import java.util.List;
import java.util.Map;
-
-
-/** converts the features from their "raw" representation as a Map
- * into a Feature class
+/**
+ * converts the features from their "raw" representation as a Map into a Feature
+ * class
+ *
* @author Andreas Prlic
- *
+ *
*/
-public class FeatureTrackConverter {
-
- public static final Color HELIX_COLOR = new Color(255,51,51);
- public static final Color STRAND_COLOR = new Color(255,204,51);
- public static final Color TURN_COLOR = new Color(204,204,204);
-
+public class FeatureTrackConverter
+{
- // some annotation types, for which there is a special treatment
- public static final String DISULFID_TYPE = "DISULFID";
- public static final String SECSTRUC_TYPE = "SECSTRUC";
- public static final String METAL_TYPE = "METAL";
- public static final String MSD_SITE_TYPE = "MSD_SITE";
+ public static final Color HELIX_COLOR = new Color(255, 51, 51);
- String type;
- public static final String TYPE_HISTOGRAM = "histogram";
- public static final String TYPE_DEFAULT = "default";
+ public static final Color STRAND_COLOR = new Color(255, 204, 51);
+ public static final Color TURN_COLOR = new Color(204, 204, 204);
- // rotate between these colors
- public static final Color[] entColors = new Color []{
- new Color(51,51,255), // blue
- new Color(102,255,255), // cyan
- new Color(153,255,153), // green
- new Color(153,255,153), // green
- new Color(255,153,153), // pink
- new Color(255,51,51), // red
- new Color(255,51,255) // pink
- };
-
- public static final String[] txtColors = new String[] {
- "blue",
- "pink",
- "green",
- "yellow",
- "red",
- "cyan",
- "pink"};
+ // some annotation types, for which there is a special treatment
+ public static final String DISULFID_TYPE = "DISULFID";
- Map[] stylesheet;
+ public static final String SECSTRUC_TYPE = "SECSTRUC";
- boolean isHistogram = false;
+ public static final String METAL_TYPE = "METAL";
+ public static final String MSD_SITE_TYPE = "MSD_SITE";
- public FeatureTrackConverter(){
- type = TYPE_DEFAULT;
- stylesheet = new Map[0];
- }
-
- public FeatureTrackConverter(Map[] stylesheet){
-
- if (stylesheet == null)
- stylesheet = new Map[0];
-
- this.stylesheet = stylesheet;
-
- }
-
-
- public FeatureTrackConverter(Map[] stylesheet, boolean isHistogram){
- this(stylesheet);
- this.isHistogram = isHistogram;
- if ( isHistogram)
- type = TYPE_HISTOGRAM;
- }
- public String getType() {
- return type;
- }
+ String type;
- public void setType(String type) {
- if ( type.equals(TYPE_HISTOGRAM))
- isHistogram = true;
- this.type = type;
- }
+ public static final String TYPE_HISTOGRAM = "histogram";
- public boolean isHistogram() {
- return isHistogram;
- }
-
-
- public void setHistogram(boolean isHistogram) {
- this.isHistogram = isHistogram;
- }
-
-
-
-
-
- public FeatureTrack[] convertMap2Features(Map[] mapfeatures){
- List features = new ArrayList();
-
- boolean first = true ;
- boolean secstruc = false ;
- boolean isGroup = false;
-
- FeatureTrack feat = null ;
- Segment segment = null ;
-
- int featuresCounter = 0;
- String prevGroup = null;
-
- for (int i = 0 ; i< mapfeatures.length;i++) {
-
- Map currentFeatureMap = mapfeatures[i];
- String type = (String) currentFeatureMap.get("TYPE") ;
-
-
-
- String group = (String) currentFeatureMap.get("GROUP");
- if ( group != null){
- if ( prevGroup != null) {
- if ( group.equals(prevGroup)){
- feat.setName(group);
- isGroup = true;
- } else {
- isGroup = false;
- }
- } else {
- isGroup = false;
- }
- } else {
- isGroup = false;
- }
-
- // we are skipping literature references for the moment
- // TODO: add a display to spice for non-positional features
- //
- if ( type.equals("reference") || type.equals("GOA")){
- continue ;
- }
-
- if (! first)
- {
- // if not first feature
-
- if ( (! secstruc ) && (! isGroup) ) {
-
- // if not secondary structure and not in a group ...
