diff --git a/rtd_phosphonetx/.classpath b/rtd_phosphonetx/.classpath index ec186f0bf310363a3b2dd6004b1d91e62f62d1a9..7e38f90e9728fc2070c06211cf59aca99c6c38a3 100644 --- a/rtd_phosphonetx/.classpath +++ b/rtd_phosphonetx/.classpath @@ -31,5 +31,6 @@ <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/> <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/> <classpathentry kind="lib" path="/libraries/fastutil/fastutil.jar" sourcepath="/libraries/fastutil/fastutil-src.zip"/> + <classpathentry kind="lib" path="/libraries/cisd-common-basic/cisd-common-basic.jar"/> <classpathentry kind="output" path="targets/www/WEB-INF/classes"/> </classpath> diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java index f0c30e2f1965268ea3dc76ddae956e65767ec195..3fa06465ca352fb1d90e1a1b388120ba60b3b0a9 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java @@ -34,6 +34,7 @@ import com.extjs.gxt.ui.client.widget.layout.FitLayout; import com.extjs.gxt.ui.client.widget.layout.RowData; import com.extjs.gxt.ui.client.widget.layout.RowLayout; +import ch.systemsx.cisd.common.shared.basic.utils.StringUtils; import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback; import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableSectionPanel; import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants; @@ -49,7 +50,6 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.Abstrac import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.RowLayoutManager; import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent; import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.PropertyGrid; -import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.StringUtils; import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder; import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier; import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder; @@ -175,7 +175,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl add(centerPanel, createBorderLayoutData(LayoutRegion.CENTER)); rowDataManager.addToContainer(propertyPanel, new RowData(1, 0.5f)); List<IndistinguishableProteinInfo> indistinguishableProteins = - details.getIndistinguishableProteinInfos(); + details.getIndistinguishableProteinInfos(); if (indistinguishableProteins.isEmpty() == false) { List<Peptide> peptides = details.getPeptides(); @@ -189,7 +189,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl layout(); } } - + private ContentPanel createIndistinguishableProteinsSection( List<IndistinguishableProteinInfo> indistinguishableProteins, List<Peptide> peptides) { @@ -209,8 +209,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl properties.put(viewContext.getMessage(Dict.ACCESSION_NUMBER), info); propertyGrid.registerPropertyValueRenderer(IndistinguishableProteinInfo.class, PropertyValueRenderers.createProteinIdentLinkRenderer(viewContext)); - properties.put(viewContext.getMessage(Dict.PROTEIN_DESCRIPTION), info - .getDescription()); + properties.put(viewContext.getMessage(Dict.PROTEIN_DESCRIPTION), info.getDescription()); String markedSequence = markPeptides(info.getSequence(), peptides); properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence); properties.put(viewContext.getMessage(Dict.COVERAGE), info.getCoverage()); @@ -225,7 +224,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl panel.add(tabPanel, new RowData(1, 1)); return panel; } - + private void recreateUIWithDatasetTable(ProteinByExperiment protein, ContentPanel propertyPanel) { BorderLayoutData layoutData = createBorderLayoutData(LayoutRegion.WEST); @@ -301,7 +300,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl String markedSequence = markPeptides(proteinDetails.getSequence(), proteinDetails.getPeptides()); properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence); - + properties.put(viewContext.getMessage(Dict.COVERAGE), proteinDetails.getCoverage()); propertyGrid.registerPropertyValueRenderer(Peptide.class, PropertyValueRenderers