From c36010655019c2ef1f4f6f80738db0b7f2e14a08 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Jul 2006 12:55:08 +0000
Subject: [PATCH] Replaced by AnnotationFile

---
 src/jalview/io/AnnotationReader.java |  281 ----------------------------------
 1 file changed, 281 deletions(-)
 delete mode 100755 src/jalview/io/AnnotationReader.java

diff --git a/src/jalview/io/AnnotationReader.java b/src/jalview/io/AnnotationReader.java
deleted file mode 100755
index cd7abfd..0000000
--- a/src/jalview/io/AnnotationReader.java
+++ /dev/null
@@ -1,281 +0,0 @@
-package jalview.io;
-
-import java.io.*;
-import jalview.datamodel.*;
-import java.util.StringTokenizer;
-import jalview.schemes.UserColourScheme;
-import java.net.URL;
-
-public class AnnotationReader
-{
-  public boolean readAnnotationFile(AlignmentI al, String file)
-  {
-
-    try
-    {
-      BufferedReader in = null;
-      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-      if (is != null)
-      {
-        in = new BufferedReader(new java.io.InputStreamReader(is));
-      }
-      else
-      {
-        try
-        {
-          URL url = new URL(file);
-          in = new BufferedReader(new InputStreamReader(url.openStream()));
-        }
-        catch (java.net.MalformedURLException ex)
-        {
-          in = new BufferedReader(new FileReader(file));
-        }
-      }
-
-      String line, label, description, token;
-      int graphStyle, index;
-      SequenceI refSeq = null;
-      int refSeqIndex = 1;
-      int existingAnnotations = 0;
-      if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
-
-      int alWidth = al.getWidth();
-
-      StringTokenizer st;
-      Annotation[] annotations;
-      AlignmentAnnotation annotation = null;
-
-      // First confirm this is an Annotation file
-      boolean jvAnnotationFile = false;
-      while ( (line = in.readLine()) != null)
-      {
-        if (line.indexOf("#") == 0 )
-          continue;
-
-        if (line.indexOf("JALVIEW_ANNOTATION") > -1)
-        {
-          jvAnnotationFile = true;
-          break;
-        }
-      }
-
-      if(!jvAnnotationFile)
-      {
-        in.close();
-        return false;
-      }
-
-      while ( (line = in.readLine()) != null)
-      {
-        if(line.indexOf("#")==0
-           || line.indexOf("JALVIEW_ANNOTATION")>-1
-           || line.length()==0)
-          continue;
-
-        st = new StringTokenizer(line, "\t");
-        token = st.nextToken();
-        if(token.equalsIgnoreCase("COLOUR"))
-        {
-          colourAnnotations(al, st.nextToken(), st.nextToken());
-          continue;
-        }
-
-        if(token.equalsIgnoreCase("COMBINE") )
-        {
-          combineAnnotations(al, st);
-          continue;
-        }
-
-        if (token.equalsIgnoreCase("GRAPHLINE"))
-        {
-          addLine(al, st);
-          continue;
-        }
-
-
-        if(token.equalsIgnoreCase("SEQUENCE_REF") )
-        {
-          refSeq = al.findName(st.nextToken());
-          try{
-            refSeqIndex = Integer.parseInt(st.nextToken());
-          }
-          catch(Exception ex)
-          {
-            refSeqIndex = 1;
-          }
-
-          continue;
-        }
-
-
-        graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
-        label = description = st.nextToken();
-
-        line = st.nextToken();
-
-        st = new StringTokenizer(line, "|", true);
-        annotations = new Annotation[alWidth];
-
-        index = 0;
-        boolean emptyColumn = true;
-
-
-        while (st.hasMoreElements() && index<alWidth)
-        {
-          token = st.nextToken().trim();
-          if(token.equals("|"))
-          {
-            if(emptyColumn)
-              index++;
-
-            emptyColumn = true;
-          }
-          else
-          {
-            annotations[index++] = parseAnnotation(token);
-            emptyColumn = false;
-          }
-        }
-
-       annotation = new AlignmentAnnotation(label,
-                                          description,
-                                          annotations,
-                                          0,
-                                          0,
-                                          graphStyle);
-
-       if(refSeq!=null)
-       {
-         annotation.createSequenceMapping(refSeq, refSeqIndex);
-         refSeq.addAlignmentAnnotation(annotation);
-       }
-
-       al.addAnnotation(annotation);
-
-       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
-      }
-
-    }catch(Exception ex)
-    {
-      ex.printStackTrace();
-      System.out.println("Problem reading annotation file: "+ex);
-      return false;
-    }
-    return true;
-  }
-
-  Annotation parseAnnotation(String string)
-  {
-    String desc = "", displayChar="";
-    char ss = ' '; // secondaryStructure
-    float value = 0;
-    boolean parsedValue = false;
-    StringTokenizer st = new StringTokenizer(string, ",");
-    String token;
-    while(st.hasMoreTokens())
-    {
-      token = st.nextToken().trim();
-      if(token.length()==0)
-        continue;
-
-      if(!parsedValue)
-      {
-        try{
-          value = new Float(token).floatValue();
-          displayChar = token;
-          parsedValue = true;
-        }catch(NumberFormatException ex){}
-      }
-
-      if(token.equals("H") || token.equals("E"))
-      {
-        // Either this character represents a helix or sheet
-        // or an integer which can be displayed
-        ss = token.charAt(0);
-      }
-      else if(desc.length()<1)
-        desc = token;
-
-    }
-
-    return new Annotation(displayChar, desc, ss, value);
-  }
-
-  void colourAnnotations(AlignmentI al, String label, String colour)
-  {
-    UserColourScheme ucs = new UserColourScheme(colour);
-    Annotation[] annotations;
-    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
-    {
-      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
-      {
-        annotations = al.getAlignmentAnnotation()[i].annotations;
-        for(int j=0; j<annotations.length; j++)
-        {
-          if(annotations[j]!=null)
-            annotations[j].colour = ucs.findColour("A");
-        }
-      }
-    }
-  }
-
-  void combineAnnotations(AlignmentI al, StringTokenizer st)
-  {
-    int graphGroup = -1;
-    String group = st.nextToken();
-    //First make sure we are not overwriting the graphIndex
-    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
-    {
-      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
-      {
-        graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;
-        al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
-        break;
-      }
-    }
-
-    //Now update groups
-    while(st.hasMoreTokens())
-    {
-      group = st.nextToken();
-      for(int i=0; i<al.getAlignmentAnnotation().length; i++)
-      {
-        if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
-        {
-          al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
-          break;
-        }
-      }
-    }
-  }
-
-  void addLine(AlignmentI al, StringTokenizer st)
-  {
-    String group = st.nextToken();
-    AlignmentAnnotation annotation = null;
-
-    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
-    {
-      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
-      {
-        annotation = al.getAlignmentAnnotation()[i];
-        break;
-      }
-    }
-
-    if(annotation==null)
-      return;
-    float value = new Float(st.nextToken()).floatValue();
-    String label = st.hasMoreTokens() ?  st.nextToken() : null;
-    java.awt.Color colour = null;
-    if(st.hasMoreTokens())
-    {
-      UserColourScheme ucs = new UserColourScheme(st.nextToken());
-      colour = ucs.findColour("A");
-    }
-
-    annotation.setThreshold(new GraphLine(value, label, colour));
-
-  }
-}
-- 
1.7.10.2