- features = testAddFeatures(features,feat);
-
-
- } else if ( !
- (
- type.equals("HELIX") ||
- type.equals("STRAND") ||
- type.equals("TURN")
- )
- )
- {
- // end of secondary structure
- secstruc = false ;
- if ( feat != null && (! isGroup)) {
- features = testAddFeatures(features,feat);
- }
-
- }
- } // end of not first
-
- first = false ;
- if ( (! secstruc) && (! isGroup)) {
- featuresCounter +=1;
- feat = getNewFeat(currentFeatureMap);
- }
-
-
-
-
- if (type.equals("STRAND")){
- secstruc = true ;
- currentFeatureMap.put("colorTxt","yellow");
- feat.setName("SECSTRUC");
- feat.setType("SECSTRUC");
- }
-
- else if (type.equals("HELIX")) {
- secstruc = true ;
- currentFeatureMap.put("colorTxt","red");
- feat.setName("SECSTRUC");
- feat.setType("SECSTRUC");
- }
-
- else if (type.equals("TURN")) {
- secstruc = true ;
- currentFeatureMap.put("colorTxt","white");
-
- feat.setName("SECSTRUC");
- feat.setType("SECSTRUC");
- }
- else {
- secstruc = false ;
- currentFeatureMap.put("colorTxt",txtColors[featuresCounter%txtColors.length]);
- if ( ! isGroup) {
- try {
- feat.setName(type);
-
- } catch ( NullPointerException e) {
- //e.printStackTrace();
- feat.setName("null");
- }
- }
- }
-
- segment = getNewSegment(currentFeatureMap);
-
- feat.addSegment(segment);
- prevGroup = group;
- }
-
- if ( feat != null)
- features =testAddFeatures(features,feat);
-
-
- return (FeatureTrack[]) features.toArray(new FeatureTrack[features.size()]);
- }
-
- /** test if this features is added as a new feature to the features list,
- * or if it is joint with an already existing one...
- *
- * @param features
- * @param newFeature
- * @return a List of FeatureTrack objects
- */
- protected List testAddFeatures(List features,FeatureTrack newFeature){
-
- //System.out.println("testing " + newFeature + " " + newFeature.getScore());
- Iterator iter = features.iterator();
-
-
- if ( isHistogramFeatureType(newFeature)) {
-
- // return histogram type features
- type = TYPE_HISTOGRAM;
-
- Segment seg = getHistogramSegmentFromFeature(newFeature);
-
- while (iter.hasNext()){
- FeatureTrack knownFeature = (FeatureTrack) iter.next() ;
- String knownType = knownFeature.getType();
-
- //System.out.println("found histogram style " + feat);
- // set type of this DAS source to being HISTOGRAM style
-
-
- if ( knownType.equals(newFeature.getType())){
- // convert the feature into a HistogramSegment and add to the already known feature
-
- knownFeature.addSegment(seg);
- // we can return now
- return features;
- }
-
-
- }
- // we could not link this to any existing feature
- // convert it to a new HistogramFeature
- HistogramFeature hfeat = new HistogramFeature();
-
- hfeat.setLink(newFeature.getLink());
- hfeat.setMethod(newFeature.getMethod());
- hfeat.setName(newFeature.getName());
- hfeat.setNote(newFeature.getNote());
- hfeat.setScore("0");
- hfeat.setSource(newFeature.getSource());
- hfeat.addSegment(seg);
- hfeat.setType(newFeature.getType());
-
- newFeature = hfeat;
- features.add(newFeature);
- return features;
- }
-
-
-
- while (iter.hasNext()){
- FeatureTrack knownFeature = (FeatureTrack) iter.next() ;
- // this only compares method source and type ...
- boolean sameFeat = false;
- if ( knownFeature.equals(newFeature))
- sameFeat = true;
-
- if ( ( knownFeature.getSource().equals(newFeature.getSource() )) &&
- ( knownFeature.getMethod().equals(newFeature.getMethod())) &&
- ( knownFeature.getNote().equals(newFeature.getNote())) &&
- isSecondaryStructureFeat(knownFeature) &&
- isSecondaryStructureFeat(newFeature))
- sameFeat =true;
-
- if ( sameFeat) {
-
- // seems to be of same type, method and source, so check if the segments can be joined
-
- List tmpsegs = knownFeature.getSegments();
- Iterator segiter = tmpsegs.iterator();
- List newsegs = newFeature.getSegments();
- Iterator newsegsiter = newsegs.iterator();
- boolean overlap = false;
- while (newsegsiter.hasNext()){
- Segment newseg = (Segment)newsegsiter.next();
-
-
- while (segiter.hasNext()){
- Segment tmpseg = (Segment) segiter.next();
-
- if ( tmpseg.overlaps(newseg))
- overlap = true;
- }
- }
-
- if ( ! overlap){
- // add all new segments to old features...
