X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f2eb8acca7ced4d1573fcffa6a08f48e44fa9ca2;hb=e224b72118c12cd77ae96f0f8d86c123e0416dc7;hp=cba91dfa22f7639d03753d4b6d63b91a01eb7ec5;hpb=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index cba91df..f2eb8ac 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,197 +1,506 @@
-package jalview.datamodel;
-
-import jalview.util.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import java.awt.*;
-
-public class SequenceFeature {
- int start;
- int end;
- String type;
- String description;
- Color color;
- Sequence sequence;
- String id;
- double score;
- int strand;
- double pvalue;
- double pid;
-
- public SequenceFeature() {
- }
-
- public SequenceFeature(Sequence sequence,String type, int start, int end, String description) {
- this.sequence = sequence;
- this.type = type;
- this.start = start;
- this.end = end;
- this.description = description;
-
- setColor();
- }
-
-
- public String toGFFString() {
- String gff = id + "\t" + type + "\tfeature\t" + start + "\t" + end + "\t" + score + "\t" + strand + "\t.";
- return gff;
- }
- public double getScore() {
- return score;
- }
-
- public void setScore(double score) {
- this.score = score;
- }
-
- public String getId() {
- return this.id;
- }
- public void setId(String id) {
- this.id = id;
- }
- public void setSequence(Sequence seq) {
- this.sequence = seq;
- }
- public void setStart(int start) {
- this.start = start;
- }
- public void setEnd(int end) {
- this.end = end;
- }
- public int getStrand() {
- return strand;
- }
- public void setStrand(int strand) {
- this.strand = strand;
- }
- public int getStart() {
- return start;
- }
-
- public int getEnd() {
- return end;
- }
-
- public String getType() {
- return type;
- }
-
- public String getDescription() {
- return description;
- }
-
- public double getPValue() {
- return pvalue;
- }
- public void setPValue(double value) {
- this.pvalue = value;
- }
- public double getPercentId() {
- return pid;
- }
- public void setPercentId(double pid) {
- this.pid = pid;
- }
- public Color getColor() {
- return color;
- }
-
- public void setColor() {
- if (type.equals("CHAIN")) {
- color = Color.white;
- } else if (type.equals("DOMAIN")) {
- color = Color.white;
- } else if (type.equals("TRANSMEM")) {
- color = Color.red.darker();
- } else if (type.equals("SIGNAL")) {
- color = Color.cyan;
- } else if (type.equals("HELIX")) {
- color = Color.magenta;
- } else if (type.equals("TURN")) {
- color = Color.cyan;
- } else if (type.equals("SHEET")) {
- color = Color.yellow;
- } else if (type.equals("STRAND")) {
- color = Color.yellow;
- } else if (type.equals("CARBOHYD")) {
- color = Color.pink;
- } else if (type.equals("ACT_SITE")) {
- color = Color.red;
- } else if (type.equals("TRANSIT")) {
- color = Color.orange;
- } else if (type.equals("VARIANT")) {
- color = Color.orange.darker();
- } else if (type.equals("BINDING")) {
- color = Color.blue;
- } else if (type.equals("DISULFID")) {
- color = Color.yellow.darker();
- } else if (type.equals("NP_BIND")) {
- color = Color.red;
- } else if (type.indexOf("BIND") > 0) {
- color = Color.red;
- } else {
- color = Color.lightGray;
- }
- }
- public String print() {
- String tmp = new Format("%15s").form(type);
- tmp = tmp + new Format("%6d").form(start);
- tmp = tmp + new Format("%6d").form(end);
- tmp = tmp + " " + description;
- return tmp;
- }
- public void draw(Graphics g, int fstart, int fend, int x1, int y1, int width, int height) {
- g.setColor(new Color((float)(Math.random()),(float)(Math.random()),(float)(Math.random())));
-
- // int xstart = sequence.findIndex(start);
- //int xend = sequence.findIndex(end);
- int xstart = start;
- int xend = end;
- long tstart = System.currentTimeMillis();
- if (!(xend < fstart && xstart > fend)) {
-
- if (xstart > fstart) {
- x1 = x1 + (xstart-fstart)*width;
- fstart = xstart;
- }
-
- if (xend < fend) {
- fend = xend;
- }
-
- for (int i = fstart; i <= fend; i++) {
- char c = sequence.sequence.charAt(i);
- if (!jalview.util.Comparison.isGap((c)))
- g.fillRect(x1+(i-fstart)*width,y1,width,height);
- else
- g.drawString("-",x1+(i-fstart)*width,y1+height);
-
- }
-
- }
- long tend = System.currentTimeMillis();
- System.out.println("Time = " + (tend-tstart) + "ms");
-
- }
-
- public static void main(String[] args) {
- SequenceFeature sf = new SequenceFeature();
-
- System.out.println("Feature " + sf);
- }
- public static int CHAIN = 0;
- public static int DOMAIN = 1;
- public static int TRANSMEM = 2;
- public static int SIGNAL = 3;
- public static int HELIX = 4;
- public static int TURN = 5;
- public static int SHEET = 6;
- public static int CARBOHYD = 7;
- public static int ACT_SITE = 8;
- public static int TRANSIT = 9;
- public static int VARIANT = 10;
- public static int BINDING = 11;
-
-}
-
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceFeature
+{
+ private static final String STATUS = "status";
+
+ private static final String STRAND = "STRAND";
+
+ // private key for Phase designed not to conflict with real GFF data
+ private static final String PHASE = "!Phase";
+
+ /*
+ * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
+ * name1=value1;name2=value2,value3;...etc
+ */
+ private static final String ATTRIBUTES = "ATTRIBUTES";
+
+ public int begin;
+
+ public int end;
+
+ public float score;
+
+ public String type;
+
+ public String description;
+
+ public Map otherDetails;
+
+ public Vector links;
+
+ // Feature group can be set from a features file
+ // as a group of features between STARTGROUP and ENDGROUP markers
+ public String featureGroup;
+
+ public SequenceFeature()
+ {
+ }
+
+ /**
+ * Constructs a duplicate feature. Note: Uses makes a shallow copy of the
+ * otherDetails map, so the new and original SequenceFeature may reference the
+ * same objects in the map.
