X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fbiojava%2Fdasobert%2Ffeature%2FFeatureTrackConverter.java;fp=src%2Forg%2Fbiojava%2Fdasobert%2Ffeature%2FFeatureTrackConverter.java;h=0000000000000000000000000000000000000000;hb=c1aff0bc80c5a64ec93acd8b6c5844da2d6da509;hp=4818e10c971b8dc2c8b07f31d92986c97c134b29;hpb=ec4ef38882bce0469ce7c65cd70ceb85421cfbd2;p=jalview.git

diff --git a/src/org/biojava/dasobert/feature/FeatureTrackConverter.java b/src/org/biojava/dasobert/feature/FeatureTrackConverter.java
deleted file mode 100644
index 4818e10..0000000
--- a/src/org/biojava/dasobert/feature/FeatureTrackConverter.java
+++ /dev/null
@@ -1,526 +0,0 @@
-/*
- *                  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;
-  }
-
-}