- newsegsiter = newsegs.iterator();
- while (newsegsiter.hasNext()){
- Segment newseg = (Segment)newsegsiter.next();
- knownFeature.addSegment(newseg);
- }
-
- return features;
- }
- }
-
- }
-
- // if we get here, the features could not be joint with any other one, so there is always some overlap
- // add to the list of known features
- features.add(newFeature);
- return features;
- }
-
- private FeatureTrack getNewFeat(Map currentFeatureMap) {
- FeatureTrack feat = new FeatureTrackImpl();
- //logger.finest(currentFeatureMap);
- //System.out.println("DrawableDasSource " + currentFeatureMap);
- feat.setSource((String)currentFeatureMap.get("dassource"));
- feat.setName( (String)currentFeatureMap.get("NAME"));
- feat.setType( (String)currentFeatureMap.get("TYPE"));
- feat.setLink( (String)currentFeatureMap.get("LINK"));
- feat.setNote( (String)currentFeatureMap.get("NOTE"));
-
- String typeID = (String) currentFeatureMap.get("TYPE_ID");
- String typeCategory = (String) currentFeatureMap.get("TYPE_CATEGORY");
- feat.setTypeID(typeID);
- feat.setTypeCategory(typeCategory);
-
- String method = (String)currentFeatureMap.get("METHOD");
- if ( method == null) { method = "";}
- feat.setMethod(method);
- feat.setScore( (String)currentFeatureMap.get("SCORE"));
- return feat ;
- }
-
- private Segment getNewSegment(Map featureMap) {
- Segment s = new SegmentImpl();
- String sstart = (String)featureMap.get("START") ;
- String send = (String)featureMap.get("END") ;
- int start = Integer.parseInt(sstart) ;
- int end = Integer.parseInt(send) ;
- s.setStart(start);
- s.setEnd(end);
- s.setName((String)featureMap.get("TYPE"));
- s.setTxtColor((String)featureMap.get("colorTxt"));
- s.setColor((Color)featureMap.get("color"));
- s.setNote((String) featureMap.get("NOTE"));
- return s ;
-
- }
-
- private boolean isSecondaryStructureFeat(FeatureTrack feat){
- String type = feat.getType();
- if (
- type.equals("HELIX") ||
- type.equals("STRAND") ||
- type.equals("TURN")
- ) return true;
- return false;
- }
-
- private boolean isHistogramFeatureType(FeatureTrack feat){
- String ftype = feat.getType();
-
- Map[] style = stylesheet;
-
- //System.out.println("is HistogramFeature type " + ftype + " " + style );
-
-
- // todo : move this info into a config file...