+ *
+ * @param cpy
+ */
+ public SequenceFeature(SequenceFeature cpy)
+ {
+ if (cpy != null)
+ {
+ begin = cpy.begin;
+ end = cpy.end;
+ score = cpy.score;
+ if (cpy.type != null)
+ {
+ type = new String(cpy.type);
+ }
+ if (cpy.description != null)
+ {
+ description = new String(cpy.description);
+ }
+ if (cpy.featureGroup != null)
+ {
+ featureGroup = new String(cpy.featureGroup);
+ }
+ if (cpy.otherDetails != null)
+ {
+ try
+ {
+ otherDetails = (Map) ((HashMap) cpy.otherDetails)
+ .clone();
+ } catch (Exception e)
+ {
+ // ignore
+ }
+ }
+ if (cpy.links != null && cpy.links.size() > 0)
+ {
+ links = new Vector();
+ for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
+ {
+ links.addElement(cpy.links.elementAt(i));
+ }
+ }
+ }
+ }
+
+ /**
+ * Constructor including a Status value
+ *
+ * @param type
+ * @param desc
+ * @param status
+ * @param begin
+ * @param end
+ * @param featureGroup
+ */
+ public SequenceFeature(String type, String desc, String status,
+ int begin, int end, String featureGroup)
+ {
+ this(type, desc, begin, end, featureGroup);
+ setStatus(status);
+ }
+
+ /**
+ * Constructor
+ *
+ * @param type
+ * @param desc
+ * @param begin
+ * @param end
+ * @param featureGroup
+ */
+ SequenceFeature(String type, String desc, int begin, int end,
+ String featureGroup)
+ {
+ this.type = type;
+ this.description = desc;
+ this.begin = begin;
+ this.end = end;
+ this.featureGroup = featureGroup;
+ }
+
+ /**
+ * Constructor including a score value
+ *
+ * @param type
+ * @param desc
+ * @param begin
+ * @param end
+ * @param score
+ * @param featureGroup
+ */
+ public SequenceFeature(String type, String desc, int begin, int end,
+ float score, String featureGroup)
+ {
+ this(type, desc, begin, end, featureGroup);
+ this.score = score;
+ }
+
+ /**
+ * Two features are considered equal if they have the same type, group,
+ * description, start, end, phase, strand, and (if present) 'Name', ID' and
+ * 'Parent' attributes.
+ *
+ * Note we need to check Parent to distinguish the same exon occurring in
+ * different transcripts (in Ensembl GFF). This allows assembly of transcript
+ * sequences from their component exon regions.
+ */
+ @Override
+ public boolean equals(Object o)
+ {
+ return equals(o, false);
+ }
+
+ /**
+ * Overloaded method allows the equality test to optionally ignore the
+ * 'Parent' attribute of a feature. This supports avoiding adding many
+ * superficially duplicate 'exon' or CDS features to genomic or protein
+ * sequence.
