+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel.features;
+import java.util.ArrayList;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
/**
* A singleton class to hold the set of attributes known for each feature type
*/
-public class FeatureAttributes
+public class FeatureAttributes implements ApplicationSingletonI
{
- private static FeatureAttributes instance = new FeatureAttributes();
+ public enum Datatype
+ {
+ Character, Number, Mixed
+ }
+
+ public static FeatureAttributes getInstance()
+ {
+ return (FeatureAttributes) ApplicationSingletonProvider
+ .getInstance(FeatureAttributes.class);
+ }
+
+ private FeatureAttributes()
+ {
+ attributes = new HashMap<>();
+ }
+
+ /*
+ * map, by feature type, of a map, by attribute name, of
+ * attribute description and min-max range (if known)
+ */
+ private Map<String, Map<String[], AttributeData>> attributes;
+
+ /*
+ * a case-insensitive comparator so that attributes are ordered e.g.
+ * AC
+ * af
+ * CSQ:AFR_MAF
+ * CSQ:Allele
+ */
+ private Comparator<String[]> comparator = new Comparator<String[]>()
+ {
+ @Override
+ public int compare(String[] o1, String[] o2)
+ {
+ int i = 0;
+ while (i < o1.length || i < o2.length)
+ {
+ if (o2.length <= i)
+ {
+ return o1.length <= i ? 0 : 1;
+ }
+ if (o1.length <= i)
+ {
+ return -1;
+ }
+ int comp = String.CASE_INSENSITIVE_ORDER.compare(o1[i], o2[i]);
+ if (comp != 0)
+ {
+ return comp;
+ }
+ i++;
+ }
+ return 0; // same length and all matched
+ }
+ };
+
+ private class AttributeData
+ {
+ /*
+ * description(s) for this attribute, if known
+ * (different feature source might have differing descriptions)
+ */
+ List<String> description;
+
+ /*
+ * minimum value (of any numeric values recorded)
+ */
+ float min = 0f;
+
+ /*
+ * maximum value (of any numeric values recorded)
+ */
+ float max = 0f;
+
+ /*
+ * flag is set true if any numeric value is detected for this attribute
+ */
+ boolean hasValue = false;
+
+ Datatype type;
+
+ /**
+ * Note one instance of this attribute, recording unique, non-null
+ * descriptions, and the min/max of any numerical values
+ *
+ * @param desc
+ * @param value
+ */
+ void addInstance(String desc, String value)
+ {
+ addDescription(desc);
+
+ if (value != null)
+ {
+ value = value.trim();
+
+ /*
+ * Parse numeric value unless we have previously
+ * seen text data for this attribute type
+ */
+ if (type == null && couldBeNumber(value) || type == Datatype.Number)
+ {
+ try
+ {
+ float f = Float.valueOf(value);
+ min = hasValue ? Math.min(min, f) : f;
+ max = hasValue ? Math.max(max, f) : f;
+ hasValue = true;
+ type = (type == null || type == Datatype.Number)
+ ? Datatype.Number
+ : Datatype.Mixed;
+ } catch (NumberFormatException e)
+ {
+ /*
+ * non-numeric data: treat attribute as Character (or Mixed)
+ */
+ type = (type == null || type == Datatype.Character)
+ ? Datatype.Character
+ : Datatype.Mixed;
+ min = 0f;
+ max = 0f;
+ hasValue = false;
+ }
+ }
+ }
+ }
- private Map<String, Set<String>> attributes;
+ /**
+ * Answers the description of the attribute, if recorded and unique, or null if either no, or more than description is recorded
+ * @return
+ */
+ public String getDescription()
+ {
+ if (description != null && description.size() == 1)
+ {
+ return description.get(0);
+ }
+ return null;
+ }
+
+ public Datatype getType()
+ {
+ return type;
+ }
+
+ /**
+ * Adds the given description to the list of known descriptions (without
+ * duplication)
+ *
+ * @param desc
+ */
+ public void addDescription(String desc)
+ {
+ if (desc != null)
+ {
+ if (description == null)
+ {
+ description = new ArrayList<>();
+ }
+ if (!description.contains(desc))
+ {
+ description.add(desc);
+ }
+ }
+ }
+ }
/**
- * Answers the singleton instance of this class
+ * Answers the attribute names known for the given feature type, in
+ * alphabetical order (not case sensitive), or an empty set if no attributes
+ * are known. An attribute name is typically 'simple' e.g. "AC", but may be
+ * 'compound' e.g. {"CSQ", "Allele"} where a feature has map-valued attributes
*
+ * @param featureType
* @return
*/
- public static FeatureAttributes getInstance()
+ public List<String[]> getAttributes(String featureType)
{
- return instance;
+ if (!attributes.containsKey(featureType))
+ {
+ return Collections.<String[]> emptyList();
+ }
+
+ return new ArrayList<>(attributes.get(featureType).keySet());
}
- private FeatureAttributes()
+ /**
+ * This quick check will save significant time avoiding numerous NumberFormatExceptions.