-
- if ( ftype.equals("hydrophobicity")){
- return true;
- }
- if ( getType().equals(TYPE_HISTOGRAM) )
- return true;
-
-
-
- if (style != null ) {
-
- for ( int i =0; i< style.length ; i++){
- Map m = style[i];
-
- // make sure the stylesheet is for this feature type
- String styleType = (String) m.get("type");
- if ( styleType != null) {
- if ( ! styleType.equals(ftype)){
- continue;
- }
- } else {
- continue;
- }
-
- String type = (String) m.get("style");
- if ( type != null) {
- //System.out.println("stylesheet type " + type);
- if ( type.equals("gradient") || ( type.equals("lineplot")) || ( type.equals("histogram"))){
-
- return true;
- }
- }
- }
- }
-
- return false;
- }
-
-
- private HistogramSegment getHistogramSegmentFromFeature(FeatureTrack feat){
- HistogramSegment s = new HistogramSegment();
-
- double score = 0.0;
-
- try {
- score = Double.parseDouble(feat.getScore());
-
- } catch (Exception e){
- //e.printStackTrace();
- }
- s.setScore(score);
- List segments = feat.getSegments();
- if (segments.size() > 0){
- Segment seg = (Segment) segments.get(0);
- s.setName(seg.getName());
- s.setStart(seg.getStart());
- s.setEnd(seg.getEnd());
- s.setNote(seg.getNote());
- s.setColor(seg.getColor());
- s.setTxtColor(seg.getTxtColor());
- }
-
-
- return s;
- }
+ public static final String TYPE_DEFAULT = "default";
+ // rotate between these colors
+ public static final Color[] entColors = new Color[]
+ { new Color(51, 51, 255), // blue
+ new Color(102, 255, 255), // cyan
+ new Color(153, 255, 153), // green
+ new Color(153, 255, 153), // green
+ new Color(255, 153, 153), // pink
+ new Color(255, 51, 51), // red
+ new Color(255, 51, 255) // pink
+ };
+
+ public static final String[] txtColors = new String[]
+ { "blue", "pink", "green", "yellow", "red", "cyan", "pink" };
+
+ Map[] stylesheet;
+
+ boolean isHistogram = false;
+
+ public FeatureTrackConverter()
+ {
+ type = TYPE_DEFAULT;
+ stylesheet = new Map[0];
+ }
+
+ public FeatureTrackConverter(Map[] stylesheet)
+ {
+
+ if (stylesheet == null)
+ stylesheet = new Map[0];
+
+ this.stylesheet = stylesheet;
+
+ }
+
+ public FeatureTrackConverter(Map[] stylesheet, boolean isHistogram)
+ {
+ this(stylesheet);
+ this.isHistogram = isHistogram;
+ if (isHistogram)
+ type = TYPE_HISTOGRAM;
+ }
+
+ public String getType()
+ {
+ return type;
+ }
+
+ public void setType(String type)
+ {
+ if (type.equals(TYPE_HISTOGRAM))
+ isHistogram = true;
+ this.type = type;
+ }
+
+ public boolean isHistogram()
+ {
+ return isHistogram;
+ }
+
+ public void setHistogram(boolean isHistogram)
+ {
+ this.isHistogram = isHistogram;
+ }
+
+ public FeatureTrack[] convertMap2Features(Map[] mapfeatures)
+ {
+ List features = new ArrayList();
+
+ boolean first = true;
+ boolean secstruc = false;
+ boolean isGroup = false;
+
+ FeatureTrack feat = null;
+ Segment segment = null;
+
+ int featuresCounter = 0;
+ String prevGroup = null;
+
+ for (int i = 0; i < mapfeatures.length; i++)
+ {
+
+ Map currentFeatureMap = mapfeatures[i];
+ String type = (String) currentFeatureMap.get("TYPE");
+
+ String group = (String) currentFeatureMap.get("GROUP");
+ if (group != null)
+ {
+ if (prevGroup != null)
+ {
+ if (group.equals(prevGroup))
+ {
+ feat.setName(group);
+ isGroup = true;
+ }
+ else
+ {
+ isGroup = false;
+ }
+ }
+ else
+ {
+ isGroup = false;
+ }
+ }
+ else
+ {
+ isGroup = false;
+ }
+
+ // we are skipping literature references for the moment
+ // TODO: add a display to spice for non-positional features
+ //
+ if (type.equals("reference") || type.equals("GOA"))
+ {
+ continue;
+ }
+
+ if (!first)
+ {
+ // if not first feature
+
+ if ((!secstruc) && (!isGroup))
+ {
+
+ // if not secondary structure and not in a group ...
