Remove Param annotation and associated broken processing code, as this was never used in the codebase
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5843 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
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43057bd15c
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@ -1,19 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
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import java.lang.annotation.Retention;
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import java.lang.annotation.RetentionPolicy;
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/**
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* @author aaron
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* <p/>
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* Annotation Param
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* <p/>
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* a description annotation for a parameter; a variable used as input to the
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* analysis, but not (nessasarally) an output. Some formats will store this
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* information in comments, others will not include it.
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*/
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@Retention(RetentionPolicy.RUNTIME)
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public @interface Param {
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String name() default ""; // the name, defaulted to the variable name
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String description(); // the description of the parameter
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}
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@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Param;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import java.lang.annotation.Annotation;
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import java.lang.annotation.Annotation;
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@ -45,7 +44,6 @@ import java.util.Map;
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public class AnalysisModuleScanner {
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public class AnalysisModuleScanner {
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// what we extracted from the class
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// what we extracted from the class
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private Map<Field, Param> parameters = new LinkedHashMap<Field, Param>(); // the parameter annotations
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private Map<Field, DataPoint> datums = new LinkedHashMap<Field, DataPoint>(); // the data we've discovered
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private Map<Field, DataPoint> datums = new LinkedHashMap<Field, DataPoint>(); // the data we've discovered
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private Analysis analysis; // the analysis annotation
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private Analysis analysis; // the analysis annotation
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@ -89,22 +87,12 @@ public class AnalysisModuleScanner {
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for ( Class superCls = cls; superCls != null; superCls=superCls.getSuperclass() ) {
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for ( Class superCls = cls; superCls != null; superCls=superCls.getSuperclass() ) {
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for (Field f : superCls.getDeclaredFields())
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for (Field f : superCls.getDeclaredFields())
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for (Annotation annotation : f.getAnnotations()) {
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for (Annotation annotation : f.getAnnotations()) {
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if (annotation.annotationType().equals(Param.class))
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parameters.put(f, (Param) annotation);
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if (annotation.annotationType().equals(DataPoint.class))
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if (annotation.annotationType().equals(DataPoint.class))
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datums.put(f,(DataPoint) annotation);
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datums.put(f,(DataPoint) annotation);
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}
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}
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}
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}
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}
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}
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/**
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*
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* @return get the list of parameters we found
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*/
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public Map<Field, Param> getParameters() {
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return parameters;
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}
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/**
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/**
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*
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*
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* @return a map of the datum annotations found
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* @return a map of the datum annotations found
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@ -1,137 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.varianteval.util;
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import java.lang.reflect.Field;
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/**
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* @author aaron
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* <p/>
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* Class ComplexDataUtils
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* <p/>
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* This class contains methods and techniques for breaking down complex data in the output system
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*/
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public class ComplexDataUtils {
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public static Object resolveObject(Field f, Object e) {
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//try {
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//return f.toGenericString();
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//return f.getName(); //f.get(e);
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//} catch (IllegalAccessException e1) {
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// throw new ReviewedStingException("Unable to access field " + f);
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//}
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return null;
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}
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/*
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private static String extractPlainObjectOrPrimitive(Object obj) {
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String value = "<null>";
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if (obj instanceof Float || obj instanceof Double)
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value = String.format("%.4f",(Double)obj);
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else
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value = obj.toString();
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return value;
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}
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*/
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/**
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* convert any string -> object pairing into a string keyed tree
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*
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* @param obj the object
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* @return a mapping of the name to the associated value tree. All non-leaf nodes will be Strings
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*/
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/*
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public static Collection<Node> resolveObjects(Object obj) { // TODO: fix this, we need a way to get the name of the list from the data point
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Collection<Node> nodes = new ArrayList<Node>();
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// the simplest case, the object is null
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if (obj == null) nodes.add(new Node("<null>", "<null>", "<null>"));
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// capture objects of type TableTable
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else if (obj instanceof TableType)
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nodes.add(tableToNode((TableType) obj, ((TableType) obj).getName()));
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// try to handle maps
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else if (obj instanceof Map) {
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throw new UnsupportedOperationException("The report generation system is currently unable to output Maps, due to their ambiguity");
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// handle collections
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} else if (obj instanceof Collection)
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nodes.addAll(listToNode((Collection) obj, "collection"));
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// arrays
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else if (obj.getClass().isArray())
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nodes.addAll(listToNode(Arrays.asList(obj), "array"));
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// else we have a simple object (at least try to handle it that way
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else
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nodes.add(extractPlainObjectOrPrimitive(obj.getClass().getSimpleName(),obj));
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// return the collection of nodes we've parsed out
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return nodes;
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}
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*/
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/**
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* extract a (hopefully) primitive value
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* @param obj the object
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*/
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/*
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private static Node extractPlainObjectOrPrimitive(String name, Object obj) {
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String value = "<null>";
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if (obj instanceof Float || obj instanceof Double)
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value = String.format("%.4f",(Double)obj);
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else
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value = obj.toString();
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return new Node(name, value, "value");
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}
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*/
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/**
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* given a TableType object, make it into a tree using maps.
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*
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* @param table the table type to convert into a map
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* @return a node representing this table
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*/
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/*
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private static Node tableToNode(TableType table, String name) {
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Node root = new Node("table", name, "Table");
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root.setTable();
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Object[] rows = table.getRowKeys();
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Object[] cols = table.getColumnKeys();
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// add the columns names
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for (int x = 0; x < table.getRowKeys().length; x++) {
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Node row = new Node("row", rows[x].toString(), "a row in a table");
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root.addChild(row);
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for (int y = 0; y < table.getColumnKeys().length; y++) {
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Node col = new Node("column", cols[y].toString(), "columns in a table");
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row.addChild(col);
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col.addChild(extractPlainObjectOrPrimitive("cell(" + x + "," + y + ")", table.getCell(x, y)));
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}
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}
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return root;
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}
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*/
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/**
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* given a Collection object, make it into a tree using maps.
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*
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* @param coll the collection to iterate, and turn into a list
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* @return a mapping of String to Object
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*/
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/*
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private static Collection<Node> listToNode(Collection coll, String name) {
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Collection<Node> nodes = new ArrayList<Node>();
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Iterator<Object> iter = coll.iterator();
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for (int x = 0; x < coll.size(); x++) {
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Node value = new Node("column " + x, String.valueOf(x), "column");
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value.addChild(new Node("value " + x, iter.next().toString(), "value"));
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nodes.add(value);
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}
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return nodes;
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}
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*/
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}
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