X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=6285cf10011eb94bc3ad9d2154d7b9a262be44a6;hb=9d8d94660cfba31f6dd39cd6a8a25e3e88284277;hp=a936dac86b2fc4245f3c10a297a406600a4c4ed4;hpb=b5fdf35e68eea0a0710cae2178020645ac17e6af;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index a936dac..6285cf1 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -33,13 +33,45 @@ public class AnnotationFile
       "JALVIEW_ANNOTATION\n"
       + "# Created: "
       + new java.util.Date() + "\n\n");
-
+  /**
+   * convenience method for pre-2.4 feature files which have no view, hidden columns or hidden row keywords.
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @return feature file as a string.
+   */
   public String printAnnotations(AlignmentAnnotation[] annotations,
                                  Vector groups,
                                  Hashtable properties)
   {
+    return printAnnotations(annotations, groups,
+            properties, null);
+
+  }
+  /**
+   * hold all the information about a particular view definition
+   * read from or written out in an annotations file.
+   */
+  public class ViewDef {
+    public String viewname;
+    public HiddenSequences hidseqs;
+    public ColumnSelection hiddencols;
+    public Vector visibleGroups;
+    public ViewDef(String viewname, HiddenSequences hidseqs,
+            ColumnSelection hiddencols)
+    {
+      this.viewname = viewname;
+      this.hidseqs = hidseqs;
+      this.hiddencols = hiddencols;
+    }
+  }
+  public String printAnnotations(AlignmentAnnotation[] annotations,
+          Vector groups,
+          Hashtable properties, ViewDef[] views)
+  {
     if (annotations != null)
     {
+      boolean oneColour = true;
       AlignmentAnnotation row;
       String comma;
       SequenceI refSeq = null;
@@ -55,12 +87,13 @@ public class AnnotationFile
       {
         row = annotations[i];
 
-        if (!row.visible)
+        if (!row.visible && !row.hasScore())
         {
           continue;
         }
 
         color = null;
+        oneColour = true;
 
         if (row.sequenceRef == null)
         {
@@ -125,7 +158,7 @@ public class AnnotationFile
           text.append(row.description + "\t");
         }
 
-        for (int j = 0; j < row.annotations.length; j++)
+        for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)
         {
           if (refSeq != null &&
               jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
@@ -151,6 +184,11 @@ public class AnnotationFile
 
             if (row.annotations[j] != null)
             {
+              if(color!=null && !color.equals(row.annotations[j].colour))
+              {
+                oneColour = false;
+              }
+
               color = row.annotations[j].colour;
               if (row.annotations[j].value != 0f)
               {
@@ -169,12 +207,12 @@ public class AnnotationFile
           text.append("|");
         }
 
-        if(!Float.isNaN(row.score))
+        if(row.hasScore())
           text.append("\t"+row.score);
 
         text.append("\n");
 
-        if (color != null && color != java.awt.Color.black)
+        if (color != null && color != java.awt.Color.black && oneColour)
         {
           colours.append("COLOUR\t"
                          + row.label + "\t"
@@ -214,7 +252,7 @@ public class AnnotationFile
       }
 
     }
-
+    
     return text.toString();
   }
 
@@ -486,7 +524,7 @@ public class AnnotationFile
 
         annotation = new AlignmentAnnotation(label,
                                              description,
-                                             annotations,
+                                             (index==0) ? null : annotations,
                                              0,
                                              0,
                                              graphStyle);
@@ -578,7 +616,8 @@ public class AnnotationFile
 
     }
 
-    if (displayChar.length() > 1
+    if (displayChar!=null
+        && displayChar.length() > 1
         &&  desc!=null
         && desc.length() == 1)
     {
@@ -586,7 +625,14 @@ public class AnnotationFile
       displayChar = desc;
       desc = tmp;
     }
-
+    /*
+     * In principle, this code will ensure that the Annotation element generated is renderable by any of the applet or application rendering code
+     * but instead we check for null strings when the display character is rendered. 
+    if (displayChar==null)
+    {
+      displayChar="";
+    }
+    */
     Annotation anot = new Annotation(displayChar, desc, ss, value);
 
     anot.colour = colour;
@@ -867,4 +913,33 @@ public class AnnotationFile
       al.setProperty(key,value);
     }
   }
+
+  /**
+   * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.
+   * @param annotations
+   * @return CSV file as a string.
+   */
+  public String printCSVAnnotations(AlignmentAnnotation[] annotations)
+  {
+    StringBuffer sp = new StringBuffer();
+    for (int i=0; i<annotations.length; i++)
+    {
+      String atos = annotations[i].toString();
+      int p = 0;
+      do {
+        int cp = atos.indexOf("\n", p);
+        sp.append(annotations[i].label);
+        sp.append(",");
+        if (cp>p)
+        {
+          sp.append(atos.substring(p, cp+1));
+        } else {
+          sp.append(atos.substring(p));
+          sp.append("\n");
+        }
+        p = cp+1;
+      } while (p>0);
+    }
+    return sp.toString();
+  }
 }