+ *
+ * @param f
+ * @return
+ */
+ public boolean couldBeNumber(String f)
{
- attributes = new HashMap<>();
+ int len = f.length();
+ if (len == 0)
+ return false;
+ char ch = f.charAt(0);
+ switch (ch) {
+ case '.':
+ case '+':
+ case '-':
+ return len > 1;
+ }
+ return (ch <= '9' && ch >= '0');
}
/**
- * Answers the attributes known for the given feature type, in alphabetical
- * order (not case sensitive), or an empty set if no attributes are known
+ * Answers true if at least one attribute is known for the given feature type,
+ * else false
*
* @param featureType
* @return
*/
- public Iterable<String> getAttributes(String featureType)
+ public boolean hasAttributes(String featureType)
{
- if (!attributes.containsKey(featureType))
+ if (attributes.containsKey(featureType))
{
- return Collections.emptySet();
+ if (!attributes.get(featureType).isEmpty())
+ {
+ return true;
+ }
}
+ return false;
+ }
- return attributes.get(featureType);
+ /**
+ * Records the given attribute name and description for the given feature
+ * type, and updates the min-max for any numeric value
+ *
+ * @param featureType
+ * @param description
+ * @param value
+ * @param attName
+ */
+ public void addAttribute(String featureType, String description,
+ Object value, String... attName)
+ {
+ if (featureType == null || attName == null)
+ {
+ return;
+ }
+
+ /*
+ * if attribute value is a map, drill down one more level to
+ * record its sub-fields
+ */
+ if (value instanceof Map<?, ?>)
+ {
+ for (Entry<?, ?> entry : ((Map<?, ?>) value).entrySet())
+ {
+ String[] attNames = new String[attName.length + 1];
+ System.arraycopy(attName, 0, attNames, 0, attName.length);
+ attNames[attName.length] = entry.getKey().toString();
+ addAttribute(featureType, description, entry.getValue(), attNames);
+ }
+ return;
+ }
+
+ String valueAsString = value.toString();
+ Map<String[], AttributeData> atts = attributes.get(featureType);
+ if (atts == null)
+ {
+ atts = new TreeMap<>(comparator);
+ attributes.put(featureType, atts);
+ }
+ AttributeData attData = atts.get(attName);
+ if (attData == null)
+ {
+ attData = new AttributeData();
+ atts.put(attName, attData);
+ }
+ attData.addInstance(description, valueAsString);
}
/**
- * Records the given attribute name for the given feature type
+ * Answers the description of the given attribute for the given feature type,
+ * if known and unique, else null
*
* @param featureType
* @param attName
+ * @return
*/
- public void addAttribute(String featureType, String attName)
+ public String getDescription(String featureType, String... attName)
+ {
+ String desc = null;
+ Map<String[], AttributeData> atts = attributes.get(featureType);
+ if (atts != null)
+ {
+ AttributeData attData = atts.get(attName);
+ if (attData != null)
+ {
+ desc = attData.getDescription();
+ }
+ }
+ return desc;
+ }
+
+ /**
+ * Answers the [min, max] value range of the given attribute for the given
+ * feature type, if known, else null. Attributes with a mixture of text and
+ * numeric values are considered text (do not return a min-max range).
+ *
+ * @param featureType
+ * @param attName
+ * @return
+ */
+ public float[] getMinMax(String featureType, String... attName)
+ {
+ Map<String[], AttributeData> atts = attributes.get(featureType);
+ if (atts != null)
+ {
+ AttributeData attData = atts.get(attName);
+ if (attData != null && attData.hasValue)
+ {
+ return new float[] { attData.min, attData.max };
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Records the given attribute description for the given feature type
+ *
+ * @param featureType
+ * @param attName
+ * @param description
+ */
+ public void addDescription(String featureType, String description,
+ String... attName)
{
if (featureType == null || attName == null)
{
return;
}
+
+ Map<String[], AttributeData> atts = attributes.get(featureType);
+ if (atts == null)
+ {
+ atts = new TreeMap<>(comparator);
+ attributes.put(featureType, atts);
+ }
+ AttributeData attData = atts.get(attName);
+ if (attData == null)
+ {
+ attData = new AttributeData();
+ atts.put(attName, attData);
+ }
+ attData.addDescription(description);
+ }
- if (!attributes.containsKey(featureType))
+ /**
+ * Answers the datatype of the feature, which is one of Character, Number or
+ * Mixed (or null if not known), as discovered from values recorded.
+ *
+ * @param featureType
+ * @param attName
+ * @return
+ */
+ public Datatype getDatatype(String featureType, String... attName)
+ {
+ Map<String[], AttributeData> atts = attributes.get(featureType);
+ if (atts != null)
+ {
+ AttributeData attData = atts.get(attName);
+ if (attData != null)
+ {
+ return attData.getType();
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Resets all attribute metadata
+ */
+ public void clear()
+ {
+ attributes.clear();
+ }
+
+ /**
+ * Resets attribute metadata for one feature type
+ *
+ * @param featureType
+ */
+ public void clear(String featureType)
+ {
+ Map<String[], AttributeData> map = attributes.get(featureType);
+ if (map != null)
{
- attributes.put(featureType, new TreeSet<String>(
- String.CASE_INSENSITIVE_ORDER));
+ map.clear();
}
- attributes.get(featureType).add(attName);
}
}
git://source.jalview.org / jalview.git / blobdiff