+ *
+ * @param o
+ * @param ignoreParent
+ * @return
+ */
+ public boolean equals(Object o, boolean ignoreParent)
+ {
+ if (o == null || !(o instanceof SequenceFeature))
+ {
+ return false;
+ }
+
+ SequenceFeature sf = (SequenceFeature) o;
+ if (begin != sf.begin || end != sf.end || score != sf.score)
+ {
+ return false;
+ }
+
+ if (getStrand() != sf.getStrand())
+ {
+ return false;
+ }
+
+ if (!(type + description + featureGroup + getPhase()).equals(sf.type
+ + sf.description + sf.featureGroup + sf.getPhase()))
+ {
+ return false;
+ }
+ if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
+ {
+ return false;
+ }
+ if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
+ {
+ return false;
+ }
+ if (!ignoreParent)
+ {
+ if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Returns true if both values are null, are both non-null and equal
+ *
+ * @param att1
+ * @param att2
+ * @return
+ */
+ protected static boolean equalAttribute(Object att1, Object att2)
+ {
+ if (att1 == null && att2 == null)
+ {
+ return true;
+ }
+ if (att1 != null)
+ {
+ return att1.equals(att2);
+ }
+ return att2.equals(att1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getBegin()
+ {
+ return begin;
+ }
+
+ public void setBegin(int start)
+ {
+ this.begin = start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ public void setEnd(int end)
+ {
+ this.end = end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ public void setType(String type)
+ {
+ this.type = type;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String desc)
+ {
+ description = desc;
+ }
+
+ public String getFeatureGroup()
+ {
+ return featureGroup;
+ }
+
+ public void setFeatureGroup(String featureGroup)
+ {
+ this.featureGroup = featureGroup;
+ }
+
+ public void addLink(String labelLink)
+ {
+ if (links == null)
+ {
+ links = new Vector();
+ }
+
+ links.insertElementAt(labelLink, 0);
+ }
+
+ public float getScore()
+ {
+ return score;
+ }
+
+ public void setScore(float value)
+ {
+ score = value;
+ }
+
+ /**
+ * Used for getting values which are not in the basic set. eg STRAND, PHASE
+ * for GFF file
+ *
+ * @param key
+ * String
+ */
+ public Object getValue(String key)
+ {
+ if (otherDetails == null)
+ {
+ return null;
+ }
+ else
+ {
+ return otherDetails.get(key);
+ }
+ }
+
+ /**
+ * Returns a property value for the given key if known, else the specified
+ * default value
+ *
+ * @param key
+ * @param defaultValue
+ * @return
+ */
+ public Object getValue(String key, Object defaultValue)
+ {
+ Object value = getValue(key);
+ return value == null ? defaultValue : value;
+ }
+
+ /**
+ * Used for setting values which are not in the basic set. eg STRAND, FRAME
+ * for GFF file
+ *
+ * @param key
+ * eg STRAND
+ * @param value
+ * eg +
+ */
+ public void setValue(String key, Object value)
+ {
+ if (value != null)
+ {
+ if (otherDetails == null)
+ {
+ otherDetails = new HashMap();
+ }
+
+ otherDetails.put(key, value);
+ }
+ }
+
+ /*
+ * The following methods are added to maintain the castor Uniprot mapping file
+ * for the moment.
+ */
+ public void setStatus(String status)
+ {
+ setValue(STATUS, status);
+ }
+
+ public String getStatus()
+ {
+ return (String) getValue(STATUS);
+ }
+
+ public void setAttributes(String attr)
+ {
+ setValue(ATTRIBUTES, attr);
+ }
+
+ public String getAttributes()
+ {
+ return (String) getValue(ATTRIBUTES);
+ }
+
+ public void setPosition(int pos)
+ {
+ begin = pos;
+ end = pos;
+ }
+
+ public int getPosition()
+ {
+ return begin;
+ }
+
+ /**
+ * Return 1 for forward strand ('+' in GFF), -1 for reverse strand ('-' in
+ * GFF), and 0 for unknown or not (validly) specified
+ *
+ * @return
+ */
+ public int getStrand()
+ {
+ int strand = 0;
+ if (otherDetails != null)
+ {
+ Object str = otherDetails.get(STRAND);
+ if ("-".equals(str))
+ {
+ strand = -1;
+ }
+ else if ("+".equals(str))
+ {
+ strand = 1;
+ }
+ }
+ return strand;
+ }
+
+ /**
+ * Set the value of strand
+ *
+ * @param strand
+ * should be "+" for forward, or "-" for reverse
+ */
+ public void setStrand(String strand)
+ {
+ setValue(STRAND, strand);
+ }
+
+ public void setPhase(String phase)
+ {
+ setValue(PHASE, phase);
+ }
+
+ public String getPhase()
+ {
+ return (String) getValue(PHASE);
+ }
+
+ /**
+ * Readable representation, for debug only, not guaranteed not to change
+ * between versions
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("%d %d %s %s", getBegin(), getEnd(), getType(),
+ getDescription());
+ }
+
+ /**
+ * Overridden to ensure that whenever two objects are equal, they have the
+ * same hashCode
+ */
+ @Override
+ public int hashCode()
+ {
+ String s = getType() + getDescription() + getFeatureGroup()
+ + getValue("ID") + getValue("Name") + getValue("Parent")
+ + getPhase();
+ return s.hashCode() + getBegin() + getEnd() + (int) getScore()
+ + getStrand();
+ }
+}