code cleaned from unchecked or unsafe operations warnings

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@278 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_Details_item.java

@@ -28,19 +28,14 @@ import org.eclipse.swt.widgets.Label;
 import org.eclipse.swt.widgets.Text;
 import org.eclipse.swt.widgets.Widget;
 
-import fr.inra.moulon.proticport.model.Controller;
-import fr.inra.moulon.proticport.model.entities.Spectrum;
-import fr.inra.moulon.proticport.model.exceptions.ProticDataNotFoundException;
 import fr.inra.moulon.svgutils.svgspectrum.SvgAaMod;
 import fr.inra.moulon.svgutils.svgspectrum.SvgAaModPhospho;
 import fr.inra.moulon.svgutils.svgspectrum.SvgPeptideSequence;
 import fr.inra.moulon.svgutils.svgspectrum.SvgSpectrumDocument;
-import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
 import fr.inra.pappso.xtandempipeline.MsException.StopException;
 import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
 import fr.inra.pappso.xtandempipeline.class_msms.Peptide;
-import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
 
 public class Peptide_Details_item extends CTabItem {
 

xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_List_item.java

@@ -44,8 +44,9 @@ public class Protein_List_item extends CTabItem {
 	private Table table;
 
 	private Label description;
-	
-	private static final Logger logger = Logger.getLogger(Protein_List_item.class);
+
+	private static final Logger logger = Logger
+			.getLogger(Protein_List_item.class);
 
 	public Protein_List_item(window_base parent, int posi) {
 		super(parent.getFolder(), SWT.CLOSE, posi);
@@ -57,7 +58,7 @@ public class Protein_List_item extends CTabItem {
 		for (Button but : buttons)
 			but.setEnabled(false);
 	}
-	
+
 	@Override
 	protected void finalize() throws Throwable {
 		logger.debug("finalize Protein_List_item");
@@ -128,10 +129,12 @@ public class Protein_List_item extends CTabItem {
 			public void widgetSelected(SelectionEvent e) {
 				logger.debug("selected");
 				TableItem item = (TableItem) e.item;
-				HashSampleScanSetProt m = (HashSampleScanSetProt) item.getData("match");
+				HashSampleScanSetProt m = (HashSampleScanSetProt) item
+						.getData("match");
 				SubGroup sg = (SubGroup) item.getData("subgroup");
 				if (e.detail == SWT.CHECK) {
-					Protein_List_item.this.changeProtValidity(sg,item.getChecked());
+					Protein_List_item.this.changeProtValidity(sg,
+							item.getChecked());
 					logger.debug("Change prot validité");
 					action_time = e.time;
 				} else if (e.time != action_time) {
@@ -147,34 +150,38 @@ public class Protein_List_item extends CTabItem {
 		return compo;
 	}
 
-	protected void changeProtValidity(SubGroup sg,boolean change) {
-		// On change la validité des peptides associé à chaque protéine du sous-groupe
+	protected void changeProtValidity(SubGroup sg, boolean change) {
+		// On change la validité des peptides associé à chaque protéine du
+		// sous-groupe
 		for (TableItem it : table.getItems()) {
 			if (it.getData("subgroup").equals(sg)) {
 				it.setChecked(change);
-				HashSampleScanSetProt hp = (HashSampleScanSetProt) it.getData("match");
-				if(change==false){
-					//unvalidate
+				HashSampleScanSetProt hp = (HashSampleScanSetProt) it
+						.getData("match");
+				if (change == false) {
+					// unvalidate
 					ArrayList<Peptide> peptidechecked = new ArrayList<Peptide>();
-					for(HashSampleScan hash : hp){
-						for(Peptide pep : hp.getMatch().getAllValidPeptideToHashSampleScan(hash)){
+					for (HashSampleScan hash : hp) {
+						for (Peptide pep : hp.getMatch()
+								.getAllValidPeptideToHashSampleScan(hash)) {
 							pep.setValidate(false);
 							peptidechecked.add(pep);
 						}
 					}
-					it.setData("peptide_checked",peptidechecked);
-				}
-				else{
-					//validate
-					ArrayList<Peptide> peptidechecked = (ArrayList<Peptide>) it.getData("peptide_checked");
-					if(peptidechecked!=null){
-						for(Peptide pep : peptidechecked){
-							pep.setValidate(true);
+					it.setData("peptide_checked", peptidechecked);
+				} else {
+					// validate
+					ArrayList<?> objectList = (ArrayList<?>) it
+							.getData("peptide_checked");
+					if (objectList != null) {
+						for (Object objectPeptide : objectList) {
+							((Peptide) objectPeptide).setValidate(true);
 						}
 					}
 				}
-				//Si analyse non phospho, on peux aussi modifier l'etat du match pour affichage
-				if(!this.data_type.getIs_phosphopeptide()){
+				// Si analyse non phospho, on peux aussi modifier l'etat du
+				// match pour affichage
+				if (!this.data_type.getIs_phosphopeptide()) {
 					hp.getMatch().setIsvalidate(change);
 				}
 			}
@@ -205,20 +212,26 @@ public class Protein_List_item extends CTabItem {
 			ident.view_result(swt);
 			// on mets à jour le texte du shell
 			if (data_type.getIs_invididual())
-				this.setText(ident.get_samples().getMsRunList().get(0).getSampleName());
+				this.setText(ident.get_samples().getMsRunList().get(0)
+						.getSampleName());
 			else if (!data_type.getIs_phosphopeptide())
 				this.setText("Combine results");
 			else
 				this.setText("Phosphosite results");
 			// on rempli la description
-			if(this.data_type.getIs_phosphopeptide()){
-			description.setText("Phosphoprotein Group : " + ident.getGrouping().getGroupList().size()
-					+ " - Phosphosite SubGroup : " + swt.getSubgroup_count()
-					+ " - Total Phosphosite (redundancy) : " + table.getItemCount());
-			}else{
-				description.setText("Protein Group : " + ident.getGrouping().getGroupList().size()
+			if (this.data_type.getIs_phosphopeptide()) {
+				description.setText("Phosphoprotein Group : "
+						+ ident.getGrouping().getGroupList().size()
+						+ " - Phosphosite SubGroup : "
+						+ swt.getSubgroup_count()
+						+ " - Total Phosphosite (redundancy) : "
+						+ table.getItemCount());
+			} else {
+				description.setText("Protein Group : "
+						+ ident.getGrouping().getGroupList().size()
 						+ " - Protein SubGroup : " + swt.getSubgroup_count()
-						+ " - Total Protein (redundancy) : " + table.getItemCount());
+						+ " - Total Protein (redundancy) : "
+						+ table.getItemCount());
 			}
 		} catch (Exception e) {
 			window.view_error(e, "Problems with drawing protein list");