X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=a211d1aa415ab7ac9761286137a3a35a77ed6d88;hb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;hp=08b58629552d758e35baf0e0989213c65870c765;hpb=51eebe77f74dda2f4ff336dfe0fea0ed68b86e5b;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 08b5862..a211d1a 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -38,7 +38,7 @@ public class AnnotationFile
 
     AlignmentAnnotation row;
     String comma;
-    String seqref = null;
+    SequenceI seqref = null;
 
     StringBuffer colours = new StringBuffer();
     StringBuffer graphLine = new StringBuffer();
@@ -55,11 +55,10 @@ public class AnnotationFile
       if( row.sequenceRef == null)
         seqref = null;
 
-      else if (seqref == null
-           || !seqref.equals(row.sequenceRef.getName()))
+      else if (seqref == null || seqref != row.sequenceRef)
       {
-        seqref = row.sequenceRef.getName();
-        text.append("\nSEQUENCE_REF\t" + seqref + "\n");
+        seqref = row.sequenceRef;
+        text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");
       }
 
 
@@ -98,24 +97,29 @@ public class AnnotationFile
 
       for(int j=0; j<row.annotations.length; j++)
       {
+        if (seqref != null && jalview.util.Comparison.isGap(seqref.getCharAt(j)))
+          continue;
+
         if(row.annotations[j]!=null)
         {
           comma = "";
-          if (row.annotations[j].displayCharacter.length() > 0
-              && !row.annotations[j].displayCharacter.equals(" "))
-          {
-            text.append(row.annotations[j].displayCharacter);
-            comma = ",";
-          }
           if (row.annotations[j].secondaryStructure!=' ')
           {
             text.append(comma + row.annotations[j].secondaryStructure);
             comma = ",";
           }
-          if (row.annotations[j].value!=0f)
+          if (row.annotations[j].displayCharacter.length() > 0
+                  && !row.annotations[j].displayCharacter.equals(" "))
+              {
+                text.append(comma + row.annotations[j].displayCharacter);
+                comma = ",";
+              }
+
+          if (row.annotations[j]!=null)
           {
             color = row.annotations[j].colour;
-            text.append(comma + row.annotations[j].value);
+            if (row.annotations[j].value!=0f)
+              text.append(comma + row.annotations[j].value);
           }
         }
         text.append("|");
@@ -239,6 +243,11 @@ public class AnnotationFile
           refSeq = al.findName(st.nextToken());
           try{
             refSeqIndex = Integer.parseInt(st.nextToken());
+            if(refSeqIndex<1)
+            {
+              refSeqIndex = 1;
+              System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+            }
           }
           catch(Exception ex)
           {
@@ -307,7 +316,7 @@ public class AnnotationFile
 
   Annotation parseAnnotation(String string)
   {
-    String desc = "", displayChar="";
+    String desc = null, displayChar="";
     char ss = ' '; // secondaryStructure
     float value = 0;
     boolean parsedValue = false;
@@ -325,6 +334,7 @@ public class AnnotationFile
           displayChar = token;
           value = new Float(token).floatValue();
           parsedValue = true;
+          continue;
         }catch(NumberFormatException ex){}
       }
 
@@ -336,11 +346,21 @@ public class AnnotationFile
         if(displayChar.equals(token.substring(0,1)))
           displayChar = "";
       }
-      else if(desc.length()<1)
+      else if(desc==null)
         desc = token;
 
     }
 
+    if(desc == null)
+      desc = value+"";
+
+    if(displayChar.length()>1 && desc.length()==1)
+    {
+      String tmp = displayChar;
+      displayChar = desc;
+      desc = tmp;
+    }
+
     return new Annotation(displayChar, desc, ss, value);
   }
 
@@ -356,7 +376,7 @@ public class AnnotationFile
         for(int j=0; j<annotations.length; j++)
         {
           if(annotations[j]!=null)
-            annotations[j].colour = ucs.findColour("A");
+            annotations[j].colour = ucs.findColour('A');
         }
       }
     }
@@ -414,7 +434,7 @@ public class AnnotationFile
     if(st.hasMoreTokens())
     {
       UserColourScheme ucs = new UserColourScheme(st.nextToken());
-      colour = ucs.findColour("A");
+      colour = ucs.findColour('A');
     }
 
     annotation.setThreshold(new GraphLine(value, label, colour));