From 88ce5193255ac106b41ec465d48fd4128dad370a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 11 Mar 2010 17:08:15 +0000
Subject: [PATCH] new ROWPROPERTIES statement for setting an individual row's
 label format

---
 src/jalview/io/AnnotationFile.java |   47 +++++++++++++++++++++++++++++++++---
 1 file changed, 44 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 0095aef..4e15c18 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -85,7 +85,7 @@ public class AnnotationFile
 
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
-
+      StringBuffer rowprops = new StringBuffer();
       Hashtable graphGroup = new Hashtable();
 
       java.awt.Color color;
@@ -276,7 +276,14 @@ public class AnnotationFile
           colours.append("COLOUR\t" + row.label + "\t"
                   + jalview.util.Format.getHexString(color) + "\n");
         }
-
+        if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels)
+        {
+          rowprops.append("ROWPROPERTIES\t"+row.label);
+          rowprops.append("\tscaletofit="+row.scaleColLabel);
+          rowprops.append("\tshowalllabs="+row.showAllColLabels);
+          rowprops.append("\tcentrelabs="+row.centreColLabels);
+          rowprops.append("\n");
+        }
       }
 
       text.append("\n");
@@ -292,6 +299,7 @@ public class AnnotationFile
           text.append(en.nextElement() + "\n");
         }
       }
+      text.append(rowprops);
     }
 
     if (groups != null)
@@ -498,7 +506,11 @@ public class AnnotationFile
           combineAnnotations(al, st);
           continue;
         }
-
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          continue;
+        }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
@@ -933,6 +945,35 @@ public class AnnotationFile
     }
   }
 
+  void addRowProperties(AlignmentI al, StringTokenizer st)
+  {
+    String label = st.nextToken(),keyValue,key,value;
+    boolean scaletofit=false,centerlab=false,showalllabs=false;
+    while (st.hasMoreTokens()) {
+      keyValue=st.nextToken();
+      key = keyValue.substring(0, keyValue.indexOf("="));
+      value = keyValue.substring(keyValue.indexOf("=") + 1);
+      if (key.equalsIgnoreCase("scaletofit")) {
+        scaletofit = Boolean.valueOf(value).booleanValue();
+      }
+        if (key.equalsIgnoreCase("showalllabs")) {
+          showalllabs = Boolean.valueOf(value).booleanValue();
+        }
+        if (key.equalsIgnoreCase("centrelabs")) {
+          centerlab = Boolean.valueOf(value).booleanValue();
+    }
+        AlignmentAnnotation[] alr = al.getAlignmentAnnotation(); 
+        for (int i = 0; i < alr.length; i++)
+        {
+          if (alr[i].label.equalsIgnoreCase(label))
+          {
+            alr[i].centreColLabels = centerlab;
+            alr[i].scaleColLabel = scaletofit;
+            alr[i].showAllColLabels = showalllabs;
+          }
+        }
+    }
+  }
   void addProperties(AlignmentI al, StringTokenizer st)
   {
 
-- 
1.7.10.2