Examples with Issue org.vcell.util.Issue used on opensource projects

Example 21 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class IssueTableModel method getComparator.

@Override
protected Comparator<Issue> getComparator(final int col, final boolean ascending) {
    return new Comparator<Issue>() {

        public int compare(Issue o1, Issue o2) {
            VCDocument vcDocument = (issueManager != null) ? (issueManager.getVCDocument()) : null;
            int scale = ascending ? 1 : -1;
            switch(col) {
                case COLUMN_DESCRIPTION:
                    {
                        Severity s1 = o1.getSeverity();
                        Severity s2 = o2.getSeverity();
                        if (s1 == s2) {
                            return scale * o1.getMessage().compareTo(o2.getMessage());
                        } else {
                            return scale * s1.compareTo(s2);
                        }
                    }
                case COLUMN_URL:
                    {
                        String u1 = o1.getHyperlink();
                        String u2 = o2.getHyperlink();
                        return u1 != null ? u1.compareTo(u2) : -1;
                    }
                case COLUMN_SOURCE:
                    return scale * getSourceObjectDescription(vcDocument, o1).compareTo(getSourceObjectDescription(vcDocument, o2));
                case COLUMN_PATH:
                    return scale * getSourceObjectPathDescription(vcDocument, o1).compareTo(getSourceObjectPathDescription(vcDocument, o2));
            }
            return 0;
        }
    };
}

Example 22 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class GeometrySpec method gatherIssues.

public void gatherIssues(IssueContext issueContext, Geometry geometry, List<Issue> issueVector) {
    // 
    if (getDimension() > 0) {
        VCImage argSampledImage = getSampledImage().getCurrentValue();
        if (argSampledImage == null) {
            return;
        }
        try {
            // 
            // make sure that each sample was assigned to a SubVolume
            // 
            int count = 0;
            byte[] samples = argSampledImage.getPixels();
            for (int i = 0; i < samples.length; i++) {
                if (samples[i] == -1) {
                    count++;
                }
            }
            if (count > 0) {
                String errorMessage = "Invalid Geometry - " + count + " of " + samples.length + " samples of geometry domain didn't map to any subdomain";
                Issue issue = new Issue(geometry, issueContext, IssueCategory.SubVolumeVerificationError, errorMessage, Issue.SEVERITY_ERROR);
                issueVector.add(issue);
            }
            // 
            // make sure that each subvolume is resolved in the geometry
            // 
            ArrayList<SubVolume> missingSubVolumeList = new ArrayList<SubVolume>();
            SubVolume[] subVolumes = getSubVolumes();
            for (int i = 0; i < subVolumes.length; i++) {
                if (argSampledImage.getPixelClassFromPixelValue(subVolumes[i].getHandle()) == null) {
                    missingSubVolumeList.add(subVolumes[i]);
                }
            }
            if (missingSubVolumeList.size() > 0) {
                for (int i = 0; i < missingSubVolumeList.size(); i++) {
                    String errorMessage = "Subdomain '" + missingSubVolumeList.get(i).getName() + "' is not resolved in geometry domain";
                    Issue issue = new Issue(geometry, issueContext, IssueCategory.SubVolumeVerificationError, errorMessage, Issue.SEVERITY_ERROR);
                    issueVector.add(issue);
                }
            }
        } catch (Exception ex) {
            Issue issue = new Issue(geometry, issueContext, IssueCategory.SubVolumeVerificationError, ex.getMessage(), Issue.SEVERITY_ERROR);
            issueVector.add(issue);
        }
    }
}

Example 23 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class FeatureMapping method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
    super.gatherIssues(issueContext, issueVector);
    if (simulationContext.getGeometry().getDimension() == 0) {
        if (!simulationContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
            String tooltip = "\nIn non-spatial application, size of structure '" + getStructure().getName() + "' must be assigned a positive value if referenced in the model.";
            String message = "In non-spatial application, size of structure '" + getStructure().getName() + "' must be assigned a positive value.";
            issueVector.add(new Issue(this, issueContext, IssueCategory.StructureMappingSizeParameterNotSet, message, Issue.SEVERITY_WARNING));
        }
    }
}

Example 24 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class MembraneMapping method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
    super.gatherIssues(issueContext, issueVector);
    if (simulationContext.getGeometry().getDimension() == 0) {
        if (!simulationContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
            String tooltip = "\nIn non-spatial application, size of structure '" + getStructure().getName() + "' must be assigned a positive value if referenced in the model.";
            String message = "In non-spatial application, size of structure '" + getStructure().getName() + "' must be assigned a positive value.";
            issueVector.add(new Issue(this, issueContext, IssueCategory.StructureMappingSizeParameterNotSet, message, Issue.SEVERITY_WARNING));
        }
    }
}

Example 25 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class MicroscopeMeasurement method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
    issueContext = issueContext.newChildContext(ContextType.MicroscopyMeasurement, this);
    if (fluorescentSpecies.size() > 0) {
        if (getConvolutionKernel() instanceof ProjectionZKernel && simulationContext.getGeometry().getDimension() != 3) {
            Issue issue = new Issue(this, issueContext, IssueCategory.Microscope_Measurement_ProjectionZKernel_Geometry_3DWarning, "Z Projection is only supported in 3D spatial applications.", Issue.SEVERITY_ERROR);
            issueVector.add(issue);
        }
    }
}