sb.toString());
        }
        pr.close();
        progressUpdated("Running R Script", 0, 1);
        RScriptRunner runner = new RScriptRunner(tempDir);
        RProgressListener listener = new RProgressListener(runner);
        runner.addProgressListener(new ProgressRecordDialog("R Session", runner));
        runner.runScript();
        while (true) {
            if (listener.cancelled()) {
                progressCancelled();
                return;
            }
            if (listener.exceptionReceived()) {
                progressExceptionReceived(listener.exception());
                return;
            }
            if (listener.complete())
                break;
            Thread.sleep(500);
        }
        // We can now parse the results and put the hits into a new probe list
        ProbeList newList;
        newList = new ProbeList(startingList, "", "", "FDR");
        File hitsFile = new File(tempDir.getAbsolutePath() + "/hits.txt");
        BufferedReader br = new BufferedReader(new FileReader(hitsFile));
        String line = br.readLine();
        while ((line = br.readLine()) != null) {
            String[] sections = line.split("\t");
            int probeIndex = Integer.parseInt(sections[0]);
            float pValue = Float.parseFloat(sections[sections.length - 1]);
            newList.addProbe(probes[probeIndex], pValue);
        }
        br.close();
        runner.cleanUp();
        // TODO: Show log of R session?
        filterFinished(newList);
    } catch (Exception ioe) {
        progressExceptionReceived(ioe);
        return;
    }
// filterFinished(newList);
}

Example 45 with Probe

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.Probe in project SeqMonk by s-andrews.

the class DifferencesFilter method generateProbeList.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
	 */
protected void generateProbeList() {
    Probe[] probes = startingList.getAllProbes();
    ProbeList newList = new ProbeList(startingList, "Filtered Probes", "", "Difference");
    HashSet<DataStore> allStoresSet = new HashSet<DataStore>();
    for (int i = 0; i < fromStores.length; i++) {
        allStoresSet.add(fromStores[i]);
    }
    for (int i = 0; i < toStores.length; i++) {
        allStoresSet.add(toStores[i]);
    }
    DataStore[] allStores = allStoresSet.toArray(new DataStore[0]);
    PROBE: for (int p = 0; p < probes.length; p++) {
        progressUpdated(p, probes.length);
        if (cancel) {
            cancel = false;
            progressCancelled();
            return;
        }
        for (int s = 0; s < allStores.length; s++) {
            if (!allStores[s].hasValueForProbe(probes[p]))
                continue PROBE;
            try {
                if (Float.isNaN(allStores[s].getValueForProbe(probes[p])))
                    continue PROBE;
            } catch (SeqMonkException sme) {
                continue;
            }
        }
        int count = 0;
        float d = 0;
        for (int fromIndex = 0; fromIndex < fromStores.length; fromIndex++) {
            for (int toIndex = 0; toIndex < toStores.length; toIndex++) {
                if (fromStores[fromIndex] == toStores[toIndex])
                    continue;
                switch(differenceType) {
                    case AVERAGE:
                        d += getDifferenceValue(toStores[toIndex], fromStores[fromIndex], probes[p]);
                        count++;
                        break;
                    case MAXIMUM:
                        float dt1 = getDifferenceValue(toStores[toIndex], fromStores[fromIndex], probes[p]);
                        if (count == 0 || dt1 > d)
                            d = dt1;
                        count++;
                        break;
                    case MINIMUM:
                        float dt2 = getDifferenceValue(toStores[toIndex], fromStores[fromIndex], probes[p]);
                        if (count == 0 || dt2 < d)
                            d = dt2;
                        count++;
                        break;
                    default:
                        progressExceptionReceived(new SeqMonkException("Unknown difference type " + differenceType));
                }
            }
        }
        if (differenceType == AVERAGE) {
            if (count > 0) {
                d /= count;
            }
        }
        // Now we have the value we need to know if it passes the test
        if (upperLimit != null)
            if (d > upperLimit) {
                continue;
            }
        if (lowerLimit != null)
            if (d < lowerLimit) {
                continue;
            }
        newList.addProbe(probes[p], new Float(d));
    }
    filterFinished(newList);
}