From: jprocter <Jim Procter>
Date: Thu, 3 Jun 2010 15:12:42 +0000 (+0000)
Subject: patch and error reports re JAL-554
X-Git-Tag: Release_2_5_1~35
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=10e588500da51e79f255e000a46e65065a49f8aa

patch and error reports re JAL-554
---

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index aeaf2f3..2721fb2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -982,45 +982,55 @@ public class AnnotationFile
     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())
+    if (al.getAlignmentAnnotation() != null)
     {
-      group = st.nextToken();
       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;
+          }
+        }
+      }
+    }
+    else
+    {
+      System.err
+              .println("Couldn't combine annotations. None are added to alignment yet!");
     }
   }
 
   void addLine(AlignmentI al, StringTokenizer st)
   {
     String group = st.nextToken();
-    AlignmentAnnotation annotation = null;
-
-    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation annotation = null, alannot[] = al
+            .getAlignmentAnnotation();
+    if (alannot != null)
     {
-      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+      for (int i = 0; i < alannot.length; i++)
       {
-        annotation = al.getAlignmentAnnotation()[i];
-        break;
+        if (alannot[i].label.equalsIgnoreCase(group))
+        {
+          annotation = alannot[i];
+          break;
+        }
       }
     }
-
     if (annotation == null)
     {
       return;
@@ -1153,13 +1163,16 @@ public class AnnotationFile
         centerlab = Boolean.valueOf(value).booleanValue();
       }
       AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
-      for (int i = 0; i < alr.length; i++)
+      if (alr != null)
       {
-        if (alr[i].label.equalsIgnoreCase(label))
+        for (int i = 0; i < alr.length; i++)
         {
-          alr[i].centreColLabels = centerlab;
-          alr[i].scaleColLabel = scaletofit;
-          alr[i].showAllColLabels = showalllabs;
+          if (alr[i].label.equalsIgnoreCase(label))
+          {
+            alr[i].centreColLabels = centerlab;
+            alr[i].scaleColLabel = scaletofit;
+            alr[i].showAllColLabels = showalllabs;
+          }
         }
       }
     }
@@ -1290,19 +1303,35 @@ public class AnnotationFile
   void setBelowAlignment(AlignmentI al, StringTokenizer st)
   {
     String token;
-    AlignmentAnnotation aa;
+    AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
+    if (ala == null)
+    {
+      System.err
+              .print("Warning - no annotation to set below for sequence associated annotation:");
+    }
     while (st.hasMoreTokens())
     {
       token = st.nextToken();
-      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+      if (ala == null)
+      {
+        System.err.print(" "+token);
+      }
+      else
       {
-        aa = al.getAlignmentAnnotation()[i];
-        if (aa.sequenceRef == refSeq && aa.label.equals(token))
+        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
-          aa.belowAlignment = true;
+          aa = al.getAlignmentAnnotation()[i];
+          if (aa.sequenceRef == refSeq && aa.label.equals(token))
+          {
+            aa.belowAlignment = true;
+          }
         }
       }
     }
+    if (ala==null)
+    {
+      System.err.print("\n");
+    }
   }
 
   void addAlignmentDetails(AlignmentI al, StringTokenizer st)