Replaced by AnnotationFile

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