From 544ccf2cea9d02873528cc8be4ca1682d56cfaad Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 14 Dec 2006 18:42:25 +0000
Subject: [PATCH] Are the labels all secondary Strutures? are the displayChars
 actually descriptions?

---
 src/jalview/datamodel/AlignmentAnnotation.java |   74 ++++++++++++++----------
 src/jalview/io/AnnotationFile.java             |   40 +++++++++----
 2 files changed, 75 insertions(+), 39 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index c3396b6..7c57e6b 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -103,21 +103,53 @@ public class AlignmentAnnotation
         this.description = description;
         this.annotations = annotations;
 
-        for (int i = 0; i < annotations.length; i++)
+       areLabelsSecondaryStructure();
+    }
+
+    void areLabelsSecondaryStructure()
+    {
+      boolean nonSSLabel = false;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if(annotations[i]==null)
+          continue;
+
+        if (annotations[i].secondaryStructure == 'H' ||
+            annotations[i].secondaryStructure == 'E')
         {
-            if ((annotations[i] != null) &&
-                    ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E')))
-            {
-                hasIcons = true;
-            }
+          hasIcons = true;
+        }
+
+        if (annotations[i].secondaryStructure != 'H'
+            && annotations[i].secondaryStructure != 'E')
+        {
+          nonSSLabel = true;
+        }
+
+        if (annotations[i].displayCharacter.length() > 0)
+        {
+          hasText = true;
+        }
+      }
+
+      if(nonSSLabel)
+      {
+        hasIcons = false;
+        for (int j = 0; j < annotations.length; j++)
+        {
+          if(annotations[j] !=null && annotations[j].secondaryStructure!=' ')
+          {
+            annotations[j].displayCharacter
+                =String.valueOf(annotations[j].secondaryStructure);
+            annotations[j].secondaryStructure = ' ';
+            if(annotations[j].description.length()<1)
+              annotations[j].description = annotations[j].displayCharacter;
+          }
 
-            if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0))
-            {
-                hasText = true;
-            }
         }
+
+      }
+
     }
 
     /**
@@ -171,23 +203,7 @@ public class AlignmentAnnotation
         graphMin = min;
         graphMax = max;
 
-        for (int i = 0; i < annotations.length; i++)
-        {
-            if (!hasIcons
-                && annotations[i] != null
-                && ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E')))
-            {
-                hasIcons = true;
-            }
-
-            if (!hasText
-                && annotations[i]!=null
-                && annotations[i].displayCharacter.length() > 0)
-            {
-                hasText = true;
-            }
-        }
+        areLabelsSecondaryStructure();
 
         if(!drawValues && graphType!=NO_GRAPH)
         {
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 77f8810..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");
       }
 
 
@@ -98,6 +97,9 @@ 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 = "";
@@ -106,16 +108,18 @@ public class AnnotationFile
             text.append(comma + row.annotations[j].secondaryStructure);
             comma = ",";
           }
-          if (row.annotations[j].displayCharacter.length() > 0 
+          if (row.annotations[j].displayCharacter.length() > 0
                   && !row.annotations[j].displayCharacter.equals(" "))
               {
                 text.append(comma + row.annotations[j].displayCharacter);
                 comma = ",";
               }
-          if (row.annotations[j].value!=0f)
+
+          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);
   }
 
-- 
1.7.10.2