X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=aac48eb0fe46c6366a736ecd868f8df285ce1ca4;hb=a9108fa3538ddb2ef02aa231e233dc978654d6f6;hp=0095aefab7cf8267e5a746a2eec74e742140adcb;hpb=16342ec2ab61d371ee70f61ac0294f2716fab638;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 0095aef..aac48eb 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;
@@ -117,7 +125,7 @@ public class AnnotationFile
           refSeq = row.sequenceRef;
           text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
         }
-        boolean hasGlyphs = false, hasLabels = false, hasValues = false, hasText = false;
+        boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
         // lookahead to check what the annotation row object actually contains.
         for (int j = 0; row.annotations != null
                 && j < row.annotations.length
@@ -202,10 +210,15 @@ public class AnnotationFile
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (hasGlyphs && row.annotations[j].secondaryStructure != ' ')
+            if (hasGlyphs) // could be also hasGlyphs || ... 
             {
 
-              text.append(comma + row.annotations[j].secondaryStructure);
+              text.append(comma);
+              if (row.annotations[j].secondaryStructure != ' ')
+              {
+                // only write out the field if its not whitespace.
+                text.append(row.annotations[j].secondaryStructure);
+              }
               comma = ",";
             }
             if (hasValues)
@@ -224,7 +237,6 @@ 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 +288,14 @@ 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 +311,7 @@ public class AnnotationFile
           text.append(en.nextElement() + "\n");
         }
       }
+      text.append(rowprops.toString());
     }
 
     if (groups != null)
@@ -413,6 +433,7 @@ public class AnnotationFile
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
+    Hashtable autoAnnots=new Hashtable();
     try
     {
       BufferedReader in = null;
@@ -442,9 +463,24 @@ public class AnnotationFile
       int graphStyle, index;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
+      // when true - will add new rows regardless of whether they are duplicate auto-annotation like consensus or conservation graphs
+      boolean overrideAutoAnnot=false; 
       if (al.getAlignmentAnnotation() != null)
       {
         existingAnnotations = al.getAlignmentAnnotation().length;
+        if (existingAnnotations>0)
+        {
+          AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
+          for (int aai=0;aai<aa.length;aai++)
+          {
+            if (aa[aai].autoCalculated)
+            {
+              // make a note of the name and description
+              autoAnnots.put(aa[aai].graph+"\t"+aa[aai].label+"\t"+aa[aai].description+"\t"+(aa[aai].sequenceRef!=null ? aa[aai].sequenceRef.getDisplayId(true) : "")
+                      ,new Integer(1));
+            }
+          }
+        }
       }
 
       int alWidth = al.getWidth();
@@ -498,7 +534,11 @@ public class AnnotationFile
           combineAnnotations(al, st);
           continue;
         }
-
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          continue;
+        }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
@@ -615,20 +655,26 @@ public class AnnotationFile
             }
             else
             {
-              annotations[index++] = parseAnnotation(token);
+              annotations[index++] = parseAnnotation(token, graphStyle);
               emptyColumn = false;
             }
           }
 
         }
-
+        
         annotation = new AlignmentAnnotation(label, description,
                 (index == 0) ? null : annotations, 0, 0, graphStyle);
 
         annotation.score = score;
-
+        if (!overrideAutoAnnot && autoAnnots.containsKey(annotation.graph+"\t"+annotation.label+"\t"+annotation.description+"\t"+(refSeq!=null ? refSeq.getDisplayId(true) : "")))
+        {
+          // skip - we've already got an automatic annotation of this type.
+          continue;
+        }
+        // otherwise add it!
         if (refSeq != null)
         {
+          
           annotation.belowAlignment = false;
           // make a copy of refSeq so we can find other matches in the alignment
           SequenceI referedSeq = refSeq;
@@ -670,8 +716,9 @@ 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;
@@ -686,40 +733,55 @@ 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;
+    int pass=0;
     while (st.hasMoreTokens())
     {
+      pass++;
       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;
         } catch (NumberFormatException ex)
         {
         }
+      } else {
+        if (token.length()==1)
+        {
+          displayChar = token;
+        }
       }
-
-      if (token.equals("H") || token.equals("E"))
+      if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
@@ -729,29 +791,31 @@ public class AnnotationFile
           displayChar = "";
         }
       }
-      else if (desc == null)
+      else if (desc == null || (parsedValue && pass>2))
       {
         desc = token;
       }
 
     }
-    if (!dcset && string.charAt(string.length() - 1) == ',')
+//    if (!dcset && string.charAt(string.length() - 1) == ',')
+//    {
+//      displayChar = " "; // empty display char symbol.
+//    }
+    if (displayChar != null && desc!=null && desc.length()==1) 
     {
-      displayChar = " "; // empty display char symbol.
-    }
-    if (displayChar != null && displayChar.length() > 1 && desc != null
-            && desc.length() == 1)
-    {
-      String tmp = displayChar;
-      displayChar = desc;
-      desc = tmp;
+      if (displayChar.length() > 1)
+      {
+        // switch desc and displayChar - legacy support  
+        String tmp = displayChar;
+        displayChar = desc;
+        desc = tmp;
+      } else {
+        if (displayChar.equals(desc)) {
+          // duplicate label - hangover from the 'robust parser' above
+          desc = null;
+        }
+      }
     }
-    /*
-     * In principle, this code will ensure that the Annotation element generated
-     * is renderable by any of the applet or application rendering code but
-     * instead we check for null strings when the display character is rendered.
-     * if (displayChar==null) { displayChar=""; }
-     */
     Annotation anot = new Annotation(displayChar, desc, ss, value);
 
     anot.colour = colour;
@@ -933,6 +997,35 @@ 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)
   {