Changeset 16256

Timestamp:

18/07/08 11:51:41 (1 month ago)

Author:

julie

Message:

checkstyle

Files:

• trunk/bio/sources/psi/main/src/org/intermine/bio/dataconversion/PsiConverter.java (modified) (15 diffs)

trunk/bio/sources/psi/main/src/org/intermine/bio/dataconversion/PsiConverter.java

@@ -59 +59 @@
-    private Map<String, String> terms = new HashMap<String, String>();
-    private Map<String, String> masterList = new HashMap<String, String>();
-    private static String datasetId;
-    //private int nextClsId;
-
-
-    /**
@@ -189 +186 @@
-            throws SAXException {
-            attName = null;
-
-            // <experimentList><experimentDescription>
-            if (qName.equals("experimentDescription")) {
-                // this experiment may have already been created
-                // we won't know until the name is processed
-                try {
-                    experimentId = attrs.getValue("id");
@@ -199 +193 @@
-                    throw new SAXException(e);
-                }
-
-
-
-
+
+
-                       && stack.search("experimentDescription") == 2) {
-                /* experiment.experimentName = shortName */
-                attName = "experimentName";
-
-
-
-
+
+
-                       && stack.search("bibref") == 2
-                       && stack.search("experimentDescription") == 3) {
@@ -217 +206 @@
-                    experimentHolder.setPublication(pub);
-                }
-
-
-
-
+
+
-                       && stack.search("experimentDescription") == 2) {
-                String name = attrs.getValue("name");
@@ -227 +214 @@
-                    setComment();
-                    comment.setAttribute("type", name);
-                    //                        String title = experimentHolder.name;
-                    //                        Item item = getInfoSource(title);
-                    //                        comment.setReference("source", item.getIdentifier());
-                    attName = "experimentAttribute";
-                } else {
-                    LOG.info("Can't create comment, bad experiment.");
-                }
-
-
-
-
+
+
-                       && stack.search("hostOrganism") == 3) {
-                attName = "hostOrganismName";
-
-
-
-
+
+
-                       && stack.search("interactionDetectionMethod") == 2) {
-
-
+
-                experimentHolder.setMethod("interactionDetectionMethod", termItemId);
-
-
-
-
+
+
-                       && stack.search("participantIdentificationMethod") == 2) {
-
-
+
-                experimentHolder.setMethod("participantIdentificationMethod", termItemId);
-
-
-
-
+
+
-                proteinId = attrs.getValue("id");
-
-
-
-
-
+
+
-                String taxId = attrs.getValue("ncbiTaxId");
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
-                       && stack.search("interactor") == 2) {
-                String db = attrs.getValue("db");
@@ -310 +277 @@
-                    protein.setCollection("dataSets", new ArrayList(Collections.singleton(
-                                                                    masterList.get("datasetId"))));
-
-
-                    // TODO this should maybe create a data source for each db
-                    Item synonym = createItem("Synonym");
-                    synonym.setAttribute("value", id);
@@ -320 +284 @@
-                    synonym.setReference("subject", proteinRefId);
-                    synonyms.add(synonym);
-
-                    // create an extra synonym for proteins that have an IntAct identifier
-                    if (db.equals("intact")) {
@@ -330 +293 @@
-                        synonyms.add(synonym);
-                    }
-
-                    // see ticket #1450
-                    Item syn2 = createItem("Synonym");
@@ -339 +301 @@
-                    synonyms.add(synonym);
-                }
-
-
-
-
-
+
+
-                attName = "sequence";
-
-
-
-
+
+
-                       && stack.search("interaction") == 2) {
-
-                attName = "interactionName";
-
-
-
-
+
+
-                       && stack.search("confidence") == 3) {
-
-                attName = "confidenceUnit";
-
-
-
-
-
+
+
-                attName = "confidence";
-
-
-
+
+
-            } else if (qName.equals("interactorRef")
-                       && stack.peek().equals("participant")) {
-
-                attName = "participantId";
-
-
-
-
-
+
+
-                attName = "proteinRole";
-
-
-
-
+
+
-                attName = "experimentRef";
-
-
-
-
-
-
+
+
+
-                attName = "startStatus";
-
-
-
-
-
-
+
+
+
-                attName = "endStatus";
-
-
-
-
-
-
+
+
-                attName = "regionName";
-
-            // <participantList><participant id="6919"><featureList><feature id="6920">
-            // <featureType><xref><primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0117"
-
-
-
-
-
+
+
-                interactorHolder.isRegionFeature = true;
-
-                // create interacting region
-                Item interactionRegion = createItem("ProteinInteractionRegion");
@@ -419 +347 @@
-                interactionRegion.setReference("protein", interactorHolder.proteinId);
-                interactionRegion.setReference("ontologyTerm", psiDagTermItemId);
-
-
-                // create new location object (start and end are coming later)
@@ -440 +367 @@
-                       && interactorHolder != null
-                       && interactorHolder.isRegionFeature) {
-
-
-
-
-
-
+
+
+
-            } else if (qName.equals("end")
-                       && stack.peek().equals("featureRange")
-                       && interactorHolder != null
-                       && interactorHolder.isRegionFeature) {
-
-
-
-
-
-
+
+
+
-                /* stuff done only once */
-                if (masterList.size() <= 1) {
@@ -472 +393 @@
-         */
-        public void characters(char[] ch, int start, int length) {
+            int st = start;
+            int l = length;
-
-            if (attName != null) {
@@ -477 +400 @@
-                // DefaultHandler may call this method more than once for a single
-                // attribute content -> hold text & create attribute in endElement
-ength
+
-                    boolean whitespace = false;
-art
+
-                    case ' ':
-                    case '\r':
@@ -492 +415 @@
-                        break;
-                    }
-art
-ength
-
-
-ength
+
+
+
+
+
-                    StringBuffer s = new StringBuffer();
-art, length
+, l
-                    attValue.append(s);
-                }
@@ -524 +447 @@
-                    if (comment != null && s != null) {
-                        //TODO store these only when valid experiment
-s != null && 
+
-                            comment.setAttribute("text", s);
-                        }