+ features = testAddFeatures(features, feat);
+
+ }
+ else if (!(type.equals("HELIX") || type.equals("STRAND") || type
+ .equals("TURN")))
+ {
+ // end of secondary structure
+ secstruc = false;
+ if (feat != null && (!isGroup))
+ {
+ features = testAddFeatures(features, feat);
+ }
+
+ }
+ } // end of not first
+
+ first = false;
+ if ((!secstruc) && (!isGroup))
+ {
+ featuresCounter += 1;
+ feat = getNewFeat(currentFeatureMap);
+ }
+
+ if (type.equals("STRAND"))
+ {
+ secstruc = true;
+ currentFeatureMap.put("colorTxt", "yellow");
+ feat.setName("SECSTRUC");
+ feat.setType("SECSTRUC");
+ }
+
+ else if (type.equals("HELIX"))
+ {
+ secstruc = true;
+ currentFeatureMap.put("colorTxt", "red");
+ feat.setName("SECSTRUC");
+ feat.setType("SECSTRUC");
+ }
+
+ else if (type.equals("TURN"))
+ {
+ secstruc = true;
+ currentFeatureMap.put("colorTxt", "white");
+
+ feat.setName("SECSTRUC");
+ feat.setType("SECSTRUC");
+ }
+ else
+ {
+ secstruc = false;
+ currentFeatureMap.put("colorTxt", txtColors[featuresCounter
+ % txtColors.length]);
+ if (!isGroup)
+ {
+ try
+ {
+ feat.setName(type);
+
+ } catch (NullPointerException e)
+ {
+ // e.printStackTrace();
+ feat.setName("null");
+ }
+ }
+ }
+
+ segment = getNewSegment(currentFeatureMap);
+
+ feat.addSegment(segment);
+ prevGroup = group;
+ }
+
+ if (feat != null)
+ features = testAddFeatures(features, feat);
+
+ return (FeatureTrack[]) features.toArray(new FeatureTrack[features
+ .size()]);
+ }
+
+ /**
+ * test if this features is added as a new feature to the features list, or if
+ * it is joint with an already existing one...
+ *
+ * @param features
+ * @param newFeature
+ * @return a List of FeatureTrack objects
+ */
+ protected List testAddFeatures(List features, FeatureTrack newFeature)
+ {
+
+ // System.out.println("testing " + newFeature + " " +
+ // newFeature.getScore());
+ Iterator iter = features.iterator();
+
+ if (isHistogramFeatureType(newFeature))
+ {
+
+ // return histogram type features
+ type = TYPE_HISTOGRAM;
+
+ Segment seg = getHistogramSegmentFromFeature(newFeature);
+
+ while (iter.hasNext())
+ {
+ FeatureTrack knownFeature = (FeatureTrack) iter.next();
+ String knownType = knownFeature.getType();
+
+ // System.out.println("found histogram style " + feat);
+ // set type of this DAS source to being HISTOGRAM style
+
+ if (knownType.equals(newFeature.getType()))
+ {
+ // convert the feature into a HistogramSegment and add to the already
+ // known feature
+
+ knownFeature.addSegment(seg);
+ // we can return now
+ return features;
+ }
+
+ }
+ // we could not link this to any existing feature
+ // convert it to a new HistogramFeature
+ HistogramFeature hfeat = new HistogramFeature();
+
+ hfeat.setLink(newFeature.getLink());
+ hfeat.setMethod(newFeature.getMethod());
+ hfeat.setName(newFeature.getName());
+ hfeat.setNote(newFeature.getNote());
+ hfeat.setScore("0");
+ hfeat.setSource(newFeature.getSource());
+ hfeat.addSegment(seg);
+ hfeat.setType(newFeature.getType());
+
+ newFeature = hfeat;
+ features.add(newFeature);
+ return features;
+ }
+
+ while (iter.hasNext())
+ {
+ FeatureTrack knownFeature = (FeatureTrack) iter.next();
+ // this only compares method source and type ...
+ boolean sameFeat = false;
+ if (knownFeature.equals(newFeature))
+ sameFeat = true;
+
+ if ((knownFeature.getSource().equals(newFeature.getSource()))
+ && (knownFeature.getMethod().equals(newFeature.getMethod()))
+ && (knownFeature.getNote().equals(newFeature.getNote()))
+ && isSecondaryStructureFeat(knownFeature)
+ && isSecondaryStructureFeat(newFeature))
+ sameFeat = true;
+
+ if (sameFeat)
+ {
+
+ // seems to be of same type, method and source, so check if the segments
+ // can be joined
+
+ List tmpsegs = knownFeature.getSegments();
+ Iterator segiter = tmpsegs.iterator();
+ List newsegs = newFeature.getSegments();
+ Iterator newsegsiter = newsegs.iterator();
+ boolean overlap = false;
+ while (newsegsiter.hasNext())
+ {
+ Segment newseg = (Segment) newsegsiter.next();
+
+ while (segiter.hasNext())
+ {
+ Segment tmpseg = (Segment) segiter.next();
+
+ if (tmpseg.overlaps(newseg))
+ overlap = true;
+ }
+ }
+
+ if (!overlap)
+ {
+ // add all new segments to old features...
