+++ /dev/null
-/*
- * BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence. This should
- * be distributed with the code. If you do not have a copy,
- * see:
- *
- * http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors. These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- * http://www.biojava.org/
- *
- * Created on Dec 5, 2007
- *
- */
-
-package org.biojava.dasobert.feature;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-/**
- * 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);
-
- // 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";
-
- String type;
-
- public static final String TYPE_HISTOGRAM = "histogram";
-
- 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