X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=01daf39a9f50ce55262a77af351c0ad1d352bc70;hb=12b928f827972f429471a5bf7a832fa634259a16;hp=aac48eb0fe46c6366a736ecd868f8df285ce1ca4;hpb=520cc5fe77f3f625c9a58cb6b8b83bbca68084b6;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index aac48eb..01daf39 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -72,8 +72,11 @@ public class AnnotationFile
       this.hiddenRepSeqs = hiddenRepSeqs;
     }
   }
+
   /**
-   * Prepare an annotation file given a set of annotations, groups, alignment properties and views. 
+   * Prepare an annotation file given a set of annotations, groups, alignment
+   * properties and views.
+   * 
    * @param annotations
    * @param groups
    * @param properties
@@ -83,13 +86,15 @@ public class AnnotationFile
   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.
+    // TODO: resolve views issue : annotationFile could contain visible region,
+    // or full data + hidden region specifications for a view.
     if (annotations != null)
     {
       boolean oneColour = true;
       AlignmentAnnotation row;
       String comma;
       SequenceI refSeq = null;
+      SequenceGroup refGroup = null;
 
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
@@ -120,11 +125,34 @@ public class AnnotationFile
           refSeq = null;
         }
 
-        else if (refSeq == null || refSeq != row.sequenceRef)
+        else
+        {
+          if (refSeq == null || refSeq != row.sequenceRef)
+          {
+            refSeq = row.sequenceRef;
+            text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+          }
+        }
+        // mark any group references for the row
+        if (row.groupRef == null)
+        {
+
+          if (refGroup != null)
+          {
+            text.append("\nGROUP_REF\tALIGNMENT\n");
+          }
+
+          refGroup = null;
+        }
+        else
         {
-          refSeq = row.sequenceRef;
-          text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+          if (refGroup == null || refGroup != row.groupRef)
+          {
+            refGroup = row.groupRef;
+            text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");
+          }
         }
+
         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
@@ -138,8 +166,8 @@ public class AnnotationFile
                     .equals(" "));
             hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
             hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
-                                                                  // be
-                                                                  // rendered..
+            // be
+            // rendered..
             hasText |= (row.annotations[j].description != null && row.annotations[j].description
                     .length() > 0);
           }
@@ -210,7 +238,7 @@ public class AnnotationFile
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (hasGlyphs) // could be also hasGlyphs || ... 
+            if (hasGlyphs) // could be also hasGlyphs || ...
             {
 
               text.append(comma);
@@ -288,12 +316,13 @@ public class AnnotationFile
           colours.append("COLOUR\t" + row.label + "\t"
                   + jalview.util.Format.getHexString(color) + "\n");
         }
-        if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels)
+        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("ROWPROPERTIES\t" + row.label);
+          rowprops.append("\tscaletofit=" + row.scaleColLabel);
+          rowprops.append("\tshowalllabs=" + row.showAllColLabels);
+          rowprops.append("\tcentrelabs=" + row.centreColLabels);
           rowprops.append("\n");
         }
       }
@@ -433,7 +462,10 @@ public class AnnotationFile
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
-    Hashtable autoAnnots=new Hashtable();
+    String groupRef = null;
+    Hashtable groupRefRows = new Hashtable();
+
+    Hashtable autoAnnots = new Hashtable();
     try
     {
       BufferedReader in = null;
@@ -463,21 +495,28 @@ 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; 
+      // 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)
+        if (existingAnnotations > 0)
         {
           AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
-          for (int aai=0;aai<aa.length;aai++)
+          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));
+              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));
             }
           }
         }
@@ -575,7 +614,28 @@ public class AnnotationFile
           }
           continue;
         }
-
+        else if (token.equalsIgnoreCase("GROUP_REF"))
+        {
+          // Group references could be forward or backwards, so they are
+          // resolved after the whole file is read in
+          groupRef = null;
+          if (st.hasMoreTokens())
+          {
+            groupRef = st.nextToken();
+            if (groupRef.length() < 1)
+            {
+              groupRef = null; // empty string
+            }
+            else
+            {
+              if (groupRefRows.get(groupRef) == null)
+              {
+                groupRefRows.put(groupRef, new Vector());
+              }
+            }
+          }
+          continue;
+        }
         else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
         {
           addGroup(al, st);
@@ -599,6 +659,7 @@ public class AnnotationFile
           continue;
         }
 
+        // Parse out the annotation row
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = st.nextToken();
 
@@ -661,12 +722,21 @@ public class AnnotationFile
           }
 
         }
-        
+
         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) : "")))
+        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;
@@ -674,7 +744,7 @@ public class AnnotationFile
         // 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;
@@ -692,6 +762,10 @@ public class AnnotationFile
             al.setAnnotationIndex(annotation,
                     al.getAlignmentAnnotation().length
                             - existingAnnotations - 1);
+            if (groupRef != null)
+            {
+              ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+            }
             // and recover our virgin copy to use again if necessary.
             annotation = ann;
 