+ newsegsiter = newsegs.iterator();
+ while (newsegsiter.hasNext())
+ {
+ Segment newseg = (Segment) newsegsiter.next();
+ knownFeature.addSegment(newseg);
+ }
+
+ return features;
+ }
+ }
+
+ }
+
+ // if we get here, the features could not be joint with any other one, so
+ // there is always some overlap
+ // add to the list of known features
+ features.add(newFeature);
+ return features;
+ }
+
+ private FeatureTrack getNewFeat(Map currentFeatureMap)
+ {
+ FeatureTrack feat = new FeatureTrackImpl();
+ // logger.finest(currentFeatureMap);
+ // System.out.println("DrawableDasSource " + currentFeatureMap);
+ feat.setSource((String) currentFeatureMap.get("dassource"));
+ feat.setName((String) currentFeatureMap.get("NAME"));
+ feat.setType((String) currentFeatureMap.get("TYPE"));
+ feat.setLink((String) currentFeatureMap.get("LINK"));
+ feat.setNote((String) currentFeatureMap.get("NOTE"));
+
+ String typeID = (String) currentFeatureMap.get("TYPE_ID");
+ String typeCategory = (String) currentFeatureMap.get("TYPE_CATEGORY");
+ feat.setTypeID(typeID);
+ feat.setTypeCategory(typeCategory);
+
+ String method = (String) currentFeatureMap.get("METHOD");
+ if (method == null)
+ {
+ method = "";
+ }
+ feat.setMethod(method);
+ feat.setScore((String) currentFeatureMap.get("SCORE"));
+ return feat;
+ }
+
+ private Segment getNewSegment(Map featureMap)
+ {
+ Segment s = new SegmentImpl();
+ String sstart = (String) featureMap.get("START");
+ String send = (String) featureMap.get("END");
+ int start = Integer.parseInt(sstart);
+ int end = Integer.parseInt(send);
+ s.setStart(start);
+ s.setEnd(end);
+ s.setName((String) featureMap.get("TYPE"));
+ s.setTxtColor((String) featureMap.get("colorTxt"));
+ s.setColor((Color) featureMap.get("color"));
+ s.setNote((String) featureMap.get("NOTE"));
+ return s;
+
+ }
+
+ private boolean isSecondaryStructureFeat(FeatureTrack feat)
+ {
+ String type = feat.getType();
+ if (type.equals("HELIX") || type.equals("STRAND")
+ || type.equals("TURN"))
+ return true;
+ return false;
+ }
+
+ private boolean isHistogramFeatureType(FeatureTrack feat)
+ {
+ String ftype = feat.getType();
+
+ Map[] style = stylesheet;
+
+ // System.out.println("is HistogramFeature type " + ftype + " " + style );
+
+ // todo : move this info into a config file...
+
+ if (ftype.equals("hydrophobicity"))
+ {
+ return true;
+ }
+ if (getType().equals(TYPE_HISTOGRAM))
+ return true;
+
+ if (style != null)
+ {
+
+ for (int i = 0; i < style.length; i++)
+ {
+ Map m = style[i];
+
+ // make sure the stylesheet is for this feature type
+ String styleType = (String) m.get("type");
+ if (styleType != null)
+ {
+ if (!styleType.equals(ftype))
+ {
+ continue;
+ }
+ }
+ else
+ {
+ continue;
+ }
+
+ String type = (String) m.get("style");
+ if (type != null)
+ {
+ // System.out.println("stylesheet type " + type);
+ if (type.equals("gradient") || (type.equals("lineplot"))
+ || (type.equals("histogram")))
+ {
+
+ return true;
+ }
+ }
+ }
+ }
+
+ return false;
+ }
+
+ private HistogramSegment getHistogramSegmentFromFeature(FeatureTrack feat)
+ {
+ HistogramSegment s = new HistogramSegment();
+
+ double score = 0.0;
+
+ try
+ {
+ score = Double.parseDouble(feat.getScore());
+
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ }
+ s.setScore(score);
+ List segments = feat.getSegments();
+ if (segments.size() > 0)
+ {
+ Segment seg = (Segment) segments.get(0);
+ s.setName(seg.getName());
+ s.setStart(seg.getStart());
+ s.setEnd(seg.getEnd());
+ s.setNote(seg.getNote());
+ s.setColor(seg.getColor());
+ s.setTxtColor(seg.getTxtColor());
+ }
+
+ return s;
+ }
}
git://source.jalview.org / jalview.git / blobdiff