X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=5bf4e885880b0285278dbb6a95bffaeef9ca0019;hb=8c2ee75d86492f03e4c01404855f9ad2dd305719;hp=cba91dfa22f7639d03753d4b6d63b91a01eb7ec5;hpb=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index cba91df..5bf4e88 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,197 +1,149 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
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;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceFeature
+{
+ int begin;
+ int end;
+ String type;
+ String description;
+ String status;
+
+ /**
+ * Creates a new SequenceFeature object.
+ */
+ public SequenceFeature()
+ {
}
- }
- 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);
+ /**
+ * Creates a new SequenceFeature object.
+ *
+ * @param type DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ * @param status DOCUMENT ME!
+ */
+ public SequenceFeature(String type, int start, int end, String description,
+ String status)
+ {
+ this.type = type;
+ this.begin = start;
+ this.end = end;
+ this.description = description;
+ this.status = status;
+ }
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStart()
+ {
+ return begin;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEnd()
+ {
+ return end;
}
- long tend = System.currentTimeMillis();
- System.out.println("Time = " + (tend-tstart) + "ms");
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getType()
+ {
+ return type;
+ }
- public static void main(String[] args) {
- SequenceFeature sf = new SequenceFeature();
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return description;
+ }
- 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;
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getStatus()
+ {
+ return status;
+ }
+ /*
+
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+ */
}
-