Examples with VCMetaData cbit.vcell.biomodel.meta.VCMetaData used on opensource projects

Example 11 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class AnnotationMapping method getComponentInfo.

private ArrayList<String> getComponentInfo(BioModel bioModel, Identifiable identifiable) {
    ArrayList<String> info = new ArrayList<String>();
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    VCID vcid = vcMetaData.getIdentifiableProvider().getVCID(identifiable);
    String modelComponentType = vcid.getClassName();
    String modelComponentName = vcid.getLocalName();
    info.add(modelComponentName);
    info.add(modelComponentType);
    return info;
}

Example 12 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class StructurePropertiesPanel method changeAnnotation.

/**
 * Comment
 */
private void changeAnnotation() {
    try {
        if (structure == null || fieldModel == null) {
            return;
        }
        VCMetaData vcMetaData = fieldModel.getVcMetaData();
        String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length() == 0 ? null : annotationTextArea.getText());
        if (!Compare.isEqualOrNull(vcMetaData.getFreeTextAnnotation(structure), textAreaStr)) {
            vcMetaData.setFreeTextAnnotation(structure, textAreaStr);
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 13 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class ReactionPropertiesPanel method changeFreeTextAnnotation.

private void changeFreeTextAnnotation() {
    try {
        if (reactionStep == null) {
            return;
        }
        // set text from annotationTextField in free text annotation for simple reactions in vcMetaData (from model)
        if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
            VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
            String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length() == 0 ? null : annotationTextArea.getText());
            if (!Compare.isEqualOrNull(vcMetaData.getFreeTextAnnotation(reactionStep), textAreaStr)) {
                vcMetaData.setFreeTextAnnotation(reactionStep, textAreaStr);
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Edit Reaction Error\n" + e.getMessage(), e);
    }
}

Example 14 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class SpeciesPropertiesPanel method changeFreeTextAnnotation.

/**
 * Comment
 */
private void changeFreeTextAnnotation() {
    try {
        if (getSpeciesContext() == null) {
            return;
        }
        // set text from annotationTextField in free text annotation for species in vcMetaData (from model)
        if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
            VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
            String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length() == 0 ? null : annotationTextArea.getText());
            if (!Compare.isEqualOrNull(vcMetaData.getFreeTextAnnotation(getSpeciesContext().getSpecies()), textAreaStr)) {
                vcMetaData.setFreeTextAnnotation(getSpeciesContext().getSpecies(), textAreaStr);
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Edit Species Error\n" + e.getMessage(), e);
    }
}

Example 15 with VCMetaData

use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.

the class ObservablePropertiesPanel method changeFreeTextAnnotation.

private void changeFreeTextAnnotation() {
    try {
        if (observable == null) {
            return;
        }
        // set text from annotationTextField in free text annotation for species in vcMetaData (from model)
        if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
            VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
            String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length() == 0 ? null : annotationTextArea.getText());
            if (!Compare.isEqualOrNull(vcMetaData.getFreeTextAnnotation(observable), textAreaStr)) {
                vcMetaData.setFreeTextAnnotation(observable, textAreaStr);
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Edit Observable Error\n" + e.getMessage(), e);
    }
}