X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=00b7ead85bde0ac4d6b5c104d33c3752c971904f;hb=96f41aa46d3e568f8734834ab36fdc9ad8e54ac1;hp=0095aefab7cf8267e5a746a2eec74e742140adcb;hpb=16342ec2ab61d371ee70f61ac0294f2716fab638;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 0095aef..00b7ead 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -72,10 +72,18 @@ public class AnnotationFile
       this.hiddenRepSeqs = hiddenRepSeqs;
     }
   }
-
+  /**
+   * Prepare an annotation file given a set of annotations, groups, alignment properties and views. 
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @param views
+   * @return annotation file
+   */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           Vector groups, Hashtable properties, ViewDef[] views)
   {
+    // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -85,7 +93,7 @@ public class AnnotationFile
 
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
-
+      StringBuffer rowprops = new StringBuffer();
       Hashtable graphGroup = new Hashtable();
 
       java.awt.Color color;
@@ -224,7 +232,6 @@ public class AnnotationFile
             if (hasLabels)
             {
               // TODO: labels are emitted after values for bar graphs.
-              text.append(comma);
               if // empty labels are allowed, so
               (row.annotations[j].displayCharacter != null
                       && row.annotations[j].displayCharacter.length() > 0
@@ -276,7 +283,14 @@ 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 +306,7 @@ public class AnnotationFile
           text.append(en.nextElement() + "\n");
         }
       }
+      text.append(rowprops.toString());
     }
 
     if (groups != null)
@@ -498,7 +513,11 @@ public class AnnotationFile
           combineAnnotations(al, st);
           continue;
         }
-
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          continue;
+        }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
@@ -615,7 +634,7 @@ public class AnnotationFile
             }
             else
             {
-              annotations[index++] = parseAnnotation(token);
+              annotations[index++] = parseAnnotation(token, graphStyle);
               emptyColumn = false;
             }
           }
@@ -670,8 +689,9 @@ public class AnnotationFile
     return true;
   }
 
-  Annotation parseAnnotation(String string)
+  Annotation parseAnnotation(String string, int graphStyle)
   {
+    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't do the glyph test if we don't want secondary structure
     String desc = null, displayChar = null;
     char ss = ' '; // secondaryStructure
     float value = 0;
@@ -686,31 +706,40 @@ public class AnnotationFile
       UserColourScheme ucs = new UserColourScheme();
 
       colour = ucs.getColourFromString(string.substring(i + 1, j));
-
+      if ( i>0 && string.charAt(i-1)==',')
+      {
+        // clip the preceding comma as well
+        i--;
+      }
       string = string.substring(0, i) + string.substring(j + 1);
     }
 
-    StringTokenizer st = new StringTokenizer(string, ",");
+    StringTokenizer st = new StringTokenizer(string, ",", true);
     String token;
+    boolean seenContent=false;
     while (st.hasMoreTokens())
     {
       token = st.nextToken().trim();
-      if (token.length() == 0)
+      if (token.equals(","))
       {
-        if (parsedValue && !dcset)
+        if (!seenContent && parsedValue && !dcset)
         {
           // allow the value below the bar/line to be empty
           dcset = true;
           displayChar = " ";
         }
+        seenContent = false;
         continue;
+      } else {
+        seenContent = true;
       }
 
       if (!parsedValue)
       {
         try
         {
-          displayChar = token;
+          displayChar = token; 
+          // foo
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
@@ -719,7 +748,7 @@ public class AnnotationFile
         }
       }
 
-      if (token.equals("H") || token.equals("E"))
+      if (hasSymbols && (token.equals("H") || token.equals("E")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
@@ -735,10 +764,10 @@ public class AnnotationFile
       }
 
     }
-    if (!dcset && string.charAt(string.length() - 1) == ',')
-    {
-      displayChar = " "; // empty display char symbol.
-    }
+//    if (!dcset && string.charAt(string.length() - 1) == ',')
+//    {
+//      displayChar = " "; // empty display char symbol.
+//    }
     if (displayChar != null && displayChar.length() > 1 && desc != null
             && desc.length() == 1)
     {
@@ -933,6 +962,35 @@ 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)
   {