@@ -704,9 +778,52 @@ public class AnnotationFile
           al.setAnnotationIndex(annotation,
                   al.getAlignmentAnnotation().length - existingAnnotations
                           - 1);
+          if (groupRef != null)
+          {
+            ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+          }
         }
       }
+      // Finally, resolve the groupRefs
+      Enumeration en = groupRefRows.keys();
+      SequenceGroup theGroup = null;
 
+      while (en.hasMoreElements())
+      {
+        groupRef = (String) en.nextElement();
+        boolean matched = false;
+        // Resolve group: TODO: add a getGroupByName method to alignments
+        Vector grps = al.getGroups();
+        for (int g = 0, gSize = grps.size(); g < gSize; g++)
+        {
+          theGroup = (SequenceGroup) grps.elementAt(g);
+          if (theGroup.getName().equals(groupRef))
+          {
+            if (matched)
+            {
+              // TODO: specify and implement duplication of alignment annotation for multiple group references.
+              System.err
+                      .println("Ignoring 1:many group reference mappings for group name '"
+                              + groupRef+"'");
+            }
+            else
+            {
+              matched = true;
+              Vector rowset = (Vector) groupRefRows.get(groupRef);
+              if (rowset != null && rowset.size() > 0)
+              {
+                AlignmentAnnotation alan = null;
+                for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
+                {
+                  alan = (AlignmentAnnotation) rowset.elementAt(elm);
+                  alan.groupRef = theGroup;
+                }
+              }
+            }
+          }
+        }
+        ((Vector) groupRefRows.get(groupRef)).removeAllElements();
+      }
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -718,7 +835,15 @@ public class AnnotationFile
 
   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
+    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;
@@ -733,7 +858,7 @@ public class AnnotationFile
       UserColourScheme ucs = new UserColourScheme();
 
       colour = ucs.getColourFromString(string.substring(i + 1, j));
-      if ( i>0 && string.charAt(i-1)==',')
+      if (i > 0 && string.charAt(i - 1) == ',')
       {
         // clip the preceding comma as well
         i--;
@@ -743,8 +868,8 @@ public class AnnotationFile
 
     StringTokenizer st = new StringTokenizer(string, ",", true);
     String token;
-    boolean seenContent=false;
-    int pass=0;
+    boolean seenContent = false;
+    int pass = 0;
     while (st.hasMoreTokens())
     {
       pass++;
@@ -759,7 +884,9 @@ public class AnnotationFile
         }
         seenContent = false;
         continue;
-      } else {
+      }
+      else
+      {
         seenContent = true;
       }
 
@@ -767,7 +894,7 @@ public class AnnotationFile
       {
         try
         {
-          displayChar = token; 
+          displayChar = token;
           // foo
           value = new Float(token).floatValue();
           parsedValue = true;
@@ -775,13 +902,17 @@ public class AnnotationFile
         } catch (NumberFormatException ex)
         {
         }
-      } else {
-        if (token.length()==1)
+      }
+      else
+      {
+        if (token.length() == 1)
         {
           displayChar = token;
         }
       }
-      if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))
+      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
@@ -791,26 +922,29 @@ public class AnnotationFile
           displayChar = "";
         }
       }
-      else if (desc == null || (parsedValue && pass>2))
+      else if (desc == null || (parsedValue && pass > 2))
       {
         desc = token;
       }
 
     }
-//    if (!dcset && string.charAt(string.length() - 1) == ',')
-//    {
-//      displayChar = " "; // empty display char symbol.
-//    }
-    if (displayChar != null && desc!=null && desc.length()==1) 
+    // if (!dcset && string.charAt(string.length() - 1) == ',')
+    // {
+    // displayChar = " "; // empty display char symbol.
+    // }
+    if (displayChar != null && desc != null && desc.length() == 1)
     {
       if (displayChar.length() > 1)
       {
-        // switch desc and displayChar - legacy support  
+        // switch desc and displayChar - legacy support
         String tmp = displayChar;
         displayChar = desc;
         desc = tmp;
-      } else {
-        if (displayChar.equals(desc)) {
+      }
+      else
+      {
+        if (displayChar.equals(desc))
+        {
           // duplicate label - hangover from the 'robust parser' above
           desc = null;
         }
@@ -999,33 +1133,38 @@ 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();
+    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")) {
+      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 (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))
         {
-          if (alr[i].label.equalsIgnoreCase(label))
-          {
-            alr[i].centreColLabels = centerlab;
-            alr[i].scaleColLabel = scaletofit;
-            alr[i].showAllColLabels = showalllabs;
-          }
+          alr[i].centreColLabels = centerlab;
+          alr[i].scaleColLabel = scaletofit;
+          alr[i].showAllColLabels = showalllabs;
         }
+      }
     }
   }
+
   void addProperties(AlignmentI al, StringTokenizer st)
   {